Mercurial > repos > hepcat72 > vcfsamplecompare
changeset 0:cdd7fecae37c draft
planemo upload commit c786cb50e512783d81d4a9ad57add9151ac5904f
| author | hepcat72 |
|---|---|
| date | Wed, 10 Oct 2018 18:53:14 -0400 |
| parents | |
| children | cc6eda569fc4 |
| files | test-data/fbse1.vcf test-data/lest1.vcf test-data/lest2.vcf test-data/test10.in3.s0.d0.af.a6.hy.fy.gy.rvcf test-data/test10.in3.s0.d0.af.a6.hy.fy.gy.vcf test-data/test7.in1.s1.s3.d1.d1.af.a6.nh.fy.gy.rvcf test-data/test7.in1.s1.s3.d1.d1.af.a6.nh.fy.gy.vcf test-data/test8.in1.s1.s3.d1.d1.gt.nh.fy.gy.rvcf test-data/test8.in1.s1.s3.d1.d1.gt.nh.fy.gy.vcf test-data/test9.in2.s0.d0.gt.hy.fy.gy.rvcf test-data/test9.in2.s0.d0.gt.hy.fy.gy.vcf vcfsamplecompare.xml |
| diffstat | 12 files changed, 1307 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fbse1.vcf Wed Oct 10 18:53:14 2018 -0400 @@ -0,0 +1,664 @@ +##fileformat=VCFv4.1 +##fileDate=20170620 +##source=freeBayes v1.0.2-29-g41c1313 +##reference=localref.fa +##contig=<ID=Chromosome,length=6537648> +##phasing=none +##commandline="freebayes --region Chromosome:0..6537648 --bam b_0.bam --bam b_1.bam --bam b_2.bam --bam b_3.bam --fasta-reference localref.fa --vcf ./vcf_output/part_Chromosome:0..6537648.vcf --theta 0.001 --ploidy 1" +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> +##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype"> +##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]"> +##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally"> +##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally"> +##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally"> +##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally"> +##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> +##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred"> +##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations"> +##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations"> +##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand"> +##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand"> +##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand"> +##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand"> +##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous"> +##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome"> +##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele"> +##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele"> +##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without."> +##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best."> +##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout."> +##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> +##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR."> +##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position."> +##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles."> +##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length"> +##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles"> +##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles"> +##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments"> +##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments"> +##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> +##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record."> +##INFO=<ID=technology.ILLUMINA,Number=A,Type=Float,Description="Fraction of observations supporting the alternate observed in reads from ILLUMINA"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=DPR,Number=A,Type=Integer,Description="Number of observation for each allele"> +##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> +##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> +##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> +##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> +##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> +##SnpEffVersion="4.3i (build 2016-12-15 22:33), by Pablo Cingolani" +##SnpEffCmd="SnpEff Pseudomonas_aeruginosa_ucbpp_pa14 /Users/rleach/PROJECT/NINA/PA14DNASEQ-20170601/SNPsSmallIndels/FreeBayes_ploidy1_filtering_FreeBayes_variants.vcf.fixed " +##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' "> +##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' "> +##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' "> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT gDNA-PA14 205w3 205w2 205w1 +Chromosome 18938 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=7;CIGAR=1X;DP=49;DPB=49;DPRA=0;EPP=18.2106;EPPR=62.7775;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=75.5575;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=1425;RO=42;RPL=0;RPP=18.2106;RPPR=8.18047;RPR=7;RUN=1;SAF=0;SAP=18.2106;SAR=7;SRF=16;SRP=8.18047;SRR=26;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|sun|PA14_00180|transcript|ABJ14973.1|protein_coding|1/1|c.1156G>C|p.Ala386Pro|1156/1305|1156/1305|386/434||,G|upstream_gene_variant|MODIFIER|PA14_00150|PA14_00150|transcript|ABJ14970.1|protein_coding||c.-2330G>C|||||2330|,G|upstream_gene_variant|MODIFIER|PA14_00160|PA14_00160|transcript|ABJ14971.1|protein_coding||c.-1698G>C|||||1698|,G|upstream_gene_variant|MODIFIER|trkA|PA14_00170|transcript|ABJ14972.1|protein_coding||c.-176G>C|||||176|,G|upstream_gene_variant|MODIFIER|PA14_00210|PA14_00210|transcript|ABJ14976.1|protein_coding||c.-2795C>G|||||2795|,G|upstream_gene_variant|MODIFIER|smf|PA14_00230|transcript|ABJ14977.1|protein_coding||c.-3955C>G|||||3955|,G|downstream_gene_variant|MODIFIER|tag|PA14_00110|transcript|ABJ14966.1|protein_coding||c.*4847C>G|||||4847|,G|downstream_gene_variant|MODIFIER|PA14_00120|PA14_00120|transcript|ABJ14967.1|protein_coding||c.*3815C>G|||||3815|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_00130|PA14_00130|transcript|ABJ14968.1|protein_coding||c.*3464C>G|||||3464|,G|downstream_gene_variant|MODIFIER|PA14_00140|PA14_00140|transcript|ABJ14969.1|protein_coding||c.*2664C>G|||||2664|,G|downstream_gene_variant|MODIFIER|fmt|PA14_00190|transcript|ABJ14974.1|protein_coding||c.*1152G>C|||||1152|,G|downstream_gene_variant|MODIFIER|def|PA14_00200|transcript|ABJ14975.1|protein_coding||c.*2150G>C|||||2150| GT:DP:DPR:RO:QR:AO:QA:GL 0:11:11,2:9:297:2:4:0,-26.6595 0:12:12,1:11:404:1:2:0,-36.5019 0:14:14,3:11:367:3:6:0,-32.7777 0:12:12,1:11:357:1:2:0,-32.2284 +Chromosome 19337 . C A 3.84232E-6 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=1.125;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=14.361;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=220;RO=9;RPL=0;RPP=7.35324;RPPR=5.18177;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=9.04217;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|sun|PA14_00180|transcript|ABJ14973.1|protein_coding|1/1|c.757G>T|p.Ala253Ser|757/1305|757/1305|253/434||,A|upstream_gene_variant|MODIFIER|PA14_00150|PA14_00150|transcript|ABJ14970.1|protein_coding||c.-2729G>T|||||2729|,A|upstream_gene_variant|MODIFIER|PA14_00160|PA14_00160|transcript|ABJ14971.1|protein_coding||c.-2097G>T|||||2097|,A|upstream_gene_variant|MODIFIER|trkA|PA14_00170|transcript|ABJ14972.1|protein_coding||c.-575G>T|||||575|,A|upstream_gene_variant|MODIFIER|PA14_00210|PA14_00210|transcript|ABJ14976.1|protein_coding||c.-2396C>A|||||2396|,A|upstream_gene_variant|MODIFIER|smf|PA14_00230|transcript|ABJ14977.1|protein_coding||c.-3556C>A|||||3556|,A|upstream_gene_variant|MODIFIER|PA14_00240|PA14_00240|transcript|ABJ14978.1|protein_coding||c.-4685C>A|||||4685|,A|downstream_gene_variant|MODIFIER|PA14_00120|PA14_00120|transcript|ABJ14967.1|protein_coding||c.*4214C>A|||||4214|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_00130|PA14_00130|transcript|ABJ14968.1|protein_coding||c.*3863C>A|||||3863|,A|downstream_gene_variant|MODIFIER|PA14_00140|PA14_00140|transcript|ABJ14969.1|protein_coding||c.*3063C>A|||||3063|,A|downstream_gene_variant|MODIFIER|fmt|PA14_00190|transcript|ABJ14974.1|protein_coding||c.*753G>T|||||753|,A|downstream_gene_variant|MODIFIER|def|PA14_00200|transcript|ABJ14975.1|protein_coding||c.*1751G>T|||||1751| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,2:1:36:2:17:0,-1.98329 0:1:1,0:1:16:0:0:0,-1.59998 0:2:2,0:2:32:0:0:0,-3.03997 0:5:5,0:5:136:0:0:0,-12.5017 +Chromosome 27657 . A G 1.36079E-16 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=46;DPB=46;DPRA=1.2;EPP=13.8677;EPPR=14.9269;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=63.9307;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=1233;RO=41;RPL=0;RPP=13.8677;RPPR=9.41879;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=15;SRP=9.41879;SRR=26;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|qor|PA14_00250|transcript|ABJ14979.1|protein_coding||c.-2091T>C|||||2091|,G|upstream_gene_variant|MODIFIER|plcB|PA14_00300|transcript|ABJ14982.1|protein_coding||c.-10A>G|||||10|,G|upstream_gene_variant|MODIFIER|PA14_00310|PA14_00310|transcript|ABJ14983.1|protein_coding||c.-977A>G|||||977|,G|upstream_gene_variant|MODIFIER|PA14_00320|PA14_00320|transcript|ABJ14984.1|protein_coding||c.-2260A>G|||||2260|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_00210|PA14_00210|transcript|ABJ14976.1|protein_coding||c.*4899A>G|||||4899|,G|downstream_gene_variant|MODIFIER|smf|PA14_00230|transcript|ABJ14977.1|protein_coding||c.*3676A>G|||||3676|,G|downstream_gene_variant|MODIFIER|PA14_00240|PA14_00240|transcript|ABJ14978.1|protein_coding||c.*3078A>G|||||3078|,G|downstream_gene_variant|MODIFIER|hemF|PA14_00280|transcript|ABJ14980.1|protein_coding||c.*983A>G|||||983|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|aroE|PA14_00290|transcript|ABJ14981.1|protein_coding||c.*101A>G|||||101|,G|downstream_gene_variant|MODIFIER|PA14_00340|PA14_00340|transcript|ABJ14985.1|protein_coding||c.*2866T>C|||||2866|,G|downstream_gene_variant|MODIFIER|PA14_00360|PA14_00360|transcript|ABJ14986.1|protein_coding||c.*4424T>C|||||4424|,G|intergenic_region|MODIFIER|aroE-plcB|PA14_00290-PA14_00300|intergenic_region|PA14_00290-PA14_00300|||n.27657A>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:11:11,1:10:308:1:13:0,-26.7132 0:10:10,0:10:293:0:0:0,-26.6512 0:13:13,3:10:266:3:40:0,-20.4646 0:12:12,1:11:366:1:14:0,-31.8504 +Chromosome 31706 . G C 9.01733E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=20;DPB=20;DPRA=2;EPP=7.35324;EPPR=10.7311;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=19.9927;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=538;RO=18;RPL=2;RPP=7.35324;RPPR=7.35324;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=13;SRP=10.7311;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_00340|PA14_00340|transcript|ABJ14985.1|protein_coding|1/1|c.371C>G|p.Ser124Trp|371/1554|371/1554|124/517||,C|upstream_gene_variant|MODIFIER|PA14_00400|PA14_00400|transcript|ABJ14988.1|protein_coding||c.-2939G>C|||||2939|,C|upstream_gene_variant|MODIFIER|PA14_00410|PA14_00410|transcript|ABJ14989.1|protein_coding||c.-3864G>C|||||3864|,C|downstream_gene_variant|MODIFIER|aroE|PA14_00290|transcript|ABJ14981.1|protein_coding||c.*4150G>C|||||4150|,C|downstream_gene_variant|MODIFIER|plcB|PA14_00300|transcript|ABJ14982.1|protein_coding||c.*3053G>C|||||3053|,C|downstream_gene_variant|MODIFIER|PA14_00310|PA14_00310|transcript|ABJ14983.1|protein_coding||c.*1786G>C|||||1786|,C|downstream_gene_variant|MODIFIER|PA14_00320|PA14_00320|transcript|ABJ14984.1|protein_coding||c.*1187G>C|||||1187|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_00360|PA14_00360|transcript|ABJ14986.1|protein_coding||c.*375C>G|||||375|,C|downstream_gene_variant|MODIFIER|betC|PA14_00380|transcript|ABJ14987.1|protein_coding||c.*1315C>G|||||1315|,C|downstream_gene_variant|MODIFIER|PA14_00420|PA14_00420|transcript|ABJ14990.1|protein_coding||c.*4220C>G|||||4220|,C|downstream_gene_variant|MODIFIER|bvga|PA14_00430|transcript|ABJ14991.1|protein_coding||c.*4593C>G|||||4593| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:74:0:0:0,-7.02486 0:8:8,0:8:226:0:0:0,-20.6087 0:2:2,0:2:36:0:0:0,-3.41897 0:8:8,2:6:202:2:16:0,-16.9895 +Chromosome 35243 . A C 2.17768E-12 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=21;DPB=21;DPRA=2.72727;EPP=7.35324;EPPR=16.8392;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=28.3229;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=627;RO=19;RPL=2;RPP=7.35324;RPPR=4.03889;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=12;SRP=5.8675;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_00400|PA14_00400|transcript|ABJ14988.1|protein_coding|1/1|c.599A>C|p.Gln200Pro|599/915|599/915|200/304||,C|upstream_gene_variant|MODIFIER|PA14_00340|PA14_00340|transcript|ABJ14985.1|protein_coding||c.-3167T>G|||||3167|,C|upstream_gene_variant|MODIFIER|PA14_00360|PA14_00360|transcript|ABJ14986.1|protein_coding||c.-2239T>G|||||2239|,C|upstream_gene_variant|MODIFIER|betC|PA14_00380|transcript|ABJ14987.1|protein_coding||c.-711T>G|||||711|,C|upstream_gene_variant|MODIFIER|PA14_00410|PA14_00410|transcript|ABJ14989.1|protein_coding||c.-327A>C|||||327|,C|upstream_gene_variant|MODIFIER|trpI|PA14_00460|transcript|ABJ14994.1|protein_coding||c.-3980A>C|||||3980|,C|upstream_gene_variant|MODIFIER|PA14_00470|PA14_00470|transcript|ABJ14995.1|protein_coding||c.-4968A>C|||||4968|,C|downstream_gene_variant|MODIFIER|PA14_00320|PA14_00320|transcript|ABJ14984.1|protein_coding||c.*4724A>C|||||4724|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_00420|PA14_00420|transcript|ABJ14990.1|protein_coding||c.*683T>G|||||683|,C|downstream_gene_variant|MODIFIER|bvga|PA14_00430|transcript|ABJ14991.1|protein_coding||c.*1056T>G|||||1056|,C|downstream_gene_variant|MODIFIER|trpA|PA14_00440|transcript|ABJ14992.1|protein_coding||c.*1865T>G|||||1865|,C|downstream_gene_variant|MODIFIER|trpB|PA14_00450|transcript|ABJ14993.1|protein_coding||c.*2668T>G|||||2668| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:70:0:0:0,-6.64733 0:5:5,0:5:191:0:0:0,-17.5575 0:4:4,0:4:146:0:0:0,-13.4974 0:10:10,2:8:220:2:4:0,-19.6854 +Chromosome 61537 . T G 7.93564E-11 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=19;DPB=19;DPRA=3.75;EPP=11.6962;EPPR=3.63072;GTI=0;LEN=1;MEANALT=1.5;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=24.7904;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=418;RO=14;RPL=0;RPP=11.6962;RPPR=8.59409;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=8;SRP=3.63072;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_00620|PA14_00620|transcript|ABJ15007.1|protein_coding|1/1|c.1555A>C|p.Ile519Leu|1555/1662|1555/1662|519/553||,G|upstream_gene_variant|MODIFIER|PA14_00550|PA14_00550|transcript|ABJ15001.1|protein_coding||c.-4553A>C|||||4553|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_00600|PA14_00600|transcript|ABJ15006.1|protein_coding||c.-389A>C|||||389|,G|upstream_gene_variant|MODIFIER|PA14_00630|PA14_00630|transcript|ABJ15008.1|protein_coding||c.-2164T>G|||||2164|,G|upstream_gene_variant|MODIFIER|phzH|PA14_00640|transcript|ABJ15009.1|protein_coding||c.-3128T>G|||||3128|,G|downstream_gene_variant|MODIFIER|exoT|PA14_00560|transcript|ABJ15002.1|protein_coding||c.*3061T>G|||||3061|,G|downstream_gene_variant|MODIFIER|PA14_00570|PA14_00570|transcript|ABJ15003.1|protein_coding||c.*1833T>G|||||1833|,G|downstream_gene_variant|MODIFIER|PA14_00580|PA14_00580|transcript|ABJ15004.1|protein_coding||c.*1449T>G|||||1449|,G|downstream_gene_variant|MODIFIER|PA14_00590|PA14_00590|transcript|ABJ15005.1|protein_coding||c.*787T>G|||||787|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:74:0:0:0,-7.02543 0:2:2,0:2:66:0:0:0,-6.26653 0:6:6,2:4:94:2:4:0,-8.30863 0:9:9,2:6:184:2:4:0,-16.4363 +Chromosome 85372 . A G 9.87353E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=21;DPB=21;DPRA=1.2;EPP=7.35324;EPPR=22.325;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=36.6267;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=692;RO=19;RPL=0;RPP=7.35324;RPPR=8.61041;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=12;SRP=5.8675;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|ppkA|PA14_00875|transcript|ABJ15671.1|protein_coding|1/1|c.2372T>C|p.Leu791Pro|2372/3099|2372/3099|791/1032||,G|upstream_gene_variant|MODIFIER|PA14_00820|PA14_00820|transcript|ABJ15027.1|protein_coding||c.-4409T>C|||||4409|,G|upstream_gene_variant|MODIFIER|PA14_00830|PA14_00830|transcript|ABJ15028.1|protein_coding||c.-2635T>C|||||2635|,G|upstream_gene_variant|MODIFIER|PA14_00850|PA14_00850|transcript|ABJ15029.1|protein_coding||c.-1443T>C|||||1443|,G|upstream_gene_variant|MODIFIER|PA14_00860|PA14_00860|transcript|ABJ15030.1|protein_coding||c.-724T>C|||||724|,G|downstream_gene_variant|MODIFIER|PA14_00890|PA14_00890|transcript|ABJ15031.1|protein_coding||c.*2379T>C|||||2379|,G|downstream_gene_variant|MODIFIER|PA14_00900|PA14_00900|transcript|ABJ15032.1|protein_coding||c.*3117T>C|||||3117|,G|downstream_gene_variant|MODIFIER|PA14_00910|PA14_00910|transcript|ABJ15033.1|protein_coding||c.*3794T>C|||||3794| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,2:4:144:2:4:0,-12.9316 0:8:8,0:8:279:0:0:0,-25.4404 0:3:3,0:3:110:0:0:0,-10.2606 0:4:4,0:4:159:0:0:0,-14.6923 +Chromosome 96406 . TCG GCC 470.465 . AB=0;ABP=0;AC=4;AF=1;AN=4;AO=18;CIGAR=1X1M1X;DP=18;DPB=18;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=3;MEANALT=1;MQM=50.7778;MQMR=0;NS=4;NUMALT=1;ODDS=20.2139;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=606;QR=0;RO=0;RPL=8;RPP=3.49285;RPPR=0;RPR=10;RUN=1;SAF=2;SAP=26.6552;SAR=16;SRF=0;SRP=0;SRR=0;TYPE=complex;technology.ILLUMINA=1;ANN=GCC|missense_variant|MODERATE|PA14_00970|PA14_00970|transcript|ABJ15036.1|protein_coding|1/1|c.46_48delCGAinsGGC|p.Arg16Gly|48/543|46/543|16/180||WARNING_TRANSCRIPT_NO_START_CODON,GCC|upstream_gene_variant|MODIFIER|PA14_00910|PA14_00910|transcript|ABJ15033.1|protein_coding||c.-3934_-3932delCGAinsGGC|||||3932|,GCC|upstream_gene_variant|MODIFIER|PA14_00925|PA14_00925|transcript|ABJ15641.1|protein_coding||c.-2363_-2361delCGAinsGGC|||||2361|,GCC|upstream_gene_variant|MODIFIER|PA14_00940|PA14_00940|transcript|ABJ15034.1|protein_coding||c.-1022_-1020delCGAinsGGC|||||1020|,GCC|upstream_gene_variant|MODIFIER|PA14_00960|PA14_00960|transcript|ABJ15035.1|protein_coding||c.-542_-540delCGAinsGGC|||||540|,GCC|upstream_gene_variant|MODIFIER|PA14_00990|PA14_00990|transcript|ABJ15038.1|protein_coding||c.-1371_-1369delTCGinsGCC|||||1371|WARNING_TRANSCRIPT_NO_START_CODON,GCC|upstream_gene_variant|MODIFIER|PA14_01010|PA14_01010|transcript|ABJ15039.1|protein_coding||c.-2494_-2492delTCGinsGCC|||||2494|,GCC|upstream_gene_variant|MODIFIER|PA14_01020|PA14_01020|transcript|ABJ15040.1|protein_coding||c.-3025_-3023delTCGinsGCC|||||3025|,GCC|upstream_gene_variant|MODIFIER|PA14_01030|PA14_01030|transcript|ABJ15041.1|protein_coding||c.-4597_-4595delTCGinsGCC|||||4597|,GCC|downstream_gene_variant|MODIFIER|PA14_00980|PA14_00980|transcript|ABJ15037.1|protein_coding||c.*42_*44delCGAinsGGC|||||44| GT:DP:DPR:RO:QR:AO:QA:GL 1:1:1,1:0:0:1:36:-3.59827,0 1:9:9,9:0:0:9:295:-24.1236,0 1:3:3,3:0:0:3:109:-9.93223,0 1:5:5,5:0:0:5:166:-14.5535,0 +Chromosome 114005 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=12;CIGAR=1X;DP=83;DPB=83;DPRA=1.39583;EPP=29.068;EPPR=9.89173;GTI=0;LEN=1;MEANALT=1;MQM=58.9167;MQMR=49.9437;NS=4;NUMALT=1;ODDS=88.7815;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=180;QR=2231;RO=71;RPL=1;RPP=21.1059;RPPR=11.8491;RPR=11;RUN=1;SAF=1;SAP=21.1059;SAR=11;SRF=13;SRP=64.9431;SRR=58;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_01160|PA14_01160|transcript|ABJ15052.1|protein_coding|1/1|c.725A>G|p.Glu242Gly|725/2226|725/2226|242/741||,G|upstream_gene_variant|MODIFIER|PA14_01120|PA14_01120|transcript|ABJ15048.1|protein_coding||c.-3046T>C|||||3046|,G|upstream_gene_variant|MODIFIER|PA14_01130|PA14_01130|transcript|ABJ15049.1|protein_coding||c.-2800T>C|||||2800|,G|upstream_gene_variant|MODIFIER|PA14_01140|PA14_01140|transcript|ABJ15050.1|protein_coding||c.-1491T>C|||||1491|,G|upstream_gene_variant|MODIFIER|PA14_01150|PA14_01150|transcript|ABJ15051.1|protein_coding||c.-978T>C|||||978|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_01170|PA14_01170|transcript|ABJ15053.1|protein_coding||c.-1529A>G|||||1529|,G|upstream_gene_variant|MODIFIER|PA14_01180|PA14_01180|transcript|ABJ15054.1|protein_coding||c.-1908A>G|||||1908|,G|upstream_gene_variant|MODIFIER|PA14_01190|PA14_01190|transcript|ABJ15055.1|protein_coding||c.-3104A>G|||||3104|,G|upstream_gene_variant|MODIFIER|PA14_01200|PA14_01200|transcript|ABJ15056.1|protein_coding||c.-4141A>G|||||4141|,G|downstream_gene_variant|MODIFIER|PA14_01110|PA14_01110|transcript|ABJ15047.1|protein_coding||c.*3445A>G|||||3445| GT:DP:DPR:RO:QR:AO:QA:GL 0:21:21,4:17:451:4:63:0,-34.4801 0:16:16,0:16:559:0:0:0,-47.3936 0:15:15,4:11:377:4:71:0,-27.4632 0:31:31,4:27:844:4:46:0,-70.0355 +Chromosome 114865 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=36;CIGAR=1X;DP=194;DPB=194;DPRA=0;EPP=3.9754;EPPR=3.88988;GTI=0;LEN=1;MEANALT=1;MQM=36.6944;MQMR=44.7152;NS=4;NUMALT=1;ODDS=189.762;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1272;QR=5876;RO=158;RPL=33;RPP=57.2971;RPPR=3.2302;RPR=3;RUN=1;SAF=13;SAP=9.04217;SAR=23;SRF=70;SRP=7.46319;SRR=88;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_01160|PA14_01160|transcript|ABJ15052.1|protein_coding|1/1|c.1585T>C|p.Tyr529His|1585/2226|1585/2226|529/741||,C|upstream_gene_variant|MODIFIER|PA14_01120|PA14_01120|transcript|ABJ15048.1|protein_coding||c.-3906A>G|||||3906|,C|upstream_gene_variant|MODIFIER|PA14_01130|PA14_01130|transcript|ABJ15049.1|protein_coding||c.-3660A>G|||||3660|,C|upstream_gene_variant|MODIFIER|PA14_01140|PA14_01140|transcript|ABJ15050.1|protein_coding||c.-2351A>G|||||2351|,C|upstream_gene_variant|MODIFIER|PA14_01150|PA14_01150|transcript|ABJ15051.1|protein_coding||c.-1838A>G|||||1838|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_01170|PA14_01170|transcript|ABJ15053.1|protein_coding||c.-669T>C|||||669|,C|upstream_gene_variant|MODIFIER|PA14_01180|PA14_01180|transcript|ABJ15054.1|protein_coding||c.-1048T>C|||||1048|,C|upstream_gene_variant|MODIFIER|PA14_01190|PA14_01190|transcript|ABJ15055.1|protein_coding||c.-2244T>C|||||2244|,C|upstream_gene_variant|MODIFIER|PA14_01200|PA14_01200|transcript|ABJ15056.1|protein_coding||c.-3281T>C|||||3281|,C|upstream_gene_variant|MODIFIER|PA14_01220|PA14_01220|transcript|ABJ15057.1|protein_coding||c.-4383T>C|||||4383|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_01110|PA14_01110|transcript|ABJ15047.1|protein_coding||c.*4305T>C|||||4305| GT:DP:DPR:RO:QR:AO:QA:GL 0:42:42,10:32:1128:10:359:0,-67.3169 0:60:60,9:51:1907:9:300:0,-135.246 0:53:53,9:44:1646:9:308:0,-107.466 0:39:39,8:31:1195:8:305:0,-73.7354 +Chromosome 138694 . C A 9.74545E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=34;DPB=34;DPRA=1.25;EPP=7.35324;EPPR=3.28173;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=40.9059;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1137;RO=32;RPL=0;RPP=7.35324;RPPR=3.28173;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=18;SRP=4.09604;SRR=14;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|PA14_01470|PA14_01470|transcript|ABJ15077.1|protein_coding|1/1|c.565C>A|p.His189Asn|565/687|565/687|189/228||,A|upstream_gene_variant|MODIFIER|elaA|PA14_01400|transcript|ABJ15072.1|protein_coding||c.-4393G>T|||||4393|,A|upstream_gene_variant|MODIFIER|PA14_01480|PA14_01480|transcript|ABJ15078.1|protein_coding||c.-223C>A|||||223|,A|upstream_gene_variant|MODIFIER|PA14_01490|PA14_01490|transcript|ABJ15079.1|protein_coding||c.-1137C>A|||||1137|,A|upstream_gene_variant|MODIFIER|PA14_01550|PA14_01550|transcript|ABJ15084.1|protein_coding||c.-4192C>A|||||4192|,A|upstream_gene_variant|MODIFIER|phnA|PA14_01560|transcript|ABJ15085.1|protein_coding||c.-4764C>A|||||4764|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_01390|PA14_01390|transcript|ABJ15071.1|protein_coding||c.*4885C>A|||||4885|,A|downstream_gene_variant|MODIFIER|PA14_01410|PA14_01410|transcript|ABJ15073.1|protein_coding||c.*3788C>A|||||3788|,A|downstream_gene_variant|MODIFIER|PA14_01430|PA14_01430|transcript|ABJ15074.1|protein_coding||c.*2804C>A|||||2804|,A|downstream_gene_variant|MODIFIER|PA14_01440|PA14_01440|transcript|ABJ15075.1|protein_coding||c.*2192C>A|||||2192|,A|downstream_gene_variant|MODIFIER|dctA|PA14_01460|transcript|ABJ15076.1|protein_coding||c.*613C>A|||||613|,A|downstream_gene_variant|MODIFIER|PA14_01500|PA14_01500|transcript|ABJ15080.1|protein_coding||c.*1579G>T|||||1579|,A|downstream_gene_variant|MODIFIER|PA14_01510|PA14_01510|transcript|ABJ15081.1|protein_coding||c.*2787G>T|||||2787|,A|downstream_gene_variant|MODIFIER|PA14_01520|PA14_01520|transcript|ABJ15082.1|protein_coding||c.*3065G>T|||||3065|,A|downstream_gene_variant|MODIFIER|PA14_01540|PA14_01540|transcript|ABJ15083.1|protein_coding||c.*3468G>T|||||3468| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:208:0:0:0,-19.0506 0:10:10,2:8:302:2:17:0,-25.9209 0:3:3,0:3:114:0:0:0,-10.6319 0:15:15,0:15:513:0:0:0,-46.474 +Chromosome 142702 . G C 2.61447E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=10;CIGAR=1X;DP=62;DPB=62;DPRA=0.958333;EPP=24.725;EPPR=19.7139;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=67.787;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=1474;RO=52;RPL=10;RPP=24.725;RPPR=3.17734;RPR=0;RUN=1;SAF=10;SAP=24.725;SAR=0;SRF=31;SRP=7.18621;SRR=21;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_01540|PA14_01540|transcript|ABJ15083.1|protein_coding|1/1|c.84C>G|p.Ser28Arg|84/624|84/624|28/207||,C|upstream_gene_variant|MODIFIER|PA14_01500|PA14_01500|transcript|ABJ15080.1|protein_coding||c.-1521C>G|||||1521|,C|upstream_gene_variant|MODIFIER|PA14_01510|PA14_01510|transcript|ABJ15081.1|protein_coding||c.-940C>G|||||940|,C|upstream_gene_variant|MODIFIER|PA14_01520|PA14_01520|transcript|ABJ15082.1|protein_coding||c.-716C>G|||||716|,C|upstream_gene_variant|MODIFIER|PA14_01550|PA14_01550|transcript|ABJ15084.1|protein_coding||c.-184G>C|||||184|,C|upstream_gene_variant|MODIFIER|phnA|PA14_01560|transcript|ABJ15085.1|protein_coding||c.-756G>C|||||756|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|dctA|PA14_01460|transcript|ABJ15076.1|protein_coding||c.*4621G>C|||||4621|,C|downstream_gene_variant|MODIFIER|PA14_01470|PA14_01470|transcript|ABJ15077.1|protein_coding||c.*3886G>C|||||3886|,C|downstream_gene_variant|MODIFIER|PA14_01480|PA14_01480|transcript|ABJ15078.1|protein_coding||c.*3051G>C|||||3051|,C|downstream_gene_variant|MODIFIER|PA14_01490|PA14_01490|transcript|ABJ15079.1|protein_coding||c.*2461G>C|||||2461|,C|downstream_gene_variant|MODIFIER|gabP|PA14_01580|transcript|ABJ15086.1|protein_coding||c.*1179C>G|||||1179|,C|downstream_gene_variant|MODIFIER|mmsA|PA14_01600|transcript|ABJ15087.1|protein_coding||c.*2775C>G|||||2775|,C|downstream_gene_variant|MODIFIER|PA14_01610|PA14_01610|transcript|ABJ15088.1|protein_coding||c.*4352C>G|||||4352|,C|downstream_gene_variant|MODIFIER|aptA|PA14_01620|transcript|ABJ15089.1|protein_coding||c.*4639C>G|||||4639| GT:DP:DPR:RO:QR:AO:QA:GL 0:16:16,0:16:490:0:0:0,-44.3732 0:13:13,3:10:240:3:6:0,-21.2647 0:12:12,4:8:242:4:8:0,-21.3268 0:21:21,3:18:502:3:6:0,-44.876 +Chromosome 150206 . C G 1.846E-8 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=20;DPB=20;DPRA=1.5;EPP=9.52472;EPPR=9.26925;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=19.2762;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=465;RO=17;RPL=0;RPP=9.52472;RPPR=9.26925;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=39.9253;SRR=17;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|guaD|PA14_01660|transcript|ABJ15091.1|protein_coding|1/1|c.1018G>C|p.Gly340Arg|1018/1371|1018/1371|340/456||,G|upstream_gene_variant|MODIFIER|gabP|PA14_01580|transcript|ABJ15086.1|protein_coding||c.-4898G>C|||||4898|,G|upstream_gene_variant|MODIFIER|mmsA|PA14_01600|transcript|ABJ15087.1|protein_coding||c.-3236G>C|||||3236|,G|upstream_gene_variant|MODIFIER|PA14_01610|PA14_01610|transcript|ABJ15088.1|protein_coding||c.-2865G>C|||||2865|,G|upstream_gene_variant|MODIFIER|aptA|PA14_01620|transcript|ABJ15089.1|protein_coding||c.-1519G>C|||||1519|,G|upstream_gene_variant|MODIFIER|PA14_01670|PA14_01670|transcript|ABJ15092.1|protein_coding||c.-2175C>G|||||2175|,G|upstream_gene_variant|MODIFIER|PA14_01680|PA14_01680|transcript|ABJ15093.1|protein_coding||c.-3746C>G|||||3746|,G|upstream_gene_variant|MODIFIER|PA14_01690|PA14_01690|transcript|ABJ15094.1|protein_coding||c.-4866C>G|||||4866|,G|downstream_gene_variant|MODIFIER|PA14_01640|PA14_01640|transcript|ABJ15090.1|protein_coding||c.*466C>G|||||466| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:37:0:0:0,-3.5137 0:6:6,1:5:182:1:2:0,-16.5336 0:6:6,0:6:140:0:0:0,-12.8269 0:6:6,2:4:106:2:4:0,-9.42015 +Chromosome 157416 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=61;DPB=61;DPRA=1.17857;EPP=11.6962;EPPR=6.88793;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=98.1665;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=45;QR=2007;RO=56;RPL=4;RPP=11.6962;RPPR=42.7172;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=13;SRP=37.909;SRR=43;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|ahpF|PA14_01720|transcript|ABJ15096.1|protein_coding|1/1|c.545A>C|p.Gln182Pro|545/1566|545/1566|182/521||,C|upstream_gene_variant|MODIFIER|PA14_01750|PA14_01750|transcript|ABJ15098.1|protein_coding||c.-2452A>C|||||2452|,C|upstream_gene_variant|MODIFIER|nuh|PA14_01760|transcript|ABJ15099.1|protein_coding||c.-3971A>C|||||3971|,C|downstream_gene_variant|MODIFIER|PA14_01670|PA14_01670|transcript|ABJ15092.1|protein_coding||c.*3464A>C|||||3464|,C|downstream_gene_variant|MODIFIER|PA14_01680|PA14_01680|transcript|ABJ15093.1|protein_coding||c.*2367A>C|||||2367|,C|downstream_gene_variant|MODIFIER|PA14_01690|PA14_01690|transcript|ABJ15094.1|protein_coding||c.*1364A>C|||||1364|,C|downstream_gene_variant|MODIFIER|ahpC|PA14_01710|transcript|ABJ15095.1|protein_coding||c.*689A>C|||||689|,C|downstream_gene_variant|MODIFIER|PA14_01730|PA14_01730|transcript|ABJ15097.1|protein_coding||c.*1101T>G|||||1101|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_01770|PA14_01770|transcript|ABJ15100.1|protein_coding||c.*4997T>G|||||4997| GT:DP:DPR:RO:QR:AO:QA:GL 0:14:14,0:14:490:0:0:0,-44.4139 0:18:18,1:17:617:1:2:0,-55.6415 0:14:14,0:13:482:0:0:0,-43.6696 0:15:15,3:12:418:3:43:0,-33.9293 +Chromosome 163771 . C G 1.99763E-6 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=3;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=2;NUMALT=1;ODDS=14.7377;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=70;RO=2;RPL=0;RPP=7.35324;RPPR=3.0103;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=7.35324;SRR=2;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_01780|PA14_01780|transcript|ABJ15101.1|protein_coding|1/1|c.152G>C|p.Arg51Pro|152/627|152/627|51/208||,G|upstream_gene_variant|MODIFIER|PA14_01730|PA14_01730|transcript|ABJ15097.1|protein_coding||c.-4358G>C|||||4358|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_01770|PA14_01770|transcript|ABJ15100.1|protein_coding||c.-510G>C|||||510|,G|upstream_gene_variant|MODIFIER|PA14_01800|PA14_01800|transcript|ABJ15103.1|protein_coding||c.-1057C>G|||||1057|,G|upstream_gene_variant|MODIFIER|PA14_01810|PA14_01810|transcript|ABJ15104.1|protein_coding||c.-2227C>G|||||2227|,G|upstream_gene_variant|MODIFIER|add|PA14_01830|transcript|ABJ15105.1|protein_coding||c.-3294C>G|||||3294|,G|upstream_gene_variant|MODIFIER|PA14_01840|PA14_01840|transcript|ABJ15106.1|protein_coding||c.-4441C>G|||||4441|,G|upstream_gene_variant|MODIFIER|PA14_01860|PA14_01860|transcript|ABJ15107.1|protein_coding||c.-4983C>G|||||4983|,G|downstream_gene_variant|MODIFIER|PA14_01750|PA14_01750|transcript|ABJ15098.1|protein_coding||c.*2554C>G|||||2554|,G|downstream_gene_variant|MODIFIER|nuh|PA14_01760|transcript|ABJ15099.1|protein_coding||c.*1395C>G|||||1395|,G|downstream_gene_variant|MODIFIER|PA14_01790|PA14_01790|transcript|ABJ15102.1|protein_coding||c.*301G>C|||||301| GT:DP:DPR:RO:QR:AO:QA:GL . . 0:1:1,0:1:31:0:0:0,-3.09945 0:3:3,2:1:39:2:4:0,-3.51656 +Chromosome 210231 . A C 8.68941E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=18;DPB=18;DPRA=3.5;EPP=9.52472;EPPR=3.15506;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=20.0297;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=528;RO=15;RPL=3;RPP=9.52472;RPPR=3.15506;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=8;SRP=3.15506;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|atsB|PA14_02340|transcript|ABJ15142.1|protein_coding|1/1|c.704T>G|p.Val235Gly|704/1617|704/1617|235/538||,C|upstream_gene_variant|MODIFIER|PA14_02290|PA14_02290|transcript|ABJ15138.1|protein_coding||c.-4416T>G|||||4416|,C|upstream_gene_variant|MODIFIER|atsA|PA14_02310|transcript|ABJ15140.1|protein_coding||c.-1837T>G|||||1837|,C|upstream_gene_variant|MODIFIER|atsC|PA14_02330|transcript|ABJ15141.1|protein_coding||c.-910T>G|||||910|,C|upstream_gene_variant|MODIFIER|atsR|PA14_02360|transcript|ABJ15143.1|protein_coding||c.-970A>C|||||970|,C|upstream_gene_variant|MODIFIER|PA14_02380|PA14_02380|transcript|ABJ15145.1|protein_coding||c.-3660A>C|||||3660|,C|downstream_gene_variant|MODIFIER|PA14_02300|PA14_02300|transcript|ABJ15139.1|protein_coding||c.*3547A>C|||||3547|,C|downstream_gene_variant|MODIFIER|PA14_02370|PA14_02370|transcript|ABJ15144.1|protein_coding||c.*2054T>G|||||2054|,C|downstream_gene_variant|MODIFIER|PA14_02390|PA14_02390|transcript|ABJ15146.1|protein_coding||c.*4409T>G|||||4409| GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:35:0:0:0,-3.49863 0:9:9,2:7:265:2:17:0,-22.5941 0:3:3,0:3:94:0:0:0,-8.76608 0:5:5,1:4:134:1:15:0,-10.8838 +Chromosome 234118 . T C 4.05295E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=45;DPB=45;DPRA=0.666667;EPP=9.52472;EPPR=6.31921;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=55.8162;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=1309;RO=42;RPL=2;RPP=3.73412;RPPR=23.691;RPR=1;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=18;SRP=4.87156;SRR=24;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|mcdM|PA14_02640|transcript|ABJ15165.1|protein_coding|1/1|c.127T>C|p.Ser43Pro|127/765|127/765|43/254||,C|upstream_gene_variant|MODIFIER|aldH|PA14_02680|transcript|ABJ15168.1|protein_coding||c.-3252T>C|||||3252|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_02690|PA14_02690|transcript|ABJ15169.1|protein_coding||c.-4800T>C|||||4800|,C|downstream_gene_variant|MODIFIER|mdcB|PA14_02560|transcript|ABJ15158.1|protein_coding||c.*4190T>C|||||4190|,C|downstream_gene_variant|MODIFIER|mdcC|PA14_02570|transcript|ABJ15159.1|protein_coding||c.*3889T>C|||||3889|,C|downstream_gene_variant|MODIFIER|mdcD|PA14_02580|transcript|ABJ15160.1|protein_coding||c.*3033T>C|||||3033|,C|downstream_gene_variant|MODIFIER|mdcE|PA14_02590|transcript|ABJ15161.1|protein_coding||c.*2230T>C|||||2230|,C|downstream_gene_variant|MODIFIER|mdcG|PA14_02610|transcript|ABJ15162.1|protein_coding||c.*1522T>C|||||1522|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|mdcH|PA14_02620|transcript|ABJ15163.1|protein_coding||c.*593T>C|||||593|,C|downstream_gene_variant|MODIFIER|mdcL|PA14_02630|transcript|ABJ15164.1|protein_coding||c.*132T>C|||||132|,C|downstream_gene_variant|MODIFIER|PA14_02650|PA14_02650|transcript|ABJ15166.1|protein_coding||c.*723A>G|||||723|,C|downstream_gene_variant|MODIFIER|PA14_02660|PA14_02660|transcript|ABJ15167.1|protein_coding||c.*1981A>G|||||1981|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,1:8:229:1:27:0,-18.1819 0:9:9,2:7:229:2:41:0,-17.0333 0:12:12,0:12:408:0:0:0,-37.0314 0:15:15,0:15:443:0:0:0,-40.1417 +Chromosome 251559 . G T 2.15768E-8 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=18;DPB=18;DPRA=1.5;EPP=7.35324;EPPR=3.55317;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=19.1202;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=499;RO=16;RPL=2;RPP=7.35324;RPPR=16.582;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=6;SRP=5.18177;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|pcaD|PA14_02840|transcript|ABJ15180.1|protein_coding|1/1|c.231G>T|p.Val77Val|231/792|231/792|77/263||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|pcaC|PA14_02850|transcript|ABJ15181.1|protein_coding||c.-572G>T|||||572|,T|upstream_gene_variant|MODIFIER|PA14_02870|PA14_02870|transcript|ABJ15182.1|protein_coding||c.-1101G>T|||||1101|,T|upstream_gene_variant|MODIFIER|PA14_02890|PA14_02890|transcript|ABJ15183.1|protein_coding||c.-2233G>T|||||2233|,T|upstream_gene_variant|MODIFIER|PA14_02910|PA14_02910|transcript|ABJ15185.1|protein_coding||c.-4857G>T|||||4857|,T|downstream_gene_variant|MODIFIER|pcaJ|PA14_02770|transcript|ABJ15176.1|protein_coding||c.*4297G>T|||||4297|,T|downstream_gene_variant|MODIFIER|pcaF|PA14_02790|transcript|ABJ15177.1|protein_coding||c.*3095G>T|||||3095|,T|downstream_gene_variant|MODIFIER|pcaT|PA14_02810|transcript|ABJ15178.1|protein_coding||c.*1647G>T|||||1647|,T|downstream_gene_variant|MODIFIER|pcaB|PA14_02830|transcript|ABJ15179.1|protein_coding||c.*245G>T|||||245|,T|downstream_gene_variant|MODIFIER|pcaK|PA14_02900|transcript|ABJ15184.1|protein_coding||c.*3205C>A|||||3205| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:37:0:0:0,-3.5137 0:6:6,0:6:186:0:0:0,-17.041 0:4:4,0:4:152:0:0:0,-14.049 0:6:6,2:4:124:2:18:0,-9.75314 +Chromosome 283291 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=9;CIGAR=1X;DP=78;DPB=78;DPRA=1.29167;EPP=22.5536;EPPR=46.0936;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=71.4747;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=135;QR=1846;RO=69;RPL=9;RPP=22.5536;RPPR=66.7383;RPR=0;RUN=1;SAF=9;SAP=22.5536;SAR=0;SRF=61;SRP=91.4113;SRR=8;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|PA14_03200|PA14_03200|transcript|ABJ15209.1|protein_coding|1/1|c.1425C>A|p.Val475Val|1425/2151|1425/2151|475/716||,T|upstream_gene_variant|MODIFIER|PA14_03170|PA14_03170|transcript|ABJ15206.1|protein_coding||c.-2734C>A|||||2734|,T|upstream_gene_variant|MODIFIER|PA14_03180|PA14_03180|transcript|ABJ15207.1|protein_coding||c.-2438C>A|||||2438|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|PA14_03190|PA14_03190|transcript|ABJ15208.1|protein_coding||c.-876C>A|||||876|,T|downstream_gene_variant|MODIFIER|PA14_03163|PA14_03163|transcript|ABJ15668.1|protein_coding||c.*4158G>T|||||4158|,T|downstream_gene_variant|MODIFIER|PA14_03166|PA14_03166|transcript|ABJ15667.1|protein_coding||c.*3760G>T|||||3760|,T|downstream_gene_variant|MODIFIER|PA14_03210|PA14_03210|transcript|ABJ15210.1|protein_coding||c.*1421C>A|||||1421|,T|downstream_gene_variant|MODIFIER|PA14_03220|PA14_03220|transcript|ABJ15211.1|protein_coding||c.*1922C>A|||||1922| GT:DP:DPR:RO:QR:AO:QA:GL 0:16:16,4:12:313:4:60:0,-22.8719 0:22:22,2:20:511:2:30:0,-43.3804 0:24:24,3:21:579:3:45:0,-48.1658 0:16:16,0:16:443:0:0:0,-40.1332 +Chromosome 287074 . T C 0.288088 . AB=0;ABP=0;AC=1;AF=0.25;AN=4;AO=4;CIGAR=1X;DP=7;DPB=7;DPRA=2;EPP=11.6962;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=7.25;MQMR=5;NS=4;NUMALT=1;ODDS=2.68773;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=109;RO=3;RPL=4;RPP=11.6962;RPPR=9.52472;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=3;SRP=9.52472;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_03220|PA14_03220|transcript|ABJ15211.1|protein_coding|1/1|c.1199A>G|p.Glu400Gly|1199/3060|1199/3060|400/1019||,C|upstream_gene_variant|MODIFIER|PA14_03190|PA14_03190|transcript|ABJ15208.1|protein_coding||c.-4659A>G|||||4659|,C|upstream_gene_variant|MODIFIER|PA14_03200|PA14_03200|transcript|ABJ15209.1|protein_coding||c.-2359A>G|||||2359|,C|upstream_gene_variant|MODIFIER|PA14_03210|PA14_03210|transcript|ABJ15210.1|protein_coding||c.-1865A>G|||||1865|,C|upstream_gene_variant|MODIFIER|PA14_03250|PA14_03250|transcript|ABJ15213.1|protein_coding||c.-4494T>C|||||4494|,C|downstream_gene_variant|MODIFIER|hcpC|PA14_03240|transcript|ABJ15212.1|protein_coding||c.*1380A>G|||||1380| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,2:1:39:2:4:0,-0.0192772 0:2:2,1:1:36:1:2:0,-0.459207 1:1:1,1:0:0:1:15:-0.813795,0 0:1:1,0:1:34:0:0:0,-0.599485 +Chromosome 316473 . A G 6.80326E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=70;DPB=70;DPRA=1;EPP=6.91895;EPPR=5.71629;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=57.9664;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=91;QR=2126;RO=65;RPL=0;RPP=13.8677;RPPR=20.6827;RPR=5;RUN=1;SAF=1;SAP=6.91895;SAR=4;SRF=31;SRP=3.31097;SRR=34;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|gabT|PA14_03450|transcript|ABJ15229.1|protein_coding|1/1|c.1115A>G|p.Glu372Gly|1115/1281|1115/1281|372/426||,G|upstream_gene_variant|MODIFIER|PA14_03390|PA14_03390|transcript|ABJ15225.1|protein_coding||c.-4299T>C|||||4299|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_03400|PA14_03400|transcript|ABJ15226.1|protein_coding||c.-3974T>C|||||3974|,G|upstream_gene_variant|MODIFIER|PA14_03410|PA14_03410|transcript|PA14_03410-1.1|protein_coding||c.-3439T>C|||||3439|WARNING_TRANSCRIPT_INCOMPLETE,G|upstream_gene_variant|MODIFIER|PA14_03420|PA14_03420|transcript|ABJ15227.1|protein_coding||c.-2835T>C|||||2835|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_03470|PA14_03470|transcript|ABJ15230.1|protein_coding||c.-492A>G|||||492|,G|upstream_gene_variant|MODIFIER|PA14_03490|PA14_03490|transcript|ABJ15232.1|protein_coding||c.-3407A>G|||||3407|,G|upstream_gene_variant|MODIFIER|PA14_03510|PA14_03510|transcript|ABJ15233.1|protein_coding||c.-3856A>G|||||3856|,G|upstream_gene_variant|MODIFIER|PA14_03520|PA14_03520|transcript|ABJ15234.1|protein_coding||c.-4297A>G|||||4297|,G|downstream_gene_variant|MODIFIER|PA14_03380|PA14_03380|transcript|ABJ15224.1|protein_coding||c.*4745A>G|||||4745|,G|downstream_gene_variant|MODIFIER|tRNA|EBG00001225076|transcript|EBT00001793389.1|protein_coding||c.*3439A>G|||||3439|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|gabD|PA14_03430|transcript|ABJ15228.1|protein_coding||c.*1359A>G|||||1359|,G|downstream_gene_variant|MODIFIER|PA14_03480|PA14_03480|transcript|ABJ15231.1|protein_coding||c.*1859T>C|||||1859|,G|downstream_gene_variant|MODIFIER|PA14_03530|PA14_03530|transcript|ABJ15235.1|protein_coding||c.*4578T>C|||||4578| GT:DP:DPR:RO:QR:AO:QA:GL 0:11:11,3:8:230:3:62:0,-15.1895 0:24:24,2:22:797:2:29:0,-69.2878 0:19:19,0:19:614:0:0:0,-55.545 0:16:16,0:16:485:0:0:0,-43.9309 +Chromosome 320133 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=7;CIGAR=1X;DP=65;DPB=65;DPRA=2.375;EPP=10.7656;EPPR=28.3192;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=72.3133;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=136;QR=1541;RO=58;RPL=1;RPP=10.7656;RPPR=36.7056;RPR=6;RUN=1;SAF=0;SAP=18.2106;SAR=7;SRF=16;SRP=28.3192;SRR=42;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_03490|PA14_03490|transcript|ABJ15232.1|protein_coding|1/1|c.254A>G|p.Glu85Gly|254/438|254/438|85/145||,G|upstream_gene_variant|MODIFIER|PA14_03480|PA14_03480|transcript|ABJ15231.1|protein_coding||c.-380T>C|||||380|,G|upstream_gene_variant|MODIFIER|PA14_03510|PA14_03510|transcript|ABJ15233.1|protein_coding||c.-196A>G|||||196|,G|upstream_gene_variant|MODIFIER|PA14_03520|PA14_03520|transcript|ABJ15234.1|protein_coding||c.-637A>G|||||637|,G|upstream_gene_variant|MODIFIER|PA14_03590|PA14_03590|transcript|ABJ15239.1|protein_coding||c.-4918A>G|||||4918|,G|downstream_gene_variant|MODIFIER|gabT|PA14_03450|transcript|ABJ15229.1|protein_coding||c.*3494A>G|||||3494|,G|downstream_gene_variant|MODIFIER|PA14_03470|PA14_03470|transcript|ABJ15230.1|protein_coding||c.*1969A>G|||||1969|,G|downstream_gene_variant|MODIFIER|PA14_03530|PA14_03530|transcript|ABJ15235.1|protein_coding||c.*918T>C|||||918|,G|downstream_gene_variant|MODIFIER|cynX|PA14_03550|transcript|ABJ15236.1|protein_coding||c.*1900T>C|||||1900|,G|downstream_gene_variant|MODIFIER|PA14_03560|PA14_03560|transcript|ABJ15237.1|protein_coding||c.*3277T>C|||||3277|,G|downstream_gene_variant|MODIFIER|PA14_03580|PA14_03580|transcript|ABJ15238.1|protein_coding||c.*4156T>C|||||4156| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:254:0:0:0,-23.1663 0:15:15,2:13:381:2:27:0,-32.0064 0:22:22,1:21:470:1:27:0,-39.8036 0:20:20,4:16:436:4:82:0,-31.9117 +Chromosome 333551 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=8;CIGAR=1X;DP=46;DPB=46;DPRA=1.2;EPP=20.3821;EPPR=6.66752;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=65.8202;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=86;QR=1236;RO=38;RPL=0;RPP=20.3821;RPPR=3.0103;RPR=8;RUN=1;SAF=0;SAP=20.3821;SAR=8;SRF=8;SRP=30.668;SRR=30;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_03720|PA14_03720|transcript|ABJ15248.1|protein_coding|1/1|c.1199T>C|p.Leu400Pro|1199/2283|1199/2283|400/760||,G|upstream_gene_variant|MODIFIER|cysA|PA14_03650|transcript|ABJ15243.1|protein_coding||c.-4469T>C|||||4469|,G|upstream_gene_variant|MODIFIER|cysW|PA14_03670|transcript|ABJ15244.1|protein_coding||c.-3596T>C|||||3596|,G|upstream_gene_variant|MODIFIER|cysT|PA14_03680|transcript|ABJ15245.1|protein_coding||c.-2767T>C|||||2767|,G|upstream_gene_variant|MODIFIER|sbp|PA14_03700|transcript|ABJ15246.1|protein_coding||c.-1607T>C|||||1607|,G|upstream_gene_variant|MODIFIER|PA14_03710|PA14_03710|transcript|ABJ15247.1|protein_coding||c.-1248T>C|||||1248|,G|upstream_gene_variant|MODIFIER|PA14_03730|PA14_03730|transcript|ABJ15249.1|protein_coding||c.-1369A>G|||||1369|,G|upstream_gene_variant|MODIFIER|PA14_03760|PA14_03760|transcript|ABJ15250.1|protein_coding||c.-2776A>G|||||2776|,G|upstream_gene_variant|MODIFIER|speB1|PA14_03770|transcript|ABJ15251.1|protein_coding||c.-4217A>G|||||4217| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,0:10:358:0:0:0,-32.5596 0:12:12,2:10:303:2:16:0,-26.0388 0:13:13,5:8:276:5:56:0,-20.0165 0:11:11,1:10:299:1:14:0,-25.7932 +Chromosome 375701 . A G 1.66728E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=28;DPB=28;DPRA=0.866667;EPP=11.6962;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=33.2754;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=851;RO=24;RPL=0;RPP=11.6962;RPPR=8.80089;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=10;SRP=4.45795;SRR=14;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_04210|PA14_04210|transcript|ABJ15285.1|protein_coding|1/1|c.1327T>C|p.Tyr443His|1327/1395|1327/1395|443/464||,G|upstream_gene_variant|MODIFIER|P2|EBG00001225124|transcript|EBT00001793415.1|sRNA||n.-4938T>C|||||4938|,G|upstream_gene_variant|MODIFIER|aphA|PA14_04190|transcript|ABJ15284.1|protein_coding||c.-84T>C|||||84|,G|downstream_gene_variant|MODIFIER|PA14_04140|PA14_04140|transcript|ABJ15280.1|protein_coding||c.*3478A>G|||||3478|,G|downstream_gene_variant|MODIFIER|ycgM|PA14_04150|transcript|ABJ15281.1|protein_coding||c.*2721A>G|||||2721|,G|downstream_gene_variant|MODIFIER|PA14_04160|PA14_04160|transcript|ABJ15282.1|protein_coding||c.*1633A>G|||||1633|,G|downstream_gene_variant|MODIFIER|PA14_04180|PA14_04180|transcript|ABJ15283.1|protein_coding||c.*1199A>G|||||1199|,G|downstream_gene_variant|MODIFIER|PA14_04220|PA14_04220|transcript|ABJ15286.1|protein_coding||c.*1747T>C|||||1747|,G|downstream_gene_variant|MODIFIER|PA14_04230|PA14_04230|transcript|ABJ15287.1|protein_coding||c.*2838T>C|||||2838|,G|downstream_gene_variant|MODIFIER|PA14_04240|PA14_04240|transcript|ABJ15288.1|protein_coding||c.*3623T>C|||||3623|,G|downstream_gene_variant|MODIFIER|PA14_04250|PA14_04250|transcript|ABJ15289.1|protein_coding||c.*4549T>C|||||4549| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:194:0:0:0,-17.8325 0:6:6,2:4:115:2:27:0,-8.06484 0:7:7,2:5:183:2:4:0,-16.4453 0:10:10,0:10:359:0:0:0,-32.6436 +Chromosome 387322 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=41;DPB=41;DPRA=0.967742;EPP=7.35324;EPPR=23.1103;GTI=0;LEN=1;MEANALT=1;MQM=49;MQMR=60;NS=4;NUMALT=1;ODDS=67.577;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1424;RO=39;RPL=2;RPP=7.35324;RPPR=19.1015;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=34;SRP=49.8362;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|ilvA1|PA14_04320|transcript|ABJ15294.1|protein_coding|1/1|c.1063A>C|p.Thr355Pro|1063/1515|1063/1515|355/504||,C|upstream_gene_variant|MODIFIER|PA14_04290|PA14_04290|transcript|ABJ15291.1|protein_coding||c.-2748T>G|||||2748|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_04300|PA14_04300|transcript|ABJ15292.1|protein_coding||c.-2115T>G|||||2115|,C|upstream_gene_variant|MODIFIER|rpiA|PA14_04310|transcript|ABJ15293.1|protein_coding||c.-1321T>G|||||1321|,C|upstream_gene_variant|MODIFIER|PA14_04330|PA14_04330|transcript|ABJ15295.1|protein_coding||c.-572A>C|||||572|,C|upstream_gene_variant|MODIFIER|PA14_04340|PA14_04340|transcript|ABJ15296.1|protein_coding||c.-1090A>C|||||1090|,C|upstream_gene_variant|MODIFIER|PA14_04350|PA14_04350|transcript|ABJ15297.1|protein_coding||c.-2358A>C|||||2358|,C|upstream_gene_variant|MODIFIER|ygdP|PA14_04390|transcript|ABJ15300.1|protein_coding||c.-4946A>C|||||4946|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_04270|PA14_04270|transcript|ABJ15290.1|protein_coding||c.*4730A>C|||||4730|,C|downstream_gene_variant|MODIFIER|PA14_04370|PA14_04370|transcript|ABJ15298.1|protein_coding||c.*2798T>G|||||2798|,C|downstream_gene_variant|MODIFIER|PA14_04380|PA14_04380|transcript|ABJ15299.1|protein_coding||c.*4089T>G|||||4089|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:264:0:0:0,-24.1173 0:10:10,2:8:283:2:17:0,-24.1891 0:9:9,0:9:356:0:0:0,-32.4032 0:15:15,0:15:521:0:0:0,-47.1956 +Chromosome 408671 . C G 9.72579E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=24;DPB=24;DPRA=2.14286;EPP=7.35324;EPPR=4.58955;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=31.4181;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=789;RO=22;RPL=0;RPP=7.35324;RPPR=12.8806;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=11;SRP=3.0103;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|yicE|PA14_04610|transcript|ABJ15316.1|protein_coding|1/1|c.1318G>C|p.Gly440Arg|1318/1386|1318/1386|440/461||,G|upstream_gene_variant|MODIFIER|glpQ|PA14_04550|transcript|ABJ15311.1|protein_coding||c.-3614G>C|||||3614|,G|upstream_gene_variant|MODIFIER|PA14_04590|PA14_04590|transcript|ABJ15315.1|protein_coding||c.-207G>C|||||207|,G|downstream_gene_variant|MODIFIER|PA14_04530|PA14_04530|transcript|ABJ15310.1|protein_coding||c.*4802C>G|||||4802|,G|downstream_gene_variant|MODIFIER|PA14_04560|PA14_04560|transcript|ABJ15312.1|protein_coding||c.*2310C>G|||||2310|,G|downstream_gene_variant|MODIFIER|PA14_04570|PA14_04570|transcript|ABJ15313.1|protein_coding||c.*1273C>G|||||1273|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|folA|PA14_04580|transcript|ABJ15314.1|protein_coding||c.*696C>G|||||696|,G|downstream_gene_variant|MODIFIER|ilvD|PA14_04630|transcript|ABJ15317.1|protein_coding||c.*1547G>C|||||1547|,G|downstream_gene_variant|MODIFIER|PA14_04640|PA14_04640|transcript|ABJ15318.1|protein_coding||c.*3713G>C|||||3713|,G|downstream_gene_variant|MODIFIER|pfpI|PA14_04650|transcript|ABJ15319.1|protein_coding||c.*4982G>C|||||4982| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:78:0:0:0,-7.40347 0:10:10,2:8:294:2:4:0,-26.427 0:4:4,0:4:158:0:0:0,-14.6007 0:8:8,0:8:259:0:0:0,-23.6146 +Chromosome 409628 . T C 2.82541E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=45;DPB=45;DPRA=0.857143;EPP=7.35324;EPPR=9.12072;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=69.7298;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=1609;RO=43;RPL=2;RPP=7.35324;RPPR=11.5447;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=11;SRP=25.2805;SRR=32;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|yicE|PA14_04610|transcript|ABJ15316.1|protein_coding|1/1|c.361A>G|p.Ser121Gly|361/1386|361/1386|121/461||,C|upstream_gene_variant|MODIFIER|glpQ|PA14_04550|transcript|ABJ15311.1|protein_coding||c.-4571A>G|||||4571|,C|upstream_gene_variant|MODIFIER|PA14_04590|PA14_04590|transcript|ABJ15315.1|protein_coding||c.-1164A>G|||||1164|,C|upstream_gene_variant|MODIFIER|PA14_04660|PA14_04660|transcript|ABJ15320.1|protein_coding||c.-4781T>C|||||4781|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_04560|PA14_04560|transcript|ABJ15312.1|protein_coding||c.*3267T>C|||||3267|,C|downstream_gene_variant|MODIFIER|PA14_04570|PA14_04570|transcript|ABJ15313.1|protein_coding||c.*2230T>C|||||2230|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|folA|PA14_04580|transcript|ABJ15314.1|protein_coding||c.*1653T>C|||||1653|,C|downstream_gene_variant|MODIFIER|ilvD|PA14_04630|transcript|ABJ15317.1|protein_coding||c.*590A>G|||||590|,C|downstream_gene_variant|MODIFIER|PA14_04640|PA14_04640|transcript|ABJ15318.1|protein_coding||c.*2756A>G|||||2756|,C|downstream_gene_variant|MODIFIER|pfpI|PA14_04650|transcript|ABJ15319.1|protein_coding||c.*4025A>G|||||4025| GT:DP:DPR:RO:QR:AO:QA:GL 0:12:12,0:12:459:0:0:0,-41.6553 0:10:10,2:8:263:2:18:0,-22.2686 0:10:10,0:10:386:0:0:0,-35.0951 0:13:13,0:13:501:0:0:0,-45.434 +Chromosome 423960 . A C 2.18859E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=35;DPB=35;DPRA=0.833333;EPP=11.6962;EPPR=3.64073;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=33.0763;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=36;QR=1118;RO=31;RPL=4;RPP=11.6962;RPPR=8.68415;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=17;SRP=3.64073;SRR=14;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_04790|PA14_04790|transcript|ABJ15330.1|protein_coding|1/1|c.239T>G|p.Val80Gly|239/549|239/549|80/182||,C|upstream_gene_variant|MODIFIER|PA14_04710|PA14_04710|transcript|ABJ15325.1|protein_coding||c.-4974T>G|||||4974|,C|upstream_gene_variant|MODIFIER|PA14_04730|PA14_04730|transcript|ABJ15326.1|protein_coding||c.-3089T>G|||||3089|,C|upstream_gene_variant|MODIFIER|fdx1|PA14_04750|transcript|ABJ15327.1|protein_coding||c.-2710T>G|||||2710|,C|upstream_gene_variant|MODIFIER|coaD|PA14_04760|transcript|ABJ15328.1|protein_coding||c.-2110T>G|||||2110|,C|upstream_gene_variant|MODIFIER|PA14_04780|PA14_04780|transcript|ABJ15329.1|protein_coding||c.-366T>G|||||366|,C|upstream_gene_variant|MODIFIER|PA14_04820|PA14_04820|transcript|ABJ15332.1|protein_coding||c.-2012A>C|||||2012|,C|downstream_gene_variant|MODIFIER|PA14_04810|PA14_04810|transcript|ABJ15331.1|protein_coding||c.*293T>G|||||293|,C|downstream_gene_variant|MODIFIER|PA14_04830|PA14_04830|transcript|ABJ15333.1|protein_coding||c.*2644T>G|||||2644|,C|downstream_gene_variant|MODIFIER|PA14_04840|PA14_04840|transcript|ABJ15334.1|protein_coding||c.*3117T>G|||||3117|,C|downstream_gene_variant|MODIFIER|PA14_04850|PA14_04850|transcript|ABJ15335.1|protein_coding||c.*4152T>G|||||4152|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|yhhF|PA14_04860|transcript|ABJ15336.1|protein_coding||c.*4721T>G|||||4721| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,0:10:363:0:0:0,-33.0063 0:9:9,1:8:292:1:2:0,-26.4273 0:11:11,1:10:357:1:2:0,-32.2617 0:5:5,2:3:106:2:32:0,-6.84792 +Chromosome 440117 . G C 2.6034E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=46;DPB=46;DPRA=0.833333;EPP=7.35324;EPPR=7.94546;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=67.8292;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1611;RO=44;RPL=2;RPP=7.35324;RPPR=4.78696;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=22;SRP=3.0103;SRR=22;TYPE=snp;technology.ILLUMINA=1;ANN=C|upstream_gene_variant|MODIFIER|mtgA|PA14_04950|transcript|ABJ15344.1|protein_coding||c.-2438C>G|||||2438|,C|upstream_gene_variant|MODIFIER|PA14_05010|PA14_05010|transcript|ABJ15349.1|protein_coding||c.-123G>C|||||123|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ftsX|PA14_04920|transcript|ABJ15341.1|protein_coding||c.*4812G>C|||||4812|,C|downstream_gene_variant|MODIFIER|rpoH|PA14_04930|transcript|ABJ15342.1|protein_coding||c.*3844G>C|||||3844|,C|downstream_gene_variant|MODIFIER|PA14_04940|PA14_04940|transcript|ABJ15343.1|protein_coding||c.*3174G>C|||||3174|,C|downstream_gene_variant|MODIFIER|PA14_04960|PA14_04960|transcript|ABJ15345.1|protein_coding||c.*2024G>C|||||2024|,C|downstream_gene_variant|MODIFIER|thiS|PA14_04970|transcript|ABJ15346.1|protein_coding||c.*1721G>C|||||1721|,C|downstream_gene_variant|MODIFIER|thiG|PA14_04980|transcript|ABJ15347.1|protein_coding||c.*865G>C|||||865|,C|downstream_gene_variant|MODIFIER|micA|PA14_05000|transcript|ABJ15348.1|protein_coding||c.*40G>C|||||40|,C|downstream_gene_variant|MODIFIER|PA14_05020|PA14_05020|transcript|ABJ15350.1|protein_coding||c.*1482C>G|||||1482|,C|downstream_gene_variant|MODIFIER|PA14_05030|PA14_05030|transcript|ABJ15351.1|protein_coding||c.*1801C>G|||||1801|,C|downstream_gene_variant|MODIFIER|PA14_05040|PA14_05040|transcript|ABJ15352.1|protein_coding||c.*2205C>G|||||2205|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_05050|PA14_05050|transcript|ABJ15353.1|protein_coding||c.*3480C>G|||||3480|,C|downstream_gene_variant|MODIFIER|PA14_05060|PA14_05060|transcript|ABJ15354.1|protein_coding||c.*4070C>G|||||4070|,C|downstream_gene_variant|MODIFIER|metW|PA14_05070|transcript|ABJ15355.1|protein_coding||c.*4621C>G|||||4621|,C|intergenic_region|MODIFIER|micA-PA14_05010|PA14_05000-PA14_05010|intergenic_region|PA14_05000-PA14_05010|||n.440117G>C|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:233:0:0:0,-21.3389 0:10:10,2:8:296:2:4:0,-26.6114 0:17:17,0:17:604:0:0:0,-54.6705 0:13:13,0:13:478:0:0:0,-43.3494 +Chromosome 455786 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=39;DPB=39;DPRA=0.774194;EPP=7.35324;EPPR=3.06899;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=52.7834;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=1283;RO=37;RPL=0;RPP=7.35324;RPPR=16.2152;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=21;SRP=4.47751;SRR=16;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|PA14_05220|PA14_05220|transcript|ABJ15366.1|protein_coding|1/1|c.412C>A|p.Gln138Lys|412/1374|412/1374|138/457||,A|upstream_gene_variant|MODIFIER|PA14_05160|PA14_05160|transcript|ABJ15361.1|protein_coding||c.-4695G>T|||||4695|,A|upstream_gene_variant|MODIFIER|czcD|PA14_05200|transcript|ABJ15364.1|protein_coding||c.-1213G>T|||||1213|,A|upstream_gene_variant|MODIFIER|PA14_05230|PA14_05230|transcript|ABJ15367.1|protein_coding||c.-959C>A|||||959|,A|downstream_gene_variant|MODIFIER|pilT|PA14_05180|transcript|ABJ15362.1|protein_coding||c.*3446C>A|||||3446|,A|downstream_gene_variant|MODIFIER|pilU|PA14_05190|transcript|ABJ15363.1|protein_coding||c.*2120C>A|||||2120|,A|downstream_gene_variant|MODIFIER|PA14_05210|PA14_05210|transcript|ABJ15365.1|protein_coding||c.*654C>A|||||654|,A|downstream_gene_variant|MODIFIER|pyrC|PA14_05250|transcript|ABJ15368.1|protein_coding||c.*2371G>T|||||2371|,A|downstream_gene_variant|MODIFIER|pyrB|PA14_05260|transcript|ABJ15369.1|protein_coding||c.*3639G>T|||||3639|,A|downstream_gene_variant|MODIFIER|pyrR|PA14_05270|transcript|ABJ15370.1|protein_coding||c.*4667G>T|||||4667| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:257:0:0:0,-23.4411 0:8:8,2:6:197:2:31:0,-15.1045 0:6:6,0:6:191:0:0:0,-17.4988 0:17:17,0:17:638:0:0:0,-57.7502 +Chromosome 484612 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=28;DPB=28;DPRA=1.66667;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=41.7211;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=923;RO=26;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=24;SRP=43.4331;SRR=2;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|PA14_05480|PA14_05480|transcript|ABJ15388.1|protein_coding|1/1|c.1452G>A|p.Lys484Lys|1452/1491|1452/1491|484/496||,A|upstream_gene_variant|MODIFIER|PA14_05440|PA14_05440|transcript|ABJ15385.1|protein_coding||c.-3878C>T|||||3878|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|PA14_05450|PA14_05450|transcript|ABJ15386.1|protein_coding||c.-3121C>T|||||3121|,A|upstream_gene_variant|MODIFIER|bioA|PA14_05460|transcript|ABJ15387.1|protein_coding||c.-1625C>T|||||1625|,A|upstream_gene_variant|MODIFIER|PA14_05500|PA14_05500|transcript|ABJ15389.1|protein_coding||c.-220G>A|||||220|,A|upstream_gene_variant|MODIFIER|yceI|PA14_05510|transcript|ABJ15390.1|protein_coding||c.-801G>A|||||801|,A|upstream_gene_variant|MODIFIER|mexA|PA14_05530|transcript|ABJ15392.1|protein_coding||c.-2163G>A|||||2163|,A|upstream_gene_variant|MODIFIER|mexB|PA14_05540|transcript|ABJ15393.1|protein_coding||c.-3330G>A|||||3330|,A|downstream_gene_variant|MODIFIER|mexR|PA14_05520|transcript|ABJ15391.1|protein_coding||c.*1445C>T|||||1445| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:140:0:0:0,-12.9448 0:10:10,2:8:284:2:4:0,-25.5203 0:6:6,0:6:222:0:0:0,-20.336 0:8:8,0:8:277:0:0:0,-25.2635 +Chromosome 500039 . T C 6.66012E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=34;DPB=34;DPRA=1.25;EPP=7.35324;EPPR=42.0968;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=44.0479;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=26;QR=947;RO=32;RPL=2;RPP=7.35324;RPPR=24.9965;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=27;SRP=35.8538;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|bfrG|PA14_05640|transcript|ABJ15401.1|protein_coding|1/1|c.325T>C|p.Phe109Leu|325/2193|325/2193|109/730||,C|upstream_gene_variant|MODIFIER|PA14_05580|PA14_05580|transcript|ABJ15396.1|protein_coding||c.-4162A>G|||||4162|,C|upstream_gene_variant|MODIFIER|metF|PA14_05590|transcript|ABJ15397.1|protein_coding||c.-3220A>G|||||3220|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_05600|PA14_05600|transcript|ABJ15398.1|protein_coding||c.-2623A>G|||||2623|,C|upstream_gene_variant|MODIFIER|sahH|PA14_05620|transcript|ABJ15399.1|protein_coding||c.-1173A>G|||||1173|,C|upstream_gene_variant|MODIFIER|PA14_05650|PA14_05650|transcript|ABJ15402.1|protein_coding||c.-1879T>C|||||1879|,C|upstream_gene_variant|MODIFIER|PA14_05660|PA14_05660|transcript|ABJ15403.1|protein_coding||c.-3442T>C|||||3442|,C|downstream_gene_variant|MODIFIER|PA14_05630|PA14_05630|transcript|ABJ15400.1|protein_coding||c.*450T>C|||||450|,C|downstream_gene_variant|MODIFIER|codA|PA14_05690|transcript|ABJ15404.1|protein_coding||c.*4099A>G|||||4099| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:132:0:0:0,-12.1988 0:11:11,0:11:274:0:0:0,-24.9032 0:10:10,2:8:288:2:26:0,-23.7938 0:9:9,0:9:253:0:0:0,-23.0419 +Chromosome 500057 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=41;DPB=41;DPRA=2.4;EPP=13.8677;EPPR=30.3709;GTI=0;LEN=1;MEANALT=1.33333;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=49.7319;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=62;QR=1141;RO=35;RPL=5;RPP=13.8677;RPPR=6.05036;RPR=0;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=22;SRP=8.03571;SRR=13;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|bfrG|PA14_05640|transcript|ABJ15401.1|protein_coding|1/1|c.343T>C|p.Tyr115His|343/2193|343/2193|115/730||,C|upstream_gene_variant|MODIFIER|PA14_05580|PA14_05580|transcript|ABJ15396.1|protein_coding||c.-4180A>G|||||4180|,C|upstream_gene_variant|MODIFIER|metF|PA14_05590|transcript|ABJ15397.1|protein_coding||c.-3238A>G|||||3238|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_05600|PA14_05600|transcript|ABJ15398.1|protein_coding||c.-2641A>G|||||2641|,C|upstream_gene_variant|MODIFIER|sahH|PA14_05620|transcript|ABJ15399.1|protein_coding||c.-1191A>G|||||1191|,C|upstream_gene_variant|MODIFIER|PA14_05650|PA14_05650|transcript|ABJ15402.1|protein_coding||c.-1861T>C|||||1861|,C|upstream_gene_variant|MODIFIER|PA14_05660|PA14_05660|transcript|ABJ15403.1|protein_coding||c.-3424T>C|||||3424|,C|downstream_gene_variant|MODIFIER|PA14_05630|PA14_05630|transcript|ABJ15400.1|protein_coding||c.*468T>C|||||468|,C|downstream_gene_variant|MODIFIER|codA|PA14_05690|transcript|ABJ15404.1|protein_coding||c.*4081A>G|||||4081| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:181:0:0:0,-16.6397 0:10:10,3:7:213:3:45:0,-15.2619 0:13:13,1:12:407:1:2:0,-36.7449 0:13:13,1:11:340:1:15:0,-29.2987 +Chromosome 512921 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=38;DPB=38;DPRA=1.07143;EPP=7.35324;EPPR=3.25157;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=76.2088;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1308;RO=36;RPL=0;RPP=7.35324;RPPR=5.18177;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=10;SRP=18.4519;SRR=26;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_05790|PA14_05790|transcript|ABJ15409.1|protein_coding|1/1|c.1300T>G|p.Trp434Gly|1300/1491|1300/1491|434/496||,G|upstream_gene_variant|MODIFIER|pydA|PA14_05740|transcript|ABJ15406.1|protein_coding||c.-4813A>C|||||4813|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|gltX|PA14_05750|transcript|ABJ15407.1|protein_coding||c.-3449A>C|||||3449|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|dhT|PA14_05770|transcript|ABJ15408.1|protein_coding||c.-1915A>C|||||1915|,G|upstream_gene_variant|MODIFIER|PA14_05775|PA14_05775|transcript|ABJ15640.1|protein_coding||c.-1692A>C|||||1692|,G|upstream_gene_variant|MODIFIER|amaB|PA14_05810|transcript|ABJ15410.1|protein_coding||c.-250T>G|||||250|,G|upstream_gene_variant|MODIFIER|PA14_05850|PA14_05850|transcript|ABJ15413.1|protein_coding||c.-4479T>G|||||4479|,G|downstream_gene_variant|MODIFIER|PA14_05820|PA14_05820|transcript|ABJ15411.1|protein_coding||c.*1734A>C|||||1734|,G|downstream_gene_variant|MODIFIER|gcdH|PA14_05840|transcript|ABJ15412.1|protein_coding||c.*3077A>C|||||3077| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,2:8:314:2:4:0,-28.2452 0:8:8,0:8:295:0:0:0,-26.9004 0:9:9,0:9:322:0:0:0,-29.3143 0:11:11,0:11:377:0:0:0,-34.245 +Chromosome 514489 . C T 4.1742E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=20;DPB=20;DPRA=2;EPP=3.0103;EPPR=3.49285;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=38.2329;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=651;RO=18;RPL=1;RPP=3.0103;RPPR=4.9405;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=7;SRP=4.9405;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=T|upstream_gene_variant|MODIFIER|dhT|PA14_05770|transcript|ABJ15408.1|protein_coding||c.-3483G>A|||||3483|,T|upstream_gene_variant|MODIFIER|PA14_05775|PA14_05775|transcript|ABJ15640.1|protein_coding||c.-3260G>A|||||3260|,T|upstream_gene_variant|MODIFIER|PA14_05850|PA14_05850|transcript|ABJ15413.1|protein_coding||c.-2911C>T|||||2911|,T|upstream_gene_variant|MODIFIER|PA14_05860|PA14_05860|transcript|ABJ15414.1|protein_coding||c.-3971C>T|||||3971|,T|downstream_gene_variant|MODIFIER|PA14_05790|PA14_05790|transcript|ABJ15409.1|protein_coding||c.*1377C>T|||||1377|,T|downstream_gene_variant|MODIFIER|amaB|PA14_05810|transcript|ABJ15410.1|protein_coding||c.*35C>T|||||35|,T|downstream_gene_variant|MODIFIER|PA14_05820|PA14_05820|transcript|ABJ15411.1|protein_coding||c.*166G>A|||||166|,T|downstream_gene_variant|MODIFIER|gcdH|PA14_05840|transcript|ABJ15412.1|protein_coding||c.*1509G>A|||||1509|,T|downstream_gene_variant|MODIFIER|PA14_05870|PA14_05870|transcript|ABJ15415.1|protein_coding||c.*4418G>A|||||4418|,T|intergenic_region|MODIFIER|amaB-PA14_05820|PA14_05810-PA14_05820|intergenic_region|PA14_05810-PA14_05820|||n.514489C>T|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:151:0:0:0,-13.9563 0:4:4,0:4:149:0:0:0,-13.7733 0:4:4,0:4:121:0:0:0,-11.1813 0:8:8,2:6:230:2:31:0,-18.1206 +Chromosome 530585 . A G 4.1114E-12 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=31;DPB=31;DPRA=0.444444;EPP=7.35324;EPPR=3.08518;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=27.6857;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1016;RO=29;RPL=0;RPP=7.35324;RPPR=4.88226;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=6;SRP=24.6501;SRR=23;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|PA14_05920|PA14_05920|transcript|ABJ15419.1|protein_coding||c.-4517T>C|||||4517|,G|upstream_gene_variant|MODIFIER|dbpA|PA14_05950|transcript|ABJ15420.1|protein_coding||c.-2879T>C|||||2879|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|emrA|PA14_05990|transcript|ABJ15423.1|protein_coding||c.-111T>C|||||111|,G|upstream_gene_variant|MODIFIER|clpA|PA14_06000|transcript|ABJ15424.1|protein_coding||c.-510A>G|||||510|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_06010|PA14_06010|transcript|ABJ15425.1|protein_coding||c.-3164A>G|||||3164|,G|upstream_gene_variant|MODIFIER|PA14_06040|PA14_06040|transcript|ABJ15426.1|protein_coding||c.-4694A>G|||||4694|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|cspB|PA14_05960|transcript|ABJ15421.1|protein_coding||c.*2322A>G|||||2322|,G|downstream_gene_variant|MODIFIER|PA14_05970|PA14_05970|transcript|ABJ15422.1|protein_coding||c.*1647A>G|||||1647|,G|downstream_gene_variant|MODIFIER|PA14_06030|PA14_06030|transcript|ABJ15427.1|protein_coding||c.*3859T>C|||||3859|,G|intergenic_region|MODIFIER|emrA-clpA|PA14_05990-PA14_06000|intergenic_region|PA14_05990-PA14_06000|||n.530585A>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,2:2:67:2:17:0,-4.7457 0:5:5,0:5:181:0:0:0,-16.6403 0:10:10,0:10:340:0:0:0,-30.918 0:12:12,0:12:428:0:0:0,-38.8463 +Chromosome 531579 . T C 1.75992E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=26;DPB=26;DPRA=1.6;EPP=9.52472;EPPR=18.9659;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=34.8604;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=28;QR=872;RO=23;RPL=3;RPP=9.52472;RPPR=7.63648;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=16;SRP=10.6577;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|clpA|PA14_06000|transcript|ABJ15424.1|protein_coding|1/1|c.485T>C|p.Leu162Pro|485/2553|485/2553|162/850||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|dbpA|PA14_05950|transcript|ABJ15420.1|protein_coding||c.-3873A>G|||||3873|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|emrA|PA14_05990|transcript|ABJ15423.1|protein_coding||c.-1105A>G|||||1105|,C|upstream_gene_variant|MODIFIER|PA14_06010|PA14_06010|transcript|ABJ15425.1|protein_coding||c.-2170T>C|||||2170|,C|upstream_gene_variant|MODIFIER|PA14_06040|PA14_06040|transcript|ABJ15426.1|protein_coding||c.-3700T>C|||||3700|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|creB|PA14_06060|transcript|ABJ15428.1|protein_coding||c.-4489T>C|||||4489|,C|downstream_gene_variant|MODIFIER|cspB|PA14_05960|transcript|ABJ15421.1|protein_coding||c.*3316T>C|||||3316|,C|downstream_gene_variant|MODIFIER|PA14_05970|PA14_05970|transcript|ABJ15422.1|protein_coding||c.*2641T>C|||||2641|,C|downstream_gene_variant|MODIFIER|PA14_06030|PA14_06030|transcript|ABJ15427.1|protein_coding||c.*2865A>G|||||2865| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:112:0:0:0,-10.4463 0:7:7,0:7:260:0:0:0,-23.7538 0:7:7,1:6:227:1:24:0,-18.3914 0:9:9,2:7:273:2:4:0,-24.5567 +Chromosome 533009 . G C 7.60232E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=49;DPB=49;DPRA=0.814815;EPP=11.6962;EPPR=3.79993;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=63.2342;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1267;RO=44;RPL=4;RPP=11.6962;RPPR=3.0103;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=36;SRP=41.702;SRR=8;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|clpA|PA14_06000|transcript|ABJ15424.1|protein_coding|1/1|c.1915G>C|p.Gly639Arg|1915/2553|1915/2553|639/850||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|emrA|PA14_05990|transcript|ABJ15423.1|protein_coding||c.-2535C>G|||||2535|,C|upstream_gene_variant|MODIFIER|PA14_06010|PA14_06010|transcript|ABJ15425.1|protein_coding||c.-740G>C|||||740|,C|upstream_gene_variant|MODIFIER|PA14_06040|PA14_06040|transcript|ABJ15426.1|protein_coding||c.-2270G>C|||||2270|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|creB|PA14_06060|transcript|ABJ15428.1|protein_coding||c.-3059G>C|||||3059|,C|upstream_gene_variant|MODIFIER|creC|PA14_06070|transcript|ABJ15429.1|protein_coding||c.-3748G>C|||||3748|,C|downstream_gene_variant|MODIFIER|cspB|PA14_05960|transcript|ABJ15421.1|protein_coding||c.*4746G>C|||||4746|,C|downstream_gene_variant|MODIFIER|PA14_05970|PA14_05970|transcript|ABJ15422.1|protein_coding||c.*4071G>C|||||4071|,C|downstream_gene_variant|MODIFIER|PA14_06030|PA14_06030|transcript|ABJ15427.1|protein_coding||c.*1435C>G|||||1435| GT:DP:DPR:RO:QR:AO:QA:GL 0:12:12,3:9:230:3:6:0,-20.3781 0:9:9,0:9:249:0:0:0,-22.6676 0:10:10,1:9:263:1:2:0,-23.7438 0:18:18,0:17:525:0:0:0,-47.4883 +Chromosome 552911 . A G 3.32127E-7 . AB=0;ABP=0;AC=0;AF=0;AN=3;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=5;EPP=7.35324;EPPR=6.91895;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=17.0726;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=77;QR=194;RO=5;RPL=1;RPP=3.0103;RPPR=6.91895;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=3;SRP=3.44459;SRR=2;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_06260|PA14_06260|transcript|ABJ15444.1|protein_coding|1/1|c.613T>C|p.Ser205Pro|613/939|613/939|205/312||,G|upstream_gene_variant|MODIFIER|PA14_06230|PA14_06230|transcript|ABJ15441.1|protein_coding||c.-2243T>C|||||2243|,G|upstream_gene_variant|MODIFIER|PA14_06240|PA14_06240|transcript|ABJ15442.1|protein_coding||c.-969T>C|||||969|,G|upstream_gene_variant|MODIFIER|catD|PA14_06270|transcript|ABJ15445.1|protein_coding||c.-716A>G|||||716|,G|upstream_gene_variant|MODIFIER|PA14_06280|PA14_06280|transcript|ABJ15446.1|protein_coding||c.-1556A>G|||||1556|,G|upstream_gene_variant|MODIFIER|PA14_06300|PA14_06300|transcript|ABJ15448.1|protein_coding||c.-4531A>G|||||4531|,G|downstream_gene_variant|MODIFIER|PA14_06200|PA14_06200|transcript|ABJ15439.1|protein_coding||c.*4623A>G|||||4623|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_06210|PA14_06210|transcript|ABJ15440.1|protein_coding||c.*4004A>G|||||4004|,G|downstream_gene_variant|MODIFIER|PA14_06250|PA14_06250|transcript|ABJ15443.1|protein_coding||c.*405A>G|||||405|,G|downstream_gene_variant|MODIFIER|glcB|PA14_06290|transcript|ABJ15447.1|protein_coding||c.*2047T>C|||||2047| GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:39:0:0:0,-3.89656 . 0:1:1,0:1:40:0:0:0,-3.99568 0:5:5,2:3:115:2:77:0,-3.41516 +Chromosome 584216 . G C 2.90074E-8 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=1.71429;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=18.8275;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=320;RO=9;RPL=2;RPP=7.35324;RPPR=3.25157;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=5.18177;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|nirJ|PA14_06670|transcript|ABJ15473.1|protein_coding|1/1|c.358C>G|p.Arg120Gly|358/1164|358/1164|120/387||,C|upstream_gene_variant|MODIFIER|nirN|PA14_06650|transcript|ABJ15471.1|protein_coding||c.-1647C>G|||||1647|,C|upstream_gene_variant|MODIFIER|nirE|PA14_06660|transcript|ABJ15472.1|protein_coding||c.-817C>G|||||817|,C|downstream_gene_variant|MODIFIER|PA14_06640|PA14_06640|transcript|ABJ15470.1|protein_coding||c.*3461G>C|||||3461|,C|downstream_gene_variant|MODIFIER|nirH|PA14_06680|transcript|ABJ15474.1|protein_coding||c.*351C>G|||||351|,C|downstream_gene_variant|MODIFIER|nirG|PA14_06690|transcript|ABJ15475.1|protein_coding||c.*841C>G|||||841|,C|downstream_gene_variant|MODIFIER|nirL|PA14_06700|transcript|ABJ15476.1|protein_coding||c.*1277C>G|||||1277|,C|downstream_gene_variant|MODIFIER|nirD|PA14_06710|transcript|ABJ15477.1|protein_coding||c.*1798C>G|||||1798|,C|downstream_gene_variant|MODIFIER|nirF|PA14_06720|transcript|ABJ15478.1|protein_coding||c.*2259C>G|||||2259|,C|downstream_gene_variant|MODIFIER|nirC|PA14_06730|transcript|ABJ15479.1|protein_coding||c.*3434C>G|||||3434|,C|downstream_gene_variant|MODIFIER|nirM|PA14_06740|transcript|ABJ15480.1|protein_coding||c.*3790C>G|||||3790|,C|downstream_gene_variant|MODIFIER|nirS|PA14_06750|transcript|ABJ15481.1|protein_coding||c.*4155C>G|||||4155| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:77:0:0:0,-7.30914 0:4:4,2:2:73:2:18:0,-5.22009 0:1:1,0:1:40:0:0:0,-3.99568 0:4:4,0:4:130:0:0:0,-12.0155 +Chromosome 585483 . C G 4.36789E-12 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=14;DPB=14;DPRA=1.66667;EPP=7.35324;EPPR=5.9056;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=27.6754;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=421;RO=12;RPL=1;RPP=3.0103;RPPR=14.5915;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=2;SRP=14.5915;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|nirG|PA14_06690|transcript|ABJ15475.1|protein_coding|1/1|c.18G>C|p.Arg6Arg|18/444|18/444|6/147||,G|upstream_gene_variant|MODIFIER|nirN|PA14_06650|transcript|ABJ15471.1|protein_coding||c.-2914G>C|||||2914|,G|upstream_gene_variant|MODIFIER|nirE|PA14_06660|transcript|ABJ15472.1|protein_coding||c.-2084G>C|||||2084|,G|upstream_gene_variant|MODIFIER|nirJ|PA14_06670|transcript|ABJ15473.1|protein_coding||c.-910G>C|||||910|,G|upstream_gene_variant|MODIFIER|nirH|PA14_06680|transcript|ABJ15474.1|protein_coding||c.-401G>C|||||401|,G|upstream_gene_variant|MODIFIER|nirQ|PA14_06770|transcript|ABJ15482.1|protein_coding||c.-4810C>G|||||4810|,G|downstream_gene_variant|MODIFIER|PA14_06640|PA14_06640|transcript|ABJ15470.1|protein_coding||c.*4728C>G|||||4728|,G|downstream_gene_variant|MODIFIER|nirL|PA14_06700|transcript|ABJ15476.1|protein_coding||c.*10G>C|||||10|,G|downstream_gene_variant|MODIFIER|nirD|PA14_06710|transcript|ABJ15477.1|protein_coding||c.*531G>C|||||531|,G|downstream_gene_variant|MODIFIER|nirF|PA14_06720|transcript|ABJ15478.1|protein_coding||c.*992G>C|||||992|,G|downstream_gene_variant|MODIFIER|nirC|PA14_06730|transcript|ABJ15479.1|protein_coding||c.*2167G>C|||||2167|,G|downstream_gene_variant|MODIFIER|nirM|PA14_06740|transcript|ABJ15480.1|protein_coding||c.*2523G>C|||||2523|,G|downstream_gene_variant|MODIFIER|nirS|PA14_06750|transcript|ABJ15481.1|protein_coding||c.*2888G>C|||||2888| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:79:0:0:0,-7.49763 0:5:5,2:3:108:2:4:0,-9.69393 0:3:3,0:3:113:0:0:0,-10.5384 0:4:4,0:4:121:0:0:0,-11.1813 +Chromosome 617338 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=35;DPB=35;DPRA=0.75;EPP=7.35324;EPPR=22.0271;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=42.0995;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=55;QR=1207;RO=33;RPL=0;RPP=7.35324;RPPR=10.9724;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=20;SRP=6.23461;SRR=13;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|tktA|PA14_07130|transcript|ABJ15511.1|protein_coding|1/1|c.1204G>A|p.Gly402Ser|1204/1998|1204/1998|402/665||,A|upstream_gene_variant|MODIFIER|metK|PA14_07090|transcript|ABJ15509.1|protein_coding||c.-2466C>T|||||2466|,A|upstream_gene_variant|MODIFIER|PA14_07110|PA14_07110|transcript|ABJ15510.1|protein_coding||c.-1449C>T|||||1449|,A|upstream_gene_variant|MODIFIER|PA14_07140|PA14_07140|transcript|ABJ15512.1|protein_coding||c.-794G>A|||||794|,A|upstream_gene_variant|MODIFIER|epd|PA14_07170|transcript|ABJ15514.1|protein_coding||c.-2851G>A|||||2851|,A|upstream_gene_variant|MODIFIER|pgk|PA14_07190|transcript|ABJ15515.1|protein_coding||c.-3918G>A|||||3918|,A|downstream_gene_variant|MODIFIER|PA14_07070|PA14_07070|transcript|ABJ15508.1|protein_coding||c.*3713G>A|||||3713|,A|downstream_gene_variant|MODIFIER|hyi|PA14_07150|transcript|ABJ15513.1|protein_coding||c.*1839C>T|||||1839| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:151:0:0:0,-13.9568 0:12:12,0:12:425:0:0:0,-38.5746 0:12:12,0:12:446:0:0:0,-40.4839 0:7:7,2:5:185:2:55:0,-11.7876 +Chromosome 619871 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=39;DPB=39;DPRA=0.95;EPP=9.52472;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=55.6667;MQMR=60;NS=4;NUMALT=1;ODDS=62.3331;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=1253;RO=36;RPL=0;RPP=9.52472;RPPR=3.0103;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=25;SRP=14.8328;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|hyi|PA14_07150|transcript|ABJ15513.1|protein_coding|1/1|c.104T>C|p.Leu35Pro|104/798|104/798|35/265||,G|upstream_gene_variant|MODIFIER|metK|PA14_07090|transcript|ABJ15509.1|protein_coding||c.-4999T>C|||||4999|,G|upstream_gene_variant|MODIFIER|PA14_07110|PA14_07110|transcript|ABJ15510.1|protein_coding||c.-3982T>C|||||3982|,G|upstream_gene_variant|MODIFIER|epd|PA14_07170|transcript|ABJ15514.1|protein_coding||c.-318A>G|||||318|,G|upstream_gene_variant|MODIFIER|pgk|PA14_07190|transcript|ABJ15515.1|protein_coding||c.-1385A>G|||||1385|,G|upstream_gene_variant|MODIFIER|PA14_07200|PA14_07200|transcript|ABJ15516.1|protein_coding||c.-2621A>G|||||2621|,G|upstream_gene_variant|MODIFIER|PA14_07210|PA14_07210|transcript|ABJ15517.1|protein_coding||c.-2981A>G|||||2981|,G|upstream_gene_variant|MODIFIER|fda|PA14_07230|transcript|ABJ15518.1|protein_coding||c.-3442A>G|||||3442|,G|upstream_gene_variant|MODIFIER|PA14_07240|PA14_07240|transcript|ABJ15519.1|protein_coding||c.-4572A>G|||||4572|,G|downstream_gene_variant|MODIFIER|tktA|PA14_07130|transcript|ABJ15511.1|protein_coding||c.*1739A>G|||||1739|,G|downstream_gene_variant|MODIFIER|PA14_07140|PA14_07140|transcript|ABJ15512.1|protein_coding||c.*675A>G|||||675| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,0:9:320:0:0:0,-29.1257 0:11:11,1:10:291:1:2:0,-26.2585 0:11:11,0:11:419:0:0:0,-38.0586 0:8:8,2:6:223:2:4:0,-20.0445 +Chromosome 623466 . G C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=56;DPB=56;DPRA=0.5;EPP=7.35324;EPPR=3.17115;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=68.0237;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1903;RO=54;RPL=2;RPP=7.35324;RPPR=8.80089;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=29;SRP=3.6537;SRR=25;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|fda|PA14_07230|transcript|ABJ15518.1|protein_coding|1/1|c.154G>C|p.Gly52Arg|154/1065|154/1065|52/354||,C|upstream_gene_variant|MODIFIER|hyi|PA14_07150|transcript|ABJ15513.1|protein_coding||c.-3492C>G|||||3492|,C|upstream_gene_variant|MODIFIER|PA14_07240|PA14_07240|transcript|ABJ15519.1|protein_coding||c.-977G>C|||||977|,C|upstream_gene_variant|MODIFIER|PA14_07260|PA14_07260|transcript|ABJ15520.1|protein_coding||c.-2116G>C|||||2116|,C|upstream_gene_variant|MODIFIER|ygjP|PA14_07290|transcript|ABJ15523.1|protein_coding||c.-4171G>C|||||4171|,C|upstream_gene_variant|MODIFIER|PA14_07300|PA14_07300|transcript|ABJ15524.1|protein_coding||c.-4685G>C|||||4685|,C|downstream_gene_variant|MODIFIER|PA14_07140|PA14_07140|transcript|ABJ15512.1|protein_coding||c.*4270G>C|||||4270|,C|downstream_gene_variant|MODIFIER|epd|PA14_07170|transcript|ABJ15514.1|protein_coding||c.*2216G>C|||||2216|,C|downstream_gene_variant|MODIFIER|pgk|PA14_07190|transcript|ABJ15515.1|protein_coding||c.*1047G>C|||||1047|,C|downstream_gene_variant|MODIFIER|PA14_07200|PA14_07200|transcript|ABJ15516.1|protein_coding||c.*774G>C|||||774|,C|downstream_gene_variant|MODIFIER|PA14_07210|PA14_07210|transcript|ABJ15517.1|protein_coding||c.*273G>C|||||273|,C|downstream_gene_variant|MODIFIER|PA14_07250|PA14_07250|transcript|ABJ15521.1|protein_coding||c.*1461C>G|||||1461|,C|downstream_gene_variant|MODIFIER|yhiN|PA14_07280|transcript|ABJ15522.1|protein_coding||c.*2880C>G|||||2880|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:11:11,0:11:379:0:0:0,-34.4345 0:18:18,0:18:599:0:0:0,-54.2046 0:19:19,0:19:700:0:0:0,-63.3114 0:8:8,2:6:225:2:4:0,-20.2294 +Chromosome 644984 . T G 2.0419E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=65;DPB=65;DPRA=0.756757;EPP=9.52472;EPPR=3.15039;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=69.7792;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=2068;RO=62;RPL=3;RPP=9.52472;RPPR=5.25182;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=25;SRP=8.05372;SRR=37;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_07500|PA14_07500|transcript|ABJ15539.1|protein_coding|1/1|c.2101A>C|p.Thr701Pro|2101/3738|2101/3738|701/1245||,G|upstream_gene_variant|MODIFIER|PA14_07460|PA14_07460|transcript|ABJ15537.1|protein_coding||c.-4706A>C|||||4706|,G|upstream_gene_variant|MODIFIER|PA14_07470|PA14_07470|transcript|PA14_07470-1.1|protein_coding||c.-4501A>C|||||4501|WARNING_TRANSCRIPT_INCOMPLETE,G|upstream_gene_variant|MODIFIER|PA14_07480|PA14_07480|transcript|ABJ15538.1|protein_coding||c.-2718A>C|||||2718|,G|downstream_gene_variant|MODIFIER|tRNA|EBG00001225084|transcript|EBT00001793438.1|protein_coding||c.*4501T>G|||||4501|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|rpoD|PA14_07520|transcript|ABJ15540.1|protein_coding||c.*2207A>C|||||2207|,G|downstream_gene_variant|MODIFIER|dnaG|PA14_07530|transcript|ABJ15541.1|protein_coding||c.*4140A>C|||||4140| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,2:7:228:2:4:0,-20.4506 0:16:16,0:16:546:0:0:0,-49.4414 0:19:19,1:18:602:1:2:0,-54.271 0:21:21,0:21:692:0:0:0,-62.5576 +Chromosome 650614 . T G 1.58557E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=34;DPB=34;DPRA=1.61538;EPP=9.52472;EPPR=3.64073;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=30.9305;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=893;RO=31;RPL=0;RPP=9.52472;RPPR=3.64073;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=7;SRP=23.254;SRR=24;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|dnaG|PA14_07530|transcript|ABJ15541.1|protein_coding|1/1|c.505A>C|p.Asn169His|505/1995|505/1995|169/664||,G|upstream_gene_variant|MODIFIER|PA14_07500|PA14_07500|transcript|ABJ15539.1|protein_coding||c.-3530A>C|||||3530|,G|upstream_gene_variant|MODIFIER|rpoD|PA14_07520|transcript|ABJ15540.1|protein_coding||c.-1570A>C|||||1570|,G|upstream_gene_variant|MODIFIER|gcp|PA14_07570|transcript|ABJ15544.1|protein_coding||c.-1522T>G|||||1522|,G|upstream_gene_variant|MODIFIER|folB|PA14_07590|transcript|ABJ15546.1|protein_coding||c.-3279T>G|||||3279|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|folK|PA14_07600|transcript|ABJ15547.1|protein_coding||c.-3623T>G|||||3623|,G|downstream_gene_variant|MODIFIER|PA14_07550|PA14_07550|transcript|ABJ15542.1|protein_coding||c.*587A>C|||||587|,G|downstream_gene_variant|MODIFIER|rpsU|PA14_07560|transcript|ABJ15543.1|protein_coding||c.*1106A>C|||||1106|,G|downstream_gene_variant|MODIFIER|PA14_07580|PA14_07580|transcript|ABJ15545.1|protein_coding||c.*2626A>C|||||2626|,G|downstream_gene_variant|MODIFIER|cca|PA14_07620|transcript|ABJ15548.1|protein_coding||c.*4138A>C|||||4138| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,0:10:278:0:0:0,-25.2754 0:12:12,1:11:314:1:2:0,-28.3179 0:3:3,0:3:71:0:0:0,-6.62261 0:9:9,2:7:230:2:4:0,-20.6318 +Chromosome 655050 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=36;DPB=36;DPRA=1.16667;EPP=11.6962;EPPR=3.08035;GTI=0;LEN=1;MEANALT=1.33333;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=45.8645;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=1115;RO=31;RPL=0;RPP=11.6962;RPPR=4.76149;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=21;SRP=11.486;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|cca|PA14_07620|transcript|ABJ15548.1|protein_coding|1/1|c.935T>C|p.Leu312Pro|935/1233|935/1233|312/410||,G|upstream_gene_variant|MODIFIER|dnaG|PA14_07530|transcript|ABJ15541.1|protein_coding||c.-3932T>C|||||3932|,G|upstream_gene_variant|MODIFIER|PA14_07550|PA14_07550|transcript|ABJ15542.1|protein_coding||c.-3400T>C|||||3400|,G|upstream_gene_variant|MODIFIER|rpsU|PA14_07560|transcript|ABJ15543.1|protein_coding||c.-3115T>C|||||3115|,G|upstream_gene_variant|MODIFIER|PA14_07580|PA14_07580|transcript|ABJ15545.1|protein_coding||c.-1241T>C|||||1241|,G|downstream_gene_variant|MODIFIER|gcp|PA14_07570|transcript|ABJ15544.1|protein_coding||c.*1889A>G|||||1889|,G|downstream_gene_variant|MODIFIER|folB|PA14_07590|transcript|ABJ15546.1|protein_coding||c.*804A>G|||||804|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|folK|PA14_07600|transcript|ABJ15547.1|protein_coding||c.*271A>G|||||271|,G|downstream_gene_variant|MODIFIER|PA14_07630|PA14_07630|transcript|ABJ15549.1|protein_coding||c.*978T>C|||||978|,G|downstream_gene_variant|MODIFIER|ycgB|PA14_07650|transcript|ABJ15550.1|protein_coding||c.*1579T>C|||||1579|,G|downstream_gene_variant|MODIFIER|PA14_07660|PA14_07660|transcript|ABJ15551.1|protein_coding||c.*3129T>C|||||3129|,G|downstream_gene_variant|MODIFIER|prkA|PA14_07680|transcript|ABJ15552.1|protein_coding||c.*4501T>C|||||4501| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,1:7:244:1:2:0,-22.0911 0:8:8,0:8:316:0:0:0,-28.8065 0:7:7,2:5:162:2:15:0,-13.4669 0:13:13,1:11:393:1:2:0,-35.4686 +Chromosome 657129 . A G 5.07049E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=32;DPB=32;DPRA=0.684211;EPP=9.52472;EPPR=4.88226;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=41.783;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=26;QR=978;RO=29;RPL=0;RPP=9.52472;RPPR=15.6647;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=12;SRP=4.88226;SRR=17;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|ycgB|PA14_07650|transcript|ABJ15550.1|protein_coding|1/1|c.1054T>C|p.Trp352Arg|1054/1554|1054/1554|352/517||,G|upstream_gene_variant|MODIFIER|PA14_07580|PA14_07580|transcript|ABJ15545.1|protein_coding||c.-3320T>C|||||3320|,G|upstream_gene_variant|MODIFIER|cca|PA14_07620|transcript|ABJ15548.1|protein_coding||c.-1145T>C|||||1145|,G|upstream_gene_variant|MODIFIER|PA14_07630|PA14_07630|transcript|ABJ15549.1|protein_coding||c.-595T>C|||||595|,G|downstream_gene_variant|MODIFIER|gcp|PA14_07570|transcript|ABJ15544.1|protein_coding||c.*3968A>G|||||3968|,G|downstream_gene_variant|MODIFIER|folB|PA14_07590|transcript|ABJ15546.1|protein_coding||c.*2883A>G|||||2883|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|folK|PA14_07600|transcript|ABJ15547.1|protein_coding||c.*2350A>G|||||2350|,G|downstream_gene_variant|MODIFIER|PA14_07660|PA14_07660|transcript|ABJ15551.1|protein_coding||c.*1050T>C|||||1050|,G|downstream_gene_variant|MODIFIER|prkA|PA14_07680|transcript|ABJ15552.1|protein_coding||c.*2422T>C|||||2422|,G|downstream_gene_variant|MODIFIER|glpE|PA14_07690|transcript|ABJ15553.1|protein_coding||c.*4623T>C|||||4623|,G|downstream_gene_variant|MODIFIER|apaH|PA14_07700|transcript|ABJ15554.1|protein_coding||c.*4999T>C|||||4999| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,2:5:168:2:24:0,-13.1639 0:6:6,1:5:194:1:2:0,-17.6317 0:13:13,0:13:473:0:0:0,-42.8988 0:6:6,0:6:143:0:0:0,-13.1035 +Chromosome 671785 . A C 2.2285E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=37;DPB=37;DPRA=0.85;EPP=9.52472;EPPR=5.30951;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=38.9843;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=1144;RO=34;RPL=3;RPP=9.52472;RPPR=3.0103;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=31;SRP=53.0819;SRR=3;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|djlA|PA14_07800|transcript|ABJ15562.1|protein_coding|1/1|c.622A>C|p.Lys208Gln|622/759|622/759|208/252||,C|upstream_gene_variant|MODIFIER|ostA|PA14_07770|transcript|ABJ15559.1|protein_coding||c.-2437T>G|||||2437|,C|upstream_gene_variant|MODIFIER|PA14_07820|PA14_07820|transcript|ABJ15564.1|protein_coding||c.-1351A>C|||||1351|,C|upstream_gene_variant|MODIFIER|uhpA|PA14_07840|transcript|ABJ15565.1|protein_coding||c.-3790A>C|||||3790|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_07850|PA14_07850|transcript|ABJ15566.1|protein_coding||c.-4551A>C|||||4551|,C|downstream_gene_variant|MODIFIER|PA14_07780|PA14_07780|transcript|ABJ15560.1|protein_coding||c.*1294A>C|||||1294|,C|downstream_gene_variant|MODIFIER|PA14_07790|PA14_07790|transcript|ABJ15561.1|protein_coding||c.*623A>C|||||623|,C|downstream_gene_variant|MODIFIER|PA14_07810|PA14_07810|transcript|ABJ15563.1|protein_coding||c.*138T>G|||||138| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,2:3:113:2:4:0,-10.1584 0:8:8,0:8:265:0:0:0,-24.1651 0:12:12,1:11:330:1:15:0,-28.479 0:12:12,0:12:436:0:0:0,-39.5766 +Chromosome 683368 . T G 8.63775E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=31;DPB=31;DPRA=0.72;EPP=7.35324;EPPR=9.07545;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=39.6044;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=878;RO=29;RPL=0;RPP=7.35324;RPPR=3.08518;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=8;SRP=15.6647;SRR=21;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|gph|PA14_07930|transcript|ABJ15572.1|protein_coding|1/1|c.458T>G|p.Leu153Arg|458/819|458/819|153/272||,G|upstream_gene_variant|MODIFIER|trpE|PA14_07940|transcript|ABJ15573.1|protein_coding||c.-434T>G|||||434|,G|upstream_gene_variant|MODIFIER|PA14_07970|PA14_07970|transcript|ABJ15576.1|protein_coding||c.-3741T>G|||||3741|,G|upstream_gene_variant|MODIFIER|PA14_07980|PA14_07980|transcript|ABJ15577.1|protein_coding||c.-3989T>G|||||3989|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|hol|PA14_07990|transcript|ABJ15578.1|protein_coding||c.-4712T>G|||||4712|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_07860|PA14_07860|transcript|ABJ15567.1|protein_coding||c.*4655T>G|||||4655|,G|downstream_gene_variant|MODIFIER|PA14_07870|PA14_07870|transcript|ABJ15568.1|protein_coding||c.*3553T>G|||||3553|,G|downstream_gene_variant|MODIFIER|PA14_07890|PA14_07890|transcript|ABJ15569.1|protein_coding||c.*2191T>G|||||2191|,G|downstream_gene_variant|MODIFIER|PA14_07900|PA14_07900|transcript|ABJ15570.1|protein_coding||c.*1255T>G|||||1255|,G|downstream_gene_variant|MODIFIER|rpe|PA14_07910|transcript|ABJ15571.1|protein_coding||c.*457T>G|||||457|,G|downstream_gene_variant|MODIFIER|prtN|PA14_07950|transcript|ABJ15574.1|protein_coding||c.*2099A>C|||||2099|,G|downstream_gene_variant|MODIFIER|prtR|PA14_07960|transcript|ABJ15575.1|protein_coding||c.*2513A>C|||||2513| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:153:0:0:0,-14.1409 0:8:8,0:8:234:0:0:0,-21.3435 0:6:6,2:4:125:2:15:0,-10.1303 0:13:13,0:13:366:0:0:0,-33.2062 +Chromosome 687865 . T A 1.96114E-16 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=58;DPB=58;DPRA=0.55102;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6667;NS=4;NUMALT=1;ODDS=55.5042;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=1662;RO=54;RPL=2;RPP=7.35324;RPPR=3.0103;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=26;SRP=3.17115;SRR=28;TYPE=snp;technology.ILLUMINA=1;ANN=A|upstream_gene_variant|MODIFIER|prtN|PA14_07950|transcript|ABJ15574.1|protein_coding||c.-2084A>T|||||2084|,A|upstream_gene_variant|MODIFIER|prtR|PA14_07960|transcript|ABJ15575.1|protein_coding||c.-1214A>T|||||1214|,A|upstream_gene_variant|MODIFIER|hol|PA14_07990|transcript|ABJ15578.1|protein_coding||c.-215T>A|||||215|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|PA14_08000|PA14_08000|transcript|ABJ15579.1|protein_coding||c.-686T>A|||||686|,A|upstream_gene_variant|MODIFIER|gpV|PA14_08010|transcript|ABJ15580.1|protein_coding||c.-1198T>A|||||1198|,A|upstream_gene_variant|MODIFIER|gpW|PA14_08020|transcript|ABJ15581.1|protein_coding||c.-1908T>A|||||1908|,A|upstream_gene_variant|MODIFIER|PA14_08030|PA14_08030|transcript|ABJ15582.1|protein_coding||c.-2231T>A|||||2231|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|gpI|PA14_08040|transcript|ABJ15583.1|protein_coding||c.-3111T>A|||||3111|,A|upstream_gene_variant|MODIFIER|PA14_08050|PA14_08050|transcript|ABJ15584.1|protein_coding||c.-3646T>A|||||3646|,A|downstream_gene_variant|MODIFIER|rpe|PA14_07910|transcript|ABJ15571.1|protein_coding||c.*4954T>A|||||4954|,A|downstream_gene_variant|MODIFIER|gph|PA14_07930|transcript|ABJ15572.1|protein_coding||c.*4136T>A|||||4136|,A|downstream_gene_variant|MODIFIER|trpE|PA14_07940|transcript|ABJ15573.1|protein_coding||c.*2585T>A|||||2585|,A|downstream_gene_variant|MODIFIER|PA14_07970|PA14_07970|transcript|ABJ15576.1|protein_coding||c.*556T>A|||||556|,A|downstream_gene_variant|MODIFIER|PA14_07980|PA14_07980|transcript|ABJ15577.1|protein_coding||c.*149T>A|||||149|WARNING_TRANSCRIPT_NO_START_CODON,A|intergenic_region|MODIFIER|PA14_07980-hol|PA14_07980-PA14_07990|intergenic_region|PA14_07980-PA14_07990|||n.687865T>A|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:18:18,0:17:577:0:0:0,-52.1854 0:9:9,2:7:195:2:31:0,-14.8716 0:12:12,0:12:307:0:0:0,-27.8633 0:19:19,0:18:583:0:0:0,-52.7141 +Chromosome 722410 . T G 4.98762E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=42;DPB=42;DPRA=0.68;EPP=11.6962;EPPR=3.06899;GTI=0;LEN=1;MEANALT=1.5;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=48.3863;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=47;QR=1296;RO=37;RPL=0;RPP=11.6962;RPPR=4.47751;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=32;SRP=45.7942;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|PA14_08440|PA14_08440|transcript|ABJ15619.1|protein_coding|1/1|c.595A>C|p.Arg199Arg|595/801|595/801|199/266||,G|upstream_gene_variant|MODIFIER|vfr|PA14_08370|transcript|ABJ15613.1|protein_coding||c.-4754A>C|||||4754|,G|upstream_gene_variant|MODIFIER|PA14_08400|PA14_08400|transcript|ABJ15616.1|protein_coding||c.-2244A>C|||||2244|,G|upstream_gene_variant|MODIFIER|PA14_08420|PA14_08420|transcript|ABJ15617.1|protein_coding||c.-1806A>C|||||1806|,G|upstream_gene_variant|MODIFIER|argC|PA14_08480|transcript|ABJ15623.1|protein_coding||c.-3557T>G|||||3557|,G|upstream_gene_variant|MODIFIER|PA14_08490|PA14_08490|transcript|ABJ15624.1|protein_coding||c.-4591T>G|||||4591|,G|downstream_gene_variant|MODIFIER|PA14_08380|PA14_08380|transcript|ABJ15614.1|protein_coding||c.*4060T>G|||||4060|,G|downstream_gene_variant|MODIFIER|speD|PA14_08390|transcript|ABJ15615.1|protein_coding||c.*2946T>G|||||2946|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_08430|PA14_08430|transcript|ABJ15618.1|protein_coding||c.*246T>G|||||246|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_08450|PA14_08450|transcript|ABJ15620.1|protein_coding||c.*655A>C|||||655|,G|downstream_gene_variant|MODIFIER|PA14_08460|PA14_08460|transcript|ABJ15621.1|protein_coding||c.*1859A>C|||||1859|,G|downstream_gene_variant|MODIFIER|PA14_08470|PA14_08470|transcript|ABJ15622.1|protein_coding||c.*2844A>C|||||2844| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,2:6:232:2:4:0,-20.8162 0:8:8,2:6:207:2:43:0,-14.8754 0:10:10,0:10:328:0:0:0,-29.8272 0:15:15,0:15:529:0:0:0,-47.9223 +Chromosome 743349 . T C 8.44493E-16 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=6;CIGAR=1X;DP=64;DPB=64;DPRA=0.733333;EPP=16.0391;EPPR=10.3484;GTI=0;LEN=1;MEANALT=1;MQM=58.1667;MQMR=59.8966;NS=4;NUMALT=1;ODDS=74.0948;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=57;QR=1778;RO=58;RPL=5;RPP=8.80089;RPPR=24.5753;RPR=1;RUN=1;SAF=5;SAP=8.80089;SAR=1;SRF=19;SRP=17.986;SRR=39;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|nusG|PA14_08710|transcript|ABJ13546.1|protein_coding|1/1|c.291T>C|p.Ala97Ala|291/534|291/534|97/177||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|tRNA|EBG00001225037|transcript|EBT00001793445.1|protein_coding||c.-2321A>G|||||2321|WARNING_TRANSCRIPT_INCOMPLETE,C|upstream_gene_variant|MODIFIER|tRNA|EBG00001225063|transcript|EBT00001793498.1|protein_coding||c.-2221A>G|||||2221|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|upstream_gene_variant|MODIFIER|tRNA|EBG00001225110|transcript|EBT00001793419.1|protein_coding||c.-2126A>G|||||2126|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|upstream_gene_variant|MODIFIER|tRNA|EBG00001225045|transcript|EBT00001793403.1|protein_coding||c.-717A>G|||||717|WARNING_TRANSCRIPT_INCOMPLETE,C|upstream_gene_variant|MODIFIER|rplK|PA14_08720|transcript|ABJ13545.1|protein_coding||c.-360T>C|||||360|,C|upstream_gene_variant|MODIFIER|rplA|PA14_08730|transcript|ABJ13544.1|protein_coding||c.-791T>C|||||791|,C|upstream_gene_variant|MODIFIER|P27|EBG00001225053|transcript|EBT00001793368.1|sRNA||n.-1493T>C|||||1493|,C|upstream_gene_variant|MODIFIER|rplJ|PA14_08740|transcript|ABJ13543.1|protein_coding||c.-1685T>C|||||1685|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|rplL|PA14_08750|transcript|ABJ13542.1|protein_coding||c.-2264T>C|||||2264|,C|upstream_gene_variant|MODIFIER|rpoB|PA14_08760|transcript|ABJ13541.1|protein_coding||c.-2854T>C|||||2854|,C|downstream_gene_variant|MODIFIER|birA|PA14_08620|transcript|ABJ13550.1|protein_coding||c.*4006T>C|||||4006|,C|downstream_gene_variant|MODIFIER|PA14_08630|PA14_08630|transcript|ABJ13549.1|protein_coding||c.*3263T>C|||||3263|,C|downstream_gene_variant|MODIFIER|PA14_08640|PA14_08640|transcript|ABJ13548.1|protein_coding||c.*2550T>C|||||2550|,C|downstream_gene_variant|MODIFIER|PA14_08650|PA14_08650|transcript|PA14_08650-1.1|protein_coding||c.*2321T>C|||||2321|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|PA14_08660|PA14_08660|transcript|PA14_08660-1.1|protein_coding||c.*2221T>C|||||2221|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|downstream_gene_variant|MODIFIER|PA14_08670|PA14_08670|transcript|PA14_08670-1.1|protein_coding||c.*2126T>C|||||2126|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|tufB|PA14_08680|transcript|ABJ13547.1|protein_coding||c.*845T>C|||||845|,C|downstream_gene_variant|MODIFIER|PA14_08690|PA14_08690|transcript|PA14_08690-1.1|protein_coding||c.*717T>C|||||717|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|secE|PA14_08695|transcript|ABJ15650.1|protein_coding||c.*300T>C|||||300|,C|downstream_gene_variant|MODIFIER|P26|EBG00001225034|transcript|EBT00001793520.1|lincRNA||n.*2638A>G|||||2638| GT:DP:DPR:RO:QR:AO:QA:GL 0:20:20,0:20:659:0:0:0,-59.5946 0:14:14,1:13:349:1:13:0,-30.3526 0:19:19,4:15:513:4:42:0,-42.5896 0:11:11,1:10:257:1:2:0,-23.165 +Chromosome 776869 . G T 7.13123E-11 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=6;CIGAR=1X;DP=38;DPB=38;DPRA=1;EPP=16.0391;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=24.8328;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=52;QR=1022;RO=32;RPL=6;RPP=16.0391;RPPR=3.28173;RPR=0;RUN=1;SAF=6;SAP=16.0391;SAR=0;SRF=31;SRP=64.083;SRR=1;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|uvrA|PA14_09180|transcript|ABJ13506.1|protein_coding|1/1|c.1194C>A|p.Ala398Ala|1194/2838|1194/2838|398/945||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|yajR|PA14_09195|transcript|ABJ15688.1|protein_coding||c.-1407G>T|||||1407|,T|upstream_gene_variant|MODIFIER|ssb|PA14_09200|transcript|ABJ13505.1|protein_coding||c.-2812G>T|||||2812|,T|downstream_gene_variant|MODIFIER|rpoA|PA14_09115|transcript|ABJ15630.1|protein_coding||c.*4473G>T|||||4473|,T|downstream_gene_variant|MODIFIER|rplQ|PA14_09130|transcript|ABJ13509.1|protein_coding||c.*4040G>T|||||4040|,T|downstream_gene_variant|MODIFIER|katA|PA14_09150|transcript|ABJ13508.1|protein_coding||c.*2311G>T|||||2311|,T|downstream_gene_variant|MODIFIER|bfrA|PA14_09160|transcript|ABJ13507.1|protein_coding||c.*1716G>T|||||1716|,T|downstream_gene_variant|MODIFIER|pchA|PA14_09210|transcript|ABJ13504.1|protein_coding||c.*3398C>A|||||3398|,T|downstream_gene_variant|MODIFIER|pchB|PA14_09220|transcript|ABJ13503.1|protein_coding||c.*4825C>A|||||4825| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,0:9:341:0:0:0,-31.046 0:7:7,3:4:64:3:19:0,-4.14615 0:12:12,3:9:281:3:33:0,-22.5099 0:10:10,0:10:336:0:0:0,-30.5589 +Chromosome 782850 . G T 9.58863E-10 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=21;DPB=21;DPRA=0.9375;EPP=3.0103;EPPR=3.12459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=22.2339;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=42;QR=627;RO=19;RPL=1;RPP=3.0103;RPPR=12.2676;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=13;SRP=8.61041;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|pchD|PA14_09240|transcript|ABJ13501.1|protein_coding|1/1|c.1545C>A|p.Arg515Arg|1545/1644|1545/1644|515/547||,T|upstream_gene_variant|MODIFIER|uvrA|PA14_09180|transcript|ABJ13506.1|protein_coding||c.-4788C>A|||||4788|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|pchA|PA14_09210|transcript|ABJ13504.1|protein_coding||c.-1153C>A|||||1153|,T|upstream_gene_variant|MODIFIER|pchB|PA14_09220|transcript|ABJ13503.1|protein_coding||c.-851C>A|||||851|,T|upstream_gene_variant|MODIFIER|pchC|PA14_09230|transcript|ABJ13502.1|protein_coding||c.-96C>A|||||96|,T|upstream_gene_variant|MODIFIER|pchR|PA14_09260|transcript|ABJ13500.1|protein_coding||c.-1774G>T|||||1774|,T|upstream_gene_variant|MODIFIER|pchE|PA14_09270|transcript|ABJ13499.1|protein_coding||c.-2858G>T|||||2858|,T|downstream_gene_variant|MODIFIER|yajR|PA14_09195|transcript|ABJ15688.1|protein_coding||c.*3186G>T|||||3186|,T|downstream_gene_variant|MODIFIER|ssb|PA14_09200|transcript|ABJ13505.1|protein_coding||c.*2672G>T|||||2672| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:102:0:0:0,-9.51603 0:5:5,2:3:92:2:42:0,-4.59123 0:3:3,0:3:81:0:0:0,-7.55658 0:10:10,0:10:352:0:0:0,-32.0083 +Chromosome 841643 . A G 4.69811E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=12;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=3.73412;EPPR=3.28173;GTI=0;LEN=1;MEANALT=1;MQM=52.25;MQMR=60;NS=4;NUMALT=1;ODDS=32.232;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=199;QR=776;RO=32;RPL=5;RPP=3.73412;RPPR=12.7819;RPR=7;RUN=1;SAF=0;SAP=29.068;SAR=12;SRF=13;SRP=5.45321;SRR=19;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_09770|PA14_09770|transcript|ABJ13462.1|protein_coding|1/1|c.65A>G|p.Glu22Gly|65/1023|65/1023|22/340||,G|upstream_gene_variant|MODIFIER|aldH|PA14_09710|transcript|ABJ13467.1|protein_coding||c.-4947T>C|||||4947|,G|upstream_gene_variant|MODIFIER|dapA|PA14_09730|transcript|ABJ13466.1|protein_coding||c.-4043T>C|||||4043|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|yaaU|PA14_09740|transcript|ABJ13465.1|protein_coding||c.-2650T>C|||||2650|,G|upstream_gene_variant|MODIFIER|PA14_09750|PA14_09750|transcript|ABJ13464.1|protein_coding||c.-1195T>C|||||1195|,G|upstream_gene_variant|MODIFIER|PA14_09760|PA14_09760|transcript|ABJ13463.1|protein_coding||c.-373T>C|||||373|,G|upstream_gene_variant|MODIFIER|PA14_09780|PA14_09780|transcript|ABJ13461.1|protein_coding||c.-984A>G|||||984|,G|upstream_gene_variant|MODIFIER|PA14_09820|PA14_09820|transcript|ABJ13458.1|protein_coding||c.-3141A>G|||||3141|,G|downstream_gene_variant|MODIFIER|PA14_09790|PA14_09790|transcript|ABJ13460.1|protein_coding||c.*1455T>C|||||1455|,G|downstream_gene_variant|MODIFIER|PA14_09810|PA14_09810|transcript|ABJ13459.1|protein_coding||c.*2121T>C|||||2121|,G|downstream_gene_variant|MODIFIER|opdN|PA14_09850|transcript|ABJ13457.1|protein_coding||c.*4827T>C|||||4827| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,3:7:235:3:42:0,-17.5525 0:6:6,1:5:115:1:35:0,-7.07692 0:12:12,5:7:185:5:81:0,-9.77928 0:16:16,3:13:241:3:41:0,-18.0437 +Chromosome 854421 . C A 1.87554E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=25;DPB=25;DPRA=0.947368;EPP=7.35324;EPPR=7.63648;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=30.815;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=831;RO=23;RPL=0;RPP=7.35324;RPPR=3.10471;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=15;SRP=7.63648;SRR=8;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|pfpI|PA14_09940|transcript|ABJ13449.1|protein_coding|1/1|c.373G>T|p.Val125Phe|373/564|373/564|125/187||,A|upstream_gene_variant|MODIFIER|prpL|PA14_09900|transcript|ABJ13453.1|protein_coding||c.-3041G>T|||||3041|,A|upstream_gene_variant|MODIFIER|lysR|PA14_09910|transcript|ABJ13452.1|protein_coding||c.-1585G>T|||||1585|,A|upstream_gene_variant|MODIFIER|PA14_09930|PA14_09930|transcript|ABJ13450.1|protein_coding||c.-214G>T|||||214|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|PA14_09960|PA14_09960|transcript|ABJ13447.1|protein_coding||c.-1521C>A|||||1521|,A|upstream_gene_variant|MODIFIER|yafB|PA14_09980|transcript|ABJ13445.1|protein_coding||c.-4765C>A|||||4765|,A|downstream_gene_variant|MODIFIER|ppiC2|PA14_09890|transcript|ABJ13454.1|protein_coding||c.*4750C>A|||||4750|,A|downstream_gene_variant|MODIFIER|PA14_09920|PA14_09920|transcript|ABJ13451.1|protein_coding||c.*1046C>A|||||1046|,A|downstream_gene_variant|MODIFIER|PA14_09950|PA14_09950|transcript|ABJ13448.1|protein_coding||c.*508G>T|||||508|,A|downstream_gene_variant|MODIFIER|fpvB|PA14_09970|transcript|ABJ13446.1|protein_coding||c.*2014G>T|||||2014| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:79:0:0:0,-7.49763 0:7:7,0:7:274:0:0:0,-25.0273 0:6:6,2:4:159:2:27:0,-12.1273 0:10:10,0:10:319:0:0:0,-29.0123 +Chromosome 855476 . A C 1.81646E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=22;DPB=22;DPRA=2.07692;EPP=7.35324;EPPR=4.03889;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=21.5949;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=591;RO=19;RPL=2;RPP=7.35324;RPPR=4.03889;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=12;SRP=5.8675;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_09950|PA14_09950|transcript|ABJ13448.1|protein_coding|1/1|c.386T>G|p.Leu129Arg|386/933|386/933|129/310||,C|upstream_gene_variant|MODIFIER|prpL|PA14_09900|transcript|ABJ13453.1|protein_coding||c.-4096T>G|||||4096|,C|upstream_gene_variant|MODIFIER|lysR|PA14_09910|transcript|ABJ13452.1|protein_coding||c.-2640T>G|||||2640|,C|upstream_gene_variant|MODIFIER|PA14_09930|PA14_09930|transcript|ABJ13450.1|protein_coding||c.-1269T>G|||||1269|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|pfpI|PA14_09940|transcript|ABJ13449.1|protein_coding||c.-683T>G|||||683|,C|upstream_gene_variant|MODIFIER|PA14_09960|PA14_09960|transcript|ABJ13447.1|protein_coding||c.-466A>C|||||466|,C|upstream_gene_variant|MODIFIER|yafB|PA14_09980|transcript|ABJ13445.1|protein_coding||c.-3710A>C|||||3710|,C|downstream_gene_variant|MODIFIER|PA14_09920|PA14_09920|transcript|ABJ13451.1|protein_coding||c.*2101A>C|||||2101|,C|downstream_gene_variant|MODIFIER|fpvB|PA14_09970|transcript|ABJ13446.1|protein_coding||c.*959T>G|||||959|,C|downstream_gene_variant|MODIFIER|PA14_09990|PA14_09990|transcript|ABJ13444.1|protein_coding||c.*4578T>G|||||4578| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:107:0:0:0,-9.9784 0:9:9,2:7:224:2:4:0,-20.0857 0:2:2,0:2:41:0:0:0,-3.89174 0:8:8,0:7:219:0:0:0,-19.9517 +Chromosome 887984 . T C 1.28667E-8 . AB=0;ABP=0;AC=0;AF=0;AN=3;AO=2;CIGAR=1X;DP=13;DPB=13;DPRA=3.2;EPP=7.35324;EPPR=4.78696;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=19.6372;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=424;RO=11;RPL=2;RPP=7.35324;RPPR=7.94546;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=8;SRP=7.94546;SRR=3;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|acoR|PA14_10290|transcript|ABJ13419.1|protein_coding|1/1|c.1508T>C|p.Leu503Pro|1508/1878|1508/1878|503/625||,C|upstream_gene_variant|MODIFIER|acoB|PA14_10250|transcript|ABJ13423.1|protein_coding||c.-4706A>G|||||4706|,C|upstream_gene_variant|MODIFIER|acoA|PA14_10260|transcript|ABJ13422.1|protein_coding||c.-3699A>G|||||3699|,C|upstream_gene_variant|MODIFIER|acoX|PA14_10270|transcript|ABJ13421.1|protein_coding||c.-2636A>G|||||2636|,C|upstream_gene_variant|MODIFIER|PA14_10280|PA14_10280|transcript|ABJ13420.1|protein_coding||c.-1839A>G|||||1839|,C|upstream_gene_variant|MODIFIER|PA14_10300|PA14_10300|transcript|ABJ13418.1|protein_coding||c.-575T>C|||||575|,C|downstream_gene_variant|MODIFIER|PA14_10320|PA14_10320|transcript|ABJ13417.1|protein_coding||c.*1173A>G|||||1173|,C|downstream_gene_variant|MODIFIER|ompK|PA14_10330|transcript|ABJ13416.1|protein_coding||c.*2159A>G|||||2159|,C|downstream_gene_variant|MODIFIER|cvaB|PA14_10340|transcript|ABJ13415.1|protein_coding||c.*3574A>G|||||3574| GT:DP:DPR:RO:QR:AO:QA:GL . 0:1:1,0:1:39:0:0:0,-3.89656 0:4:4,0:4:154:0:0:0,-14.2326 0:8:8,2:6:231:2:18:0,-19.4466 +Chromosome 890503 . T C 4.07812E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=34;DPB=34;DPRA=1.08333;EPP=11.6962;EPPR=21.5402;GTI=0;LEN=1;MEANALT=1;MQM=58.5;MQMR=60;NS=4;NUMALT=1;ODDS=32.509;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=1117;RO=30;RPL=4;RPP=11.6962;RPPR=7.64277;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=12;SRP=5.61607;SRR=18;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|ompK|PA14_10330|transcript|ABJ13416.1|protein_coding|1/1|c.1056A>G|p.Glu352Glu|1056/1416|1056/1416|352/471||,C|upstream_gene_variant|MODIFIER|PA14_10280|PA14_10280|transcript|ABJ13420.1|protein_coding||c.-4358A>G|||||4358|,C|upstream_gene_variant|MODIFIER|PA14_10320|PA14_10320|transcript|ABJ13417.1|protein_coding||c.-456A>G|||||456|,C|downstream_gene_variant|MODIFIER|acoR|PA14_10290|transcript|ABJ13419.1|protein_coding||c.*2149T>C|||||2149|,C|downstream_gene_variant|MODIFIER|PA14_10300|PA14_10300|transcript|ABJ13418.1|protein_coding||c.*1333T>C|||||1333|,C|downstream_gene_variant|MODIFIER|cvaB|PA14_10340|transcript|ABJ13415.1|protein_coding||c.*1055A>G|||||1055|,C|downstream_gene_variant|MODIFIER|PA14_10350|PA14_10350|transcript|ABJ13414.1|protein_coding||c.*3224A>G|||||3224|,C|downstream_gene_variant|MODIFIER|PA14_10360|PA14_10360|transcript|ABJ13413.1|protein_coding||c.*4577A>G|||||4577| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:255:0:0:0,-23.2467 0:4:4,2:2:79:2:4:0,-7.11763 0:7:7,1:6:236:1:15:0,-20.112 0:15:15,1:14:547:1:2:0,-49.3743 +Chromosome 932701 . T C 2.83271E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=27;DPB=27;DPRA=1.5;EPP=9.52472;EPPR=6.26751;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=55.4103;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=932;RO=24;RPL=3;RPP=9.52472;RPPR=4.45795;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=11;SRP=3.37221;SRR=13;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|ampC|PA14_10790|transcript|ABJ13380.1|protein_coding|1/1|c.1124A>G|p.Glu375Gly|1124/1194|1124/1194|375/397||,C|upstream_gene_variant|MODIFIER|PA14_10780|PA14_10780|transcript|ABJ13381.1|protein_coding||c.-135A>G|||||135|,C|upstream_gene_variant|MODIFIER|ampR|PA14_10800|transcript|ABJ13379.1|protein_coding||c.-1272T>C|||||1272|,C|downstream_gene_variant|MODIFIER|PA14_10770|PA14_10770|transcript|ABJ13382.1|protein_coding||c.*697T>C|||||697|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_10820|PA14_10820|transcript|ABJ13378.1|protein_coding||c.*2721A>G|||||2721|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_10830|PA14_10830|transcript|ABJ13377.1|protein_coding||c.*4248A>G|||||4248|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:194:0:0:0,-17.8321 0:7:7,0:7:269:0:0:0,-24.5739 0:9:9,3:6:237:3:17:0,-20.117 0:6:6,0:6:232:0:0:0,-21.2479 +Chromosome 950017 . C G 2.87062E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=33;DPB=33;DPRA=1.35714;EPP=13.8677;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=58.1913;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=36;QR=983;RO=28;RPL=0;RPP=13.8677;RPPR=3.0103;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=13;SRP=3.32051;SRR=15;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_10980|PA14_10980|transcript|ABJ13365.1|protein_coding|1/1|c.414C>G|p.Ile138Met|414/855|414/855|138/284||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|phlE|PA14_10910|transcript|ABJ13371.1|protein_coding||c.-4988G>C|||||4988|,G|upstream_gene_variant|MODIFIER|dad|PA14_10920|transcript|ABJ13370.1|protein_coding||c.-4384G>C|||||4384|,G|upstream_gene_variant|MODIFIER|PA14_10960|PA14_10960|transcript|ABJ13367.1|protein_coding||c.-1518G>C|||||1518|,G|upstream_gene_variant|MODIFIER|PA14_10970|PA14_10970|transcript|ABJ13366.1|protein_coding||c.-524G>C|||||524|,G|downstream_gene_variant|MODIFIER|PA14_10940|PA14_10940|transcript|ABJ13369.1|protein_coding||c.*3104C>G|||||3104|,G|downstream_gene_variant|MODIFIER|PA14_10950|PA14_10950|transcript|ABJ13368.1|protein_coding||c.*2640C>G|||||2640|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|hpaC|PA14_10990|transcript|ABJ13364.1|protein_coding||c.*485G>C|||||485|,G|downstream_gene_variant|MODIFIER|hpaA|PA14_11000|transcript|ABJ13363.1|protein_coding||c.*1027G>C|||||1027|,G|downstream_gene_variant|MODIFIER|PA14_11010|PA14_11010|transcript|ABJ13362.1|protein_coding||c.*2755G>C|||||2755|,G|downstream_gene_variant|MODIFIER|fabG|PA14_11020|transcript|ABJ13361.1|protein_coding||c.*3348G>C|||||3348|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_11030|PA14_11030|transcript|ABJ13360.1|protein_coding||c.*4106G>C|||||4106| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:209:0:0:0,-19.1469 0:8:8,0:8:308:0:0:0,-28.0805 0:7:7,1:6:230:1:15:0,-19.566 0:12:12,4:8:236:4:21:0,-19.5804 +Chromosome 953358 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=44;DPB=44;DPRA=0.913043;EPP=11.6962;EPPR=4.96463;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=53.0987;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=1114;RO=40;RPL=0;RPP=11.6962;RPPR=24.725;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=15;SRP=8.43898;SRR=25;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|PA14_10960|PA14_10960|transcript|ABJ13367.1|protein_coding||c.-4859T>C|||||4859|,G|upstream_gene_variant|MODIFIER|PA14_10970|PA14_10970|transcript|ABJ13366.1|protein_coding||c.-3865T>C|||||3865|,G|upstream_gene_variant|MODIFIER|hpaC|PA14_10990|transcript|ABJ13364.1|protein_coding||c.-2344T>C|||||2344|,G|upstream_gene_variant|MODIFIER|hpaA|PA14_11000|transcript|ABJ13363.1|protein_coding||c.-752T>C|||||752|,G|upstream_gene_variant|MODIFIER|PA14_11010|PA14_11010|transcript|ABJ13362.1|protein_coding||c.-296T>C|||||296|,G|upstream_gene_variant|MODIFIER|cupB1|PA14_11060|transcript|ABJ13358.1|protein_coding||c.-3454A>G|||||3454|,G|upstream_gene_variant|MODIFIER|cupB2|PA14_11070|transcript|ABJ13357.1|protein_coding||c.-4054A>G|||||4054|,G|downstream_gene_variant|MODIFIER|PA14_10980|PA14_10980|transcript|ABJ13365.1|protein_coding||c.*2900A>G|||||2900|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|fabG|PA14_11020|transcript|ABJ13361.1|protein_coding||c.*7T>C|||||7|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_11030|PA14_11030|transcript|ABJ13360.1|protein_coding||c.*765T>C|||||765|,G|downstream_gene_variant|MODIFIER|moaF|PA14_11050|transcript|ABJ13359.1|protein_coding||c.*2159T>C|||||2159|,G|intergenic_region|MODIFIER|PA14_11010-fabG|PA14_11010-PA14_11020|intergenic_region|PA14_11010-PA14_11020|||n.953358A>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:11:11,0:11:350:0:0:0,-31.7981 0:11:11,1:10:271:1:2:0,-24.4439 0:10:10,3:7:196:3:28:0,-15.2985 0:12:12,0:12:297:0:0:0,-26.9599 +Chromosome 955757 . G C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=45;DPB=45;DPRA=0.75;EPP=7.35324;EPPR=25.2805;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=56.8141;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1523;RO=43;RPL=2;RPP=7.35324;RPPR=3.46479;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=20;SRP=3.46479;SRR=23;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|moaF|PA14_11050|transcript|ABJ13359.1|protein_coding|1/1|c.585C>G|p.Gly195Gly|585/825|585/825|195/274||,C|upstream_gene_variant|MODIFIER|hpaC|PA14_10990|transcript|ABJ13364.1|protein_coding||c.-4743C>G|||||4743|,C|upstream_gene_variant|MODIFIER|hpaA|PA14_11000|transcript|ABJ13363.1|protein_coding||c.-3151C>G|||||3151|,C|upstream_gene_variant|MODIFIER|PA14_11010|PA14_11010|transcript|ABJ13362.1|protein_coding||c.-2695C>G|||||2695|,C|upstream_gene_variant|MODIFIER|fabG|PA14_11020|transcript|ABJ13361.1|protein_coding||c.-1631C>G|||||1631|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_11030|PA14_11030|transcript|ABJ13360.1|protein_coding||c.-249C>G|||||249|,C|upstream_gene_variant|MODIFIER|cupB1|PA14_11060|transcript|ABJ13358.1|protein_coding||c.-1055G>C|||||1055|,C|upstream_gene_variant|MODIFIER|cupB2|PA14_11070|transcript|ABJ13357.1|protein_coding||c.-1655G>C|||||1655|,C|upstream_gene_variant|MODIFIER|cupB3|PA14_11080|transcript|ABJ13356.1|protein_coding||c.-2723G>C|||||2723|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:261:0:0:0,-23.8425 0:9:9,2:7:198:2:4:0,-17.7095 0:10:10,0:10:373:0:0:0,-33.9163 0:19:19,0:19:691:0:0:0,-62.5032 +Chromosome 964316 . G C 1.46247E-8 . AB=0;ABP=0;AC=0;AF=0;AN=3;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=3;EPP=7.35324;EPPR=5.80219;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=19.5861;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=194;RO=7;RPL=2;RPP=7.35324;RPPR=3.32051;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=4;SRP=3.32051;SRR=3;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|cupB5|PA14_11100|transcript|ABJ13354.1|protein_coding|1/1|c.2478G>C|p.Thr826Thr|2478/3057|2478/3057|826/1018||,C|upstream_gene_variant|MODIFIER|cupB6|PA14_11110|transcript|ABJ13353.1|protein_coding||c.-679G>C|||||679|,C|upstream_gene_variant|MODIFIER|rcsB|PA14_11120|transcript|ABJ13352.1|protein_coding||c.-2469G>C|||||2469|,C|downstream_gene_variant|MODIFIER|cupB3|PA14_11080|transcript|ABJ13356.1|protein_coding||c.*3302G>C|||||3302|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|cupB4|PA14_11090|transcript|ABJ13355.1|protein_coding||c.*2565G>C|||||2565|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_11130|PA14_11130|transcript|ABJ13351.1|protein_coding||c.*3128C>G|||||3128|,C|downstream_gene_variant|MODIFIER|PA14_11140|PA14_11140|transcript|ABJ13350.1|protein_coding||c.*3907C>G|||||3907| GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:39:0:0:0,-3.89656 0:6:6,2:3:92:2:4:0,-8.12782 . 0:3:3,0:3:63:0:0:0,-5.87878 +Chromosome 1019395 . G C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=37;DPB=37;DPRA=0.964286;EPP=7.35324;EPPR=25.4075;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=53.7627;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1070;RO=35;RPL=2;RPP=7.35324;RPPR=25.4075;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=31;SRP=48.239;SRR=4;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|eutB|PA14_11770|transcript|ABJ13297.1|protein_coding|1/1|c.1347C>G|p.Gly449Gly|1347/1395|1347/1395|449/464||,C|upstream_gene_variant|MODIFIER|PA14_11700|PA14_11700|transcript|ABJ13303.1|protein_coding||c.-4786C>G|||||4786|,C|upstream_gene_variant|MODIFIER|PA14_11720|PA14_11720|transcript|ABJ13302.1|protein_coding||c.-4118C>G|||||4118|,C|upstream_gene_variant|MODIFIER|PA14_11740|PA14_11740|transcript|ABJ13300.1|protein_coding||c.-1555C>G|||||1555|,C|upstream_gene_variant|MODIFIER|PA14_11750|PA14_11750|transcript|ABJ13299.1|protein_coding||c.-1044C>G|||||1044|,C|upstream_gene_variant|MODIFIER|eutC|PA14_11760|transcript|ABJ13298.1|protein_coding||c.-59C>G|||||59|,C|upstream_gene_variant|MODIFIER|PA14_11830|PA14_11830|transcript|ABJ13294.1|protein_coding||c.-4922G>C|||||4922|,C|downstream_gene_variant|MODIFIER|PA14_11730|PA14_11730|transcript|ABJ13301.1|protein_coding||c.*2341G>C|||||2341|,C|downstream_gene_variant|MODIFIER|PA14_11790|PA14_11790|transcript|ABJ13296.1|protein_coding||c.*1405C>G|||||1405|,C|downstream_gene_variant|MODIFIER|PA14_11810|PA14_11810|transcript|ABJ13295.1|protein_coding||c.*3063C>G|||||3063| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:207:0:0:0,-18.9669 0:10:10,0:10:324:0:0:0,-29.4664 0:12:12,0:12:313:0:0:0,-28.42 0:9:9,2:7:226:2:4:0,-20.2719 +Chromosome 1022354 . T G 1.03613E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=6;CIGAR=1X;DP=49;DPB=49;DPRA=0.923077;EPP=16.0391;EPPR=9.12072;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=76.6665;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=1578;RO=43;RPL=0;RPP=16.0391;RPPR=5.48477;RPR=6;RUN=1;SAF=0;SAP=16.0391;SAR=6;SRF=24;SRP=4.27278;SRR=19;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|PA14_11740|PA14_11740|transcript|ABJ13300.1|protein_coding||c.-4514A>C|||||4514|,G|upstream_gene_variant|MODIFIER|PA14_11750|PA14_11750|transcript|ABJ13299.1|protein_coding||c.-4003A>C|||||4003|,G|upstream_gene_variant|MODIFIER|eutC|PA14_11760|transcript|ABJ13298.1|protein_coding||c.-3018A>C|||||3018|,G|upstream_gene_variant|MODIFIER|eutB|PA14_11770|transcript|ABJ13297.1|protein_coding||c.-1613A>C|||||1613|,G|upstream_gene_variant|MODIFIER|PA14_11790|PA14_11790|transcript|ABJ13296.1|protein_coding||c.-106A>C|||||106|,G|upstream_gene_variant|MODIFIER|PA14_11830|PA14_11830|transcript|ABJ13294.1|protein_coding||c.-1963T>G|||||1963|,G|upstream_gene_variant|MODIFIER|mpl|PA14_11845|transcript|ABJ15687.1|protein_coding||c.-4052T>G|||||4052|,G|downstream_gene_variant|MODIFIER|PA14_11810|PA14_11810|transcript|ABJ13295.1|protein_coding||c.*104A>C|||||104|,G|intergenic_region|MODIFIER|PA14_11790-PA14_11810|PA14_11790-PA14_11810|intergenic_region|PA14_11790-PA14_11810|||n.1022354T>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,1:8:305:1:22:0,-25.6059 0:13:13,0:13:501:0:0:0,-45.435 0:14:14,2:12:460:2:4:0,-41.3688 0:13:13,3:10:312:3:6:0,-27.8079 +Chromosome 1025662 . T G 8.12441E-12 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=24;DPB=24;DPRA=0.846154;EPP=9.52472;EPPR=5.59539;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=27.0058;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=26;QR=771;RO=21;RPL=0;RPP=9.52472;RPPR=3.1137;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=12;SRP=3.94093;SRR=9;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_11830|PA14_11830|transcript|ABJ13294.1|protein_coding|1/1|c.1346T>G|p.Val449Gly|1346/1932|1346/1932|449/643||,G|upstream_gene_variant|MODIFIER|eutB|PA14_11770|transcript|ABJ13297.1|protein_coding||c.-4921A>C|||||4921|,G|upstream_gene_variant|MODIFIER|PA14_11790|PA14_11790|transcript|ABJ13296.1|protein_coding||c.-3414A>C|||||3414|,G|upstream_gene_variant|MODIFIER|PA14_11810|PA14_11810|transcript|ABJ13295.1|protein_coding||c.-1684A>C|||||1684|,G|upstream_gene_variant|MODIFIER|mpl|PA14_11845|transcript|ABJ15687.1|protein_coding||c.-744T>G|||||744|,G|upstream_gene_variant|MODIFIER|PA14_11860|PA14_11860|transcript|ABJ13293.1|protein_coding||c.-2108T>G|||||2108|,G|upstream_gene_variant|MODIFIER|PA14_11880|PA14_11880|transcript|ABJ13292.1|protein_coding||c.-2739T>G|||||2739|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_11890|PA14_11890|transcript|ABJ13291.1|protein_coding||c.*3034A>C|||||3034|,G|downstream_gene_variant|MODIFIER|PA14_11900|PA14_11900|transcript|ABJ13290.1|protein_coding||c.*3722A>C|||||3722| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,2:2:79:2:24:0,-5.2177 0:7:7,1:6:193:1:2:0,-17.4826 0:4:4,0:4:150:0:0:0,-13.8654 0:9:9,0:9:349:0:0:0,-31.7674 +Chromosome 1026459 . G T 1.5901E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=61;DPB=61;DPRA=0.588235;EPP=7.35324;EPPR=22.4799;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=56.6584;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1669;RO=59;RPL=2;RPP=7.35324;RPPR=11.2913;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=37;SRP=11.2913;SRR=22;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|mpl|PA14_11845|transcript|ABJ15687.1|protein_coding|1/1|c.54G>T|p.Val18Val|54/1356|54/1356|18/451||,T|upstream_gene_variant|MODIFIER|PA14_11790|PA14_11790|transcript|ABJ13296.1|protein_coding||c.-4211C>A|||||4211|,T|upstream_gene_variant|MODIFIER|PA14_11810|PA14_11810|transcript|ABJ13295.1|protein_coding||c.-2481C>A|||||2481|,T|upstream_gene_variant|MODIFIER|PA14_11860|PA14_11860|transcript|ABJ13293.1|protein_coding||c.-1311G>T|||||1311|,T|upstream_gene_variant|MODIFIER|PA14_11880|PA14_11880|transcript|ABJ13292.1|protein_coding||c.-1942G>T|||||1942|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|PA14_11830|PA14_11830|transcript|ABJ13294.1|protein_coding||c.*211G>T|||||211|,T|downstream_gene_variant|MODIFIER|PA14_11890|PA14_11890|transcript|ABJ13291.1|protein_coding||c.*2237C>A|||||2237|,T|downstream_gene_variant|MODIFIER|PA14_11900|PA14_11900|transcript|ABJ13290.1|protein_coding||c.*2925C>A|||||2925|,T|downstream_gene_variant|MODIFIER|PA14_11910|PA14_11910|transcript|ABJ13289.1|protein_coding||c.*4855C>A|||||4855| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,2:8:189:2:17:0,-15.6214 0:15:15,0:15:461:0:0:0,-41.7731 0:23:23,0:23:668:0:0:0,-60.3772 0:13:13,0:13:351:0:0:0,-31.8474 +Chromosome 1047262 . C A 1.11618E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=34;DPB=34;DPRA=1.25;EPP=7.35324;EPPR=9.79615;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=37.5561;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=1109;RO=32;RPL=0;RPP=7.35324;RPPR=3.0103;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=7;SRP=24.9965;SRR=25;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|dacC|PA14_12100|transcript|ABJ13273.1|protein_coding|1/1|c.1155C>A|p.Phe385Leu|1155/1161|1155/1161|385/386||,A|upstream_gene_variant|MODIFIER|PA14_12110|PA14_12110|transcript|ABJ13272.1|protein_coding||c.-77C>A|||||77|,A|upstream_gene_variant|MODIFIER|lipB|PA14_12120|transcript|ABJ13271.1|protein_coding||c.-358C>A|||||358|,A|upstream_gene_variant|MODIFIER|lis|PA14_12130|transcript|ABJ13270.1|protein_coding||c.-1008C>A|||||1008|,A|upstream_gene_variant|MODIFIER|PA14_12150|PA14_12150|transcript|ABJ13268.1|protein_coding||c.-3137C>A|||||3137|,A|downstream_gene_variant|MODIFIER|pbpA|PA14_12060|transcript|ABJ13277.1|protein_coding||c.*4408C>A|||||4408|,A|downstream_gene_variant|MODIFIER|rodA|PA14_12070|transcript|ABJ13276.1|protein_coding||c.*3273C>A|||||3273|,A|downstream_gene_variant|MODIFIER|sltB1|PA14_12080|transcript|ABJ13275.1|protein_coding||c.*2242C>A|||||2242|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_12090|PA14_12090|transcript|ABJ13274.1|protein_coding||c.*1220C>A|||||1220|,A|downstream_gene_variant|MODIFIER|PA14_12140|PA14_12140|transcript|ABJ13269.1|protein_coding||c.*2136G>T|||||2136|,A|downstream_gene_variant|MODIFIER|PA14_12160|PA14_12160|transcript|ABJ13266.1|protein_coding||c.*4230G>T|||||4230| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:175:0:0:0,-16.0907 0:3:3,0:3:106:0:0:0,-9.88729 0:10:10,2:8:285:2:15:0,-24.5588 0:16:16,0:16:543:0:0:0,-49.1696 +Chromosome 1052348 . G C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=38;DPB=38;DPRA=1.07143;EPP=7.35324;EPPR=6.8707;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=42.727;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1305;RO=36;RPL=2;RPP=7.35324;RPPR=3.9754;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=18;SRP=3.0103;SRR=18;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_12160|PA14_12160|transcript|ABJ13266.1|protein_coding|1/1|c.491C>G|p.Ala164Gly|491/1347|491/1347|164/448||,C|upstream_gene_variant|MODIFIER|PA14_12140|PA14_12140|transcript|ABJ13269.1|protein_coding||c.-2057C>G|||||2057|,C|upstream_gene_variant|MODIFIER|PA14_12170|PA14_12170|transcript|ABJ13267.1|protein_coding||c.-719G>C|||||719|,C|downstream_gene_variant|MODIFIER|PA14_12110|PA14_12110|transcript|ABJ13272.1|protein_coding||c.*4728G>C|||||4728|,C|downstream_gene_variant|MODIFIER|lipB|PA14_12120|transcript|ABJ13271.1|protein_coding||c.*4075G>C|||||4075|,C|downstream_gene_variant|MODIFIER|lis|PA14_12130|transcript|ABJ13270.1|protein_coding||c.*3095G>C|||||3095|,C|downstream_gene_variant|MODIFIER|PA14_12150|PA14_12150|transcript|ABJ13268.1|protein_coding||c.*1059G>C|||||1059|,C|downstream_gene_variant|MODIFIER|PA14_12180|PA14_12180|transcript|ABJ13265.1|protein_coding||c.*1053C>G|||||1053|,C|downstream_gene_variant|MODIFIER|holA|PA14_12200|transcript|ABJ13264.1|protein_coding||c.*1297C>G|||||1297|,C|downstream_gene_variant|MODIFIER|PA14_12210|PA14_12210|transcript|ABJ13263.1|protein_coding||c.*2372C>G|||||2372|,C|downstream_gene_variant|MODIFIER|leuS|PA14_12230|transcript|ABJ13262.1|protein_coding||c.*3062C>G|||||3062| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:118:0:0:0,-11.0027 0:14:14,0:14:516:0:0:0,-46.7748 0:11:11,0:11:365:0:0:0,-33.1585 0:10:10,2:8:306:2:4:0,-27.5206 +Chromosome 1054441 . A G 5.13806E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=39;DPB=39;DPRA=1.03448;EPP=7.35324;EPPR=10.1116;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=65.0102;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=80;QR=1285;RO=37;RPL=2;RPP=7.35324;RPPR=5.88603;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=17;SRP=3.5385;SRR=20;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|holA|PA14_12200|transcript|ABJ13264.1|protein_coding|1/1|c.242T>C|p.Leu81Pro|242/1038|242/1038|81/345||,G|upstream_gene_variant|MODIFIER|PA14_12140|PA14_12140|transcript|ABJ13269.1|protein_coding||c.-4150T>C|||||4150|,G|upstream_gene_variant|MODIFIER|PA14_12160|PA14_12160|transcript|ABJ13266.1|protein_coding||c.-1603T>C|||||1603|,G|upstream_gene_variant|MODIFIER|PA14_12180|PA14_12180|transcript|ABJ13265.1|protein_coding||c.-888T>C|||||888|,G|upstream_gene_variant|MODIFIER|PA14_12260|PA14_12260|transcript|ABJ13261.1|protein_coding||c.-3761A>G|||||3761|,G|upstream_gene_variant|MODIFIER|PA14_12270|PA14_12270|transcript|ABJ13260.1|protein_coding||c.-4265A>G|||||4265|,G|downstream_gene_variant|MODIFIER|PA14_12150|PA14_12150|transcript|ABJ13268.1|protein_coding||c.*3152A>G|||||3152|,G|downstream_gene_variant|MODIFIER|PA14_12170|PA14_12170|transcript|ABJ13267.1|protein_coding||c.*1156A>G|||||1156|,G|downstream_gene_variant|MODIFIER|PA14_12210|PA14_12210|transcript|ABJ13263.1|protein_coding||c.*279T>C|||||279|,G|downstream_gene_variant|MODIFIER|leuS|PA14_12230|transcript|ABJ13262.1|protein_coding||c.*969T>C|||||969| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:294:0:0:0,-26.8082 0:10:10,0:10:318:0:0:0,-28.9183 0:10:10,2:8:306:2:80:0,-20.3078 0:11:11,0:11:367:0:0:0,-33.3393 +Chromosome 1056787 . G T 3.32331E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=24;DPB=24;DPRA=2.14286;EPP=3.0103;EPPR=12.8806;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=30.6214;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=614;RO=22;RPL=1;RPP=3.0103;RPPR=17.2236;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=19;SRP=28.2783;SRR=3;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|leuS|PA14_12230|transcript|ABJ13262.1|protein_coding|1/1|c.1245C>A|p.Ala415Ala|1245/2622|1245/2622|415/873||,T|upstream_gene_variant|MODIFIER|PA14_12160|PA14_12160|transcript|ABJ13266.1|protein_coding||c.-3949C>A|||||3949|,T|upstream_gene_variant|MODIFIER|PA14_12180|PA14_12180|transcript|ABJ13265.1|protein_coding||c.-3234C>A|||||3234|,T|upstream_gene_variant|MODIFIER|holA|PA14_12200|transcript|ABJ13264.1|protein_coding||c.-2105C>A|||||2105|,T|upstream_gene_variant|MODIFIER|PA14_12210|PA14_12210|transcript|ABJ13263.1|protein_coding||c.-1444C>A|||||1444|,T|upstream_gene_variant|MODIFIER|PA14_12260|PA14_12260|transcript|ABJ13261.1|protein_coding||c.-1415G>T|||||1415|,T|upstream_gene_variant|MODIFIER|PA14_12270|PA14_12270|transcript|ABJ13260.1|protein_coding||c.-1919G>T|||||1919|,T|downstream_gene_variant|MODIFIER|PA14_12170|PA14_12170|transcript|ABJ13267.1|protein_coding||c.*3502G>T|||||3502|,T|downstream_gene_variant|MODIFIER|cutE|PA14_12280|transcript|ABJ13259.1|protein_coding||c.*2730C>A|||||2730|,T|downstream_gene_variant|MODIFIER|PA14_12300|PA14_12300|transcript|ABJ13258.1|protein_coding||c.*4451C>A|||||4451| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:174:0:0:0,-15.9411 0:5:5,0:5:117:0:0:0,-10.7609 0:3:3,0:3:85:0:0:0,-7.93102 0:10:10,2:8:238:2:18:0,-19.9995 +Chromosome 1063071 . C A 8.91613E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=25;DPB=25;DPRA=0.923077;EPP=9.52472;EPPR=9.32731;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=20.0507;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=47;QR=577;RO=22;RPL=0;RPP=9.52472;RPPR=4.58955;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=8;SRP=6.56362;SRR=14;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|PA14_12330|PA14_12330|transcript|ABJ13256.1|protein_coding|1/1|c.498G>T|p.Val166Val|498/1023|498/1023|166/340||,A|upstream_gene_variant|MODIFIER|cutE|PA14_12280|transcript|ABJ13259.1|protein_coding||c.-2019G>T|||||2019|,A|upstream_gene_variant|MODIFIER|PA14_12300|PA14_12300|transcript|ABJ13258.1|protein_coding||c.-994G>T|||||994|,A|upstream_gene_variant|MODIFIER|PA14_12310|PA14_12310|transcript|ABJ13257.1|protein_coding||c.-515G>T|||||515|,A|upstream_gene_variant|MODIFIER|PA14_12360|PA14_12360|transcript|ABJ13254.1|protein_coding||c.-2135C>A|||||2135|,A|downstream_gene_variant|MODIFIER|PA14_12260|PA14_12260|transcript|ABJ13261.1|protein_coding||c.*4438C>A|||||4438|,A|downstream_gene_variant|MODIFIER|PA14_12270|PA14_12270|transcript|ABJ13260.1|protein_coding||c.*3604C>A|||||3604|,A|downstream_gene_variant|MODIFIER|orf2|PA14_12350|transcript|ABJ13255.1|protein_coding||c.*666G>T|||||666|,A|downstream_gene_variant|MODIFIER|PA14_12370|PA14_12370|transcript|ABJ13253.1|protein_coding||c.*2483G>T|||||2483|,A|downstream_gene_variant|MODIFIER|hemL|PA14_12390|transcript|ABJ13252.1|protein_coding||c.*3240G>T|||||3240|,A|downstream_gene_variant|MODIFIER|thiE|PA14_12400|transcript|ABJ13251.1|protein_coding||c.*4561G>T|||||4561| GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:40:0:0:0,-3.99568 0:6:6,1:5:143:1:15:0,-11.6531 0:6:6,2:4:60:2:32:0,-2.50602 0:12:12,0:12:334:0:0:0,-30.3232 +Chromosome 1085004 . G C 7.86224E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=34;DPB=34;DPRA=0.545455;EPP=9.52472;EPPR=3.64073;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=34.8824;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=1140;RO=31;RPL=3;RPP=9.52472;RPPR=11.486;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=12;SRP=6.44263;SRR=19;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|PA14_12630|PA14_12630|transcript|ABJ13237.1|protein_coding|1/1|c.2286G>C|p.Pro762Pro|2286/2493|2286/2493|762/830||,C|upstream_gene_variant|MODIFIER|PA14_12570|PA14_12570|transcript|ABJ13241.1|protein_coding||c.-4977C>G|||||4977|,C|upstream_gene_variant|MODIFIER|P24|EBG00001225128|transcript|EBT00001793494.1|lincRNA||n.-4696C>G|||||4696|,C|upstream_gene_variant|MODIFIER|PA14_12590|PA14_12590|transcript|ABJ13240.1|protein_coding||c.-3810C>G|||||3810|,C|upstream_gene_variant|MODIFIER|cepA|PA14_12610|transcript|ABJ13239.1|protein_coding||c.-2957C>G|||||2957|,C|upstream_gene_variant|MODIFIER|PA14_12620|PA14_12620|transcript|ABJ13238.1|protein_coding||c.-2452C>G|||||2452|,C|upstream_gene_variant|MODIFIER|PA14_12680|PA14_12680|transcript|ABJ13233.1|protein_coding||c.-2674G>C|||||2674|,C|downstream_gene_variant|MODIFIER|PA14_12640|PA14_12640|transcript|ABJ13236.1|protein_coding||c.*218C>G|||||218|,C|downstream_gene_variant|MODIFIER|PA14_12650|PA14_12650|transcript|ABJ13235.1|protein_coding||c.*649C>G|||||649|,C|downstream_gene_variant|MODIFIER|PA14_12670|PA14_12670|transcript|ABJ13234.1|protein_coding||c.*1473C>G|||||1473|,C|downstream_gene_variant|MODIFIER|PA14_12690|PA14_12690|transcript|ABJ13232.1|protein_coding||c.*3517C>G|||||3517|,C|downstream_gene_variant|MODIFIER|PA14_12700|PA14_12700|transcript|ABJ13231.1|protein_coding||c.*4018C>G|||||4018|,C|downstream_gene_variant|MODIFIER|PA14_12710|PA14_12710|transcript|ABJ13230.1|protein_coding||c.*4758C>G|||||4758| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,0:10:368:0:0:0,-33.4616 0:5:5,2:3:113:2:30:0,-7.68902 0:12:12,0:12:448:0:0:0,-40.6623 0:7:7,1:6:211:1:2:0,-19.1279 +Chromosome 1087304 . T G 3.24731E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=32;DPB=32;DPRA=1.8;EPP=9.52472;EPPR=3.68421;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=52.4838;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=976;RO=29;RPL=0;RPP=9.52472;RPPR=6.67934;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=8;SRP=15.6647;SRR=21;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_12670|PA14_12670|transcript|ABJ13234.1|protein_coding|1/1|c.313A>C|p.Thr105Pro|313/1140|313/1140|105/379||,G|upstream_gene_variant|MODIFIER|PA14_12620|PA14_12620|transcript|ABJ13238.1|protein_coding||c.-4752A>C|||||4752|,G|upstream_gene_variant|MODIFIER|PA14_12640|PA14_12640|transcript|ABJ13236.1|protein_coding||c.-1675A>C|||||1675|,G|upstream_gene_variant|MODIFIER|PA14_12650|PA14_12650|transcript|ABJ13235.1|protein_coding||c.-917A>C|||||917|,G|upstream_gene_variant|MODIFIER|PA14_12680|PA14_12680|transcript|ABJ13233.1|protein_coding||c.-374T>G|||||374|,G|upstream_gene_variant|MODIFIER|PA14_12740|PA14_12740|transcript|ABJ13228.1|protein_coding||c.-4532T>G|||||4532|,G|downstream_gene_variant|MODIFIER|PA14_12630|PA14_12630|transcript|ABJ13237.1|protein_coding||c.*2093T>G|||||2093|,G|downstream_gene_variant|MODIFIER|PA14_12690|PA14_12690|transcript|ABJ13232.1|protein_coding||c.*1217A>C|||||1217|,G|downstream_gene_variant|MODIFIER|PA14_12700|PA14_12700|transcript|ABJ13231.1|protein_coding||c.*1718A>C|||||1718|,G|downstream_gene_variant|MODIFIER|PA14_12710|PA14_12710|transcript|ABJ13230.1|protein_coding||c.*2458A>C|||||2458|,G|downstream_gene_variant|MODIFIER|PA14_12730|PA14_12730|transcript|ABJ13229.1|protein_coding||c.*3710A>C|||||3710| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:192:0:0:0,-17.6486 0:6:6,0:6:188:0:0:0,-17.2181 0:12:12,3:9:275:3:6:0,-24.4799 0:9:9,0:9:321:0:0:0,-29.2205 +Chromosome 1095769 . G T 6.69002E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=14;CIGAR=1X;DP=81;DPB=81;DPRA=0;EPP=8.59409;EPPR=3.04271;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=72.0207;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=228;QR=1952;RO=67;RPL=10;RPP=8.59409;RPPR=5.63551;RPR=4;RUN=1;SAF=14;SAP=33.4109;SAR=0;SRF=35;SRP=3.30199;SRR=32;TYPE=snp;technology.ILLUMINA=1;ANN=T|upstream_gene_variant|MODIFIER|PA14_12710|PA14_12710|transcript|ABJ13230.1|protein_coding||c.-4913C>A|||||4913|,T|upstream_gene_variant|MODIFIER|PA14_12730|PA14_12730|transcript|ABJ13229.1|protein_coding||c.-4174C>A|||||4174|,T|upstream_gene_variant|MODIFIER|PA14_12770|PA14_12770|transcript|ABJ13225.1|protein_coding||c.-164C>A|||||164|,T|upstream_gene_variant|MODIFIER|PA14_12810|PA14_12810|transcript|ABJ13223.1|protein_coding||c.-1106G>T|||||1106|,T|upstream_gene_variant|MODIFIER|PA14_12820|PA14_12820|transcript|ABJ13222.1|protein_coding||c.-2386G>T|||||2386|,T|downstream_gene_variant|MODIFIER|PA14_12740|PA14_12740|transcript|ABJ13228.1|protein_coding||c.*3358G>T|||||3358|,T|downstream_gene_variant|MODIFIER|PA14_12750|PA14_12750|transcript|ABJ13227.1|protein_coding||c.*2789G>T|||||2789|,T|downstream_gene_variant|MODIFIER|PA14_12760|PA14_12760|transcript|ABJ13226.1|protein_coding||c.*1362G>T|||||1362|,T|downstream_gene_variant|MODIFIER|PA14_12780|PA14_12780|transcript|ABJ13224.1|protein_coding||c.*195C>A|||||195|,T|intergenic_region|MODIFIER|PA14_12770-PA14_12780|PA14_12770-PA14_12780|intergenic_region|PA14_12770-PA14_12780|||n.1095769G>T|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:15:15,3:12:281:3:45:0,-21.3106 0:20:20,4:16:429:4:60:0,-33.3051 0:24:24,5:19:643:5:93:0,-49.6142 0:22:22,2:20:599:2:30:0,-51.3301 +Chromosome 1110075 . G C 2.89504E-7 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=22;DPB=22;DPRA=1.125;EPP=7.35324;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=16.5237;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=616;RO=20;RPL=2;RPP=7.35324;RPPR=3.44459;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=12;SRP=4.74748;SRR=8;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_12960|PA14_12960|transcript|ABJ13212.1|protein_coding|1/1|c.760G>C|p.Ala254Pro|760/819|760/819|254/272||,C|upstream_gene_variant|MODIFIER|PA14_12900|PA14_12900|transcript|ABJ13216.1|protein_coding||c.-3373C>G|||||3373|,C|upstream_gene_variant|MODIFIER|tauD|PA14_12970|transcript|ABJ13211.1|protein_coding||c.-166G>C|||||166|,C|upstream_gene_variant|MODIFIER|PA14_12980|PA14_12980|transcript|ABJ13210.1|protein_coding||c.-1162G>C|||||1162|,C|downstream_gene_variant|MODIFIER|tesB|PA14_12870|transcript|ABJ13218.1|protein_coding||c.*4371G>C|||||4371|,C|downstream_gene_variant|MODIFIER|PA14_12890|PA14_12890|transcript|ABJ13217.1|protein_coding||c.*3778G>C|||||3778|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_12910|PA14_12910|transcript|ABJ13215.1|protein_coding||c.*2824G>C|||||2824|,C|downstream_gene_variant|MODIFIER|PA14_12920|PA14_12920|transcript|ABJ13214.1|protein_coding||c.*1604G>C|||||1604|,C|downstream_gene_variant|MODIFIER|PA14_12940|PA14_12940|transcript|ABJ13213.1|protein_coding||c.*749G>C|||||749|,C|downstream_gene_variant|MODIFIER|PA14_12990|PA14_12990|transcript|ABJ13209.1|protein_coding||c.*3306C>G|||||3306| GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:14:0:0:0,-1.39999 0:5:5,0:5:185:0:0:0,-17.0061 0:6:6,2:4:107:2:30:0,-7.04257 0:10:10,0:10:310:0:0:0,-28.1911 +Chromosome 1148998 . C G 4.73123E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=47;DPB=47;DPRA=0.710526;EPP=7.35324;EPPR=20.4303;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=69.8087;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=26;QR=1619;RO=45;RPL=0;RPP=7.35324;RPPR=3.05855;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=30;SRP=13.8677;SRR=15;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_13350|PA14_13350|transcript|ABJ13181.1|protein_coding|1/1|c.644G>C|p.Arg215Pro|644/720|644/720|215/239||,G|upstream_gene_variant|MODIFIER|P10|EBG00001225072|transcript|EBT00001793431.1|sRNA||n.-2623C>G|||||2623|,G|upstream_gene_variant|MODIFIER|PA14_13420|PA14_13420|transcript|ABJ13175.1|protein_coding||c.-4906C>G|||||4906|,G|downstream_gene_variant|MODIFIER|PA14_13320|PA14_13320|transcript|ABJ13184.1|protein_coding||c.*4591C>G|||||4591|,G|downstream_gene_variant|MODIFIER|PA14_13330|PA14_13330|transcript|ABJ13183.1|protein_coding||c.*2777C>G|||||2777|,G|downstream_gene_variant|MODIFIER|PA14_13340|PA14_13340|transcript|ABJ13182.1|protein_coding||c.*398C>G|||||398|,G|downstream_gene_variant|MODIFIER|PA14_13360|PA14_13360|transcript|ABJ13180.1|protein_coding||c.*640G>C|||||640|,G|downstream_gene_variant|MODIFIER|PA14_13370|PA14_13370|transcript|ABJ13179.1|protein_coding||c.*1422G>C|||||1422|,G|downstream_gene_variant|MODIFIER|PA14_13380|PA14_13380|transcript|ABJ13178.1|protein_coding||c.*1798G>C|||||1798|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_13390|PA14_13390|transcript|ABJ13177.1|protein_coding||c.*2322G>C|||||2322|,G|downstream_gene_variant|MODIFIER|PA14_13410|PA14_13410|transcript|ABJ13176.1|protein_coding||c.*3102G>C|||||3102| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:278:0:0:0,-25.3488 0:16:16,0:16:556:0:0:0,-50.3473 0:9:9,2:7:273:2:26:0,-22.4667 0:14:14,0:14:512:0:0:0,-46.406 +Chromosome 1165356 . A G 7.47539E-8 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=19;DPB=19;DPRA=2.8;EPP=13.8677;EPPR=5.49198;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=17.9526;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=360;RO=14;RPL=5;RPP=13.8677;RPPR=3.63072;RPR=0;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=7;SRP=3.0103;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_13530|PA14_13530|transcript|ABJ13166.1|protein_coding|1/1|c.1198A>G|p.Met400Val|1198/2196|1198/2196|400/731||,G|upstream_gene_variant|MODIFIER|PA14_13500|PA14_13500|transcript|ABJ13169.1|protein_coding||c.-3978T>C|||||3978|,G|upstream_gene_variant|MODIFIER|PA14_13510|PA14_13510|transcript|ABJ13168.1|protein_coding||c.-2930T>C|||||2930|,G|upstream_gene_variant|MODIFIER|PA14_13560|PA14_13560|transcript|ABJ13165.1|protein_coding||c.-1225A>G|||||1225|,G|downstream_gene_variant|MODIFIER|PA14_13490|PA14_13490|transcript|ABJ13170.1|protein_coding||c.*4973A>G|||||4973|,G|downstream_gene_variant|MODIFIER|PA14_13520|PA14_13520|transcript|ABJ13167.1|protein_coding||c.*1194A>G|||||1194|,G|downstream_gene_variant|MODIFIER|PA14_13580|PA14_13580|transcript|ABJ13164.1|protein_coding||c.*2261T>C|||||2261|,G|downstream_gene_variant|MODIFIER|PA14_13590|PA14_13590|transcript|ABJ13163.1|protein_coding||c.*3437T>C|||||3437|,G|downstream_gene_variant|MODIFIER|PA14_13600|PA14_13600|transcript|ABJ13162.1|protein_coding||c.*4099T>C|||||4099| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:69:0:0:0,-6.38099 0:1:1,0:1:36:0:0:0,-3.59827 0:4:4,3:1:14:3:6:0,-0.83999 0:10:10,2:8:241:2:4:0,-21.5966 +Chromosome 1171410 . G T 3.1597E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=6.91895;EPPR=13.4954;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=38.8569;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=86;QR=1121;RO=35;RPL=4;RPP=6.91895;RPPR=20.9405;RPR=1;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=31;SRP=48.239;SRR=4;TYPE=snp;technology.ILLUMINA=1;ANN=T|upstream_gene_variant|MODIFIER|PA14_13580|PA14_13580|transcript|ABJ13164.1|protein_coding||c.-2630C>A|||||2630|,T|upstream_gene_variant|MODIFIER|PA14_13590|PA14_13590|transcript|ABJ13163.1|protein_coding||c.-1955C>A|||||1955|,T|upstream_gene_variant|MODIFIER|PA14_13600|PA14_13600|transcript|ABJ13162.1|protein_coding||c.-1020C>A|||||1020|,T|upstream_gene_variant|MODIFIER|PA14_13610|PA14_13610|transcript|ABJ13161.1|protein_coding||c.-298C>A|||||298|,T|upstream_gene_variant|MODIFIER|nhaP|PA14_13620|transcript|ABJ13160.1|protein_coding||c.-144G>T|||||144|,T|downstream_gene_variant|MODIFIER|PA14_13560|PA14_13560|transcript|ABJ13165.1|protein_coding||c.*3921G>T|||||3921|,T|downstream_gene_variant|MODIFIER|PA14_13630|PA14_13630|transcript|ABJ13159.1|protein_coding||c.*1477C>A|||||1477|,T|downstream_gene_variant|MODIFIER|PA14_13650|PA14_13650|transcript|ABJ13158.1|protein_coding||c.*1753C>A|||||1753|,T|downstream_gene_variant|MODIFIER|PA14_13660|PA14_13660|transcript|ABJ13157.1|protein_coding||c.*2757C>A|||||2757|,T|downstream_gene_variant|MODIFIER|PA14_13670|PA14_13670|transcript|ABJ13156.1|protein_coding||c.*3508C>A|||||3508|,T|downstream_gene_variant|MODIFIER|PA14_13680|PA14_13680|transcript|ABJ13155.1|protein_coding||c.*3915C>A|||||3915|,T|downstream_gene_variant|MODIFIER|PA14_13690|PA14_13690|transcript|ABJ13154.1|protein_coding||c.*4833C>A|||||4833|,T|intergenic_region|MODIFIER|PA14_13610-nhaP|PA14_13610-PA14_13620|intergenic_region|PA14_13610-PA14_13620|||n.1171410G>T|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,1:6:192:1:15:0,-16.092 0:15:15,1:14:425:1:27:0,-35.834 0:7:7,2:5:168:2:30:0,-12.5953 0:11:11,1:10:336:1:14:0,-29.1571 +Chromosome 1172803 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=41;DPB=41;DPRA=0.727273;EPP=7.35324;EPPR=9.74743;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=55.4312;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=26;QR=1186;RO=39;RPL=2;RPP=7.35324;RPPR=4.40227;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=26;SRP=12.42;SRR=13;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|nhaP|PA14_13620|transcript|ABJ13160.1|protein_coding|1/1|c.1250T>C|p.Leu417Pro|1250/1275|1250/1275|417/424||,C|upstream_gene_variant|MODIFIER|PA14_13580|PA14_13580|transcript|ABJ13164.1|protein_coding||c.-4023A>G|||||4023|,C|upstream_gene_variant|MODIFIER|PA14_13590|PA14_13590|transcript|ABJ13163.1|protein_coding||c.-3348A>G|||||3348|,C|upstream_gene_variant|MODIFIER|PA14_13600|PA14_13600|transcript|ABJ13162.1|protein_coding||c.-2413A>G|||||2413|,C|upstream_gene_variant|MODIFIER|PA14_13610|PA14_13610|transcript|ABJ13161.1|protein_coding||c.-1691A>G|||||1691|,C|downstream_gene_variant|MODIFIER|PA14_13630|PA14_13630|transcript|ABJ13159.1|protein_coding||c.*84A>G|||||84|,C|downstream_gene_variant|MODIFIER|PA14_13650|PA14_13650|transcript|ABJ13158.1|protein_coding||c.*360A>G|||||360|,C|downstream_gene_variant|MODIFIER|PA14_13660|PA14_13660|transcript|ABJ13157.1|protein_coding||c.*1364A>G|||||1364|,C|downstream_gene_variant|MODIFIER|PA14_13670|PA14_13670|transcript|ABJ13156.1|protein_coding||c.*2115A>G|||||2115|,C|downstream_gene_variant|MODIFIER|PA14_13680|PA14_13680|transcript|ABJ13155.1|protein_coding||c.*2522A>G|||||2522|,C|downstream_gene_variant|MODIFIER|PA14_13690|PA14_13690|transcript|ABJ13154.1|protein_coding||c.*3440A>G|||||3440|,C|downstream_gene_variant|MODIFIER|PA14_13710|PA14_13710|transcript|ABJ13153.1|protein_coding||c.*4205A>G|||||4205|,C|downstream_gene_variant|MODIFIER|PA14_13720|PA14_13720|transcript|ABJ13152.1|protein_coding||c.*4835A>G|||||4835| GT:DP:DPR:RO:QR:AO:QA:GL 0:13:13,0:13:352:0:0:0,-31.9324 0:8:8,2:6:211:2:26:0,-16.8588 0:6:6,0:6:185:0:0:0,-16.9486 0:14:14,0:14:438:0:0:0,-39.7118 +Chromosome 1174074 . C G 2.26278E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=27;DPB=27;DPRA=1.5;EPP=7.35324;EPPR=3.79203;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=33.0605;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=783;RO=25;RPL=0;RPP=7.35324;RPPR=17.6895;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=11;SRP=3.79203;SRR=14;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|PA14_13590|PA14_13590|transcript|ABJ13163.1|protein_coding||c.-4619G>C|||||4619|,G|upstream_gene_variant|MODIFIER|PA14_13600|PA14_13600|transcript|ABJ13162.1|protein_coding||c.-3684G>C|||||3684|,G|upstream_gene_variant|MODIFIER|PA14_13610|PA14_13610|transcript|ABJ13161.1|protein_coding||c.-2962G>C|||||2962|,G|upstream_gene_variant|MODIFIER|PA14_13630|PA14_13630|transcript|ABJ13159.1|protein_coding||c.-942G>C|||||942|,G|upstream_gene_variant|MODIFIER|PA14_13650|PA14_13650|transcript|ABJ13158.1|protein_coding||c.-12G>C|||||12|,G|downstream_gene_variant|MODIFIER|nhaP|PA14_13620|transcript|ABJ13160.1|protein_coding||c.*1246C>G|||||1246|,G|downstream_gene_variant|MODIFIER|PA14_13660|PA14_13660|transcript|ABJ13157.1|protein_coding||c.*93G>C|||||93|,G|downstream_gene_variant|MODIFIER|PA14_13670|PA14_13670|transcript|ABJ13156.1|protein_coding||c.*844G>C|||||844|,G|downstream_gene_variant|MODIFIER|PA14_13680|PA14_13680|transcript|ABJ13155.1|protein_coding||c.*1251G>C|||||1251|,G|downstream_gene_variant|MODIFIER|PA14_13690|PA14_13690|transcript|ABJ13154.1|protein_coding||c.*2169G>C|||||2169|,G|downstream_gene_variant|MODIFIER|PA14_13710|PA14_13710|transcript|ABJ13153.1|protein_coding||c.*2934G>C|||||2934|,G|downstream_gene_variant|MODIFIER|PA14_13720|PA14_13720|transcript|ABJ13152.1|protein_coding||c.*3564G>C|||||3564|,G|downstream_gene_variant|MODIFIER|narL|PA14_13730|transcript|ABJ13151.1|protein_coding||c.*4044G>C|||||4044|,G|downstream_gene_variant|MODIFIER|narX|PA14_13740|transcript|ABJ13150.1|protein_coding||c.*4700G>C|||||4700|,G|intergenic_region|MODIFIER|PA14_13650-PA14_13660|PA14_13650-PA14_13660|intergenic_region|PA14_13650-PA14_13660|||n.1174074C>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:237:0:0:0,-21.6476 0:3:3,0:3:81:0:0:0,-7.55276 0:8:8,0:8:253:0:0:0,-23.0706 0:9:9,2:7:212:2:4:0,-18.9921 +Chromosome 1178787 . T C 8.43057E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=29;DPB=29;DPRA=1.57895;EPP=9.52472;EPPR=11.3621;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=41.5039;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=833;RO=26;RPL=3;RPP=9.52472;RPPR=3.34437;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=20;SRP=19.3799;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|narX|PA14_13740|transcript|ABJ13150.1|protein_coding|1/1|c.1856A>G|p.Glu619Gly|1856/1869|1856/1869|619/622||,C|upstream_gene_variant|MODIFIER|PA14_13650|PA14_13650|transcript|ABJ13158.1|protein_coding||c.-4725A>G|||||4725|,C|upstream_gene_variant|MODIFIER|PA14_13660|PA14_13660|transcript|ABJ13157.1|protein_coding||c.-3964A>G|||||3964|,C|upstream_gene_variant|MODIFIER|PA14_13670|PA14_13670|transcript|ABJ13156.1|protein_coding||c.-3483A>G|||||3483|,C|upstream_gene_variant|MODIFIER|PA14_13680|PA14_13680|transcript|ABJ13155.1|protein_coding||c.-2632A>G|||||2632|,C|upstream_gene_variant|MODIFIER|PA14_13690|PA14_13690|transcript|ABJ13154.1|protein_coding||c.-1795A>G|||||1795|,C|upstream_gene_variant|MODIFIER|PA14_13710|PA14_13710|transcript|ABJ13153.1|protein_coding||c.-1315A>G|||||1315|,C|upstream_gene_variant|MODIFIER|PA14_13720|PA14_13720|transcript|ABJ13152.1|protein_coding||c.-754A>G|||||754|,C|upstream_gene_variant|MODIFIER|narL|PA14_13730|transcript|ABJ13151.1|protein_coding||c.-10A>G|||||10|,C|upstream_gene_variant|MODIFIER|narK1|PA14_13750|transcript|ABJ13149.1|protein_coding||c.-2030T>C|||||2030|,C|upstream_gene_variant|MODIFIER|narK2|PA14_13770|transcript|ABJ13148.1|protein_coding||c.-3338T>C|||||3338|,C|upstream_gene_variant|MODIFIER|narG|PA14_13780|transcript|ABJ13147.1|protein_coding||c.-4820T>C|||||4820| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:148:0:0:0,-13.6055 0:5:5,0:5:135:0:0:0,-12.41 0:9:9,0:9:278:0:0:0,-25.3122 0:10:10,3:7:272:3:6:0,-24.2865 +Chromosome 1191206 . G C 1.83811E-12 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=34;DPB=34;DPRA=0.517241;EPP=7.35324;EPPR=4.09604;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=28.4924;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=828;RO=32;RPL=2;RPP=7.35324;RPPR=7.35324;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=28;SRP=42.0968;SRR=4;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_13840|PA14_13840|transcript|ABJ13143.1|protein_coding|1/1|c.775G>C|p.Glu259Gln|775/819|775/819|259/272||,C|upstream_gene_variant|MODIFIER|moaA1|PA14_13850|transcript|ABJ13142.1|protein_coding||c.-101G>C|||||101|,C|upstream_gene_variant|MODIFIER|PA14_13920|PA14_13920|transcript|ABJ13137.1|protein_coding||c.-4259G>C|||||4259|,C|downstream_gene_variant|MODIFIER|narG|PA14_13780|transcript|ABJ13147.1|protein_coding||c.*3814G>C|||||3814|,C|downstream_gene_variant|MODIFIER|narH|PA14_13800|transcript|ABJ13146.1|protein_coding||c.*2261G>C|||||2261|,C|downstream_gene_variant|MODIFIER|narJ|PA14_13810|transcript|ABJ13145.1|protein_coding||c.*1515G>C|||||1515|,C|downstream_gene_variant|MODIFIER|narI|PA14_13830|transcript|ABJ13144.1|protein_coding||c.*829G>C|||||829|,C|downstream_gene_variant|MODIFIER|PA14_13860|PA14_13860|transcript|ABJ13141.1|protein_coding||c.*1097C>G|||||1097|,C|downstream_gene_variant|MODIFIER|PA14_13870|PA14_13870|transcript|ABJ13140.1|protein_coding||c.*1411C>G|||||1411|,C|downstream_gene_variant|MODIFIER|PA14_13880|PA14_13880|transcript|ABJ13139.1|protein_coding||c.*1837C>G|||||1837|,C|downstream_gene_variant|MODIFIER|PA14_13890|PA14_13890|transcript|ABJ13138.1|protein_coding||c.*1985C>G|||||1985| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:166:0:0:0,-15.1423 0:6:6,0:6:142:0:0:0,-13.0144 0:5:5,2:3:82:2:17:0,-6.03769 0:15:15,0:15:438:0:0:0,-39.6892 +Chromosome 1200013 . A G 5.87637E-16 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=7;CIGAR=1X;DP=38;DPB=38;DPRA=1.25;EPP=18.2106;EPPR=11.486;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=56.4462;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=51;QR=1040;RO=31;RPL=0;RPP=18.2106;RPPR=11.486;RPR=7;RUN=1;SAF=0;SAP=18.2106;SAR=7;SRF=13;SRP=4.76149;SRR=18;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_13990|PA14_13990|transcript|ABJ13132.1|protein_coding|1/1|c.772A>G|p.Ser258Gly|772/792|772/792|258/263||,G|upstream_gene_variant|MODIFIER|PA14_13960|PA14_13960|transcript|ABJ13134.1|protein_coding||c.-1587T>C|||||1587|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_13970|PA14_13970|transcript|ABJ13133.1|protein_coding||c.-1319T>C|||||1319|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_14060|PA14_14060|transcript|ABJ13127.1|protein_coding||c.-4804A>G|||||4804|,G|downstream_gene_variant|MODIFIER|PA14_13920|PA14_13920|transcript|ABJ13137.1|protein_coding||c.*4390A>G|||||4390|,G|downstream_gene_variant|MODIFIER|PA14_13940|PA14_13940|transcript|ABJ13136.1|protein_coding||c.*2089A>G|||||2089|,G|downstream_gene_variant|MODIFIER|PA14_13950|PA14_13950|transcript|ABJ13135.1|protein_coding||c.*1751A>G|||||1751|,G|downstream_gene_variant|MODIFIER|PA14_14000|PA14_14000|transcript|ABJ13131.1|protein_coding||c.*44T>C|||||44|,G|downstream_gene_variant|MODIFIER|PA14_14010|PA14_14010|transcript|ABJ13130.1|protein_coding||c.*739T>C|||||739|,G|downstream_gene_variant|MODIFIER|PA14_14020|PA14_14020|transcript|ABJ13129.1|protein_coding||c.*1889T>C|||||1889|,G|downstream_gene_variant|MODIFIER|rhl|PA14_14040|transcript|ABJ13128.1|protein_coding||c.*2997T>C|||||2997|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,1:7:254:1:2:0,-23.0092 0:11:11,2:9:314:2:17:0,-26.9728 0:8:8,0:8:257:0:0:0,-23.4386 0:11:11,4:7:215:4:32:0,-16.6854 +Chromosome 1206180 . T C 9.94698E-16 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=47;DPB=47;DPRA=0.711111;EPP=13.8677;EPPR=6.31921;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=64.0488;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1406;RO=42;RPL=5;RPP=13.8677;RPPR=16.2459;RPR=0;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=28;SRP=13.1438;SRR=14;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_14060|PA14_14060|transcript|ABJ13127.1|protein_coding|1/1|c.1364T>C|p.Leu455Pro|1364/1899|1364/1899|455/632||,C|upstream_gene_variant|MODIFIER|PA14_14010|PA14_14010|transcript|ABJ13130.1|protein_coding||c.-4301A>G|||||4301|,C|upstream_gene_variant|MODIFIER|PA14_14020|PA14_14020|transcript|ABJ13129.1|protein_coding||c.-3331A>G|||||3331|,C|upstream_gene_variant|MODIFIER|rhl|PA14_14040|transcript|ABJ13128.1|protein_coding||c.-1977A>G|||||1977|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|yhdW|PA14_14100|transcript|ABJ13125.1|protein_coding||c.-1479T>C|||||1479|,C|upstream_gene_variant|MODIFIER|pcs|PA14_14110|transcript|ABJ13124.1|protein_coding||c.-2618T>C|||||2618|,C|upstream_gene_variant|MODIFIER|PA14_14130|PA14_14130|transcript|ABJ13123.1|protein_coding||c.-3405T>C|||||3405|,C|upstream_gene_variant|MODIFIER|PA14_14140|PA14_14140|transcript|ABJ13122.1|protein_coding||c.-3954T>C|||||3954|,C|upstream_gene_variant|MODIFIER|PA14_14150|PA14_14150|transcript|ABJ13121.1|protein_coding||c.-4648T>C|||||4648|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_14160|PA14_14160|transcript|ABJ13120.1|protein_coding||c.-4991T>C|||||4991|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|estB|PA14_14080|transcript|ABJ13126.1|protein_coding||c.*551A>G|||||551| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,1:6:225:1:2:0,-20.4087 0:15:15,0:15:463:0:0:0,-41.9515 0:9:9,2:7:264:2:4:0,-23.7394 0:16:16,2:14:454:2:4:0,-40.7752 +Chromosome 1223709 . A G 1.5369E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=30;DPB=30;DPRA=1.33333;EPP=13.8677;EPPR=7.26639;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=53.9316;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=62;QR=901;RO=25;RPL=0;RPP=13.8677;RPPR=7.26639;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=19;SRP=17.6895;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|ybiN|PA14_14340|transcript|ABJ13106.1|protein_coding|1/1|c.314T>C|p.Leu105Pro|314/1011|314/1011|105/336||,G|upstream_gene_variant|MODIFIER|PA14_14280|PA14_14280|transcript|ABJ13112.1|protein_coding||c.-4466T>C|||||4466|,G|upstream_gene_variant|MODIFIER|PA14_14300|PA14_14300|transcript|ABJ13110.1|protein_coding||c.-2447T>C|||||2447|,G|upstream_gene_variant|MODIFIER|PA14_14310|PA14_14310|transcript|ABJ13109.1|protein_coding||c.-2214T>C|||||2214|,G|upstream_gene_variant|MODIFIER|PA14_14330|PA14_14330|transcript|ABJ13107.1|protein_coding||c.-885T>C|||||885|,G|downstream_gene_variant|MODIFIER|PA14_14290|PA14_14290|transcript|ABJ13111.1|protein_coding||c.*3731A>G|||||3731|,G|downstream_gene_variant|MODIFIER|PA14_14320|PA14_14320|transcript|ABJ13108.1|protein_coding||c.*1527A>G|||||1527|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_14360|PA14_14360|transcript|ABJ13105.1|protein_coding||c.*405T>C|||||405|,G|downstream_gene_variant|MODIFIER|PA14_14370|PA14_14370|transcript|ABJ13104.1|protein_coding||c.*2356T>C|||||2356|,G|downstream_gene_variant|MODIFIER|PA14_14380|PA14_14380|transcript|ABJ13103.1|protein_coding||c.*3153T>C|||||3153|,G|downstream_gene_variant|MODIFIER|PA14_14390|PA14_14390|transcript|ABJ13102.1|protein_coding||c.*4127T>C|||||4127| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:207:0:0:0,-18.9592 0:8:8,1:7:254:1:14:0,-21.8076 0:9:9,3:6:228:3:33:0,-17.8022 0:7:7,1:6:212:1:15:0,-17.9168 +Chromosome 1225464 . G T 8.56617E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=22;DPB=22;DPRA=1.125;EPP=7.35324;EPPR=9.95901;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=29.6658;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=624;RO=20;RPL=2;RPP=7.35324;RPPR=6.91895;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=15;SRP=13.8677;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|PA14_14360|PA14_14360|transcript|ABJ13105.1|protein_coding|1/1|c.483C>A|p.Val161Val|483/1833|483/1833|161/610||,T|upstream_gene_variant|MODIFIER|PA14_14300|PA14_14300|transcript|ABJ13110.1|protein_coding||c.-4202C>A|||||4202|,T|upstream_gene_variant|MODIFIER|PA14_14310|PA14_14310|transcript|ABJ13109.1|protein_coding||c.-3969C>A|||||3969|,T|upstream_gene_variant|MODIFIER|PA14_14330|PA14_14330|transcript|ABJ13107.1|protein_coding||c.-2640C>A|||||2640|,T|upstream_gene_variant|MODIFIER|ybiN|PA14_14340|transcript|ABJ13106.1|protein_coding||c.-1442C>A|||||1442|,T|upstream_gene_variant|MODIFIER|PA14_14400|PA14_14400|transcript|ABJ13101.1|protein_coding||c.-3472G>T|||||3472|,T|upstream_gene_variant|MODIFIER|PA14_14420|PA14_14420|transcript|ABJ13100.1|protein_coding||c.-3699G>T|||||3699|,T|downstream_gene_variant|MODIFIER|PA14_14320|PA14_14320|transcript|ABJ13108.1|protein_coding||c.*3282G>T|||||3282|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|PA14_14370|PA14_14370|transcript|ABJ13104.1|protein_coding||c.*601C>A|||||601|,T|downstream_gene_variant|MODIFIER|PA14_14380|PA14_14380|transcript|ABJ13103.1|protein_coding||c.*1398C>A|||||1398|,T|downstream_gene_variant|MODIFIER|PA14_14390|PA14_14390|transcript|ABJ13102.1|protein_coding||c.*2372C>A|||||2372| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:166:0:0:0,-15.2622 0:2:2,0:2:73:0:0:0,-6.9307 0:9:9,0:9:279:0:0:0,-25.4075 0:6:6,2:4:106:2:30:0,-6.94973 +Chromosome 1237025 . G C 1.01598E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=36;DPB=36;DPRA=0.8;EPP=9.52472;EPPR=4.65535;GTI=0;LEN=1;MEANALT=1;MQM=50.6667;MQMR=60;NS=4;NUMALT=1;ODDS=39.9748;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=1063;RO=33;RPL=3;RPP=9.52472;RPPR=3.60252;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=11;SRP=10.9724;SRR=22;TYPE=snp;technology.ILLUMINA=1;ANN=C|upstream_gene_variant|MODIFIER|valS|PA14_14440|transcript|ABJ13098.1|protein_coding||c.-2592C>G|||||2592|,C|upstream_gene_variant|MODIFIER|PA14_14450|PA14_14450|transcript|ABJ13097.1|protein_coding||c.-2103C>G|||||2103|,C|upstream_gene_variant|MODIFIER|holC|PA14_14460|transcript|ABJ13096.1|protein_coding||c.-1663C>G|||||1663|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|pepA|PA14_14470|transcript|ABJ13095.1|protein_coding||c.-179C>G|||||179|,C|upstream_gene_variant|MODIFIER|PA14_14480|PA14_14480|transcript|ABJ13094.1|protein_coding||c.-158G>C|||||158|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_14490|PA14_14490|transcript|ABJ13093.1|protein_coding||c.-1054G>C|||||1054|,C|upstream_gene_variant|MODIFIER|yjgP|PA14_14500|transcript|ABJ13092.1|protein_coding||c.-2170G>C|||||2170|,C|upstream_gene_variant|MODIFIER|yjgQ|PA14_14510|transcript|ABJ13091.1|protein_coding||c.-3281G>C|||||3281|,C|downstream_gene_variant|MODIFIER|PA14_14520|PA14_14520|transcript|ABJ13090.1|protein_coding||c.*4480C>G|||||4480|,C|intergenic_region|MODIFIER|pepA-PA14_14480|PA14_14470-PA14_14480|intergenic_region|PA14_14470-PA14_14480|||n.1237025G>C|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:309:0:0:0,-28.1717 0:7:7,1:6:130:1:15:0,-10.419 0:12:12,0:12:394:0:0:0,-35.7563 0:9:9,2:7:230:2:4:0,-20.6321 +Chromosome 1237076 . C A 1.53692E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=52;DPB=52;DPRA=0.857143;EPP=11.6962;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=34.2785;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=49;QR=1580;RO=48;RPL=0;RPP=11.6962;RPPR=3.19126;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=21;SRP=4.6389;SRR=27;TYPE=snp;technology.ILLUMINA=1;ANN=A|upstream_gene_variant|MODIFIER|valS|PA14_14440|transcript|ABJ13098.1|protein_coding||c.-2643G>T|||||2643|,A|upstream_gene_variant|MODIFIER|PA14_14450|PA14_14450|transcript|ABJ13097.1|protein_coding||c.-2154G>T|||||2154|,A|upstream_gene_variant|MODIFIER|holC|PA14_14460|transcript|ABJ13096.1|protein_coding||c.-1714G>T|||||1714|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|pepA|PA14_14470|transcript|ABJ13095.1|protein_coding||c.-230G>T|||||230|,A|upstream_gene_variant|MODIFIER|PA14_14480|PA14_14480|transcript|ABJ13094.1|protein_coding||c.-107C>A|||||107|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|PA14_14490|PA14_14490|transcript|ABJ13093.1|protein_coding||c.-1003C>A|||||1003|,A|upstream_gene_variant|MODIFIER|yjgP|PA14_14500|transcript|ABJ13092.1|protein_coding||c.-2119C>A|||||2119|,A|upstream_gene_variant|MODIFIER|yjgQ|PA14_14510|transcript|ABJ13091.1|protein_coding||c.-3230C>A|||||3230|,A|downstream_gene_variant|MODIFIER|PA14_14520|PA14_14520|transcript|ABJ13090.1|protein_coding||c.*4429G>T|||||4429|,A|intergenic_region|MODIFIER|pepA-PA14_14480|PA14_14470-PA14_14480|intergenic_region|PA14_14470-PA14_14480|||n.1237076C>A|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,2:3:94:2:31:0,-5.82193 0:11:11,0:11:378:0:0:0,-34.3388 0:17:17,0:17:577:0:0:0,-52.2429 0:19:19,2:17:531:2:18:0,-46.3605 +Chromosome 1239158 . GCCCCCG GCCCCG 1736.22 . AB=0;ABP=0;AC=4;AF=1;AN=4;AO=56;CIGAR=1M1D5M;DP=57;DPB=63.7143;DPRA=0;EPP=29.2231;EPPR=0;GTI=0;LEN=1;MEANALT=1.25;MQM=60;MQMR=0;NS=4;NUMALT=1;ODDS=74.7963;PAIRED=0;PAIREDR=0;PAO=15;PQA=211;PQR=247;PRO=10;QA=2091;QR=0;RO=0;RPL=41;RPP=29.2231;RPPR=0;RPR=15;RUN=1;SAF=14;SAP=33.4109;SAR=42;SRF=0;SRP=0;SRR=0;TYPE=del;technology.ILLUMINA=1;ANN=GCCCCG|upstream_gene_variant|MODIFIER|valS|PA14_14440|transcript|ABJ13098.1|protein_coding||c.-4730delG|||||4730|,GCCCCG|upstream_gene_variant|MODIFIER|PA14_14450|PA14_14450|transcript|ABJ13097.1|protein_coding||c.-4241delG|||||4241|,GCCCCG|upstream_gene_variant|MODIFIER|holC|PA14_14460|transcript|ABJ13096.1|protein_coding||c.-3801delG|||||3801|WARNING_TRANSCRIPT_NO_START_CODON,GCCCCG|upstream_gene_variant|MODIFIER|pepA|PA14_14470|transcript|ABJ13095.1|protein_coding||c.-2317delG|||||2317|,GCCCCG|upstream_gene_variant|MODIFIER|yjgP|PA14_14500|transcript|ABJ13092.1|protein_coding||c.-32delC|||||32|,GCCCCG|upstream_gene_variant|MODIFIER|yjgQ|PA14_14510|transcript|ABJ13091.1|protein_coding||c.-1143delC|||||1143|,GCCCCG|upstream_gene_variant|MODIFIER|PA14_14530|PA14_14530|transcript|ABJ13089.1|protein_coding||c.-2969delC|||||2969|,GCCCCG|upstream_gene_variant|MODIFIER|PA14_14540|PA14_14540|transcript|ABJ13088.1|protein_coding||c.-4777delC|||||4777|,GCCCCG|upstream_gene_variant|MODIFIER|PA14_14550|PA14_14550|transcript|ABJ13087.1|protein_coding||c.-4925delC|||||4925|,GCCCCG|downstream_gene_variant|MODIFIER|PA14_14480|PA14_14480|transcript|ABJ13094.1|protein_coding||c.*1168delC|||||1168|WARNING_TRANSCRIPT_NO_START_CODON,GCCCCG|downstream_gene_variant|MODIFIER|PA14_14490|PA14_14490|transcript|ABJ13093.1|protein_coding||c.*161delC|||||161|,GCCCCG|downstream_gene_variant|MODIFIER|PA14_14520|PA14_14520|transcript|ABJ13090.1|protein_coding||c.*2342delG|||||2342|,GCCCCG|intergenic_region|MODIFIER|PA14_14490-yjgP|PA14_14490-PA14_14500|intergenic_region|PA14_14490-PA14_14500|||n.1239163delC|||||| GT:DP:DPR:RO:QR:AO:QA:GL 1:15:15,14:0:0:14:514:-46.5547,0 1:7:7,7:0:0:7:254:-20.7626,0 1:14:14,14:0:0:14:548:-50.0675,0 1:21:21,21:0:0:21:775:-67.6245,0 +Chromosome 1270600 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=35;DPB=35;DPRA=1.2;EPP=7.35324;EPPR=4.65535;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=62.965;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=1207;RO=33;RPL=0;RPP=7.35324;RPPR=3.60252;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=20;SRP=6.23461;SRR=13;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|yafV|PA14_14960|transcript|ABJ13058.1|protein_coding|1/1|c.373C>A|p.His125Asn|373/795|373/795|125/264||,A|upstream_gene_variant|MODIFIER|PA14_14975|PA14_14975|transcript|ABJ15677.1|protein_coding||c.-556C>A|||||556|,A|upstream_gene_variant|MODIFIER|PA14_15000|PA14_15000|transcript|ABJ13056.1|protein_coding||c.-2363C>A|||||2363|,A|upstream_gene_variant|MODIFIER|PA14_15020|PA14_15020|transcript|ABJ13055.1|protein_coding||c.-2872C>A|||||2872|,A|downstream_gene_variant|MODIFIER|PA14_14900|PA14_14900|transcript|ABJ13062.1|protein_coding||c.*4508C>A|||||4508|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_14910|PA14_14910|transcript|ABJ13061.1|protein_coding||c.*3364C>A|||||3364|,A|downstream_gene_variant|MODIFIER|engA|PA14_14930|transcript|ABJ13060.1|protein_coding||c.*1805C>A|||||1805|,A|downstream_gene_variant|MODIFIER|ybdL|PA14_14940|transcript|ABJ13059.1|protein_coding||c.*360C>A|||||360|,A|downstream_gene_variant|MODIFIER|mocA|PA14_14990|transcript|ABJ13057.1|protein_coding||c.*1232G>T|||||1232|,A|downstream_gene_variant|MODIFIER|leuA|PA14_15030|transcript|ABJ13054.1|protein_coding||c.*3274G>T|||||3274|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:228:0:0:0,-20.8838 0:10:10,2:8:280:2:30:0,-22.6808 0:9:9,0:9:336:0:0:0,-30.589 0:10:10,0:10:363:0:0:0,-33.0135 +Chromosome 1271760 . CGG CG 771.025 . AB=0;ABP=0;AC=4;AF=1;AN=4;AO=26;CIGAR=1M1D1M;DP=28;DPB=19.3333;DPRA=0;EPP=3.34437;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=28.3074;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=929;QR=69;RO=2;RPL=12;RPP=3.34437;RPPR=3.0103;RPR=14;RUN=1;SAF=12;SAP=3.34437;SAR=14;SRF=1;SRP=3.0103;SRR=1;TYPE=del;technology.ILLUMINA=1;ANN=CG|upstream_gene_variant|MODIFIER|PA14_15000|PA14_15000|transcript|ABJ13056.1|protein_coding||c.-1201delG|||||1201|,CG|upstream_gene_variant|MODIFIER|PA14_15020|PA14_15020|transcript|ABJ13055.1|protein_coding||c.-1710delG|||||1710|,CG|upstream_gene_variant|MODIFIER|PA14_15050|PA14_15050|transcript|ABJ13053.1|protein_coding||c.-4263delG|||||4263|WARNING_TRANSCRIPT_NO_START_CODON,CG|upstream_gene_variant|MODIFIER|oprC|PA14_15070|transcript|ABJ13052.1|protein_coding||c.-4845delG|||||4845|,CG|downstream_gene_variant|MODIFIER|PA14_14910|PA14_14910|transcript|ABJ13061.1|protein_coding||c.*4526delG|||||4526|,CG|downstream_gene_variant|MODIFIER|engA|PA14_14930|transcript|ABJ13060.1|protein_coding||c.*2967delG|||||2967|,CG|downstream_gene_variant|MODIFIER|ybdL|PA14_14940|transcript|ABJ13059.1|protein_coding||c.*1522delG|||||1522|,CG|downstream_gene_variant|MODIFIER|yafV|PA14_14960|transcript|ABJ13058.1|protein_coding||c.*740delG|||||740|,CG|downstream_gene_variant|MODIFIER|PA14_14975|PA14_14975|transcript|ABJ15677.1|protein_coding||c.*19delG|||||19|,CG|downstream_gene_variant|MODIFIER|mocA|PA14_14990|transcript|ABJ13057.1|protein_coding||c.*70delC|||||70|,CG|downstream_gene_variant|MODIFIER|leuA|PA14_15030|transcript|ABJ13054.1|protein_coding||c.*2112delC|||||2112|WARNING_TRANSCRIPT_NO_START_CODON,CG|intergenic_region|MODIFIER|PA14_14975-mocA|PA14_14975-PA14_14990|intergenic_region|PA14_14975-PA14_14990|||n.1271762delG|||||| GT:DP:DPR:RO:QR:AO:QA:GL 1:7:7,7:0:0:7:231:-21.1062,0 1:5:5,5:0:0:5:192:-17.6498,0 1:6:6,4:2:69:4:137:-6.11424,0 1:10:10,10:0:0:10:369:-33.5539,0 +Chromosome 1296110 . T G 3.67071E-12 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=19;DPB=19;DPRA=2.7;EPP=7.35324;EPPR=4.1599;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=28.0723;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=511;RO=17;RPL=0;RPP=7.35324;RPPR=3.13803;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=31.7504;SRR=16;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_15280|PA14_15280|transcript|ABJ13033.1|protein_coding|1/1|c.208A>C|p.Lys70Gln|208/897|208/897|70/298||,G|upstream_gene_variant|MODIFIER|xseA|PA14_15230|transcript|ABJ13038.1|protein_coding||c.-4851A>C|||||4851|,G|upstream_gene_variant|MODIFIER|PA14_15240|PA14_15240|transcript|ABJ13037.1|protein_coding||c.-3906A>C|||||3906|,G|upstream_gene_variant|MODIFIER|PA14_15260|PA14_15260|transcript|ABJ13035.1|protein_coding||c.-1889A>C|||||1889|,G|upstream_gene_variant|MODIFIER|PA14_15270|PA14_15270|transcript|ABJ13034.1|protein_coding||c.-702A>C|||||702|,G|upstream_gene_variant|MODIFIER|guaB|PA14_15310|transcript|ABJ13031.1|protein_coding||c.-1583T>G|||||1583|,G|upstream_gene_variant|MODIFIER|guaA|PA14_15340|transcript|ABJ13030.1|protein_coding||c.-3132T>G|||||3132|,G|downstream_gene_variant|MODIFIER|PA14_15250|PA14_15250|transcript|ABJ13036.1|protein_coding||c.*3016T>G|||||3016|,G|downstream_gene_variant|MODIFIER|PA14_15290|PA14_15290|transcript|ABJ13032.1|protein_coding||c.*342A>C|||||342| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:85:0:0:0,-7.92878 0:5:5,0:5:133:0:0:0,-12.2257 0:2:2,0:2:70:0:0:0,-6.64548 0:9:9,2:7:223:2:15:0,-18.9539 +Chromosome 1300283 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=54;DPB=54;DPRA=0.666667;EPP=11.6962;EPPR=3.70517;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=81.2281;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1814;RO=50;RPL=4;RPP=11.6962;RPPR=3.70517;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=32;SRP=11.5225;SRR=18;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|guaA|PA14_15340|transcript|ABJ13030.1|protein_coding|1/1|c.1042A>C|p.Lys348Gln|1042/1578|1042/1578|348/525||,C|upstream_gene_variant|MODIFIER|PA14_15270|PA14_15270|transcript|ABJ13034.1|protein_coding||c.-4875T>G|||||4875|,C|upstream_gene_variant|MODIFIER|PA14_15280|PA14_15280|transcript|ABJ13033.1|protein_coding||c.-3966T>G|||||3966|,C|upstream_gene_variant|MODIFIER|PA14_15290|PA14_15290|transcript|ABJ13032.1|protein_coding||c.-2854T>G|||||2854|,C|upstream_gene_variant|MODIFIER|PA14_15350|PA14_15350|transcript|ABJ13029.1|protein_coding||c.-843A>C|||||843|,C|upstream_gene_variant|MODIFIER|repA|PA14_15380|transcript|ABJ13027.1|protein_coding||c.-3769A>C|||||3769|,C|upstream_gene_variant|MODIFIER|repC|PA14_15400|transcript|ABJ13025.1|protein_coding||c.-4619A>C|||||4619|,C|downstream_gene_variant|MODIFIER|guaB|PA14_15310|transcript|ABJ13031.1|protein_coding||c.*1121A>C|||||1121|,C|downstream_gene_variant|MODIFIER|PA14_15360|PA14_15360|transcript|ABJ13028.1|protein_coding||c.*2460T>G|||||2460|,C|downstream_gene_variant|MODIFIER|PA14_15370|PA14_15370|transcript|ABJ13026.1|protein_coding||c.*3574T>G|||||3574|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:13:13,1:12:393:1:2:0,-35.4699 0:18:18,0:18:682:0:0:0,-61.7015 0:10:10,2:8:301:2:4:0,-27.062 0:13:13,1:12:438:1:2:0,-39.5449 +Chromosome 1308336 . G C 7.72439E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=14;DPB=14;DPRA=4;EPP=7.35324;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=20.1481;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=430;RO=12;RPL=2;RPP=7.35324;RPPR=9.52472;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=6;SRP=3.0103;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|merD|PA14_15450|transcript|ABJ13023.1|protein_coding|1/1|c.350C>G|p.Ala117Gly|350/366|350/366|117/121||,C|upstream_gene_variant|MODIFIER|PA14_15360|PA14_15360|transcript|ABJ13028.1|protein_coding||c.-4613C>G|||||4613|,C|upstream_gene_variant|MODIFIER|PA14_15370|PA14_15370|transcript|ABJ13026.1|protein_coding||c.-4252C>G|||||4252|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|tnpR|PA14_15430|transcript|ABJ13024.1|protein_coding||c.-1366C>G|||||1366|,C|upstream_gene_variant|MODIFIER|PA14_15435|PA14_15435|transcript|ABJ15638.1|protein_coding||c.-246C>G|||||246|,C|upstream_gene_variant|MODIFIER|merE|PA14_15445|transcript|ABJ15637.1|protein_coding||c.-13C>G|||||13|,C|upstream_gene_variant|MODIFIER|merR|PA14_15480|transcript|ABJ13020.1|protein_coding||c.-2834G>C|||||2834|,C|upstream_gene_variant|MODIFIER|PA14_15490|PA14_15490|transcript|ABJ13019.1|protein_coding||c.-3522G>C|||||3522|,C|upstream_gene_variant|MODIFIER|traK|PA14_15500|transcript|ABJ13018.1|protein_coding||c.-3738G>C|||||3738|,C|upstream_gene_variant|MODIFIER|traJ|PA14_15510|transcript|ABJ13017.1|protein_coding||c.-4319G>C|||||4319|,C|upstream_gene_variant|MODIFIER|trbJ|PA14_15520|transcript|ABJ13016.1|protein_coding||c.-4955G>C|||||4955|,C|downstream_gene_variant|MODIFIER|repA|PA14_15380|transcript|ABJ13027.1|protein_coding||c.*3406G>C|||||3406|,C|downstream_gene_variant|MODIFIER|repC|PA14_15400|transcript|ABJ13025.1|protein_coding||c.*2547G>C|||||2547|,C|downstream_gene_variant|MODIFIER|merA|PA14_15460|transcript|ABJ13022.1|protein_coding||c.*367C>G|||||367|,C|downstream_gene_variant|MODIFIER|merP|PA14_15470|transcript|ABJ13021.1|protein_coding||c.*2124C>G|||||2124|,C|downstream_gene_variant|MODIFIER|merT|PA14_15475|transcript|ABJ15636.1|protein_coding||c.*2412C>G|||||2412| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:115:0:0:0,-10.724 0:8:8,2:6:195:2:30:0,-15.0127 0:2:2,0:2:80:0:0:0,-7.59179 0:1:1,0:1:40:0:0:0,-3.99568 +Chromosome 1336903 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=43;DPB=43;DPRA=0.861111;EPP=11.6962;EPPR=5.73856;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=46.5333;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=56;QR=1332;RO=39;RPL=4;RPP=11.6962;RPPR=3.06598;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=16;SRP=5.73856;SRR=23;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|yfhD|PA14_15720|transcript|ABJ12999.1|protein_coding|1/1|c.1261C>A|p.Gln421Lys|1261/1356|1261/1356|421/451||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|purL|PA14_15740|transcript|ABJ12998.1|protein_coding||c.-1661G>T|||||1661|,T|downstream_gene_variant|MODIFIER|PA14_15660|PA14_15660|transcript|ABJ13004.1|protein_coding||c.*4558G>T|||||4558|,T|downstream_gene_variant|MODIFIER|cumA|PA14_15670|transcript|ABJ13003.1|protein_coding||c.*3003G>T|||||3003|,T|downstream_gene_variant|MODIFIER|cumB|PA14_15680|transcript|ABJ13002.1|protein_coding||c.*2464G>T|||||2464|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|PA14_15700|PA14_15700|transcript|ABJ13001.1|protein_coding||c.*819G>T|||||819|,T|downstream_gene_variant|MODIFIER|PA14_15710|PA14_15710|transcript|ABJ13000.1|protein_coding||c.*109G>T|||||109| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,2:6:175:2:39:0,-12.3307 0:12:12,0:12:432:0:0:0,-39.209 0:9:9,1:8:294:1:2:0,-26.6013 0:14:14,1:13:431:1:15:0,-37.5891 +Chromosome 1337235 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=56;DPB=56;DPRA=1.43478;EPP=13.8677;EPPR=3.70517;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=80.8832;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1611;RO=50;RPL=0;RPP=13.8677;RPPR=9.26414;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=16;SRP=17.0814;SRR=34;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|yfhD|PA14_15720|transcript|ABJ12999.1|protein_coding|1/1|c.929T>C|p.Leu310Pro|929/1356|929/1356|310/451||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|purL|PA14_15740|transcript|ABJ12998.1|protein_coding||c.-1329A>G|||||1329|,G|downstream_gene_variant|MODIFIER|PA14_15660|PA14_15660|transcript|ABJ13004.1|protein_coding||c.*4890A>G|||||4890|,G|downstream_gene_variant|MODIFIER|cumA|PA14_15670|transcript|ABJ13003.1|protein_coding||c.*3335A>G|||||3335|,G|downstream_gene_variant|MODIFIER|cumB|PA14_15680|transcript|ABJ13002.1|protein_coding||c.*2796A>G|||||2796|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_15700|PA14_15700|transcript|ABJ13001.1|protein_coding||c.*1151A>G|||||1151|,G|downstream_gene_variant|MODIFIER|PA14_15710|PA14_15710|transcript|ABJ13000.1|protein_coding||c.*441A>G|||||441| GT:DP:DPR:RO:QR:AO:QA:GL 0:17:17,4:13:367:4:8:0,-32.5577 0:10:10,0:10:305:0:0:0,-27.7363 0:16:16,1:15:508:1:2:0,-45.8182 0:13:13,0:12:431:0:0:0,-39.0717 +Chromosome 1349835 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=44;DPB=44;DPRA=0.882353;EPP=7.35324;EPPR=6.31921;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=75.7558;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=36;QR=1588;RO=42;RPL=2;RPP=7.35324;RPPR=3.83753;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=28;SRP=13.1438;SRR=14;TYPE=snp;technology.ILLUMINA=1;ANN=C|start_lost|HIGH|nagA|PA14_15820|transcript|ABJ12992.1|protein_coding|1/1|c.2T>G|p.Met1?|2/1092|2/1092|1/363||,C|upstream_gene_variant|MODIFIER|nagE|PA14_15780|transcript|ABJ12995.1|protein_coding||c.-4679T>G|||||4679|,C|upstream_gene_variant|MODIFIER|nagF|PA14_15790|transcript|ABJ12994.1|protein_coding||c.-2126T>G|||||2126|,C|upstream_gene_variant|MODIFIER|glmS|PA14_15810|transcript|ABJ12993.1|protein_coding||c.-1087T>G|||||1087|,C|upstream_gene_variant|MODIFIER|PA14_15860|PA14_15860|transcript|ABJ12988.1|protein_coding||c.-2262A>C|||||2262|,C|upstream_gene_variant|MODIFIER|PA14_15870|PA14_15870|transcript|ABJ12987.1|protein_coding||c.-2911A>C|||||2911|,C|upstream_gene_variant|MODIFIER|PA14_15880|PA14_15880|transcript|ABJ12986.1|protein_coding||c.-3432A>C|||||3432|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|purT|PA14_15890|transcript|ABJ12985.1|protein_coding||c.-3664A>C|||||3664|,C|upstream_gene_variant|MODIFIER|PA14_15910|PA14_15910|transcript|ABJ12984.1|protein_coding||c.-4847A>C|||||4847|,C|downstream_gene_variant|MODIFIER|PA14_15830|PA14_15830|transcript|ABJ12991.1|protein_coding||c.*18T>G|||||18|,C|downstream_gene_variant|MODIFIER|PA14_15840|PA14_15840|transcript|ABJ12990.1|protein_coding||c.*1004T>G|||||1004|,C|downstream_gene_variant|MODIFIER|PA14_15850|PA14_15850|transcript|ABJ12989.1|protein_coding||c.*1567T>G|||||1567|;LOF=(nagA|PA14_15820|1|1.00) GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,2:8:317:2:36:0,-25.4782 0:9:9,0:9:320:0:0:0,-29.1317 0:16:16,0:16:612:0:0:0,-55.4129 0:9:9,0:9:339:0:0:0,-30.8633 +Chromosome 1371323 . A C 5.86201E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=6;CIGAR=1X;DP=52;DPB=52;DPRA=1.11111;EPP=16.0391;EPPR=25.858;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=71.2365;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=1554;RO=46;RPL=6;RPP=16.0391;RPPR=3.19912;RPR=0;RUN=1;SAF=6;SAP=16.0391;SAR=0;SRF=16;SRP=12.2627;SRR=30;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_16100|PA14_16100|transcript|ABJ12968.1|protein_coding|1/1|c.1175T>G|p.Leu392Arg|1175/1221|1175/1221|392/406||,C|upstream_gene_variant|MODIFIER|PA14_16110|PA14_16110|transcript|ABJ12967.1|protein_coding||c.-1271A>C|||||1271|,C|upstream_gene_variant|MODIFIER|PA14_16140|PA14_16140|transcript|ABJ12965.1|protein_coding||c.-3453A>C|||||3453|,C|upstream_gene_variant|MODIFIER|PA14_16150|PA14_16150|transcript|ABJ12964.1|protein_coding||c.-3911A>C|||||3911|,C|upstream_gene_variant|MODIFIER|PA14_16160|PA14_16160|transcript|ABJ12963.1|protein_coding||c.-4662A>C|||||4662|,C|downstream_gene_variant|MODIFIER|xerD|PA14_16040|transcript|ABJ12972.1|protein_coding||c.*3935A>C|||||3935|,C|downstream_gene_variant|MODIFIER|dsbC|PA14_16050|transcript|ABJ12971.1|protein_coding||c.*3080A>C|||||3080|,C|downstream_gene_variant|MODIFIER|hom|PA14_16070|transcript|ABJ12970.1|protein_coding||c.*1562A>C|||||1562|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|thrC|PA14_16090|transcript|ABJ12969.1|protein_coding||c.*100A>C|||||100|,C|downstream_gene_variant|MODIFIER|PA14_16130|PA14_16130|transcript|ABJ12966.1|protein_coding||c.*1742T>G|||||1742| GT:DP:DPR:RO:QR:AO:QA:GL 0:13:13,3:10:290:3:25:0,-24.0408 0:9:9,1:8:282:1:2:0,-25.517 0:12:12,0:12:372:0:0:0,-33.7642 0:18:18,2:16:610:2:4:0,-54.8562 +Chromosome 1373692 . G T 4.24029E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=30;DPB=30;DPRA=1.28571;EPP=3.0103;EPPR=14.1779;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=29.9592;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=956;RO=28;RPL=1;RPP=3.0103;RPPR=3.32051;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=13;SRP=3.32051;SRR=15;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|PA14_16130|PA14_16130|transcript|ABJ12966.1|protein_coding|1/1|c.603C>A|p.Val201Val|603/1230|603/1230|201/409||,T|upstream_gene_variant|MODIFIER|PA14_16100|PA14_16100|transcript|ABJ12968.1|protein_coding||c.-1195C>A|||||1195|,T|upstream_gene_variant|MODIFIER|PA14_16140|PA14_16140|transcript|ABJ12965.1|protein_coding||c.-1084G>T|||||1084|,T|upstream_gene_variant|MODIFIER|PA14_16150|PA14_16150|transcript|ABJ12964.1|protein_coding||c.-1542G>T|||||1542|,T|upstream_gene_variant|MODIFIER|PA14_16160|PA14_16160|transcript|ABJ12963.1|protein_coding||c.-2293G>T|||||2293|,T|upstream_gene_variant|MODIFIER|PA14_16180|PA14_16180|transcript|ABJ12962.1|protein_coding||c.-2970G>T|||||2970|,T|downstream_gene_variant|MODIFIER|hom|PA14_16070|transcript|ABJ12970.1|protein_coding||c.*3931G>T|||||3931|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|thrC|PA14_16090|transcript|ABJ12969.1|protein_coding||c.*2469G>T|||||2469|,T|downstream_gene_variant|MODIFIER|PA14_16110|PA14_16110|transcript|ABJ12967.1|protein_coding||c.*814G>T|||||814| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:69:0:0:0,-6.55132 0:10:10,0:10:317:0:0:0,-28.8302 0:9:9,0:9:311:0:0:0,-28.3171 0:9:9,2:7:259:2:31:0,-20.7161 +Chromosome 1383031 . G C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=12;CIGAR=1X;DP=107;DPB=107;DPRA=0;EPP=29.068;EPPR=3.58174;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=140.62;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=46;QR=3259;RO=95;RPL=12;RPP=29.068;RPPR=24.9765;RPR=0;RUN=1;SAF=12;SAP=29.068;SAR=0;SRF=41;SRP=6.87324;SRR=54;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_16190|PA14_16190|transcript|ABJ12961.1|protein_coding|1/1|c.4154G>C|p.Arg1385Pro|4154/5241|4154/5241|1385/1746||,C|upstream_gene_variant|MODIFIER|PA14_16200|PA14_16200|transcript|ABJ12960.1|protein_coding||c.-1106G>C|||||1106|,C|upstream_gene_variant|MODIFIER|PA14_16210|PA14_16210|transcript|ABJ12959.1|protein_coding||c.-1905G>C|||||1905|,C|upstream_gene_variant|MODIFIER|recJ|PA14_16220|transcript|ABJ12958.1|protein_coding||c.-2488G>C|||||2488|,C|upstream_gene_variant|MODIFIER|lasB|PA14_16250|transcript|ABJ12957.1|protein_coding||c.-4490G>C|||||4490|,C|downstream_gene_variant|MODIFIER|PA14_16180|PA14_16180|transcript|ABJ12962.1|protein_coding||c.*4303G>C|||||4303| GT:DP:DPR:RO:QR:AO:QA:GL 0:20:20,1:19:654:1:2:0,-58.9576 0:29:29,2:27:973:2:4:0,-87.4694 0:34:34,4:30:1061:4:8:0,-95.0243 0:24:24,5:19:571:5:32:0,-48.704 +Chromosome 1384434 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=10;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=24.725;EPPR=57.1301;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=61.1064;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=1530;RO=52;RPL=10;RPP=24.725;RPPR=3.17734;RPR=0;RUN=1;SAF=10;SAP=24.725;SAR=0;SRF=29;SRP=4.51363;SRR=23;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_16200|PA14_16200|transcript|ABJ12960.1|protein_coding|1/1|c.298A>G|p.Lys100Glu|298/693|298/693|100/230||,G|upstream_gene_variant|MODIFIER|PA14_16210|PA14_16210|transcript|ABJ12959.1|protein_coding||c.-502A>G|||||502|,G|upstream_gene_variant|MODIFIER|recJ|PA14_16220|transcript|ABJ12958.1|protein_coding||c.-1085A>G|||||1085|,G|upstream_gene_variant|MODIFIER|lasB|PA14_16250|transcript|ABJ12957.1|protein_coding||c.-3087A>G|||||3087|,G|upstream_gene_variant|MODIFIER|PA14_16260|PA14_16260|transcript|ABJ12956.1|protein_coding||c.-4753A>G|||||4753|,G|downstream_gene_variant|MODIFIER|PA14_16190|PA14_16190|transcript|ABJ12961.1|protein_coding||c.*316A>G|||||316| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,1:6:200:1:2:0,-18.1152 0:16:16,1:15:427:1:2:0,-38.4814 0:20:20,4:16:413:4:8:0,-36.6567 0:19:19,4:15:490:4:8:0,-43.6494 +Chromosome 1395968 . G A 4.32761E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=18;DPB=18;DPRA=1.90909;EPP=7.35324;EPPR=3.55317;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=20.7268;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=52;QR=547;RO=16;RPL=1;RPP=3.0103;RPPR=3.55317;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=2;SRP=22.5536;SRR=14;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|PA14_16330|PA14_16330|transcript|ABJ12949.1|protein_coding|1/1|c.1659G>A|p.Glu553Glu|1659/1707|1659/1707|553/568||,A|upstream_gene_variant|MODIFIER|PA14_16280|PA14_16280|transcript|ABJ12954.1|protein_coding||c.-4483C>T|||||4483|,A|upstream_gene_variant|MODIFIER|fkbP-1|PA14_16320|transcript|ABJ12950.1|protein_coding||c.-1869C>T|||||1869|,A|upstream_gene_variant|MODIFIER|PA14_16370|PA14_16370|transcript|ABJ12945.1|protein_coding||c.-4200G>A|||||4200|,A|downstream_gene_variant|MODIFIER|PA14_16290|PA14_16290|transcript|ABJ12953.1|protein_coding||c.*3855G>A|||||3855|,A|downstream_gene_variant|MODIFIER|PA14_16300|PA14_16300|transcript|ABJ12952.1|protein_coding||c.*3686G>A|||||3686|,A|downstream_gene_variant|MODIFIER|PA14_16310|PA14_16310|transcript|ABJ12951.1|protein_coding||c.*2297G>A|||||2297|,A|downstream_gene_variant|MODIFIER|PA14_16340|PA14_16340|transcript|ABJ12948.1|protein_coding||c.*127C>T|||||127|,A|downstream_gene_variant|MODIFIER|PA14_16350|PA14_16350|transcript|ABJ12947.1|protein_coding||c.*1051C>T|||||1051|,A|downstream_gene_variant|MODIFIER|PA14_16360|PA14_16360|transcript|ABJ12946.1|protein_coding||c.*2016C>T|||||2016|,A|downstream_gene_variant|MODIFIER|PA14_16380|PA14_16380|transcript|ABJ12944.1|protein_coding||c.*4932C>T|||||4932| GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:40:0:0:0,-3.99568 0:3:3,0:3:103:0:0:0,-9.60749 0:7:7,2:5:174:2:52:0,-11.0624 0:7:7,0:7:230:0:0:0,-21.0186 +Chromosome 1398452 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=31;DPB=31;DPRA=1.42857;EPP=7.35324;EPPR=9.07545;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=46.8075;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=954;RO=29;RPL=0;RPP=7.35324;RPPR=19.8579;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=11;SRP=6.67934;SRR=18;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|PA14_16360|PA14_16360|transcript|ABJ12946.1|protein_coding|1/1|c.1395G>C|p.Pro465Pro|1395/1863|1395/1863|465/620||,G|upstream_gene_variant|MODIFIER|fkbP-1|PA14_16320|transcript|ABJ12950.1|protein_coding||c.-4353G>C|||||4353|,G|upstream_gene_variant|MODIFIER|PA14_16340|PA14_16340|transcript|ABJ12948.1|protein_coding||c.-1554G>C|||||1554|,G|upstream_gene_variant|MODIFIER|PA14_16350|PA14_16350|transcript|ABJ12947.1|protein_coding||c.-792G>C|||||792|,G|upstream_gene_variant|MODIFIER|PA14_16370|PA14_16370|transcript|ABJ12945.1|protein_coding||c.-1716C>G|||||1716|,G|upstream_gene_variant|MODIFIER|PA14_16390|PA14_16390|transcript|ABJ12943.1|protein_coding||c.-3525C>G|||||3525|,G|downstream_gene_variant|MODIFIER|PA14_16310|PA14_16310|transcript|ABJ12951.1|protein_coding||c.*4781C>G|||||4781|,G|downstream_gene_variant|MODIFIER|PA14_16330|PA14_16330|transcript|ABJ12949.1|protein_coding||c.*2436C>G|||||2436|,G|downstream_gene_variant|MODIFIER|PA14_16380|PA14_16380|transcript|ABJ12944.1|protein_coding||c.*2448G>C|||||2448| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,0:9:283:0:0:0,-25.7689 0:6:6,0:6:214:0:0:0,-19.604 0:6:6,0:6:161:0:0:0,-14.7471 0:10:10,2:8:296:2:4:0,-26.6119 +Chromosome 1400739 . T C 7.00668E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=25;DPB=25;DPRA=1.6875;EPP=7.35324;EPPR=18.9659;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=45.8674;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=79;QR=870;RO=23;RPL=2;RPP=7.35324;RPPR=7.63648;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=9;SRP=5.3706;SRR=14;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_16370|PA14_16370|transcript|ABJ12945.1|protein_coding|1/1|c.572T>C|p.Val191Ala|572/696|572/696|191/231||,C|upstream_gene_variant|MODIFIER|PA14_16340|PA14_16340|transcript|ABJ12948.1|protein_coding||c.-3841A>G|||||3841|,C|upstream_gene_variant|MODIFIER|PA14_16350|PA14_16350|transcript|ABJ12947.1|protein_coding||c.-3079A>G|||||3079|,C|upstream_gene_variant|MODIFIER|PA14_16360|PA14_16360|transcript|ABJ12946.1|protein_coding||c.-893A>G|||||893|,C|upstream_gene_variant|MODIFIER|PA14_16390|PA14_16390|transcript|ABJ12943.1|protein_coding||c.-1238T>C|||||1238|,C|upstream_gene_variant|MODIFIER|PA14_16410|PA14_16410|transcript|ABJ12942.1|protein_coding||c.-3020T>C|||||3020|,C|upstream_gene_variant|MODIFIER|wspA|PA14_16430|transcript|ABJ12941.1|protein_coding||c.-4906T>C|||||4906|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_16330|PA14_16330|transcript|ABJ12949.1|protein_coding||c.*4723T>C|||||4723|,C|downstream_gene_variant|MODIFIER|PA14_16380|PA14_16380|transcript|ABJ12944.1|protein_coding||c.*161A>G|||||161| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:198:0:0:0,-18.1978 0:9:9,2:7:241:2:79:0,-14.5202 0:5:5,0:5:199:0:0:0,-18.2889 0:6:6,0:6:232:0:0:0,-21.248 +Chromosome 1416086 . T A 3.83471E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=43;DPB=43;DPRA=0.583333;EPP=7.35324;EPPR=41.6201;GTI=0;LEN=1;MEANALT=1;MQM=26;MQMR=59.7073;NS=4;NUMALT=1;ODDS=53.3879;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1314;RO=41;RPL=0;RPP=7.35324;RPPR=11.961;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=24;SRP=5.60547;SRR=17;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|lysS|PA14_16530|transcript|ABJ12933.1|protein_coding|1/1|c.487T>A|p.Tyr163Asn|487/1506|487/1506|163/501||,A|upstream_gene_variant|MODIFIER|PA14_16550|PA14_16550|transcript|ABJ12932.1|protein_coding||c.-1231T>A|||||1231|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|PA14_16560|PA14_16560|transcript|ABJ12931.1|protein_coding||c.-2041T>A|||||2041|,A|upstream_gene_variant|MODIFIER|PA14_16580|PA14_16580|transcript|ABJ12930.1|protein_coding||c.-2601T>A|||||2601|,A|upstream_gene_variant|MODIFIER|PA14_16590|PA14_16590|transcript|ABJ12929.1|protein_coding||c.-3965T>A|||||3965|,A|upstream_gene_variant|MODIFIER|PA14_16600|PA14_16600|transcript|ABJ12928.1|protein_coding||c.-4708T>A|||||4708|,A|downstream_gene_variant|MODIFIER|wspE|PA14_16470|transcript|ABJ12937.1|protein_coding||c.*4040T>A|||||4040|,A|downstream_gene_variant|MODIFIER|wspF|PA14_16480|transcript|ABJ12936.1|protein_coding||c.*3036T>A|||||3036|,A|downstream_gene_variant|MODIFIER|wspR|PA14_16500|transcript|ABJ12935.1|protein_coding||c.*1885T>A|||||1885|,A|downstream_gene_variant|MODIFIER|PA14_16510|PA14_16510|transcript|ABJ12934.1|protein_coding||c.*667T>A|||||667| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:241:0:0:0,-22.0187 0:16:16,0:16:527:0:0:0,-47.7219 0:13:13,0:13:385:0:0:0,-34.9174 0:7:7,2:5:161:2:4:0,-14.4182 +Chromosome 1422627 . A G 2.60717E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=49;DPB=49;DPRA=0.96;EPP=11.6962;EPPR=20.4303;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=58.9467;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=1588;RO=45;RPL=0;RPP=11.6962;RPPR=28.5372;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=33;SRP=24.2907;SRR=12;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_16630|PA14_16630|transcript|ABJ12925.1|protein_coding|1/1|c.772T>C|p.Ser258Pro|772/786|772/786|258/261||,G|upstream_gene_variant|MODIFIER|cadR|PA14_16670|transcript|ABJ12922.1|protein_coding||c.-3968A>G|||||3968|,G|upstream_gene_variant|MODIFIER|ppc|PA14_16690|transcript|ABJ12920.1|protein_coding||c.-4999A>G|||||4999|,G|downstream_gene_variant|MODIFIER|PA14_16550|PA14_16550|transcript|ABJ12932.1|protein_coding||c.*4597A>G|||||4597|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_16560|PA14_16560|transcript|ABJ12931.1|protein_coding||c.*3949A>G|||||3949|,G|downstream_gene_variant|MODIFIER|PA14_16580|PA14_16580|transcript|ABJ12930.1|protein_coding||c.*2645A>G|||||2645|,G|downstream_gene_variant|MODIFIER|PA14_16590|PA14_16590|transcript|ABJ12929.1|protein_coding||c.*1830A>G|||||1830|,G|downstream_gene_variant|MODIFIER|PA14_16600|PA14_16600|transcript|ABJ12928.1|protein_coding||c.*928A>G|||||928|,G|downstream_gene_variant|MODIFIER|PA14_16610|PA14_16610|transcript|ABJ12927.1|protein_coding||c.*608A>G|||||608|,G|downstream_gene_variant|MODIFIER|PA14_16620|PA14_16620|transcript|ABJ12926.1|protein_coding||c.*90A>G|||||90|,G|downstream_gene_variant|MODIFIER|PA14_16640|PA14_16640|transcript|ABJ12924.1|protein_coding||c.*820T>C|||||820|,G|downstream_gene_variant|MODIFIER|cadA|PA14_16660|transcript|ABJ12923.1|protein_coding||c.*1626T>C|||||1626|,G|downstream_gene_variant|MODIFIER|PA14_16680|PA14_16680|transcript|ABJ12921.1|protein_coding||c.*4447T>C|||||4447| GT:DP:DPR:RO:QR:AO:QA:GL 0:14:14,2:12:421:2:16:0,-36.6877 0:19:19,0:19:702:0:0:0,-63.4888 0:10:10,2:8:262:2:4:0,-23.5165 0:6:6,0:6:203:0:0:0,-18.5923 +Chromosome 1441656 . G T 9.65905E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=35;DPB=35;DPRA=1.33333;EPP=6.91895;EPPR=4.16842;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=34.7102;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=64;QR=850;RO=30;RPL=4;RPP=6.91895;RPPR=7.64277;RPR=1;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=20;SRP=10.2485;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|PA14_16820|PA14_16820|transcript|ABJ12909.1|protein_coding|1/1|c.2904G>T|p.Leu968Leu|2904/3078|2904/3078|968/1025||,T|upstream_gene_variant|MODIFIER|PA14_16790|PA14_16790|transcript|ABJ12911.1|protein_coding||c.-4107C>A|||||4107|,T|upstream_gene_variant|MODIFIER|PA14_16870|PA14_16870|transcript|ABJ12905.1|protein_coding||c.-4363G>T|||||4363|,T|downstream_gene_variant|MODIFIER|PA14_16780|PA14_16780|transcript|ABJ12912.1|protein_coding||c.*4752G>T|||||4752|,T|downstream_gene_variant|MODIFIER|PA14_16800|PA14_16800|transcript|ABJ12910.1|protein_coding||c.*2908G>T|||||2908|,T|downstream_gene_variant|MODIFIER|PA14_16830|PA14_16830|transcript|ABJ12908.1|protein_coding||c.*217C>A|||||217|,T|downstream_gene_variant|MODIFIER|PA14_16840|PA14_16840|transcript|ABJ12907.1|protein_coding||c.*1034C>A|||||1034|,T|downstream_gene_variant|MODIFIER|plsB|PA14_16860|transcript|ABJ12906.1|protein_coding||c.*1575C>A|||||1575| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,1:4:110:1:16:0,-8.56846 0:7:7,0:7:239:0:0:0,-21.8379 0:11:11,1:10:275:1:16:0,-23.4134 0:12:12,3:9:226:3:32:0,-17.5983 +Chromosome 1454379 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=61;DPB=61;DPRA=0.90625;EPP=11.6962;EPPR=4.877;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=79.2797;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=61;QR=1754;RO=57;RPL=4;RPP=11.6962;RPPR=6.09608;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=29;SRP=3.0484;SRR=28;TYPE=snp;technology.ILLUMINA=1;ANN=T|upstream_gene_variant|MODIFIER|sufE|PA14_16920|transcript|ABJ12901.1|protein_coding||c.-3435C>A|||||3435|,T|upstream_gene_variant|MODIFIER|csdA|PA14_16930|transcript|ABJ12900.1|protein_coding||c.-2233C>A|||||2233|,T|upstream_gene_variant|MODIFIER|dapD|PA14_16950|transcript|ABJ12899.1|protein_coding||c.-1104C>A|||||1104|,T|upstream_gene_variant|MODIFIER|PA14_16960|PA14_16960|transcript|ABJ12898.1|protein_coding||c.-451C>A|||||451|,T|upstream_gene_variant|MODIFIER|PA14_16970|PA14_16970|transcript|ABJ12897.1|protein_coding||c.-91C>A|||||91|,T|upstream_gene_variant|MODIFIER|PA14_16980|PA14_16980|transcript|ABJ12896.1|protein_coding||c.-212G>T|||||212|,T|upstream_gene_variant|MODIFIER|yjcE|PA14_17010|transcript|ABJ12893.1|protein_coding||c.-1792G>T|||||1792|,T|downstream_gene_variant|MODIFIER|PA14_16890|PA14_16890|transcript|ABJ12903.1|protein_coding||c.*4848G>T|||||4848|,T|downstream_gene_variant|MODIFIER|PA14_16910|PA14_16910|transcript|ABJ12902.1|protein_coding||c.*3864G>T|||||3864|,T|downstream_gene_variant|MODIFIER|PA14_16990|PA14_16990|transcript|ABJ12895.1|protein_coding||c.*580C>A|||||580|,T|downstream_gene_variant|MODIFIER|PA14_17000|PA14_17000|transcript|ABJ12894.1|protein_coding||c.*1195C>A|||||1195|,T|downstream_gene_variant|MODIFIER|dapC|PA14_17030|transcript|ABJ12892.1|protein_coding||c.*3588C>A|||||3588|,T|downstream_gene_variant|MODIFIER|glnD|PA14_17040|transcript|ABJ12891.1|protein_coding||c.*4814C>A|||||4814|,T|intergenic_region|MODIFIER|PA14_16970-PA14_16980|PA14_16970-PA14_16980|intergenic_region|PA14_16970-PA14_16980|||n.1454379G>T|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:15:15,1:14:437:1:15:0,-38.1223 0:14:14,3:11:325:3:46:0,-25.2348 0:16:16,0:16:539:0:0:0,-48.8102 0:16:16,0:16:453:0:0:0,-41.0367 +Chromosome 1470273 . A G 3.49569E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=56;DPB=56;DPRA=1.07407;EPP=11.6962;EPPR=19.7139;GTI=0;LEN=1;MEANALT=1;MQM=53.25;MQMR=60;NS=4;NUMALT=1;ODDS=84.9008;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=44;QR=1879;RO=52;RPL=4;RPP=11.6962;RPPR=9.02361;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=18;SRP=13.7006;SRR=34;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|yaeL|PA14_17140|transcript|ABJ12882.1|protein_coding|1/1|c.1133A>G|p.Asp378Gly|1133/1353|1133/1353|378/450||,G|upstream_gene_variant|MODIFIER|PA14_17150|PA14_17150|transcript|ABJ12881.1|protein_coding||c.-291A>G|||||291|,G|upstream_gene_variant|MODIFIER|ompH|PA14_17170|transcript|ABJ12880.1|protein_coding||c.-2726A>G|||||2726|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|lpxD|PA14_17180|transcript|ABJ12879.1|protein_coding||c.-3232A>G|||||3232|,G|upstream_gene_variant|MODIFIER|fabZ|PA14_17190|transcript|ABJ12878.1|protein_coding||c.-4339A>G|||||4339|,G|upstream_gene_variant|MODIFIER|lpxA|PA14_17210|transcript|ABJ12877.1|protein_coding||c.-4776A>G|||||4776|,G|downstream_gene_variant|MODIFIER|pyrH|PA14_17080|transcript|ABJ12887.1|protein_coding||c.*4485A>G|||||4485|,G|downstream_gene_variant|MODIFIER|frr|PA14_17100|transcript|ABJ12886.1|protein_coding||c.*3925A>G|||||3925|,G|downstream_gene_variant|MODIFIER|uppS|PA14_17110|transcript|ABJ12885.1|protein_coding||c.*3154A>G|||||3154|,G|downstream_gene_variant|MODIFIER|cdsA|PA14_17120|transcript|ABJ12884.1|protein_coding||c.*2345A>G|||||2345|,G|downstream_gene_variant|MODIFIER|dxr|PA14_17130|transcript|ABJ12883.1|protein_coding||c.*1158A>G|||||1158| GT:DP:DPR:RO:QR:AO:QA:GL 0:15:15,0:15:526:0:0:0,-47.6565 0:14:14,3:11:361:3:42:0,-28.8731 0:15:15,1:14:517:1:2:0,-46.6598 0:12:12,0:12:475:0:0:0,-43.1026 +Chromosome 1479581 . A G 4.67353E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=22;DPB=22;DPRA=2.5;EPP=3.0103;EPPR=4.74748;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=20.6499;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=699;RO=20;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=8;SRP=4.74748;SRR=12;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|dnaE|PA14_17260|transcript|ABJ12873.1|protein_coding|1/1|c.250A>G|p.Ser84Gly|250/3522|250/3522|84/1173||,G|upstream_gene_variant|MODIFIER|accA|PA14_17270|transcript|ABJ12872.1|protein_coding||c.-3422A>G|||||3422|,G|upstream_gene_variant|MODIFIER|mesJ|PA14_17280|transcript|ABJ12871.1|protein_coding||c.-4442A>G|||||4442|,G|downstream_gene_variant|MODIFIER|fabZ|PA14_17190|transcript|ABJ12878.1|protein_coding||c.*4529A>G|||||4529|,G|downstream_gene_variant|MODIFIER|lpxA|PA14_17210|transcript|ABJ12877.1|protein_coding||c.*3756A>G|||||3756|,G|downstream_gene_variant|MODIFIER|lpxB|PA14_17220|transcript|ABJ12876.1|protein_coding||c.*2616A>G|||||2616|,G|downstream_gene_variant|MODIFIER|rnhB|PA14_17230|transcript|ABJ12875.1|protein_coding||c.*2011A>G|||||2011|,G|downstream_gene_variant|MODIFIER|yaaJ|PA14_17250|transcript|ABJ12874.1|protein_coding||c.*379A>G|||||379| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:168:0:0:0,-15.449 0:1:1,0:1:31:0:0:0,-3.09945 0:6:6,0:6:218:0:0:0,-19.9696 0:10:10,2:8:282:2:30:0,-22.8617 +Chromosome 1482220 . C A 7.31533E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=61;DPB=61;DPRA=0.893617;EPP=3.73412;EPPR=10.3484;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=85.5424;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=1988;RO=58;RPL=1;RPP=3.73412;RPPR=6.75422;RPR=2;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=20;SRP=15.1406;SRR=38;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|dnaE|PA14_17260|transcript|ABJ12873.1|protein_coding|1/1|c.2889C>A|p.Leu963Leu|2889/3522|2889/3522|963/1173||,A|upstream_gene_variant|MODIFIER|accA|PA14_17270|transcript|ABJ12872.1|protein_coding||c.-783C>A|||||783|,A|upstream_gene_variant|MODIFIER|mesJ|PA14_17280|transcript|ABJ12871.1|protein_coding||c.-1803C>A|||||1803|,A|upstream_gene_variant|MODIFIER|pyrG|PA14_17290|transcript|ABJ12870.1|protein_coding||c.-3302C>A|||||3302|,A|upstream_gene_variant|MODIFIER|kdsA|PA14_17310|transcript|ABJ12869.1|protein_coding||c.-4933C>A|||||4933|,A|downstream_gene_variant|MODIFIER|rnhB|PA14_17230|transcript|ABJ12875.1|protein_coding||c.*4650C>A|||||4650|,A|downstream_gene_variant|MODIFIER|yaaJ|PA14_17250|transcript|ABJ12874.1|protein_coding||c.*3018C>A|||||3018| GT:DP:DPR:RO:QR:AO:QA:GL 0:13:13,0:13:463:0:0:0,-41.9965 0:14:14,3:11:350:3:33:0,-28.7209 0:21:21,0:21:714:0:0:0,-64.5591 0:13:13,0:13:461:0:0:0,-41.8168 +Chromosome 1483383 . C A 5.00998E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=52;DPB=52;DPRA=1;EPP=11.6962;EPPR=4.16534;GTI=0;LEN=1;MEANALT=1.33333;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=54.7055;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=56;QR=1708;RO=47;RPL=0;RPP=11.6962;RPPR=10.8184;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=26;SRP=4.16534;SRR=21;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|accA|PA14_17270|transcript|ABJ12872.1|protein_coding|1/1|c.381C>A|p.Arg127Arg|381/951|381/951|127/316||,A|upstream_gene_variant|MODIFIER|mesJ|PA14_17280|transcript|ABJ12871.1|protein_coding||c.-640C>A|||||640|,A|upstream_gene_variant|MODIFIER|pyrG|PA14_17290|transcript|ABJ12870.1|protein_coding||c.-2139C>A|||||2139|,A|upstream_gene_variant|MODIFIER|kdsA|PA14_17310|transcript|ABJ12869.1|protein_coding||c.-3770C>A|||||3770|,A|upstream_gene_variant|MODIFIER|eno|PA14_17320|transcript|ABJ12868.1|protein_coding||c.-4661C>A|||||4661|,A|downstream_gene_variant|MODIFIER|yaaJ|PA14_17250|transcript|ABJ12874.1|protein_coding||c.*4181C>A|||||4181|,A|downstream_gene_variant|MODIFIER|dnaE|PA14_17260|transcript|ABJ12873.1|protein_coding||c.*530C>A|||||530| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,2:6:209:2:39:0,-15.3867 0:13:13,1:12:444:1:2:0,-40.0991 0:13:13,0:13:499:0:0:0,-45.256 0:17:17,1:16:556:1:15:0,-48.8523 +Chromosome 1490965 . T C 1.72924E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=52;DPB=52;DPRA=1.11111;EPP=11.6962;EPPR=5.27418;GTI=0;LEN=1;MEANALT=1.33333;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=64.7624;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1707;RO=47;RPL=0;RPP=11.6962;RPPR=3.42611;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=18;SRP=8.60069;SRR=29;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|yedE|PA14_17370|transcript|ABJ12864.1|protein_coding|1/1|c.943A>G|p.Met315Val|943/1227|943/1227|315/408||,C|upstream_gene_variant|MODIFIER|PA14_17350|PA14_17350|transcript|ABJ12865.1|protein_coding||c.-250A>G|||||250|,C|upstream_gene_variant|MODIFIER|adhC|PA14_17400|transcript|ABJ12862.1|protein_coding||c.-2058T>C|||||2058|,C|upstream_gene_variant|MODIFIER|PA14_17410|PA14_17410|transcript|ABJ12861.1|protein_coding||c.-3224T>C|||||3224|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ispF|PA14_17420|transcript|ABJ12860.1|protein_coding||c.-4146T>C|||||4146|,C|upstream_gene_variant|MODIFIER|PA14_17440|PA14_17440|transcript|ABJ12859.1|protein_coding||c.-4616T>C|||||4616|,C|downstream_gene_variant|MODIFIER|pyrG|PA14_17290|transcript|ABJ12870.1|protein_coding||c.*3815T>C|||||3815|,C|downstream_gene_variant|MODIFIER|kdsA|PA14_17310|transcript|ABJ12869.1|protein_coding||c.*2967T>C|||||2967|,C|downstream_gene_variant|MODIFIER|eno|PA14_17320|transcript|ABJ12868.1|protein_coding||c.*1632T>C|||||1632|,C|downstream_gene_variant|MODIFIER|PA14_17330|PA14_17330|transcript|ABJ12867.1|protein_coding||c.*1283T>C|||||1283|,C|downstream_gene_variant|MODIFIER|ispD|PA14_17340|transcript|ABJ12866.1|protein_coding||c.*559T>C|||||559|,C|downstream_gene_variant|MODIFIER|PA14_17380|PA14_17380|transcript|ABJ12863.1|protein_coding||c.*1018A>G|||||1018| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,2:6:219:2:4:0,-19.6075 0:12:12,0:12:458:0:0:0,-41.5673 0:21:21,1:20:701:1:2:0,-63.1895 0:10:10,1:9:329:1:2:0,-29.7554 +Chromosome 1504880 . A G 7.31533E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=36;DPB=36;DPRA=1.15385;EPP=7.35324;EPPR=9.39698;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=48.7252;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=65;QR=1112;RO=34;RPL=0;RPP=7.35324;RPPR=4.03217;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=9;SRP=19.3602;SRR=25;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|cinA|PA14_17520|transcript|ABJ12851.1|protein_coding|1/1|c.116A>G|p.Glu39Gly|116/507|116/507|39/168||,G|upstream_gene_variant|MODIFIER|PrrB_RsmZ|EBG00001225027|transcript|EBT00001793507.1|sRNA||n.-4412T>C|||||4412|,G|upstream_gene_variant|MODIFIER|fdxA|PA14_17490|transcript|ABJ12854.1|protein_coding||c.-4030T>C|||||4030|,G|upstream_gene_variant|MODIFIER|mutS|PA14_17500|transcript|ABJ12853.1|protein_coding||c.-1396T>C|||||1396|,G|upstream_gene_variant|MODIFIER|PA14_17510|PA14_17510|transcript|ABJ12852.1|protein_coding||c.-263T>C|||||263|,G|upstream_gene_variant|MODIFIER|recA|PA14_17530|transcript|ABJ12850.1|protein_coding||c.-525A>G|||||525|,G|upstream_gene_variant|MODIFIER|recX|PA14_17540|transcript|ABJ12849.1|protein_coding||c.-1571A>G|||||1571|,G|upstream_gene_variant|MODIFIER|PA14_17580|PA14_17580|transcript|ABJ12846.1|protein_coding||c.-4790A>G|||||4790|,G|downstream_gene_variant|MODIFIER|rpoS|PA14_17480|transcript|ABJ12855.1|protein_coding||c.*4779A>G|||||4779|,G|downstream_gene_variant|MODIFIER|PA14_17550|PA14_17550|transcript|ABJ12848.1|protein_coding||c.*2054T>C|||||2054|,G|downstream_gene_variant|MODIFIER|PA14_17570|PA14_17570|transcript|ABJ12847.1|protein_coding||c.*3207T>C|||||3207| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,0:10:353:0:0:0,-32.1004 0:10:10,2:8:227:2:65:0,-14.529 0:9:9,0:9:296:0:0:0,-26.9497 0:7:7,0:7:236:0:0:0,-21.567 +Chromosome 1516153 . C G 3.79493E-12 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=22;DPB=22;DPRA=1.4;EPP=7.35324;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=27.7677;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=29;QR=707;RO=20;RPL=0;RPP=7.35324;RPPR=3.44459;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=14;SRP=9.95901;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|potA|PA14_17640|transcript|ABJ12840.1|protein_coding|1/1|c.778G>C|p.Gly260Arg|778/1092|778/1092|260/363||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_17590|PA14_17590|transcript|ABJ12845.1|protein_coding||c.-3733G>C|||||3733|,G|upstream_gene_variant|MODIFIER|PA14_17600|PA14_17600|transcript|ABJ12844.1|protein_coding||c.-3304G>C|||||3304|,G|upstream_gene_variant|MODIFIER|potD|PA14_17610|transcript|ABJ12843.1|protein_coding||c.-2064G>C|||||2064|,G|upstream_gene_variant|MODIFIER|potC|PA14_17620|transcript|ABJ12842.1|protein_coding||c.-1205G>C|||||1205|,G|upstream_gene_variant|MODIFIER|potB|PA14_17630|transcript|ABJ12841.1|protein_coding||c.-319G>C|||||319|,G|upstream_gene_variant|MODIFIER|PA14_17650|PA14_17650|transcript|ABJ12839.1|protein_coding||c.-1036C>G|||||1036|,G|upstream_gene_variant|MODIFIER|PA14_17670|PA14_17670|transcript|ABJ12837.1|protein_coding||c.-2815C>G|||||2815|,G|upstream_gene_variant|MODIFIER|dgkA|PA14_17675|transcript|ABJ15695.1|protein_coding||c.-3540C>G|||||3540|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_17580|PA14_17580|transcript|ABJ12846.1|protein_coding||c.*4078C>G|||||4078|,G|downstream_gene_variant|MODIFIER|PA14_17660|PA14_17660|transcript|ABJ12838.1|protein_coding||c.*1756G>C|||||1756|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_17690|PA14_17690|transcript|ABJ12836.1|protein_coding||c.*3981G>C|||||3981| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:67:0:0:0,-6.36148 0:7:7,2:5:157:2:29:0,-11.6765 0:10:10,0:10:373:0:0:0,-33.9193 0:3:3,0:3:110:0:0:0,-10.2601 +Chromosome 1518635 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=59;DPB=59;DPRA=1.30556;EPP=11.6962;EPPR=11.8936;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=64.1486;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=48;QR=1689;RO=55;RPL=0;RPP=11.6962;RPPR=20.4216;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=17;SRP=20.4216;SRR=38;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|PA14_17660|PA14_17660|transcript|ABJ12838.1|protein_coding|1/1|c.201G>T|p.Leu67Leu|201/927|201/927|67/308||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|potD|PA14_17610|transcript|ABJ12843.1|protein_coding||c.-4546G>T|||||4546|,A|upstream_gene_variant|MODIFIER|potC|PA14_17620|transcript|ABJ12842.1|protein_coding||c.-3687G>T|||||3687|,A|upstream_gene_variant|MODIFIER|potB|PA14_17630|transcript|ABJ12841.1|protein_coding||c.-2801G>T|||||2801|,A|upstream_gene_variant|MODIFIER|potA|PA14_17640|transcript|ABJ12840.1|protein_coding||c.-1705G>T|||||1705|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|PA14_17670|PA14_17670|transcript|ABJ12837.1|protein_coding||c.-333C>A|||||333|,A|upstream_gene_variant|MODIFIER|dgkA|PA14_17675|transcript|ABJ15695.1|protein_coding||c.-1058C>A|||||1058|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|rpmE|PA14_17700|transcript|ABJ12835.1|protein_coding||c.-3353C>A|||||3353|,A|upstream_gene_variant|MODIFIER|PA14_17710|PA14_17710|transcript|ABJ12834.1|protein_coding||c.-3616C>A|||||3616|,A|upstream_gene_variant|MODIFIER|PA14_17730|PA14_17730|transcript|ABJ12832.1|protein_coding||c.-4709C>A|||||4709|,A|downstream_gene_variant|MODIFIER|PA14_17650|PA14_17650|transcript|ABJ12839.1|protein_coding||c.*730C>A|||||730|,A|downstream_gene_variant|MODIFIER|PA14_17690|PA14_17690|transcript|ABJ12836.1|protein_coding||c.*1499G>T|||||1499|,A|downstream_gene_variant|MODIFIER|PA14_17720|PA14_17720|transcript|ABJ12833.1|protein_coding||c.*3796G>T|||||3796| GT:DP:DPR:RO:QR:AO:QA:GL 0:12:12,0:12:374:0:0:0,-33.9522 0:10:10,2:8:229:2:17:0,-19.271 0:16:16,1:15:484:1:15:0,-42.3548 0:21:21,1:20:602:1:16:0,-52.8555 +Chromosome 1519584 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=40;DPB=40;DPRA=1;EPP=9.52472;EPPR=3.06899;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=60.042;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=1289;RO=37;RPL=3;RPP=9.52472;RPPR=7.76406;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=18;SRP=3.06899;SRR=19;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_17670|PA14_17670|transcript|ABJ12837.1|protein_coding|1/1|c.617T>C|p.Leu206Pro|617/654|617/654|206/217||,C|upstream_gene_variant|MODIFIER|potC|PA14_17620|transcript|ABJ12842.1|protein_coding||c.-4636A>G|||||4636|,C|upstream_gene_variant|MODIFIER|potB|PA14_17630|transcript|ABJ12841.1|protein_coding||c.-3750A>G|||||3750|,C|upstream_gene_variant|MODIFIER|potA|PA14_17640|transcript|ABJ12840.1|protein_coding||c.-2654A>G|||||2654|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_17660|PA14_17660|transcript|ABJ12838.1|protein_coding||c.-749A>G|||||749|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|dgkA|PA14_17675|transcript|ABJ15695.1|protein_coding||c.-109T>C|||||109|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|rpmE|PA14_17700|transcript|ABJ12835.1|protein_coding||c.-2404T>C|||||2404|,C|upstream_gene_variant|MODIFIER|PA14_17710|PA14_17710|transcript|ABJ12834.1|protein_coding||c.-2667T>C|||||2667|,C|upstream_gene_variant|MODIFIER|PA14_17730|PA14_17730|transcript|ABJ12832.1|protein_coding||c.-3760T>C|||||3760|,C|upstream_gene_variant|MODIFIER|ycjJ|PA14_17740|transcript|ABJ12831.1|protein_coding||c.-4775T>C|||||4775|,C|downstream_gene_variant|MODIFIER|PA14_17650|PA14_17650|transcript|ABJ12839.1|protein_coding||c.*1679T>C|||||1679|,C|downstream_gene_variant|MODIFIER|PA14_17690|PA14_17690|transcript|ABJ12836.1|protein_coding||c.*550A>G|||||550|,C|downstream_gene_variant|MODIFIER|PA14_17720|PA14_17720|transcript|ABJ12833.1|protein_coding||c.*2847A>G|||||2847| GT:DP:DPR:RO:QR:AO:QA:GL 0:12:12,0:12:433:0:0:0,-39.3021 0:9:9,2:7:222:2:17:0,-18.6677 0:11:11,1:10:385:1:16:0,-33.4026 0:8:8,0:8:249:0:0:0,-22.7033 +Chromosome 1538987 . G T 7.1987E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=7;CIGAR=1X;DP=27;DPB=27;DPRA=2.66667;EPP=18.2106;EPPR=9.95901;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=29.6035;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=93;QR=728;RO=20;RPL=7;RPP=18.2106;RPPR=24.2907;RPR=0;RUN=1;SAF=7;SAP=18.2106;SAR=0;SRF=3;SRP=24.2907;SRR=17;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|lipG|PA14_17910|transcript|ABJ12820.1|protein_coding|1/1|c.423G>T|p.Val141Val|423/987|423/987|141/328||,T|upstream_gene_variant|MODIFIER|metR|PA14_17900|transcript|ABJ12821.1|protein_coding||c.-721C>A|||||721|,T|downstream_gene_variant|MODIFIER|paaH|PA14_17860|transcript|ABJ12824.1|protein_coding||c.*4178G>T|||||4178|,T|downstream_gene_variant|MODIFIER|paaJ|PA14_17880|transcript|ABJ12823.1|protein_coding||c.*2950G>T|||||2950|,T|downstream_gene_variant|MODIFIER|PA14_17890|PA14_17890|transcript|ABJ12822.1|protein_coding||c.*1647G>T|||||1647|,T|downstream_gene_variant|MODIFIER|glpM|PA14_17920|transcript|ABJ12819.1|protein_coding||c.*581C>A|||||581|,T|downstream_gene_variant|MODIFIER|glpD|PA14_17930|transcript|ABJ12818.1|protein_coding||c.*1043C>A|||||1043|,T|downstream_gene_variant|MODIFIER|glpR|PA14_17940|transcript|ABJ12817.1|protein_coding||c.*2860C>A|||||2860|,T|downstream_gene_variant|MODIFIER|glpK|PA14_17960|transcript|ABJ12816.1|protein_coding||c.*3821C>A|||||3821| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:106:0:0:0,-9.88589 0:6:6,1:5:188:1:15:0,-15.7826 0:13:13,4:9:314:4:47:0,-24.2389 0:5:5,2:3:120:2:31:0,-8.24293 +Chromosome 1544118 . G T 1.05325E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=8;CIGAR=1X;DP=56;DPB=56;DPRA=1.22222;EPP=20.3821;EPPR=3.19126;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=40.7673;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=104;QR=1600;RO=48;RPL=8;RPP=20.3821;RPPR=14.5915;RPR=0;RUN=1;SAF=8;SAP=20.3821;SAR=0;SRF=27;SRP=4.6389;SRR=21;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|glpK|PA14_17960|transcript|ABJ12816.1|protein_coding|1/1|c.208C>A|p.Gln70Lys|208/1518|208/1518|70/505||,T|upstream_gene_variant|MODIFIER|glpM|PA14_17920|transcript|ABJ12819.1|protein_coding||c.-4221C>A|||||4221|,T|upstream_gene_variant|MODIFIER|glpD|PA14_17930|transcript|ABJ12818.1|protein_coding||c.-2550C>A|||||2550|,T|upstream_gene_variant|MODIFIER|glpR|PA14_17940|transcript|ABJ12817.1|protein_coding||c.-1516C>A|||||1516|,T|upstream_gene_variant|MODIFIER|ybaK|PA14_17990|transcript|ABJ12814.1|protein_coding||c.-1351G>T|||||1351|,T|upstream_gene_variant|MODIFIER|glpK|PA14_18010|transcript|ABJ12813.1|protein_coding||c.-1885G>T|||||1885|,T|upstream_gene_variant|MODIFIER|PA14_18020|PA14_18020|transcript|ABJ12812.1|protein_coding||c.-3565G>T|||||3565|,T|downstream_gene_variant|MODIFIER|lipG|PA14_17910|transcript|ABJ12820.1|protein_coding||c.*4567G>T|||||4567|,T|downstream_gene_variant|MODIFIER|glpF|PA14_17980|transcript|ABJ12815.1|protein_coding||c.*247C>A|||||247| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,1:5:106:1:2:0,-9.54656 0:14:14,3:11:366:3:55:0,-28.1158 0:12:12,0:12:408:0:0:0,-37.0322 0:24:24,4:20:720:4:47:0,-60.7598 +Chromosome 1562680 . A G 4.52028E-16 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=33;DPB=33;DPRA=0.766667;EPP=5.18177;EPPR=4.88226;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=52.2534;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=63;QR=1103;RO=29;RPL=0;RPP=11.6962;RPPR=3.08518;RPR=4;RUN=1;SAF=1;SAP=5.18177;SAR=3;SRF=21;SRP=15.6647;SRR=8;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|fruR|PA14_18230|transcript|ABJ12796.1|protein_coding|1/1|c.712T>C|p.Tyr238His|712/990|712/990|238/329||,G|upstream_gene_variant|MODIFIER|PA14_18160|PA14_18160|transcript|ABJ12800.1|protein_coding||c.-2687T>C|||||2687|,G|upstream_gene_variant|MODIFIER|PA14_18180|PA14_18180|transcript|ABJ12799.1|protein_coding||c.-2372T>C|||||2372|,G|upstream_gene_variant|MODIFIER|PA14_18210|PA14_18210|transcript|ABJ12797.1|protein_coding||c.-391T>C|||||391|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|fruB|PA14_18250|transcript|ABJ12795.1|protein_coding||c.-1039A>G|||||1039|,G|upstream_gene_variant|MODIFIER|fruK|PA14_18260|transcript|ABJ12794.1|protein_coding||c.-3909A>G|||||3909|,G|upstream_gene_variant|MODIFIER|fruA|PA14_18275|transcript|ABJ15652.1|protein_coding||c.-4855A>G|||||4855|,G|downstream_gene_variant|MODIFIER|acsL|PA14_18150|transcript|ABJ12801.1|protein_coding||c.*3758A>G|||||3758|,G|downstream_gene_variant|MODIFIER|PA14_18200|PA14_18200|transcript|ABJ12798.1|protein_coding||c.*1356A>G|||||1356| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,1:7:261:1:13:0,-22.5448 0:7:7,1:6:206:1:2:0,-18.6694 0:10:10,0:10:397:0:0:0,-36.0901 0:8:8,2:6:239:2:48:0,-17.3264 +Chromosome 1569403 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=26;DPB=26;DPRA=0.857143;EPP=9.52472;EPPR=9.32731;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=41.8153;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=710;RO=22;RPL=3;RPP=9.52472;RPPR=22.3561;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=19;SRP=28.2783;SRR=3;TYPE=snp;technology.ILLUMINA=1;ANN=C|downstream_gene_variant|MODIFIER|fruB|PA14_18250|transcript|ABJ12795.1|protein_coding||c.*2814A>C|||||2814|,C|downstream_gene_variant|MODIFIER|fruK|PA14_18260|transcript|ABJ12794.1|protein_coding||c.*1870A>C|||||1870|,C|downstream_gene_variant|MODIFIER|fruA|PA14_18275|transcript|ABJ15652.1|protein_coding||c.*111A>C|||||111|,C|downstream_gene_variant|MODIFIER|PA14_18300|PA14_18300|transcript|ABJ12793.1|protein_coding||c.*42T>G|||||42|,C|downstream_gene_variant|MODIFIER|PA14_18310|PA14_18310|transcript|ABJ12792.1|protein_coding||c.*1433T>G|||||1433|,C|downstream_gene_variant|MODIFIER|PA14_18320|PA14_18320|transcript|ABJ12791.1|protein_coding||c.*1843T>G|||||1843|,C|downstream_gene_variant|MODIFIER|arnT|PA14_18330|transcript|ABJ12790.1|protein_coding||c.*2187T>G|||||2187|,C|downstream_gene_variant|MODIFIER|PA14_18340|PA14_18340|transcript|ABJ12789.1|protein_coding||c.*3833T>G|||||3833|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|fmt|PA14_18350|transcript|ABJ12788.1|protein_coding||c.*4717T>G|||||4717|,C|intergenic_region|MODIFIER|fruA-PA14_18300|PA14_18275-PA14_18300|intergenic_region|PA14_18275-PA14_18300|||n.1569403A>C|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,1:4:158:1:2:0,-14.4007 0:7:7,2:5:143:2:4:0,-12.7712 0:9:9,0:8:251:0:0:0,-22.8372 0:5:5,0:5:158:0:0:0,-14.5232 +Chromosome 1569551 . T G 1.20188E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=6;CIGAR=1X;DP=60;DPB=60;DPRA=1;EPP=16.0391;EPPR=3.17115;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=92.1749;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=1927;RO=54;RPL=0;RPP=16.0391;RPPR=10.8919;RPR=6;RUN=1;SAF=0;SAP=16.0391;SAR=6;SRF=36;SRP=16.0391;SRR=18;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_18300|PA14_18300|transcript|ABJ12793.1|protein_coding|1/1|c.1289A>C|p.His430Pro|1289/1395|1289/1395|430/464||,G|downstream_gene_variant|MODIFIER|fruB|PA14_18250|transcript|ABJ12795.1|protein_coding||c.*2962T>G|||||2962|,G|downstream_gene_variant|MODIFIER|fruK|PA14_18260|transcript|ABJ12794.1|protein_coding||c.*2018T>G|||||2018|,G|downstream_gene_variant|MODIFIER|fruA|PA14_18275|transcript|ABJ15652.1|protein_coding||c.*259T>G|||||259|,G|downstream_gene_variant|MODIFIER|PA14_18310|PA14_18310|transcript|ABJ12792.1|protein_coding||c.*1285A>C|||||1285|,G|downstream_gene_variant|MODIFIER|PA14_18320|PA14_18320|transcript|ABJ12791.1|protein_coding||c.*1695A>C|||||1695|,G|downstream_gene_variant|MODIFIER|arnT|PA14_18330|transcript|ABJ12790.1|protein_coding||c.*2039A>C|||||2039|,G|downstream_gene_variant|MODIFIER|PA14_18340|PA14_18340|transcript|ABJ12789.1|protein_coding||c.*3685A>C|||||3685|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|fmt|PA14_18350|transcript|ABJ12788.1|protein_coding||c.*4569A>C|||||4569| GT:DP:DPR:RO:QR:AO:QA:GL 0:15:15,0:15:544:0:0:0,-49.2782 0:14:14,3:11:359:3:6:0,-32.0449 0:16:16,2:14:530:2:4:0,-47.6603 0:15:15,1:14:494:1:2:0,-44.5739 +Chromosome 1569806 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=42;DPB=42;DPRA=2;EPP=5.18177;EPPR=17.6392;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=58.0406;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=45;QR=1293;RO=38;RPL=1;RPP=5.18177;RPPR=5.06748;RPR=3;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=21;SRP=3.9246;SRR=17;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_18300|PA14_18300|transcript|ABJ12793.1|protein_coding|1/1|c.1034T>C|p.Leu345Pro|1034/1395|1034/1395|345/464||,G|downstream_gene_variant|MODIFIER|fruB|PA14_18250|transcript|ABJ12795.1|protein_coding||c.*3217A>G|||||3217|,G|downstream_gene_variant|MODIFIER|fruK|PA14_18260|transcript|ABJ12794.1|protein_coding||c.*2273A>G|||||2273|,G|downstream_gene_variant|MODIFIER|fruA|PA14_18275|transcript|ABJ15652.1|protein_coding||c.*514A>G|||||514|,G|downstream_gene_variant|MODIFIER|PA14_18310|PA14_18310|transcript|ABJ12792.1|protein_coding||c.*1030T>C|||||1030|,G|downstream_gene_variant|MODIFIER|PA14_18320|PA14_18320|transcript|ABJ12791.1|protein_coding||c.*1440T>C|||||1440|,G|downstream_gene_variant|MODIFIER|arnT|PA14_18330|transcript|ABJ12790.1|protein_coding||c.*1784T>C|||||1784|,G|downstream_gene_variant|MODIFIER|PA14_18340|PA14_18340|transcript|ABJ12789.1|protein_coding||c.*3430T>C|||||3430|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|fmt|PA14_18350|transcript|ABJ12788.1|protein_coding||c.*4314T>C|||||4314| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:267:0:0:0,-24.3456 0:6:6,0:6:198:0:0:0,-18.1374 0:14:14,3:11:394:3:43:0,-31.7811 0:14:14,1:13:434:1:2:0,-39.1684 +Chromosome 1578763 . T C 2.32041E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=68;DPB=68;DPRA=1;EPP=13.8677;EPPR=5.80219;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=97.7141;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=23;QR=2176;RO=63;RPL=5;RPP=13.8677;RPPR=3.32051;RPR=0;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=30;SRP=3.32051;SRR=33;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|algA|PA14_18380|transcript|ABJ12785.1|protein_coding|1/1|c.1340A>G|p.Glu447Gly|1340/1446|1340/1446|447/481||,C|upstream_gene_variant|MODIFIER|PA14_18340|PA14_18340|transcript|ABJ12789.1|protein_coding||c.-4640A>G|||||4640|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|fmt|PA14_18350|transcript|ABJ12788.1|protein_coding||c.-2655A>G|||||2655|,C|upstream_gene_variant|MODIFIER|prmF|PA14_18360|transcript|ABJ12787.1|protein_coding||c.-1639A>G|||||1639|,C|upstream_gene_variant|MODIFIER|arnB|PA14_18370|transcript|ABJ12786.1|protein_coding||c.-494A>G|||||494|,C|downstream_gene_variant|MODIFIER|algF|PA14_18410|transcript|ABJ12784.1|protein_coding||c.*1536A>G|||||1536|,C|downstream_gene_variant|MODIFIER|algJ|PA14_18430|transcript|ABJ12783.1|protein_coding||c.*2259A>G|||||2259|,C|downstream_gene_variant|MODIFIER|algI|PA14_18450|transcript|ABJ12782.1|protein_coding||c.*3449A>G|||||3449| GT:DP:DPR:RO:QR:AO:QA:GL 0:18:18,1:17:579:1:2:0,-52.2119 0:15:15,3:12:380:3:19:0,-32.7267 0:17:17,0:17:637:0:0:0,-57.6587 0:18:18,1:17:580:1:2:0,-52.3053 +Chromosome 1584714 . A G 1.98135E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=23;DPB=23;DPRA=0.833333;EPP=3.0103;EPPR=3.94093;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=21.7988;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=78;QR=809;RO=21;RPL=1;RPP=3.0103;RPPR=5.59539;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=8;SRP=5.59539;SRR=13;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|algL|PA14_18470|transcript|ABJ12781.1|protein_coding|1/1|c.406T>C|p.Phe136Leu|406/1104|406/1104|136/367||,G|upstream_gene_variant|MODIFIER|algA|PA14_18380|transcript|ABJ12785.1|protein_coding||c.-4612T>C|||||4612|,G|upstream_gene_variant|MODIFIER|algF|PA14_18410|transcript|ABJ12784.1|protein_coding||c.-3765T>C|||||3765|,G|upstream_gene_variant|MODIFIER|algJ|PA14_18430|transcript|ABJ12783.1|protein_coding||c.-2517T>C|||||2517|,G|upstream_gene_variant|MODIFIER|algI|PA14_18450|transcript|ABJ12782.1|protein_coding||c.-940T>C|||||940|,G|downstream_gene_variant|MODIFIER|algX|PA14_18480|transcript|ABJ12780.1|protein_coding||c.*409T>C|||||409|,G|downstream_gene_variant|MODIFIER|algG|PA14_18500|transcript|ABJ12779.1|protein_coding||c.*1846T>C|||||1846|,G|downstream_gene_variant|MODIFIER|algE|PA14_18510|transcript|ABJ12778.1|protein_coding||c.*3498T>C|||||3498|,G|downstream_gene_variant|MODIFIER|algK|PA14_18520|transcript|ABJ12777.1|protein_coding||c.*4967T>C|||||4967| GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:40:0:0:0,-3.99568 0:5:5,2:3:116:2:78:0,-3.41393 0:6:6,0:6:227:0:0:0,-20.7913 0:11:11,0:11:426:0:0:0,-38.6925 +Chromosome 1603634 . C A 2.01371E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=19;DPB=19;DPRA=2.18182;EPP=9.52472;EPPR=3.55317;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=21.4918;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=45;QR=534;RO=16;RPL=0;RPP=9.52472;RPPR=7.89611;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=4;SRP=11.6962;SRR=12;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|PA14_18640|PA14_18640|transcript|ABJ12769.1|protein_coding|1/1|c.108C>A|p.Ile36Ile|108/2109|108/2109|36/702||,A|upstream_gene_variant|MODIFIER|argF|PA14_18610|transcript|ABJ12772.1|protein_coding||c.-4533G>T|||||4533|,A|upstream_gene_variant|MODIFIER|eprS|PA14_18630|transcript|ABJ12770.1|protein_coding||c.-406G>T|||||406|,A|upstream_gene_variant|MODIFIER|ydhD|PA14_18650|transcript|ABJ12768.1|protein_coding||c.-2114C>A|||||2114|,A|upstream_gene_variant|MODIFIER|PA14_18660|PA14_18660|transcript|ABJ12767.1|protein_coding||c.-2523C>A|||||2523|,A|upstream_gene_variant|MODIFIER|ahpC|PA14_18690|transcript|ABJ12764.1|protein_coding||c.-4909C>A|||||4909|,A|downstream_gene_variant|MODIFIER|PA14_18620|PA14_18620|transcript|ABJ12771.1|protein_coding||c.*3787C>A|||||3787|,A|downstream_gene_variant|MODIFIER|bfrB|PA14_18670|transcript|ABJ12766.1|protein_coding||c.*3742G>T|||||3742|,A|downstream_gene_variant|MODIFIER|bfd|PA14_18680|transcript|ABJ12765.1|protein_coding||c.*4428G>T|||||4428| GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:39:0:0:0,-3.89656 0:6:6,0:6:178:0:0:0,-16.3085 0:4:4,0:4:129:0:0:0,-11.9249 0:8:8,3:5:188:3:45:0,-13.0832 +Chromosome 1603950 . G C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=43;DPB=43;DPRA=0.685714;EPP=7.35324;EPPR=11.961;GTI=0;LEN=1;MEANALT=1;MQM=57;MQMR=60;NS=4;NUMALT=1;ODDS=59.8263;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=26;QR=1414;RO=41;RPL=2;RPP=7.35324;RPPR=7.30028;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=21;SRP=3.06326;SRR=20;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_18640|PA14_18640|transcript|ABJ12769.1|protein_coding|1/1|c.424G>C|p.Asp142His|424/2109|424/2109|142/702||,C|upstream_gene_variant|MODIFIER|argF|PA14_18610|transcript|ABJ12772.1|protein_coding||c.-4849C>G|||||4849|,C|upstream_gene_variant|MODIFIER|eprS|PA14_18630|transcript|ABJ12770.1|protein_coding||c.-722C>G|||||722|,C|upstream_gene_variant|MODIFIER|ydhD|PA14_18650|transcript|ABJ12768.1|protein_coding||c.-1798G>C|||||1798|,C|upstream_gene_variant|MODIFIER|PA14_18660|PA14_18660|transcript|ABJ12767.1|protein_coding||c.-2207G>C|||||2207|,C|upstream_gene_variant|MODIFIER|ahpC|PA14_18690|transcript|ABJ12764.1|protein_coding||c.-4593G>C|||||4593|,C|downstream_gene_variant|MODIFIER|PA14_18620|PA14_18620|transcript|ABJ12771.1|protein_coding||c.*4103G>C|||||4103|,C|downstream_gene_variant|MODIFIER|bfrB|PA14_18670|transcript|ABJ12766.1|protein_coding||c.*3426C>G|||||3426|,C|downstream_gene_variant|MODIFIER|bfd|PA14_18680|transcript|ABJ12765.1|protein_coding||c.*4112C>G|||||4112| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,2:6:221:2:26:0,-17.7719 0:11:11,0:11:379:0:0:0,-34.4297 0:9:9,0:9:318:0:0:0,-28.9568 0:15:15,0:15:496:0:0:0,-44.9437 +Chromosome 1606659 . C A 8.58148E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=30;DPB=30;DPRA=1.28571;EPP=3.73412;EPPR=16.6021;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=39.244;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=965;RO=27;RPL=2;RPP=3.73412;RPPR=3.09072;RPR=1;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=10;SRP=6.95112;SRR=17;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|PA14_18660|PA14_18660|transcript|ABJ12767.1|protein_coding|1/1|c.503C>A|p.Ala168Glu|503/1152|503/1152|168/383||,A|upstream_gene_variant|MODIFIER|eprS|PA14_18630|transcript|ABJ12770.1|protein_coding||c.-3431G>T|||||3431|,A|upstream_gene_variant|MODIFIER|ahpC|PA14_18690|transcript|ABJ12764.1|protein_coding||c.-1884C>A|||||1884|,A|upstream_gene_variant|MODIFIER|motY|PA14_18720|transcript|ABJ12761.1|protein_coding||c.-4515C>A|||||4515|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_18640|PA14_18640|transcript|ABJ12769.1|protein_coding||c.*1024C>A|||||1024|,A|downstream_gene_variant|MODIFIER|ydhD|PA14_18650|transcript|ABJ12768.1|protein_coding||c.*585C>A|||||585|,A|downstream_gene_variant|MODIFIER|bfrB|PA14_18670|transcript|ABJ12766.1|protein_coding||c.*717G>T|||||717|,A|downstream_gene_variant|MODIFIER|bfd|PA14_18680|transcript|ABJ12765.1|protein_coding||c.*1403G>T|||||1403|,A|downstream_gene_variant|MODIFIER|rnt|PA14_18700|transcript|ABJ12763.1|protein_coding||c.*2665G>T|||||2665|,A|downstream_gene_variant|MODIFIER|pyrC|PA14_18710|transcript|ABJ12762.1|protein_coding||c.*3336G>T|||||3336| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:120:0:0:0,-11.1879 0:9:9,3:6:178:3:34:0,-13.1324 0:12:12,0:12:430:0:0:0,-39.029 0:6:6,0:6:237:0:0:0,-21.7037 +Chromosome 1618168 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=59;DPB=59;DPRA=0.612245;EPP=7.35324;EPPR=26.8203;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=75.7279;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1922;RO=57;RPL=0;RPP=7.35324;RPPR=7.61992;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=19;SRP=16.763;SRR=38;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|mexF|PA14_18780|transcript|ABJ12757.1|protein_coding|1/1|c.2686A>G|p.Ser896Gly|2686/3162|2686/3162|896/1053||,G|upstream_gene_variant|MODIFIER|gloA1|PA14_18750|transcript|ABJ12759.1|protein_coding||c.-4216T>C|||||4216|,G|upstream_gene_variant|MODIFIER|opmE|PA14_18790|transcript|ABJ12756.1|protein_coding||c.-473A>G|||||473|,G|upstream_gene_variant|MODIFIER|PA14_18800|PA14_18800|transcript|ABJ12755.1|protein_coding||c.-2519A>G|||||2519|,G|upstream_gene_variant|MODIFIER|PA14_18810|PA14_18810|transcript|ABJ12754.1|protein_coding||c.-3114A>G|||||3114|,G|upstream_gene_variant|MODIFIER|PA14_18820|PA14_18820|transcript|ABJ12753.1|protein_coding||c.-4184A>G|||||4184|,G|downstream_gene_variant|MODIFIER|argG|PA14_18740|transcript|ABJ12760.1|protein_coding||c.*4694A>G|||||4694|,G|downstream_gene_variant|MODIFIER|mexE|PA14_18760|transcript|ABJ12758.1|protein_coding||c.*2682A>G|||||2682| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,2:8:274:2:17:0,-23.3703 0:16:16,0:16:557:0:0:0,-50.4393 0:17:17,0:17:552:0:0:0,-49.9771 0:16:16,0:16:539:0:0:0,-48.8187 +Chromosome 1624511 . GT GG 1.15611E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1M1X;DP=24;DPB=24;DPRA=2.33333;EPP=11.6962;EPPR=9.95901;GTI=0;LEN=1;MEANALT=1;MQM=56.75;MQMR=60;NS=4;NUMALT=1;ODDS=35.4588;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=616;RO=20;RPL=4;RPP=11.6962;RPPR=3.0103;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=6;SRP=9.95901;SRR=14;TYPE=snp;technology.ILLUMINA=1;ANN=GG|missense_variant|MODERATE|PA14_18830|PA14_18830|transcript|ABJ12752.1|protein_coding|1/1|c.1144T>G|p.Phe382Val|1144/1434|1144/1434|382/477||,GG|upstream_gene_variant|MODIFIER|PA14_18850|PA14_18850|transcript|ABJ12751.1|protein_coding||c.-290T>G|||||290|,GG|upstream_gene_variant|MODIFIER|PA14_18860|PA14_18860|transcript|ABJ12750.1|protein_coding||c.-1791T>G|||||1791|,GG|downstream_gene_variant|MODIFIER|opmE|PA14_18790|transcript|ABJ12756.1|protein_coding||c.*4396T>G|||||4396|,GG|downstream_gene_variant|MODIFIER|PA14_18800|PA14_18800|transcript|ABJ12755.1|protein_coding||c.*3631T>G|||||3631|,GG|downstream_gene_variant|MODIFIER|PA14_18810|PA14_18810|transcript|ABJ12754.1|protein_coding||c.*2193T>G|||||2193|,GG|downstream_gene_variant|MODIFIER|PA14_18820|PA14_18820|transcript|ABJ12753.1|protein_coding||c.*1174T>G|||||1174|,GG|downstream_gene_variant|MODIFIER|PA14_18870|PA14_18870|transcript|ABJ12749.1|protein_coding||c.*3064A>C|||||3064|,GG|downstream_gene_variant|MODIFIER|nth|PA14_18880|transcript|ABJ12748.1|protein_coding||c.*3352A>C|||||3352|,GG|downstream_gene_variant|MODIFIER|rnfE|PA14_18890|transcript|ABJ12747.1|protein_coding||c.*3987A>C|||||3987|,GG|downstream_gene_variant|MODIFIER|rnfG|PA14_18900|transcript|ABJ12746.1|protein_coding||c.*4696A>C|||||4696| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,2:5:111:2:4:0,-9.82594 0:5:5,1:4:115:1:2:0,-10.4299 0:3:3,0:3:113:0:0:0,-10.5384 0:9:9,1:8:277:1:2:0,-25.0522 +Chromosome 1632138 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=29;DPB=29;DPRA=1.35;EPP=3.0103;EPPR=3.09072;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=54.2997;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=55;QR=937;RO=27;RPL=2;RPP=7.35324;RPPR=9.52472;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=17;SRP=6.95112;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|rnfC|PA14_18920|transcript|ABJ12744.1|protein_coding|1/1|c.1076A>G|p.Glu359Gly|1076/2325|1076/2325|359/774||,C|upstream_gene_variant|MODIFIER|PA14_18870|PA14_18870|transcript|ABJ12749.1|protein_coding||c.-4383A>G|||||4383|,C|upstream_gene_variant|MODIFIER|nth|PA14_18880|transcript|ABJ12748.1|protein_coding||c.-3636A>G|||||3636|,C|upstream_gene_variant|MODIFIER|rnfE|PA14_18890|transcript|ABJ12747.1|protein_coding||c.-2923A>G|||||2923|,C|upstream_gene_variant|MODIFIER|rnfG|PA14_18900|transcript|ABJ12746.1|protein_coding||c.-2286A>G|||||2286|,C|upstream_gene_variant|MODIFIER|rnfD|PA14_18910|transcript|ABJ12745.1|protein_coding||c.-1252A>G|||||1252|,C|downstream_gene_variant|MODIFIER|PA14_18860|PA14_18860|transcript|ABJ12750.1|protein_coding||c.*4762T>C|||||4762|,C|downstream_gene_variant|MODIFIER|rnfB|PA14_18930|transcript|ABJ12743.1|protein_coding||c.*1072A>G|||||1072|,C|downstream_gene_variant|MODIFIER|rnfA|PA14_18950|transcript|ABJ12742.1|protein_coding||c.*1635A>G|||||1635|,C|downstream_gene_variant|MODIFIER|PA14_18960|PA14_18960|transcript|ABJ12741.1|protein_coding||c.*2397A>G|||||2397|,C|downstream_gene_variant|MODIFIER|pldA|PA14_18970|transcript|ABJ12740.1|protein_coding||c.*3524A>G|||||3524| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:276:0:0:0,-25.173 0:5:5,0:5:191:0:0:0,-17.5575 0:7:7,0:7:202:0:0:0,-18.4599 0:9:9,2:7:268:2:55:0,-19.2597 +Chromosome 1634578 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=6;CIGAR=1X;DP=61;DPB=61;DPRA=1.11905;EPP=16.0391;EPPR=31.7922;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=68.5982;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=1820;RO=55;RPL=0;RPP=16.0391;RPPR=6.20829;RPR=6;RUN=1;SAF=0;SAP=16.0391;SAR=6;SRF=17;SRP=20.4216;SRR=38;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_18960|PA14_18960|transcript|ABJ12741.1|protein_coding|1/1|c.656T>C|p.Leu219Pro|656/699|656/699|219/232||,G|upstream_gene_variant|MODIFIER|rnfG|PA14_18900|transcript|ABJ12746.1|protein_coding||c.-4726T>C|||||4726|,G|upstream_gene_variant|MODIFIER|rnfD|PA14_18910|transcript|ABJ12745.1|protein_coding||c.-3692T>C|||||3692|,G|upstream_gene_variant|MODIFIER|rnfC|PA14_18920|transcript|ABJ12744.1|protein_coding||c.-1365T>C|||||1365|,G|upstream_gene_variant|MODIFIER|rnfB|PA14_18930|transcript|ABJ12743.1|protein_coding||c.-802T>C|||||802|,G|upstream_gene_variant|MODIFIER|rnfA|PA14_18950|transcript|ABJ12742.1|protein_coding||c.-221T>C|||||221|,G|downstream_gene_variant|MODIFIER|pldA|PA14_18970|transcript|ABJ12740.1|protein_coding||c.*1084T>C|||||1084|,G|downstream_gene_variant|MODIFIER|PA14_18985|PA14_18985|transcript|ABJ15661.1|protein_coding||c.*4399T>C|||||4399| GT:DP:DPR:RO:QR:AO:QA:GL 0:18:18,1:17:551:1:13:0,-48.5794 0:10:10,2:8:266:2:29:0,-21.5002 0:14:14,0:14:517:0:0:0,-46.8641 0:19:19,3:16:486:3:17:0,-42.4221 +Chromosome 1666642 . C A 8.09555E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=25;DPB=25;DPRA=0.947368;EPP=7.35324;EPPR=3.10471;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=35.1676;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=654;RO=23;RPL=0;RPP=7.35324;RPPR=3.86001;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=7;SRP=10.6577;SRR=16;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|PA14_19320|PA14_19320|transcript|ABJ12720.1|protein_coding|1/1|c.982C>A|p.Gln328Lys|982/1326|982/1326|328/441||,A|upstream_gene_variant|MODIFIER|PA14_19270|PA14_19270|transcript|ABJ12723.1|protein_coding||c.-4561G>T|||||4561|,A|upstream_gene_variant|MODIFIER|PA14_19310|PA14_19310|transcript|ABJ12721.1|protein_coding||c.-1198G>T|||||1198|,A|downstream_gene_variant|MODIFIER|srmB|PA14_19290|transcript|ABJ12722.1|protein_coding||c.*3035C>A|||||3035|,A|downstream_gene_variant|MODIFIER|PA14_19330|PA14_19330|transcript|ABJ12719.1|protein_coding||c.*473G>T|||||473|,A|downstream_gene_variant|MODIFIER|PA14_19340|PA14_19340|transcript|ABJ12718.1|protein_coding||c.*754G>T|||||754|,A|downstream_gene_variant|MODIFIER|PA14_19350|PA14_19350|transcript|ABJ12717.1|protein_coding||c.*3647G>T|||||3647|,A|downstream_gene_variant|MODIFIER|PA14_19360|PA14_19360|transcript|ABJ12716.1|protein_coding||c.*4840G>T|||||4840| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:123:0:0:0,-11.3718 0:8:8,0:8:169:0:0:0,-15.4129 0:6:6,2:4:98:2:4:0,-8.67699 0:7:7,0:7:264:0:0:0,-24.118 +Chromosome 1680494 . GCCG CCCC,GCCC 2.88174E-9 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=4;AO=3,5;CIGAR=1X2M1X,3M1X;DP=27;DPB=27.5;DPRA=0.8,0;EPP=9.52472,13.8677;EPPR=8.61041;GTI=0;LEN=4,1;MEANALT=2,1.5;MQM=45.3333,57.8;MQMR=60;NS=4;NUMALT=2;ODDS=21.7299;PAIRED=0,0;PAIREDR=0;PAO=0,0.5;PQA=0,16.5;PQR=16.5;PRO=0.5;QA=18,35;QR=559;RO=19;RPL=0,1;RPP=9.52472,6.91895;RPPR=12.2676;RPR=3,4;RUN=1,1;SAF=0,1;SAP=9.52472,6.91895;SAR=3,4;SRF=12;SRP=5.8675;SRR=7;TYPE=complex,snp;technology.ILLUMINA=1,1;ANN=CCCC|upstream_gene_variant|MODIFIER|PA14_19390|PA14_19390|transcript|ABJ12713.1|protein_coding||c.-3824_-3821delCGGCinsGGGG|||||3821|,GCCC|upstream_gene_variant|MODIFIER|PA14_19390|PA14_19390|transcript|ABJ12713.1|protein_coding||c.-3824C>G|||||3824|,CCCC|upstream_gene_variant|MODIFIER|PA14_19400|PA14_19400|transcript|ABJ12712.1|protein_coding||c.-1759_-1756delCGGCinsGGGG|||||1756|,GCCC|upstream_gene_variant|MODIFIER|PA14_19400|PA14_19400|transcript|ABJ12712.1|protein_coding||c.-1759C>G|||||1759|,CCCC|upstream_gene_variant|MODIFIER|PA14_19430|PA14_19430|transcript|ABJ12710.1|protein_coding||c.-31_-28delGCCGinsCCCC|||||31|,GCCC|upstream_gene_variant|MODIFIER|PA14_19430|PA14_19430|transcript|ABJ12710.1|protein_coding||c.-28G>C|||||28|,CCCC|upstream_gene_variant|MODIFIER|PA14_19450|PA14_19450|transcript|ABJ12709.1|protein_coding||c.-1344_-1341delGCCGinsCCCC|||||1344|,GCCC|upstream_gene_variant|MODIFIER|PA14_19450|PA14_19450|transcript|ABJ12709.1|protein_coding||c.-1341G>C|||||1341|,CCCC|upstream_gene_variant|MODIFIER|lsfA|PA14_19490|transcript|ABJ12706.1|protein_coding||c.-4422_-4419delGCCGinsCCCC|||||4422|,GCCC|upstream_gene_variant|MODIFIER|lsfA|PA14_19490|transcript|ABJ12706.1|protein_coding||c.-4419G>C|||||4419|,CCCC|downstream_gene_variant|MODIFIER|PA14_19380|PA14_19380|transcript|ABJ12714.1|protein_coding||c.*4829_*4832delGCCGinsCCCC|||||4829|,GCCC|downstream_gene_variant|MODIFIER|PA14_19380|PA14_19380|transcript|ABJ12714.1|protein_coding||c.*4832G>C|||||4832|,CCCC|downstream_gene_variant|MODIFIER|PA14_19410|PA14_19410|transcript|ABJ12711.1|protein_coding||c.*122_*125delGCCGinsCCCC|||||122|,GCCC|downstream_gene_variant|MODIFIER|PA14_19410|PA14_19410|transcript|ABJ12711.1|protein_coding||c.*125G>C|||||125|,CCCC|downstream_gene_variant|MODIFIER|mqoA|PA14_19470|transcript|ABJ12708.1|protein_coding||c.*2230_*2233delCGGCinsGGGG|||||2233|,GCCC|downstream_gene_variant|MODIFIER|mqoA|PA14_19470|transcript|ABJ12708.1|protein_coding||c.*2230C>G|||||2230|,CCCC|downstream_gene_variant|MODIFIER|PA14_19480|PA14_19480|transcript|ABJ12707.1|protein_coding||c.*4004_*4007delCGGCinsGGGG|||||4007|,GCCC|downstream_gene_variant|MODIFIER|PA14_19480|PA14_19480|transcript|ABJ12707.1|protein_coding||c.*4004C>G|||||4004|,CCCC|intergenic_region|MODIFIER|PA14_19410-PA14_19430|PA14_19410-PA14_19430|intergenic_region|PA14_19410-PA14_19430|||n.1680494_1680497delGCCGinsCCCC||||||,GCCC|intergenic_region|MODIFIER|PA14_19410-PA14_19430|PA14_19410-PA14_19430|intergenic_region|PA14_19410-PA14_19430|||n.1680497G>C|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,1,1:4:152:1,1:14,27:0,-12.5626,-11.3668 0:10:10,0,1:9:279:0,1:0,2:0,-25.3579,-25.2069 0:6:6,2,1:3:86:2,1:4,2:0,-7.53288,-7.71808 0:5:5,0,2:3:42:0,2:0,4:0,-3.84949,-3.53745 +Chromosome 1711074 . A T 1.00727E-5 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=1.71429;EPP=3.0103;EPPR=9.04217;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=12.9747;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=328;RO=9;RPL=2;RPP=7.35324;RPPR=5.18177;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=3;SRP=5.18177;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_19850|PA14_19850|transcript|ABJ12676.1|protein_coding|1/1|c.1123A>T|p.Ile375Phe|1123/2484|1123/2484|375/827||,T|upstream_gene_variant|MODIFIER|PA14_19800|PA14_19800|transcript|ABJ12679.1|protein_coding||c.-4741T>A|||||4741|,T|upstream_gene_variant|MODIFIER|ldh|PA14_19870|transcript|ABJ12674.1|protein_coding||c.-2426A>T|||||2426|,T|upstream_gene_variant|MODIFIER|PA14_19900|PA14_19900|transcript|ABJ12673.1|protein_coding||c.-3593A>T|||||3593|,T|upstream_gene_variant|MODIFIER|pdhB|PA14_19910|transcript|ABJ12672.1|protein_coding||c.-4683A>T|||||4683|,T|downstream_gene_variant|MODIFIER|PA14_19810|PA14_19810|transcript|ABJ12678.1|protein_coding||c.*2699A>T|||||2699|,T|downstream_gene_variant|MODIFIER|PA14_19830|PA14_19830|transcript|ABJ12677.1|protein_coding||c.*1272A>T|||||1272|,T|downstream_gene_variant|MODIFIER|PA14_19860|PA14_19860|transcript|ABJ12675.1|protein_coding||c.*1368T>A|||||1368| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,2:2:79:2:31:0,-4.55266 0:1:1,0:1:16:0:0:0,-1.59998 0:2:2,0:2:74:0:0:0,-7.02486 0:4:4,0:4:159:0:0:0,-14.6923 +Chromosome 1712295 . T C 6.05023E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=23;DPB=23;DPRA=2.30769;EPP=7.35324;EPPR=3.94093;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=20.3917;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=749;RO=21;RPL=2;RPP=7.35324;RPPR=3.94093;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=9;SRP=3.94093;SRR=12;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_19850|PA14_19850|transcript|ABJ12676.1|protein_coding|1/1|c.2344T>C|p.Ser782Pro|2344/2484|2344/2484|782/827||,C|upstream_gene_variant|MODIFIER|ldh|PA14_19870|transcript|ABJ12674.1|protein_coding||c.-1205T>C|||||1205|,C|upstream_gene_variant|MODIFIER|PA14_19900|PA14_19900|transcript|ABJ12673.1|protein_coding||c.-2372T>C|||||2372|,C|upstream_gene_variant|MODIFIER|pdhB|PA14_19910|transcript|ABJ12672.1|protein_coding||c.-3462T>C|||||3462|,C|upstream_gene_variant|MODIFIER|PA14_19920|PA14_19920|transcript|ABJ12671.1|protein_coding||c.-4481T>C|||||4481|,C|downstream_gene_variant|MODIFIER|PA14_19810|PA14_19810|transcript|ABJ12678.1|protein_coding||c.*3920T>C|||||3920|,C|downstream_gene_variant|MODIFIER|PA14_19830|PA14_19830|transcript|ABJ12677.1|protein_coding||c.*2493T>C|||||2493|,C|downstream_gene_variant|MODIFIER|PA14_19860|PA14_19860|transcript|ABJ12675.1|protein_coding||c.*147A>G|||||147| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:259:0:0:0,-23.6616 0:10:10,2:8:300:2:17:0,-25.7389 0:2:2,0:2:32:0:0:0,-3.03997 0:4:4,0:4:158:0:0:0,-14.6005 +Chromosome 1757873 . G C 2.24648E-7 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=20;DPB=20;DPRA=0.529412;EPP=7.35324;EPPR=4.9405;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=16.7773;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=653;RO=18;RPL=2;RPP=7.35324;RPPR=7.35324;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=9;SRP=3.0103;SRR=9;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|phnN|PA14_20440|transcript|ABJ12627.1|protein_coding|1/1|c.277G>C|p.Asp93His|277/558|277/558|93/185||,C|upstream_gene_variant|MODIFIER|phnP|PA14_20450|transcript|ABJ12626.1|protein_coding||c.-272G>C|||||272|,C|upstream_gene_variant|MODIFIER|PA14_20500|PA14_20500|transcript|PA14_20500-1.1|protein_coding||c.-2662G>C|||||2662|WARNING_TRANSCRIPT_INCOMPLETE,C|upstream_gene_variant|MODIFIER|PA14_20510|PA14_20510|transcript|ABJ12621.1|protein_coding||c.-4635G>C|||||4635|,C|downstream_gene_variant|MODIFIER|phnH|PA14_20370|transcript|ABJ12633.1|protein_coding||c.*4989G>C|||||4989|,C|downstream_gene_variant|MODIFIER|phnI|PA14_20380|transcript|ABJ12632.1|protein_coding||c.*3889G>C|||||3889|,C|downstream_gene_variant|MODIFIER|phnJ|PA14_20390|transcript|ABJ12631.1|protein_coding||c.*3008G>C|||||3008|,C|downstream_gene_variant|MODIFIER|phnK|PA14_20400|transcript|ABJ12630.1|protein_coding||c.*2196G>C|||||2196|,C|downstream_gene_variant|MODIFIER|phnL|PA14_20420|transcript|ABJ12629.1|protein_coding||c.*1429G>C|||||1429|,C|downstream_gene_variant|MODIFIER|phnM|PA14_20430|transcript|ABJ12628.1|protein_coding||c.*276G>C|||||276|,C|downstream_gene_variant|MODIFIER|PA14_20460|PA14_20460|transcript|ABJ12625.1|protein_coding||c.*1081C>G|||||1081|,C|downstream_gene_variant|MODIFIER|PA14_20470|PA14_20470|transcript|ABJ12624.1|protein_coding||c.*1318C>G|||||1318|,C|downstream_gene_variant|MODIFIER|PA14_20480|PA14_20480|transcript|ABJ12623.1|protein_coding||c.*1553C>G|||||1553|,C|downstream_gene_variant|MODIFIER|PA14_20491|PA14_20491|transcript|ABJ12622.1|protein_coding||c.*2024C>G|||||2024|,C|downstream_gene_variant|MODIFIER|tRNA|EBG00001225096|transcript|EBT00001793400.1|protein_coding||c.*2662C>G|||||2662|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,2:1:15:2:4:0,-1.11999 0:3:3,0:3:105:0:0:0,-9.795 0:7:7,0:7:268:0:0:0,-24.4822 0:7:7,0:7:265:0:0:0,-24.207 +Chromosome 1788192 . T C 2.01833E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=49;DPB=49;DPRA=0.769231;EPP=3.73412;EPPR=4.70971;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=38.1612;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=46;QR=1342;RO=46;RPL=1;RPP=3.73412;RPPR=15.095;RPR=2;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=27;SRP=6.03148;SRR=19;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_20780|PA14_20780|transcript|ABJ12597.1|protein_coding|1/1|c.332T>C|p.Leu111Pro|332/1716|332/1716|111/571||,C|upstream_gene_variant|MODIFIER|PA14_20700|PA14_20700|transcript|ABJ12604.1|protein_coding||c.-4638A>G|||||4638|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|flgN|PA14_20720|transcript|ABJ12603.1|protein_coding||c.-4139A>G|||||4139|,C|upstream_gene_variant|MODIFIER|flgM|PA14_20730|transcript|ABJ12602.1|protein_coding||c.-3761A>G|||||3761|,C|upstream_gene_variant|MODIFIER|flgA|PA14_20740|transcript|ABJ12601.1|protein_coding||c.-2918A>G|||||2918|,C|upstream_gene_variant|MODIFIER|PA14_20800|PA14_20800|transcript|ABJ12596.1|protein_coding||c.-1450T>C|||||1450|,C|upstream_gene_variant|MODIFIER|recQ|PA14_20810|transcript|ABJ12595.1|protein_coding||c.-1884T>C|||||1884|,C|upstream_gene_variant|MODIFIER|PA14_20820|PA14_20820|transcript|ABJ12594.1|protein_coding||c.-4111T>C|||||4111|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_20750|PA14_20750|transcript|ABJ12600.1|protein_coding||c.*1854T>C|||||1854|,C|downstream_gene_variant|MODIFIER|cheR|PA14_20760|transcript|ABJ12599.1|protein_coding||c.*953T>C|||||953|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_20770|PA14_20770|transcript|ABJ12598.1|protein_coding||c.*333T>C|||||333| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,3:7:155:3:46:0,-9.87051 0:13:13,0:13:356:0:0:0,-32.3006 0:14:14,0:14:477:0:0:0,-43.2404 0:12:12,0:12:354:0:0:0,-32.1384 +Chromosome 1803983 . G T 1.41551E-5 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=10;DPB=10;DPRA=4.5;EPP=9.52472;EPPR=5.80219;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=12.6531;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=197;RO=7;RPL=3;RPP=9.52472;RPPR=3.32051;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=2;SRP=5.80219;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|fabH2|PA14_20950|transcript|ABJ12584.1|protein_coding|1/1|c.556C>A|p.His186Asn|556/993|556/993|186/330||,T|upstream_gene_variant|MODIFIER|PA14_20870|PA14_20870|transcript|ABJ12590.1|protein_coding||c.-4276C>A|||||4276|,T|upstream_gene_variant|MODIFIER|PA14_20900|PA14_20900|transcript|ABJ12587.1|protein_coding||c.-1652C>A|||||1652|,T|upstream_gene_variant|MODIFIER|PA14_20920|PA14_20920|transcript|ABJ12586.1|protein_coding||c.-808C>A|||||808|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|PA14_20940|PA14_20940|transcript|ABJ12585.1|protein_coding||c.-451C>A|||||451|,T|downstream_gene_variant|MODIFIER|PA14_20880|PA14_20880|transcript|ABJ12589.1|protein_coding||c.*3917G>T|||||3917|,T|downstream_gene_variant|MODIFIER|rfaD|PA14_20890|transcript|ABJ12588.1|protein_coding||c.*2829G>T|||||2829|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|PA14_20960|PA14_20960|transcript|ABJ12583.1|protein_coding||c.*559C>A|||||559|,T|downstream_gene_variant|MODIFIER|cyp23|PA14_20970|transcript|ABJ12582.1|protein_coding||c.*981C>A|||||981|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|PA14_20980|PA14_20980|transcript|ABJ12581.1|protein_coding||c.*2230C>A|||||2230|,T|downstream_gene_variant|MODIFIER|PA14_21000|PA14_21000|transcript|ABJ12580.1|protein_coding||c.*3146C>A|||||3146|,T|downstream_gene_variant|MODIFIER|PA14_21010|PA14_21010|transcript|ABJ12579.1|protein_coding||c.*4471C>A|||||4471| GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:35:0:0:0,-3.49863 0:1:1,0:1:31:0:0:0,-3.09945 0:2:2,0:2:18:0:0:0,-1.70998 0:6:6,3:3:113:3:31:0,-7.6451 +Chromosome 1805739 . T C 1.50676E-4 . AB=0;ABP=0;AC=1;AF=0.25;AN=4;AO=4;CIGAR=1X;DP=15;DPB=15;DPRA=4.66667;EPP=5.18177;EPPR=7.94546;GTI=0;LEN=1;MEANALT=1;MQM=56;MQMR=60;NS=4;NUMALT=1;ODDS=10.2882;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=44;QR=242;RO=11;RPL=3;RPP=5.18177;RPPR=4.78696;RPR=1;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=7;SRP=4.78696;SRR=4;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|cyp23|PA14_20970|transcript|ABJ12582.1|protein_coding|1/1|c.482A>G|p.Glu161Gly|482/1257|482/1257|161/418||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_20900|PA14_20900|transcript|ABJ12587.1|protein_coding||c.-3408A>G|||||3408|,C|upstream_gene_variant|MODIFIER|PA14_20920|PA14_20920|transcript|ABJ12586.1|protein_coding||c.-2564A>G|||||2564|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_20940|PA14_20940|transcript|ABJ12585.1|protein_coding||c.-2207A>G|||||2207|,C|upstream_gene_variant|MODIFIER|fabH2|PA14_20950|transcript|ABJ12584.1|protein_coding||c.-1201A>G|||||1201|,C|upstream_gene_variant|MODIFIER|PA14_20960|PA14_20960|transcript|ABJ12583.1|protein_coding||c.-772A>G|||||772|,C|downstream_gene_variant|MODIFIER|rfaD|PA14_20890|transcript|ABJ12588.1|protein_coding||c.*4585T>C|||||4585|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_20980|PA14_20980|transcript|ABJ12581.1|protein_coding||c.*474A>G|||||474|,C|downstream_gene_variant|MODIFIER|PA14_21000|PA14_21000|transcript|ABJ12580.1|protein_coding||c.*1390A>G|||||1390|,C|downstream_gene_variant|MODIFIER|PA14_21010|PA14_21010|transcript|ABJ12579.1|protein_coding||c.*2715A>G|||||2715|,C|downstream_gene_variant|MODIFIER|PA14_21020|PA14_21020|transcript|ABJ12578.1|protein_coding||c.*3878A>G|||||3878| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,1:3:56:1:14:0,-3.82263 0:1:1,0:1:14:0:0:0,-1.39999 1:3:3,2:1:2:2:16:-1.31998,0 0:7:7,1:6:170:1:14:0,-14.1769 +Chromosome 1808366 . A C 2.54581E-12 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=23;DPB=23;DPRA=0.833333;EPP=7.35324;EPPR=15.5221;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=28.1652;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=26;QR=621;RO=21;RPL=2;RPP=7.35324;RPPR=20.4855;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=18;SRP=26.2761;SRR=3;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_21000|PA14_21000|transcript|ABJ12580.1|protein_coding|1/1|c.92T>G|p.Val31Gly|92/1329|92/1329|31/442||,C|upstream_gene_variant|MODIFIER|PA14_20940|PA14_20940|transcript|ABJ12585.1|protein_coding||c.-4834T>G|||||4834|,C|upstream_gene_variant|MODIFIER|fabH2|PA14_20950|transcript|ABJ12584.1|protein_coding||c.-3828T>G|||||3828|,C|upstream_gene_variant|MODIFIER|PA14_20960|PA14_20960|transcript|ABJ12583.1|protein_coding||c.-3399T>G|||||3399|,C|upstream_gene_variant|MODIFIER|cyp23|PA14_20970|transcript|ABJ12582.1|protein_coding||c.-2146T>G|||||2146|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_20980|PA14_20980|transcript|ABJ12581.1|protein_coding||c.-1239T>G|||||1239|,C|downstream_gene_variant|MODIFIER|PA14_21010|PA14_21010|transcript|ABJ12579.1|protein_coding||c.*88T>G|||||88|,C|downstream_gene_variant|MODIFIER|PA14_21020|PA14_21020|transcript|ABJ12578.1|protein_coding||c.*1251T>G|||||1251| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:158:0:0:0,-14.5255 0:6:6,0:6:156:0:0:0,-14.2911 0:5:5,2:3:108:2:26:0,-7.60451 0:7:7,0:7:199:0:0:0,-18.1872 +Chromosome 1823651 . A G 2.04169E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=30;DPB=30;DPRA=0.913043;EPP=7.35324;EPPR=5.80219;GTI=0;LEN=1;MEANALT=1;MQM=59.5;MQMR=60;NS=4;NUMALT=1;ODDS=36.6615;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=65;QR=991;RO=28;RPL=0;RPP=7.35324;RPPR=5.80219;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=20;SRP=14.1779;SRR=8;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|toxR|PA14_21080|transcript|ABJ12572.1|protein_coding|1/1|c.50T>C|p.Val17Ala|50/915|50/915|17/304||,G|upstream_gene_variant|MODIFIER|PA14_21040|PA14_21040|transcript|ABJ12576.1|protein_coding||c.-4657T>C|||||4657|,G|upstream_gene_variant|MODIFIER|PA14_21050|PA14_21050|transcript|ABJ12575.1|protein_coding||c.-2869T>C|||||2869|,G|upstream_gene_variant|MODIFIER|PA14_21060|PA14_21060|transcript|ABJ12574.1|protein_coding||c.-1997T>C|||||1997|,G|upstream_gene_variant|MODIFIER|PA14_21090|PA14_21090|transcript|ABJ12571.1|protein_coding||c.-138A>G|||||138|,G|upstream_gene_variant|MODIFIER|plcN|PA14_21110|transcript|ABJ12570.1|protein_coding||c.-825A>G|||||825|,G|downstream_gene_variant|MODIFIER|PA14_21070|PA14_21070|transcript|ABJ12573.1|protein_coding||c.*873A>G|||||873|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_21120|PA14_21120|transcript|ABJ12569.1|protein_coding||c.*2961T>C|||||2961|,G|downstream_gene_variant|MODIFIER|PA14_21130|PA14_21130|transcript|ABJ12568.1|protein_coding||c.*3527T>C|||||3527|,G|downstream_gene_variant|MODIFIER|PA14_21140|PA14_21140|transcript|ABJ12567.1|protein_coding||c.*4362T>C|||||4362| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:211:0:0:0,-19.3235 0:7:7,2:5:166:2:65:0,-9.08835 0:5:5,0:5:181:0:0:0,-16.6389 0:12:12,0:12:433:0:0:0,-39.2991 +Chromosome 1831200 . T G 9.53827E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=31;DPB=31;DPRA=1.65;EPP=3.73412;EPPR=5.80219;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=39.1211;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=29;QR=990;RO=28;RPL=1;RPP=3.73412;RPPR=4.25114;RPR=2;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=15;SRP=3.32051;SRR=13;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_21175|PA14_21175|transcript|ABJ15693.1|protein_coding|1/1|c.215A>C|p.His72Pro|215/1008|215/1008|72/335||,G|upstream_gene_variant|MODIFIER|PA14_21120|PA14_21120|transcript|ABJ12569.1|protein_coding||c.-4088A>C|||||4088|,G|upstream_gene_variant|MODIFIER|PA14_21130|PA14_21130|transcript|ABJ12568.1|protein_coding||c.-3294A>C|||||3294|,G|upstream_gene_variant|MODIFIER|PA14_21140|PA14_21140|transcript|ABJ12567.1|protein_coding||c.-2417A>C|||||2417|,G|upstream_gene_variant|MODIFIER|PA14_21150|PA14_21150|transcript|ABJ12566.1|protein_coding||c.-1587A>C|||||1587|,G|upstream_gene_variant|MODIFIER|PA14_21160|PA14_21160|transcript|ABJ12565.1|protein_coding||c.-790A>C|||||790|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_21180|PA14_21180|transcript|ABJ12564.1|protein_coding||c.-213T>G|||||213|,G|upstream_gene_variant|MODIFIER|PA14_21210|PA14_21210|transcript|ABJ12562.1|protein_coding||c.-3619T>G|||||3619|,G|downstream_gene_variant|MODIFIER|plcN|PA14_21110|transcript|ABJ12570.1|protein_coding||c.*4646T>G|||||4646|,G|downstream_gene_variant|MODIFIER|PA14_21190|PA14_21190|transcript|ABJ12563.1|protein_coding||c.*1107A>C|||||1107| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:115:0:0:0,-10.7245 0:8:8,0:8:255:0:0:0,-23.2528 0:9:9,0:9:329:0:0:0,-29.9571 0:11:11,3:8:291:3:29:0,-23.8227 +Chromosome 1841263 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=78;DPB=78;DPRA=1.19608;EPP=13.8677;EPPR=13.7487;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8082;NS=4;NUMALT=1;ODDS=73.6704;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=54;QR=2518;RO=73;RPL=0;RPP=13.8677;RPPR=3.04005;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=60;SRP=68.7196;SRR=13;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|alkB|PA14_21250|transcript|ABJ12558.1|protein_coding|1/1|c.533T>G|p.Val178Gly|533/603|533/603|178/200||,G|upstream_gene_variant|MODIFIER|PA14_21220|PA14_21220|transcript|ABJ12561.1|protein_coding||c.-4265A>C|||||4265|,G|upstream_gene_variant|MODIFIER|hepA|PA14_21230|transcript|ABJ12560.1|protein_coding||c.-1130A>C|||||1130|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_21260|PA14_21260|transcript|ABJ12557.1|protein_coding||c.-477T>G|||||477|,G|upstream_gene_variant|MODIFIER|PA14_21280|PA14_21280|transcript|ABJ12556.1|protein_coding||c.-798T>G|||||798|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_21290|PA14_21290|transcript|ABJ12555.1|protein_coding||c.-3010T>G|||||3010|,G|downstream_gene_variant|MODIFIER|PA14_21210|PA14_21210|transcript|ABJ12562.1|protein_coding||c.*4789T>G|||||4789|,G|downstream_gene_variant|MODIFIER|PA14_21240|PA14_21240|transcript|ABJ12559.1|protein_coding||c.*586T>G|||||586|,G|downstream_gene_variant|MODIFIER|PhrS|EBG00001225085|transcript|EBT00001793519.1|sRNA||n.*439A>C|||||439|,G|downstream_gene_variant|MODIFIER|P18|EBG00001225175|transcript|EBT00001793397.1|sRNA||n.*2803A>C|||||2803|,G|downstream_gene_variant|MODIFIER|PA14_21300|PA14_21300|transcript|ABJ12554.1|protein_coding||c.*3848A>C|||||3848| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,2:8:240:2:17:0,-20.2691 0:24:24,2:22:751:2:21:0,-65.881 0:17:17,0:17:570:0:0:0,-51.5864 0:27:27,1:26:957:1:16:0,-84.8219 +Chromosome 1847966 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=20;CIGAR=1X;DP=88;DPB=88;DPRA=0;EPP=46.4397;EPPR=14.7103;GTI=0;LEN=1;MEANALT=1.25;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=72.5906;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=40;QR=1504;RO=67;RPL=20;RPP=46.4397;RPPR=6.93191;RPR=0;RUN=1;SAF=20;SAP=46.4397;SAR=0;SRF=35;SRP=3.30199;SRR=32;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|P18|EBG00001225175|transcript|EBT00001793397.1|sRNA||n.-3766G>C|||||3766|,G|upstream_gene_variant|MODIFIER|PA14_21300|PA14_21300|transcript|ABJ12554.1|protein_coding||c.-1680G>C|||||1680|,G|upstream_gene_variant|MODIFIER|phaJ1|PA14_21310|transcript|ABJ12553.1|protein_coding||c.-1059G>C|||||1059|,G|upstream_gene_variant|MODIFIER|PA14_21320|PA14_21320|transcript|ABJ12552.1|protein_coding||c.-112G>C|||||112|,G|upstream_gene_variant|MODIFIER|fadD2|PA14_21340|transcript|ABJ12551.1|protein_coding||c.-135C>G|||||135|,G|upstream_gene_variant|MODIFIER|fadD1|PA14_21370|transcript|ABJ12550.1|protein_coding||c.-2058C>G|||||2058|,G|upstream_gene_variant|MODIFIER|PA14_21380|PA14_21380|transcript|ABJ12549.1|protein_coding||c.-3776C>G|||||3776|,G|upstream_gene_variant|MODIFIER|hrpA|PA14_21400|transcript|ABJ12548.1|protein_coding||c.-4254C>G|||||4254|,G|downstream_gene_variant|MODIFIER|PA14_21280|PA14_21280|transcript|ABJ12556.1|protein_coding||c.*3911C>G|||||3911|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_21290|PA14_21290|transcript|ABJ12555.1|protein_coding||c.*2836C>G|||||2836|,G|intergenic_region|MODIFIER|PA14_21320-fadD2|PA14_21320-PA14_21340|intergenic_region|PA14_21320-PA14_21340|||n.1847966C>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:18:18,5:13:247:5:10:0,-21.4845 0:23:23,4:19:455:4:8:0,-40.4191 0:29:29,9:20:494:9:18:0,-43.0438 0:18:18,2:15:308:2:4:0,-27.5192 +Chromosome 1847968 . A G 3.37538E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=59;DPB=59;DPRA=1.45455;EPP=13.8677;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=70.5278;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1593;RO=54;RPL=5;RPP=13.8677;RPPR=5.5839;RPR=0;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=21;SRP=8.80089;SRR=33;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|P18|EBG00001225175|transcript|EBT00001793397.1|sRNA||n.-3768T>C|||||3768|,G|upstream_gene_variant|MODIFIER|PA14_21300|PA14_21300|transcript|ABJ12554.1|protein_coding||c.-1682T>C|||||1682|,G|upstream_gene_variant|MODIFIER|phaJ1|PA14_21310|transcript|ABJ12553.1|protein_coding||c.-1061T>C|||||1061|,G|upstream_gene_variant|MODIFIER|PA14_21320|PA14_21320|transcript|ABJ12552.1|protein_coding||c.-114T>C|||||114|,G|upstream_gene_variant|MODIFIER|fadD2|PA14_21340|transcript|ABJ12551.1|protein_coding||c.-133A>G|||||133|,G|upstream_gene_variant|MODIFIER|fadD1|PA14_21370|transcript|ABJ12550.1|protein_coding||c.-2056A>G|||||2056|,G|upstream_gene_variant|MODIFIER|PA14_21380|PA14_21380|transcript|ABJ12549.1|protein_coding||c.-3774A>G|||||3774|,G|upstream_gene_variant|MODIFIER|hrpA|PA14_21400|transcript|ABJ12548.1|protein_coding||c.-4252A>G|||||4252|,G|downstream_gene_variant|MODIFIER|PA14_21280|PA14_21280|transcript|ABJ12556.1|protein_coding||c.*3913A>G|||||3913|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_21290|PA14_21290|transcript|ABJ12555.1|protein_coding||c.*2838A>G|||||2838|,G|intergenic_region|MODIFIER|PA14_21320-fadD2|PA14_21320-PA14_21340|intergenic_region|PA14_21320-PA14_21340|||n.1847968A>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,2:8:242:2:4:0,-21.6834 0:19:19,2:17:494:2:4:0,-44.3329 0:19:19,1:18:572:1:2:0,-51.5605 0:11:11,0:11:285:0:0:0,-25.8863 +Chromosome 1850530 . C A 2.83271E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=9;CIGAR=1X;DP=74;DPB=74;DPRA=1.42857;EPP=14.8328;EPPR=15.0703;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=109.808;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=166;QR=2203;RO=65;RPL=1;RPP=14.8328;RPPR=10.5269;RPR=8;RUN=1;SAF=0;SAP=22.5536;SAR=9;SRF=12;SRP=59.1679;SRR=53;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|fadD1|PA14_21370|transcript|ABJ12550.1|protein_coding|1/1|c.507C>A|p.Val169Val|507/1689|507/1689|169/562||,A|upstream_gene_variant|MODIFIER|PA14_21300|PA14_21300|transcript|ABJ12554.1|protein_coding||c.-4244G>T|||||4244|,A|upstream_gene_variant|MODIFIER|phaJ1|PA14_21310|transcript|ABJ12553.1|protein_coding||c.-3623G>T|||||3623|,A|upstream_gene_variant|MODIFIER|PA14_21320|PA14_21320|transcript|ABJ12552.1|protein_coding||c.-2676G>T|||||2676|,A|upstream_gene_variant|MODIFIER|PA14_21380|PA14_21380|transcript|ABJ12549.1|protein_coding||c.-1212C>A|||||1212|,A|upstream_gene_variant|MODIFIER|hrpA|PA14_21400|transcript|ABJ12548.1|protein_coding||c.-1690C>A|||||1690|,A|downstream_gene_variant|MODIFIER|fadD2|PA14_21340|transcript|ABJ12551.1|protein_coding||c.*741C>A|||||741| GT:DP:DPR:RO:QR:AO:QA:GL 0:21:21,3:18:629:3:45:0,-52.7164 0:21:21,2:19:611:2:42:0,-51.2818 0:14:14,0:14:454:0:0:0,-41.1633 0:18:18,4:14:509:4:79:0,-38.8344 +Chromosome 1855405 . G T 1.69817E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=36;DPB=36;DPRA=2.06667;EPP=11.6962;EPPR=24.9965;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=40.699;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1074;RO=32;RPL=4;RPP=11.6962;RPPR=3.28173;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=10;SRP=12.7819;SRR=22;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|hrpA|PA14_21400|transcript|ABJ12548.1|protein_coding|1/1|c.3186G>T|p.Leu1062Phe|3186/3981|3186/3981|1062/1326||,T|upstream_gene_variant|MODIFIER|PA14_21440|PA14_21440|transcript|ABJ12546.1|protein_coding||c.-2503G>T|||||2503|,T|upstream_gene_variant|MODIFIER|PA14_21450|PA14_21450|transcript|ABJ12545.1|protein_coding||c.-3169G>T|||||3169|,T|downstream_gene_variant|MODIFIER|fadD1|PA14_21370|transcript|ABJ12550.1|protein_coding||c.*3693G>T|||||3693|,T|downstream_gene_variant|MODIFIER|PA14_21380|PA14_21380|transcript|ABJ12549.1|protein_coding||c.*3361G>T|||||3361|,T|downstream_gene_variant|MODIFIER|phoA|PA14_21410|transcript|ABJ12547.1|protein_coding||c.*868C>A|||||868| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:123:0:0:0,-11.3088 0:10:10,1:9:329:1:2:0,-29.748 0:6:6,2:4:142:2:17:0,-11.511 0:15:15,1:14:480:1:15:0,-42.0136 +Chromosome 1877404 . T G 6.13276E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=7;CIGAR=1X;DP=70;DPB=70;DPRA=2;EPP=18.2106;EPPR=21.2438;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=104.064;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=92;QR=2373;RO=63;RPL=0;RPP=18.2106;RPPR=8.83536;RPR=7;RUN=1;SAF=0;SAP=18.2106;SAR=7;SRF=29;SRP=3.872;SRR=34;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|PA14_21650|PA14_21650|transcript|ABJ12526.1|protein_coding||c.-231T>G|||||231|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_21660|PA14_21660|transcript|ABJ12525.1|protein_coding||c.-650T>G|||||650|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_21680|PA14_21680|transcript|ABJ12524.1|protein_coding||c.-1296T>G|||||1296|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|lhr1|PA14_21690|transcript|ABJ12522.1|protein_coding||c.-1964T>G|||||1964|,G|downstream_gene_variant|MODIFIER|PA14_21600|PA14_21600|transcript|ABJ12531.1|protein_coding||c.*4751T>G|||||4751|,G|downstream_gene_variant|MODIFIER|oprO|PA14_21610|transcript|ABJ12530.1|protein_coding||c.*3188T>G|||||3188|,G|downstream_gene_variant|MODIFIER|oprP|PA14_21620|transcript|ABJ12529.1|protein_coding||c.*1407T>G|||||1407|,G|downstream_gene_variant|MODIFIER|PA14_21630|PA14_21630|transcript|ABJ12528.1|protein_coding||c.*939T>G|||||939|,G|downstream_gene_variant|MODIFIER|PA14_21640|PA14_21640|transcript|ABJ12527.1|protein_coding||c.*2T>G|||||2|,G|downstream_gene_variant|MODIFIER|PA14_21670|PA14_21670|transcript|ABJ12523.1|protein_coding||c.*1058A>C|||||1058|,G|intergenic_region|MODIFIER|PA14_21640-PA14_21650|PA14_21640-PA14_21650|intergenic_region|PA14_21640-PA14_21650|||n.1877404T>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,0:10:390:0:0:0,-35.4564 0:24:24,5:19:731:5:62:0,-60.4145 0:23:23,1:22:786:1:15:0,-69.5414 0:13:13,1:12:466:1:15:0,-40.7905 +Chromosome 1881807 . C A 1.66784E-5 . AB=0;ABP=0;AC=1;AF=0.25;AN=4;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0.857143;EPP=7.35324;EPPR=18.2106;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=12.4931;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=262;RO=7;RPL=0;RPP=7.35324;RPPR=10.7656;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=10.7656;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|lhr1|PA14_21690|transcript|ABJ12522.1|protein_coding|1/1|c.2440C>A|p.Gln814Lys|2440/4347|2440/4347|814/1448||,A|upstream_gene_variant|MODIFIER|PA14_21670|PA14_21670|transcript|ABJ12523.1|protein_coding||c.-3058G>T|||||3058|,A|downstream_gene_variant|MODIFIER|PA14_21640|PA14_21640|transcript|ABJ12527.1|protein_coding||c.*4405C>A|||||4405|,A|downstream_gene_variant|MODIFIER|PA14_21650|PA14_21650|transcript|ABJ12526.1|protein_coding||c.*3750C>A|||||3750|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_21660|PA14_21660|transcript|ABJ12525.1|protein_coding||c.*3424C>A|||||3424|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_21680|PA14_21680|transcript|ABJ12524.1|protein_coding||c.*2508C>A|||||2508|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_21700|PA14_21700|transcript|ABJ12521.1|protein_coding||c.*1915G>T|||||1915| GT:DP:DPR:RO:QR:AO:QA:GL 1:2:2,2:0:0:2:4:-0.38,0 0:3:3,0:3:109:0:0:0,-10.1657 0:1:1,0:1:36:0:0:0,-3.59827 0:3:3,0:3:117:0:0:0,-10.9104 +Chromosome 1885620 . T G 2.78774E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=45;DPB=45;DPRA=0.857143;EPP=7.35324;EPPR=4.27278;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=72.066;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=1581;RO=43;RPL=0;RPP=7.35324;RPPR=9.12072;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=18;SRP=5.48477;SRR=25;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_21700|PA14_21700|transcript|ABJ12521.1|protein_coding|1/1|c.1582A>C|p.Ile528Leu|1582/3480|1582/3480|528/1159||,G|upstream_gene_variant|MODIFIER|PA14_21710|PA14_21710|transcript|ABJ12520.1|protein_coding||c.-1847T>G|||||1847|,G|upstream_gene_variant|MODIFIER|PA14_21720|PA14_21720|transcript|ABJ12519.1|protein_coding||c.-2501T>G|||||2501|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|fecA|PA14_21730|transcript|ABJ12518.1|protein_coding||c.-3452T>G|||||3452|,G|downstream_gene_variant|MODIFIER|lhr1|PA14_21690|transcript|ABJ12522.1|protein_coding||c.*1906T>G|||||1906| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,0:9:340:0:0:0,-30.9533 0:10:10,2:8:286:2:30:0,-23.2247 0:14:14,0:14:497:0:0:0,-45.0506 0:12:12,0:12:458:0:0:0,-41.5674 +Chromosome 1894226 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=10;CIGAR=1X;DP=67;DPB=67;DPRA=0;EPP=24.725;EPPR=3.0484;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=105.192;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=1998;RO=57;RPL=0;RPP=24.725;RPPR=23.1631;RPR=10;RUN=1;SAF=0;SAP=24.725;SAR=10;SRF=26;SRP=3.9627;SRR=31;TYPE=snp;technology.ILLUMINA=1;ANN=A|stop_lost&splice_region_variant|HIGH|PA14_21780|PA14_21780|transcript|ABJ12514.1|protein_coding|1/1|c.935G>T|p.Ter312Leuext*?|935/936|935/936|312/311||,A|upstream_gene_variant|MODIFIER|capB|PA14_21760|transcript|ABJ12516.1|protein_coding||c.-670G>T|||||670|,A|upstream_gene_variant|MODIFIER|sugE|PA14_21770|transcript|ABJ12515.1|protein_coding||c.-141G>T|||||141|,A|upstream_gene_variant|MODIFIER|PA14_21800|PA14_21800|transcript|PA14_21800-1.1|protein_coding||c.-2106C>A|||||2106|WARNING_TRANSCRIPT_INCOMPLETE,A|upstream_gene_variant|MODIFIER|PA14_21810|PA14_21810|transcript|PA14_21810-1.1|protein_coding||c.-2198C>A|||||2198|WARNING_TRANSCRIPT_INCOMPLETE,A|upstream_gene_variant|MODIFIER|PA14_21820|PA14_21820|transcript|ABJ12512.1|protein_coding||c.-2531C>A|||||2531|,A|upstream_gene_variant|MODIFIER|PA14_21830|PA14_21830|transcript|ABJ12511.1|protein_coding||c.-3662C>A|||||3662|,A|upstream_gene_variant|MODIFIER|PA14_21850|PA14_21850|transcript|ABJ12509.1|protein_coding||c.-4931C>A|||||4931|,A|downstream_gene_variant|MODIFIER|fecA|PA14_21730|transcript|ABJ12518.1|protein_coding||c.*2989C>A|||||2989|,A|downstream_gene_variant|MODIFIER|PA14_21750|PA14_21750|transcript|ABJ12517.1|protein_coding||c.*940C>A|||||940|,A|downstream_gene_variant|MODIFIER|rdgC|PA14_21790|transcript|ABJ12513.1|protein_coding||c.*1021G>T|||||1021|,A|downstream_gene_variant|MODIFIER|tRNA|EBG00001225062|transcript|EBT00001793441.1|protein_coding||c.*2106G>T|||||2106|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|tRNA|EBG00001225157|transcript|EBT00001793503.1|protein_coding||c.*2198G>T|||||2198|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,A|downstream_gene_variant|MODIFIER|PA14_21840|PA14_21840|transcript|ABJ12510.1|protein_coding||c.*4081G>T|||||4081|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:19:19,4:15:517:4:8:0,-46.0986 0:13:13,2:11:409:2:4:0,-36.7733 0:20:20,2:18:635:2:4:0,-57.0773 0:15:15,2:13:437:2:4:0,-39.2604 +Chromosome 1895386 . T C 1.33652E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=30;DPB=30;DPRA=1.09091;EPP=7.35324;EPPR=14.1779;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=39.2186;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=932;RO=28;RPL=2;RPP=7.35324;RPPR=4.25114;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=16;SRP=4.25114;SRR=12;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|rdgC|PA14_21790|transcript|ABJ12513.1|protein_coding|1/1|c.782A>G|p.Glu261Gly|782/921|782/921|261/306||,C|upstream_gene_variant|MODIFIER|capB|PA14_21760|transcript|ABJ12516.1|protein_coding||c.-1830A>G|||||1830|,C|upstream_gene_variant|MODIFIER|sugE|PA14_21770|transcript|ABJ12515.1|protein_coding||c.-1301A>G|||||1301|,C|upstream_gene_variant|MODIFIER|PA14_21780|PA14_21780|transcript|ABJ12514.1|protein_coding||c.-226A>G|||||226|,C|upstream_gene_variant|MODIFIER|PA14_21800|PA14_21800|transcript|PA14_21800-1.1|protein_coding||c.-946T>C|||||946|WARNING_TRANSCRIPT_INCOMPLETE,C|upstream_gene_variant|MODIFIER|PA14_21810|PA14_21810|transcript|PA14_21810-1.1|protein_coding||c.-1038T>C|||||1038|WARNING_TRANSCRIPT_INCOMPLETE,C|upstream_gene_variant|MODIFIER|PA14_21820|PA14_21820|transcript|ABJ12512.1|protein_coding||c.-1371T>C|||||1371|,C|upstream_gene_variant|MODIFIER|PA14_21830|PA14_21830|transcript|ABJ12511.1|protein_coding||c.-2502T>C|||||2502|,C|upstream_gene_variant|MODIFIER|PA14_21850|PA14_21850|transcript|ABJ12509.1|protein_coding||c.-3771T>C|||||3771|,C|upstream_gene_variant|MODIFIER|PA14_21860|PA14_21860|transcript|ABJ12508.1|protein_coding||c.-4440T>C|||||4440|,C|downstream_gene_variant|MODIFIER|fecA|PA14_21730|transcript|ABJ12518.1|protein_coding||c.*4149T>C|||||4149|,C|downstream_gene_variant|MODIFIER|PA14_21750|PA14_21750|transcript|ABJ12517.1|protein_coding||c.*2100T>C|||||2100|,C|downstream_gene_variant|MODIFIER|tRNA|EBG00001225062|transcript|EBT00001793441.1|protein_coding||c.*946A>G|||||946|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|tRNA|EBG00001225157|transcript|EBT00001793503.1|protein_coding||c.*1038A>G|||||1038|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|downstream_gene_variant|MODIFIER|PA14_21840|PA14_21840|transcript|ABJ12510.1|protein_coding||c.*2921A>G|||||2921|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_21870|PA14_21870|transcript|ABJ12507.1|protein_coding||c.*4933A>G|||||4933|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,2:6:220:2:38:0,-16.5426 0:8:8,0:8:276:0:0:0,-25.1662 0:4:4,0:4:123:0:0:0,-11.3714 0:10:10,0:10:313:0:0:0,-28.4676 +Chromosome 1899851 . T G 9.29372E-7 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=11;DPB=11;DPRA=1.75;EPP=9.52472;EPPR=5.80219;GTI=0;LEN=1;MEANALT=1.5;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=15.9309;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=29;QR=225;RO=7;RPL=0;RPP=9.52472;RPPR=10.7656;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=4;SRP=3.32051;SRR=3;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_21860|PA14_21860|transcript|ABJ12508.1|protein_coding|1/1|c.26T>G|p.Leu9Arg|26/480|26/480|9/159||,G|upstream_gene_variant|MODIFIER|PA14_21780|PA14_21780|transcript|ABJ12514.1|protein_coding||c.-4691A>C|||||4691|,G|upstream_gene_variant|MODIFIER|rdgC|PA14_21790|transcript|ABJ12513.1|protein_coding||c.-3684A>C|||||3684|,G|upstream_gene_variant|MODIFIER|tRNA|EBG00001225062|transcript|EBT00001793441.1|protein_coding||c.-3447A>C|||||3447|WARNING_TRANSCRIPT_INCOMPLETE,G|upstream_gene_variant|MODIFIER|tRNA|EBG00001225157|transcript|EBT00001793503.1|protein_coding||c.-3354A>C|||||3354|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,G|upstream_gene_variant|MODIFIER|PA14_21840|PA14_21840|transcript|ABJ12510.1|protein_coding||c.-798A>C|||||798|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|qor|PA14_21890|transcript|ABJ12505.1|protein_coding||c.-4538T>G|||||4538|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_21800|PA14_21800|transcript|PA14_21800-1.1|protein_coding||c.*3447T>G|||||3447|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|PA14_21810|PA14_21810|transcript|PA14_21810-1.1|protein_coding||c.*3354T>G|||||3354|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|PA14_21820|PA14_21820|transcript|ABJ12512.1|protein_coding||c.*2333T>G|||||2333|,G|downstream_gene_variant|MODIFIER|PA14_21830|PA14_21830|transcript|ABJ12511.1|protein_coding||c.*1532T>G|||||1532|,G|downstream_gene_variant|MODIFIER|PA14_21850|PA14_21850|transcript|ABJ12509.1|protein_coding||c.*383T>G|||||383|,G|downstream_gene_variant|MODIFIER|PA14_21870|PA14_21870|transcript|ABJ12507.1|protein_coding||c.*468A>C|||||468|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|tsp|PA14_21880|transcript|ABJ12506.1|protein_coding||c.*2312A>C|||||2312| GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:39:0:0:0,-3.89656 0:3:3,0:3:117:0:0:0,-10.9104 0:3:3,2:1:27:2:15:0,-1.27479 0:4:4,1:2:42:1:14:0,-2.58264 +Chromosome 1911455 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=54;DPB=54;DPRA=0.446809;EPP=7.35324;EPPR=45.7716;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=43.3633;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=26;QR=1570;RO=52;RPL=2;RPP=7.35324;RPPR=5.68288;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=34;SRP=13.7006;SRR=18;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_21970|PA14_21970|transcript|ABJ12498.1|protein_coding|1/1|c.484T>C|p.Ser162Pro|484/717|484/717|162/238||,C|upstream_gene_variant|MODIFIER|PA14_21910|PA14_21910|transcript|ABJ12503.1|protein_coding||c.-4392A>G|||||4392|,C|upstream_gene_variant|MODIFIER|PA14_21920|PA14_21920|transcript|ABJ12502.1|protein_coding||c.-3592A>G|||||3592|,C|upstream_gene_variant|MODIFIER|PA14_21930|PA14_21930|transcript|ABJ12501.1|protein_coding||c.-2766A>G|||||2766|,C|upstream_gene_variant|MODIFIER|PA14_21940|PA14_21940|transcript|ABJ12500.1|protein_coding||c.-1960A>G|||||1960|,C|upstream_gene_variant|MODIFIER|PA14_21960|PA14_21960|transcript|ABJ12499.1|protein_coding||c.-847A>G|||||847|,C|upstream_gene_variant|MODIFIER|PA14_21980|PA14_21980|transcript|ABJ12497.1|protein_coding||c.-299T>C|||||299|,C|downstream_gene_variant|MODIFIER|PA14_21990|PA14_21990|transcript|ABJ12496.1|protein_coding||c.*893A>G|||||893|,C|downstream_gene_variant|MODIFIER|rluA|PA14_22000|transcript|ABJ12495.1|protein_coding||c.*2351A>G|||||2351|,C|downstream_gene_variant|MODIFIER|minE|PA14_22010|transcript|ABJ12494.1|protein_coding||c.*3090A>G|||||3090|,C|downstream_gene_variant|MODIFIER|minD|PA14_22020|transcript|ABJ12493.1|protein_coding||c.*3341A>G|||||3341|,C|downstream_gene_variant|MODIFIER|minC|PA14_22040|transcript|ABJ12492.1|protein_coding||c.*4218A>G|||||4218| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,2:5:131:2:26:0,-9.57613 0:12:12,0:12:368:0:0:0,-33.4081 0:15:15,0:15:476:0:0:0,-43.1317 0:20:20,0:20:595:0:0:0,-53.8169 +Chromosome 1913087 . T C 4.13004E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=19;DPB=19;DPRA=2.18182;EPP=7.35324;EPPR=3.13803;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=20.7738;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=592;RO=17;RPL=2;RPP=7.35324;RPPR=6.20364;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=10;SRP=4.1599;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_21990|PA14_21990|transcript|ABJ12496.1|protein_coding|1/1|c.551A>G|p.Glu184Gly|551/1290|551/1290|184/429||,C|upstream_gene_variant|MODIFIER|PA14_21930|PA14_21930|transcript|ABJ12501.1|protein_coding||c.-4398A>G|||||4398|,C|upstream_gene_variant|MODIFIER|PA14_21940|PA14_21940|transcript|ABJ12500.1|protein_coding||c.-3592A>G|||||3592|,C|upstream_gene_variant|MODIFIER|PA14_21960|PA14_21960|transcript|ABJ12499.1|protein_coding||c.-2479A>G|||||2479|,C|upstream_gene_variant|MODIFIER|htrB|PA14_22050|transcript|ABJ12491.1|protein_coding||c.-3537T>C|||||3537|,C|upstream_gene_variant|MODIFIER|PA14_22060|PA14_22060|transcript|ABJ12490.1|protein_coding||c.-4543T>C|||||4543|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_21970|PA14_21970|transcript|ABJ12498.1|protein_coding||c.*1399T>C|||||1399|,C|downstream_gene_variant|MODIFIER|PA14_21980|PA14_21980|transcript|ABJ12497.1|protein_coding||c.*782T>C|||||782|,C|downstream_gene_variant|MODIFIER|rluA|PA14_22000|transcript|ABJ12495.1|protein_coding||c.*719A>G|||||719|,C|downstream_gene_variant|MODIFIER|minE|PA14_22010|transcript|ABJ12494.1|protein_coding||c.*1458A>G|||||1458|,C|downstream_gene_variant|MODIFIER|minD|PA14_22020|transcript|ABJ12493.1|protein_coding||c.*1709A>G|||||1709|,C|downstream_gene_variant|MODIFIER|minC|PA14_22040|transcript|ABJ12492.1|protein_coding||c.*2586A>G|||||2586| GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:36:0:0:0,-3.59827 0:2:2,0:2:78:0:0:0,-7.40347 0:8:8,0:8:259:0:0:0,-23.6198 0:8:8,2:6:219:2:4:0,-19.6812 +Chromosome 1914228 . T C 3.95476E-11 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=40;DPB=40;DPRA=0.555556;EPP=11.6962;EPPR=6.05036;GTI=0;LEN=1;MEANALT=1.33333;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=25.4222;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=22;QR=778;RO=35;RPL=4;RPP=11.6962;RPPR=16.9698;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=23;SRP=10.5174;SRR=12;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|rluA|PA14_22000|transcript|ABJ12495.1|protein_coding|1/1|c.214A>G|p.Ser72Gly|214/636|214/636|72/211||,C|upstream_gene_variant|MODIFIER|PA14_21940|PA14_21940|transcript|ABJ12500.1|protein_coding||c.-4733A>G|||||4733|,C|upstream_gene_variant|MODIFIER|PA14_21960|PA14_21960|transcript|ABJ12499.1|protein_coding||c.-3620A>G|||||3620|,C|upstream_gene_variant|MODIFIER|PA14_21990|PA14_21990|transcript|ABJ12496.1|protein_coding||c.-591A>G|||||591|,C|upstream_gene_variant|MODIFIER|htrB|PA14_22050|transcript|ABJ12491.1|protein_coding||c.-2396T>C|||||2396|,C|upstream_gene_variant|MODIFIER|PA14_22060|PA14_22060|transcript|ABJ12490.1|protein_coding||c.-3402T>C|||||3402|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_21970|PA14_21970|transcript|ABJ12498.1|protein_coding||c.*2540T>C|||||2540|,C|downstream_gene_variant|MODIFIER|PA14_21980|PA14_21980|transcript|ABJ12497.1|protein_coding||c.*1923T>C|||||1923|,C|downstream_gene_variant|MODIFIER|minE|PA14_22010|transcript|ABJ12494.1|protein_coding||c.*317A>G|||||317|,C|downstream_gene_variant|MODIFIER|minD|PA14_22020|transcript|ABJ12493.1|protein_coding||c.*568A>G|||||568|,C|downstream_gene_variant|MODIFIER|minC|PA14_22040|transcript|ABJ12492.1|protein_coding||c.*1445A>G|||||1445|,C|downstream_gene_variant|MODIFIER|PA14_22075|PA14_22075|transcript|ABJ15635.1|protein_coding||c.*4635A>G|||||4635| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,2:3:44:2:4:0,-3.69479 0:11:11,1:10:186:1:16:0,-15.3242 0:8:8,1:7:173:1:2:0,-15.6056 0:15:15,0:15:375:0:0:0,-33.9784 +Chromosome 1950765 . A G 2.0812E-7 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=3.75;EPP=7.35324;EPPR=5.80219;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=17.4595;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=186;RO=7;RPL=0;RPP=7.35324;RPPR=3.32051;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=5.80219;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_22410|PA14_22410|transcript|ABJ12462.1|protein_coding|1/1|c.121A>G|p.Ser41Gly|121/1125|121/1125|41/374||,G|downstream_gene_variant|MODIFIER|yjcH|PA14_22340|transcript|ABJ12467.1|protein_coding||c.*4828A>G|||||4828|,G|downstream_gene_variant|MODIFIER|yjcG|PA14_22350|transcript|ABJ12466.1|protein_coding||c.*3176A>G|||||3176|,G|downstream_gene_variant|MODIFIER|PA14_22370|PA14_22370|transcript|ABJ12465.1|protein_coding||c.*1287A>G|||||1287|,G|downstream_gene_variant|MODIFIER|PA14_22380|PA14_22380|transcript|ABJ12464.1|protein_coding||c.*664A>G|||||664|,G|downstream_gene_variant|MODIFIER|PA14_22400|PA14_22400|transcript|ABJ12463.1|protein_coding||c.*397A>G|||||397|,G|downstream_gene_variant|MODIFIER|PA14_22420|PA14_22420|transcript|ABJ12461.1|protein_coding||c.*1037T>C|||||1037|,G|downstream_gene_variant|MODIFIER|bapA|PA14_22440|transcript|ABJ12460.1|protein_coding||c.*1585T>C|||||1585|,G|downstream_gene_variant|MODIFIER|ppiA|PA14_22450|transcript|ABJ12459.1|protein_coding||c.*3480T>C|||||3480|,G|downstream_gene_variant|MODIFIER|PA14_22460|PA14_22460|transcript|ABJ12458.1|protein_coding||c.*4025T>C|||||4025|,G|downstream_gene_variant|MODIFIER|PA14_22470|PA14_22470|transcript|ABJ12457.1|protein_coding||c.*4859T>C|||||4859| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:40:0:0:0,-3.79741 0:1:1,0:1:39:0:0:0,-3.89656 0:1:1,0:1:39:0:0:0,-3.89656 0:5:5,2:3:68:2:30:0,-3.49264 +Chromosome 1952276 . C A 7.35586E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=42;DPB=42;DPRA=0.826087;EPP=3.73412;EPPR=19.1015;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=29.4102;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=48;QR=1024;RO=39;RPL=2;RPP=3.73412;RPPR=9.74743;RPR=1;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=7;SRP=37.8095;SRR=32;TYPE=snp;technology.ILLUMINA=1;ANN=A|upstream_gene_variant|MODIFIER|PA14_22420|PA14_22420|transcript|ABJ12461.1|protein_coding||c.-208G>T|||||208|,A|upstream_gene_variant|MODIFIER|PA14_22480|PA14_22480|transcript|ABJ12456.1|protein_coding||c.-4477C>A|||||4477|,A|upstream_gene_variant|MODIFIER|acpD|PA14_22490|transcript|ABJ12455.1|protein_coding||c.-4941C>A|||||4941|,A|downstream_gene_variant|MODIFIER|yjcG|PA14_22350|transcript|ABJ12466.1|protein_coding||c.*4687C>A|||||4687|,A|downstream_gene_variant|MODIFIER|PA14_22370|PA14_22370|transcript|ABJ12465.1|protein_coding||c.*2798C>A|||||2798|,A|downstream_gene_variant|MODIFIER|PA14_22380|PA14_22380|transcript|ABJ12464.1|protein_coding||c.*2175C>A|||||2175|,A|downstream_gene_variant|MODIFIER|PA14_22400|PA14_22400|transcript|ABJ12463.1|protein_coding||c.*1908C>A|||||1908|,A|downstream_gene_variant|MODIFIER|PA14_22410|PA14_22410|transcript|ABJ12462.1|protein_coding||c.*507C>A|||||507|,A|downstream_gene_variant|MODIFIER|bapA|PA14_22440|transcript|ABJ12460.1|protein_coding||c.*74G>T|||||74|,A|downstream_gene_variant|MODIFIER|ppiA|PA14_22450|transcript|ABJ12459.1|protein_coding||c.*1969G>T|||||1969|,A|downstream_gene_variant|MODIFIER|PA14_22460|PA14_22460|transcript|ABJ12458.1|protein_coding||c.*2514G>T|||||2514|,A|downstream_gene_variant|MODIFIER|PA14_22470|PA14_22470|transcript|ABJ12457.1|protein_coding||c.*3348G>T|||||3348|,A|intergenic_region|MODIFIER|PA14_22420-bapA|PA14_22420-PA14_22440|intergenic_region|PA14_22420-PA14_22440|||n.1952276C>A|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,2:6:111:2:32:0,-7.13445 0:8:8,0:8:167:0:0:0,-15.233 0:11:11,1:10:327:1:16:0,-28.1423 0:15:15,0:15:419:0:0:0,-37.9707 +Chromosome 1975105 . C G 1.86109E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=39;DPB=39;DPRA=1.03448;EPP=7.35324;EPPR=12.9286;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=53.5908;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1090;RO=37;RPL=0;RPP=7.35324;RPPR=39.6906;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=25;SRP=12.9286;SRR=12;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|PA14_22650|PA14_22650|transcript|ABJ12440.1|protein_coding||c.-4486G>C|||||4486|,G|upstream_gene_variant|MODIFIER|PA14_22660|PA14_22660|transcript|ABJ12439.1|protein_coding||c.-3551G>C|||||3551|,G|upstream_gene_variant|MODIFIER|yrbF|PA14_22670|transcript|ABJ12438.1|protein_coding||c.-2755G>C|||||2755|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|yrbE|PA14_22680|transcript|ABJ12437.1|protein_coding||c.-1613G>C|||||1613|,G|upstream_gene_variant|MODIFIER|trkH|PA14_22690|transcript|ABJ12436.1|protein_coding||c.-92G>C|||||92|,G|upstream_gene_variant|MODIFIER|ykgJ|PA14_22700|transcript|ABJ12435.1|protein_coding||c.-66C>G|||||66|,G|upstream_gene_variant|MODIFIER|ydjA|PA14_22710|transcript|ABJ12434.1|protein_coding||c.-502C>G|||||502|,G|downstream_gene_variant|MODIFIER|PA14_22720|PA14_22720|transcript|ABJ12433.1|protein_coding||c.*1043G>C|||||1043|,G|downstream_gene_variant|MODIFIER|PA14_22730|PA14_22730|transcript|ABJ12432.1|protein_coding||c.*1563G>C|||||1563|,G|downstream_gene_variant|MODIFIER|PA14_22740|PA14_22740|transcript|ABJ12431.1|protein_coding||c.*3015G>C|||||3015|,G|downstream_gene_variant|MODIFIER|cpxR|PA14_22760|transcript|ABJ12430.1|protein_coding||c.*3584G>C|||||3584|,G|downstream_gene_variant|MODIFIER|PA14_22770|PA14_22770|transcript|ABJ12429.1|protein_coding||c.*4272G>C|||||4272|,G|downstream_gene_variant|MODIFIER|yciI|PA14_22780|transcript|ABJ12428.1|protein_coding||c.*4816G>C|||||4816|,G|intergenic_region|MODIFIER|trkH-ykgJ|PA14_22690-PA14_22700|intergenic_region|PA14_22690-PA14_22700|||n.1975105C>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,0:10:324:0:0:0,-29.4599 0:7:7,0:7:169:0:0:0,-15.4412 0:12:12,0:12:334:0:0:0,-30.3145 0:10:10,2:8:263:2:4:0,-23.6015 +Chromosome 1978349 . T C 6.13276E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=29;DPB=29;DPRA=0.8125;EPP=9.52472;EPPR=11.3621;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=42.223;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=938;RO=26;RPL=2;RPP=3.73412;RPPR=6.01695;RPR=1;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=6;SRP=19.3799;SRR=20;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_22740|PA14_22740|transcript|ABJ12431.1|protein_coding|1/1|c.212A>G|p.Lys71Arg|212/441|212/441|71/146||,C|upstream_gene_variant|MODIFIER|yrbE|PA14_22680|transcript|ABJ12437.1|protein_coding||c.-4857A>G|||||4857|,C|upstream_gene_variant|MODIFIER|trkH|PA14_22690|transcript|ABJ12436.1|protein_coding||c.-3336A>G|||||3336|,C|upstream_gene_variant|MODIFIER|PA14_22720|PA14_22720|transcript|ABJ12433.1|protein_coding||c.-1725A>G|||||1725|,C|upstream_gene_variant|MODIFIER|PA14_22730|PA14_22730|transcript|ABJ12432.1|protein_coding||c.-344A>G|||||344|,C|upstream_gene_variant|MODIFIER|yciV|PA14_22820|transcript|ABJ12426.1|protein_coding||c.-2675T>C|||||2675|,C|upstream_gene_variant|MODIFIER|yciO|PA14_22830|transcript|ABJ12425.1|protein_coding||c.-3559T>C|||||3559|,C|upstream_gene_variant|MODIFIER|ypuG|PA14_22840|transcript|ABJ12424.1|protein_coding||c.-4361T>C|||||4361|,C|downstream_gene_variant|MODIFIER|ykgJ|PA14_22700|transcript|ABJ12435.1|protein_coding||c.*2807T>C|||||2807|,C|downstream_gene_variant|MODIFIER|ydjA|PA14_22710|transcript|ABJ12434.1|protein_coding||c.*2182T>C|||||2182|,C|downstream_gene_variant|MODIFIER|cpxR|PA14_22760|transcript|ABJ12430.1|protein_coding||c.*340A>G|||||340|,C|downstream_gene_variant|MODIFIER|PA14_22770|PA14_22770|transcript|ABJ12429.1|protein_coding||c.*1028A>G|||||1028|,C|downstream_gene_variant|MODIFIER|yciI|PA14_22780|transcript|ABJ12428.1|protein_coding||c.*1572A>G|||||1572|,C|downstream_gene_variant|MODIFIER|yciB|PA14_22800|transcript|ABJ12427.1|protein_coding||c.*1873A>G|||||1873| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,0:9:333:0:0:0,-30.3101 0:6:6,1:5:170:1:15:0,-14.1273 0:7:7,2:5:198:2:55:0,-12.9769 0:7:7,0:7:237:0:0:0,-21.6518 +Chromosome 1982762 . T C 1.37419E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=6;CIGAR=1X;DP=55;DPB=55;DPRA=0.97619;EPP=16.0391;EPPR=4.11819;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=51.3601;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=114;QR=1497;RO=49;RPL=6;RPP=16.0391;RPPR=30.7077;RPR=0;RUN=1;SAF=6;SAP=16.0391;SAR=0;SRF=33;SRP=15.8176;SRR=16;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|ypuG|PA14_22840|transcript|ABJ12424.1|protein_coding|1/1|c.53T>C|p.Leu18Pro|53/753|53/753|18/250||,C|upstream_gene_variant|MODIFIER|PA14_22730|PA14_22730|transcript|ABJ12432.1|protein_coding||c.-4757A>G|||||4757|,C|upstream_gene_variant|MODIFIER|PA14_22740|PA14_22740|transcript|ABJ12431.1|protein_coding||c.-4202A>G|||||4202|,C|upstream_gene_variant|MODIFIER|cpxR|PA14_22760|transcript|ABJ12430.1|protein_coding||c.-3396A>G|||||3396|,C|upstream_gene_variant|MODIFIER|PA14_22770|PA14_22770|transcript|ABJ12429.1|protein_coding||c.-3017A>G|||||3017|,C|upstream_gene_variant|MODIFIER|yciI|PA14_22780|transcript|ABJ12428.1|protein_coding||c.-2542A>G|||||2542|,C|upstream_gene_variant|MODIFIER|yciB|PA14_22800|transcript|ABJ12427.1|protein_coding||c.-1953A>G|||||1953|,C|upstream_gene_variant|MODIFIER|PA14_22860|PA14_22860|transcript|ABJ12423.1|protein_coding||c.-845T>C|||||845|,C|upstream_gene_variant|MODIFIER|PA14_22870|PA14_22870|transcript|ABJ12422.1|protein_coding||c.-1919T>C|||||1919|,C|upstream_gene_variant|MODIFIER|PA14_22880|PA14_22880|transcript|ABJ12421.1|protein_coding||c.-2534T>C|||||2534|,C|upstream_gene_variant|MODIFIER|edd|PA14_22910|transcript|ABJ12419.1|protein_coding||c.-3887T>C|||||3887|,C|downstream_gene_variant|MODIFIER|yciV|PA14_22820|transcript|ABJ12426.1|protein_coding||c.*851T>C|||||851|,C|downstream_gene_variant|MODIFIER|yciO|PA14_22830|transcript|ABJ12425.1|protein_coding||c.*225T>C|||||225|,C|downstream_gene_variant|MODIFIER|gapA|PA14_22890|transcript|ABJ12420.1|protein_coding||c.*2753A>G|||||2753| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,2:6:207:2:54:0,-13.833 0:14:14,0:14:378:0:0:0,-34.2694 0:18:18,2:16:478:2:30:0,-40.4389 0:15:15,2:13:434:2:30:0,-36.5119 +Chromosome 1987633 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=33;DPB=33;DPRA=1.125;EPP=7.35324;EPPR=28.2974;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=53.0517;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=1124;RO=31;RPL=2;RPP=7.35324;RPPR=3.64073;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=14;SRP=3.64073;SRR=17;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|edd|PA14_22910|transcript|ABJ12419.1|protein_coding|1/1|c.985G>T|p.Val329Leu|985/1827|985/1827|329/608||,T|upstream_gene_variant|MODIFIER|gapA|PA14_22890|transcript|ABJ12420.1|protein_coding||c.-1114C>A|||||1114|,T|upstream_gene_variant|MODIFIER|glk|PA14_22930|transcript|ABJ12418.1|protein_coding||c.-945G>T|||||945|,T|upstream_gene_variant|MODIFIER|gltR|PA14_22940|transcript|ABJ12417.1|protein_coding||c.-1975G>T|||||1975|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|PA14_22960|PA14_22960|transcript|ABJ12416.1|protein_coding||c.-2727G>T|||||2727|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|gltB|PA14_22980|transcript|ABJ12415.1|protein_coding||c.-4673G>T|||||4673|,T|downstream_gene_variant|MODIFIER|ypuG|PA14_22840|transcript|ABJ12424.1|protein_coding||c.*4171G>T|||||4171|,T|downstream_gene_variant|MODIFIER|PA14_22860|PA14_22860|transcript|ABJ12423.1|protein_coding||c.*3034G>T|||||3034|,T|downstream_gene_variant|MODIFIER|PA14_22870|PA14_22870|transcript|ABJ12422.1|protein_coding||c.*2422G>T|||||2422|,T|downstream_gene_variant|MODIFIER|PA14_22880|PA14_22880|transcript|ABJ12421.1|protein_coding||c.*2125G>T|||||2125| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:182:0:0:0,-16.678 0:9:9,2:7:268:2:31:0,-21.5372 0:11:11,0:11:416:0:0:0,-37.7881 0:7:7,0:7:258:0:0:0,-23.5733 +Chromosome 2021195 . A G 7.55688E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=27;DPB=27;DPRA=1.46667;EPP=11.6962;EPPR=5.3706;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=38.6388;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=828;RO=23;RPL=0;RPP=11.6962;RPPR=3.86001;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=8;SRP=7.63648;SRR=15;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_23310|PA14_23310|transcript|ABJ12389.1|protein_coding|1/1|c.236A>G|p.Gln79Arg|236/2241|236/2241|79/746||,G|upstream_gene_variant|MODIFIER|cmk|PA14_23320|transcript|ABJ12388.1|protein_coding||c.-2005A>G|||||2005|,G|upstream_gene_variant|MODIFIER|rpsA|PA14_23330|transcript|ABJ12387.1|protein_coding||c.-2962A>G|||||2962|,G|upstream_gene_variant|MODIFIER|himD|PA14_23340|transcript|ABJ12386.1|protein_coding||c.-4778A>G|||||4778|,G|downstream_gene_variant|MODIFIER|gyrA|PA14_23260|transcript|ABJ12393.1|protein_coding||c.*3676A>G|||||3676|,G|downstream_gene_variant|MODIFIER|serC|PA14_23270|transcript|ABJ12392.1|protein_coding||c.*2503A>G|||||2503|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|pheA|PA14_23280|transcript|ABJ12391.1|protein_coding||c.*1406A>G|||||1406|,G|downstream_gene_variant|MODIFIER|hisC2|PA14_23290|transcript|ABJ12390.1|protein_coding||c.*228A>G|||||228| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:198:0:0:0,-18.1978 0:5:5,2:3:114:2:4:0,-10.2515 0:9:9,1:8:288:1:2:0,-26.062 0:8:8,1:7:228:1:2:0,-20.6391 +Chromosome 2059830 . C A 1.06302E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=32;DPB=32;DPRA=1.17391;EPP=7.35324;EPPR=21.5402;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5667;NS=4;NUMALT=1;ODDS=37.4753;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1006;RO=30;RPL=0;RPP=7.35324;RPPR=3.0103;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=14;SRP=3.29983;SRR=16;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|PA14_23690|PA14_23690|transcript|ABJ12357.1|protein_coding|1/1|c.1114G>T|p.Ala372Ser|1114/1329|1114/1329|372/442||,A|upstream_gene_variant|MODIFIER|ygfF|PA14_23650|transcript|ABJ12360.1|protein_coding||c.-1686G>T|||||1686|,A|upstream_gene_variant|MODIFIER|PA14_23670|PA14_23670|transcript|ABJ12359.1|protein_coding||c.-866G>T|||||866|,A|upstream_gene_variant|MODIFIER|PA14_23700|PA14_23700|transcript|ABJ12356.1|protein_coding||c.-1225C>A|||||1225|,A|upstream_gene_variant|MODIFIER|PA14_23720|PA14_23720|transcript|ABJ12355.1|protein_coding||c.-2216C>A|||||2216|,A|upstream_gene_variant|MODIFIER|leuC|PA14_23750|transcript|ABJ12353.1|protein_coding||c.-3742C>A|||||3742|,A|downstream_gene_variant|MODIFIER|PA14_23610|PA14_23610|transcript|ABJ12364.1|protein_coding||c.*4696C>A|||||4696|,A|downstream_gene_variant|MODIFIER|kdgA|PA14_23620|transcript|ABJ12363.1|protein_coding||c.*3936C>A|||||3936|,A|downstream_gene_variant|MODIFIER|PA14_23630|PA14_23630|transcript|ABJ12362.1|protein_coding||c.*3499C>A|||||3499|,A|downstream_gene_variant|MODIFIER|PA14_23640|PA14_23640|transcript|ABJ12361.1|protein_coding||c.*2447C>A|||||2447|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ibpA|PA14_23680|transcript|ABJ12358.1|protein_coding||c.*259C>A|||||259|,A|downstream_gene_variant|MODIFIER|PA14_23730|PA14_23730|transcript|ABJ12354.1|protein_coding||c.*2686G>T|||||2686| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:192:0:0:0,-17.592 0:9:9,2:7:247:2:17:0,-20.9497 0:3:3,0:3:95:0:0:0,-8.85941 0:14:14,0:14:472:0:0:0,-42.7835 +Chromosome 2093368 . C G 7.20985E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=27;DPB=27;DPRA=1.76471;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=38.803;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=907;RO=25;RPL=0;RPP=7.35324;RPPR=7.26639;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=20;SRP=22.5536;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_24140|PA14_24140|transcript|ABJ12326.1|protein_coding|1/1|c.790G>C|p.Ala264Pro|790/1038|790/1038|264/345||,G|upstream_gene_variant|MODIFIER|tRNA|EBG00001225033|transcript|EBT00001793383.1|protein_coding||c.-823G>C|||||823|WARNING_TRANSCRIPT_INCOMPLETE,G|upstream_gene_variant|MODIFIER|tRNA|EBG00001225140|transcript|EBT00001793439.1|protein_coding||c.-730G>C|||||730|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,G|upstream_gene_variant|MODIFIER|tRNA|EBG00001225171|transcript|EBT00001793482.1|protein_coding||c.-539G>C|||||539|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,G|upstream_gene_variant|MODIFIER|fadH1|PA14_24170|transcript|ABJ12324.1|protein_coding||c.-2119C>G|||||2119|,G|upstream_gene_variant|MODIFIER|PA14_24180|PA14_24180|transcript|ABJ12323.1|protein_coding||c.-4495C>G|||||4495|,G|downstream_gene_variant|MODIFIER|xcpU|PA14_24040|transcript|ABJ12332.1|protein_coding||c.*4799C>G|||||4799|,G|downstream_gene_variant|MODIFIER|xcpV|PA14_24050|transcript|ABJ12331.1|protein_coding||c.*4413C>G|||||4413|,G|downstream_gene_variant|MODIFIER|xcpW|PA14_24060|transcript|ABJ12330.1|protein_coding||c.*3703C>G|||||3703|,G|downstream_gene_variant|MODIFIER|xcpX|PA14_24070|transcript|ABJ12329.1|protein_coding||c.*2705C>G|||||2705|,G|downstream_gene_variant|MODIFIER|xcpY|PA14_24080|transcript|ABJ12328.1|protein_coding||c.*1560C>G|||||1560|,G|downstream_gene_variant|MODIFIER|xcpZ|PA14_24100|transcript|ABJ12327.1|protein_coding||c.*1034C>G|||||1034|,G|downstream_gene_variant|MODIFIER|PA14_24110|PA14_24110|transcript|PA14_24110-1.1|protein_coding||c.*823C>G|||||823|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|PA14_24120|PA14_24120|transcript|PA14_24120-1.1|protein_coding||c.*730C>G|||||730|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|PA14_24130|PA14_24130|transcript|PA14_24130-1.1|protein_coding||c.*539C>G|||||539|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|PA14_24150|PA14_24150|transcript|ABJ12325.1|protein_coding||c.*786G>C|||||786| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:116:0:0:0,-10.7216 0:6:6,0:6:214:0:0:0,-19.6025 0:7:7,0:7:273:0:0:0,-24.9361 0:10:10,2:8:304:2:4:0,-27.3346 +Chromosome 2094637 . G C 9.06341E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=27;DPB=27;DPRA=2;EPP=5.18177;EPPR=3.86001;GTI=0;LEN=1;MEANALT=1;MQM=58.5;MQMR=60;NS=4;NUMALT=1;ODDS=39.8479;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=22;QR=781;RO=23;RPL=3;RPP=5.18177;RPPR=3.86001;RPR=1;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=6;SRP=14.4341;SRR=17;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|PA14_24150|PA14_24150|transcript|ABJ12325.1|protein_coding|1/1|c.636C>G|p.Leu212Leu|636/1119|636/1119|212/372||,C|upstream_gene_variant|MODIFIER|tRNA|EBG00001225033|transcript|EBT00001793383.1|protein_coding||c.-2092C>G|||||2092|WARNING_TRANSCRIPT_INCOMPLETE,C|upstream_gene_variant|MODIFIER|tRNA|EBG00001225140|transcript|EBT00001793439.1|protein_coding||c.-1999C>G|||||1999|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|upstream_gene_variant|MODIFIER|tRNA|EBG00001225171|transcript|EBT00001793482.1|protein_coding||c.-1808C>G|||||1808|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|upstream_gene_variant|MODIFIER|PA14_24140|PA14_24140|transcript|ABJ12326.1|protein_coding||c.-480C>G|||||480|,C|upstream_gene_variant|MODIFIER|fadH1|PA14_24170|transcript|ABJ12324.1|protein_coding||c.-850G>C|||||850|,C|upstream_gene_variant|MODIFIER|PA14_24180|PA14_24180|transcript|ABJ12323.1|protein_coding||c.-3226G>C|||||3226|,C|upstream_gene_variant|MODIFIER|PA14_24190|PA14_24190|transcript|ABJ12322.1|protein_coding||c.-4670G>C|||||4670|,C|downstream_gene_variant|MODIFIER|xcpW|PA14_24060|transcript|ABJ12330.1|protein_coding||c.*4972G>C|||||4972|,C|downstream_gene_variant|MODIFIER|xcpX|PA14_24070|transcript|ABJ12329.1|protein_coding||c.*3974G>C|||||3974|,C|downstream_gene_variant|MODIFIER|xcpY|PA14_24080|transcript|ABJ12328.1|protein_coding||c.*2829G>C|||||2829|,C|downstream_gene_variant|MODIFIER|xcpZ|PA14_24100|transcript|ABJ12327.1|protein_coding||c.*2303G>C|||||2303|,C|downstream_gene_variant|MODIFIER|PA14_24110|PA14_24110|transcript|PA14_24110-1.1|protein_coding||c.*2092G>C|||||2092|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|PA14_24120|PA14_24120|transcript|PA14_24120-1.1|protein_coding||c.*1999G>C|||||1999|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|PA14_24130|PA14_24130|transcript|PA14_24130-1.1|protein_coding||c.*1808G>C|||||1808|WARNING_TRANSCRIPT_INCOMPLETE GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,3:4:153:3:20:0,-12.2737 0:5:5,0:5:122:0:0:0,-11.2137 0:11:11,1:10:375:1:2:0,-33.8958 0:4:4,0:4:131:0:0:0,-12.108 +Chromosome 2094748 . G C 1.15081E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=26;DPB=26;DPRA=0.9;EPP=7.35324;EPPR=26.1727;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=37.5876;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=706;RO=24;RPL=2;RPP=7.35324;RPPR=12.0581;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=15;SRP=6.26751;SRR=9;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|PA14_24150|PA14_24150|transcript|ABJ12325.1|protein_coding|1/1|c.525C>G|p.Val175Val|525/1119|525/1119|175/372||,C|upstream_gene_variant|MODIFIER|tRNA|EBG00001225033|transcript|EBT00001793383.1|protein_coding||c.-2203C>G|||||2203|WARNING_TRANSCRIPT_INCOMPLETE,C|upstream_gene_variant|MODIFIER|tRNA|EBG00001225140|transcript|EBT00001793439.1|protein_coding||c.-2110C>G|||||2110|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|upstream_gene_variant|MODIFIER|tRNA|EBG00001225171|transcript|EBT00001793482.1|protein_coding||c.-1919C>G|||||1919|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|upstream_gene_variant|MODIFIER|PA14_24140|PA14_24140|transcript|ABJ12326.1|protein_coding||c.-591C>G|||||591|,C|upstream_gene_variant|MODIFIER|fadH1|PA14_24170|transcript|ABJ12324.1|protein_coding||c.-739G>C|||||739|,C|upstream_gene_variant|MODIFIER|PA14_24180|PA14_24180|transcript|ABJ12323.1|protein_coding||c.-3115G>C|||||3115|,C|upstream_gene_variant|MODIFIER|PA14_24190|PA14_24190|transcript|ABJ12322.1|protein_coding||c.-4559G>C|||||4559|,C|downstream_gene_variant|MODIFIER|xcpX|PA14_24070|transcript|ABJ12329.1|protein_coding||c.*4085G>C|||||4085|,C|downstream_gene_variant|MODIFIER|xcpY|PA14_24080|transcript|ABJ12328.1|protein_coding||c.*2940G>C|||||2940|,C|downstream_gene_variant|MODIFIER|xcpZ|PA14_24100|transcript|ABJ12327.1|protein_coding||c.*2414G>C|||||2414|,C|downstream_gene_variant|MODIFIER|PA14_24110|PA14_24110|transcript|PA14_24110-1.1|protein_coding||c.*2203G>C|||||2203|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|PA14_24120|PA14_24120|transcript|PA14_24120-1.1|protein_coding||c.*2110G>C|||||2110|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|PA14_24130|PA14_24130|transcript|PA14_24130-1.1|protein_coding||c.*1919G>C|||||1919|WARNING_TRANSCRIPT_INCOMPLETE GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,2:4:144:2:4:0,-12.933 0:4:4,0:4:117:0:0:0,-10.8132 0:5:5,0:5:152:0:0:0,-13.974 0:11:11,0:11:293:0:0:0,-26.6203 +Chromosome 2106623 . A G 7.53144E-10 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=17;DPB=17;DPRA=1.83333;EPP=9.52472;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=57;MQMR=59;NS=4;NUMALT=1;ODDS=22.4802;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=420;RO=14;RPL=0;RPP=9.52472;RPPR=12.937;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=4;SRP=8.59409;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|pepN|PA14_24270|transcript|ABJ12316.1|protein_coding|1/1|c.1371A>G|p.Glu457Glu|1371/2658|1371/2658|457/885||,G|upstream_gene_variant|MODIFIER|gbt|PA14_24290|transcript|ABJ12315.1|protein_coding||c.-1734A>G|||||1734|,G|upstream_gene_variant|MODIFIER|PA14_24300|PA14_24300|transcript|ABJ12314.1|protein_coding||c.-3757A>G|||||3757|,G|downstream_gene_variant|MODIFIER|PA14_24220|PA14_24220|transcript|ABJ12320.1|protein_coding||c.*4406A>G|||||4406|,G|downstream_gene_variant|MODIFIER|PA14_24230|PA14_24230|transcript|ABJ12319.1|protein_coding||c.*3426A>G|||||3426|,G|downstream_gene_variant|MODIFIER|PA14_24240|PA14_24240|transcript|ABJ12318.1|protein_coding||c.*2569A>G|||||2569|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_24245|PA14_24245|transcript|ABJ15700.1|protein_coding||c.*2222A>G|||||2222|,G|downstream_gene_variant|MODIFIER|PA14_24260|PA14_24260|transcript|ABJ12317.1|protein_coding||c.*1389A>G|||||1389| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:119:0:0:0,-11.0954 0:6:6,1:5:173:1:15:0,-14.4017 0:5:5,2:3:43:2:4:0,-3.63013 0:3:3,0:3:85:0:0:0,-7.93064 +Chromosome 2107457 . C A 5.69579E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=61;DPB=61;DPRA=1.51515;EPP=11.6962;EPPR=19.8106;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=63.7513;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=61;QR=1901;RO=57;RPL=0;RPP=11.6962;RPPR=4.877;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=19;SRP=16.763;SRR=38;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|pepN|PA14_24270|transcript|ABJ12316.1|protein_coding|1/1|c.2205C>A|p.Val735Val|2205/2658|2205/2658|735/885||,A|upstream_gene_variant|MODIFIER|gbt|PA14_24290|transcript|ABJ12315.1|protein_coding||c.-900C>A|||||900|,A|upstream_gene_variant|MODIFIER|PA14_24300|PA14_24300|transcript|ABJ12314.1|protein_coding||c.-2923C>A|||||2923|,A|upstream_gene_variant|MODIFIER|PA14_24310|PA14_24310|transcript|ABJ12313.1|protein_coding||c.-4470C>A|||||4470|,A|downstream_gene_variant|MODIFIER|PA14_24230|PA14_24230|transcript|ABJ12319.1|protein_coding||c.*4260C>A|||||4260|,A|downstream_gene_variant|MODIFIER|PA14_24240|PA14_24240|transcript|ABJ12318.1|protein_coding||c.*3403C>A|||||3403|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_24245|PA14_24245|transcript|ABJ15700.1|protein_coding||c.*3056C>A|||||3056|,A|downstream_gene_variant|MODIFIER|PA14_24260|PA14_24260|transcript|ABJ12317.1|protein_coding||c.*2223C>A|||||2223| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,2:8:245:2:31:0,-19.3987 0:20:20,1:19:614:1:15:0,-54.055 0:20:20,1:19:642:1:15:0,-56.584 0:11:11,0:11:400:0:0:0,-36.3399 +Chromosome 2107810 . A G 1.03613E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=30;DPB=30;DPRA=1.28571;EPP=3.0103;EPPR=4.25114;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=51.5166;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=977;RO=28;RPL=1;RPP=3.0103;RPPR=4.25114;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=14;SRP=3.0103;SRR=14;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|pepN|PA14_24270|transcript|ABJ12316.1|protein_coding|1/1|c.2558A>G|p.Glu853Gly|2558/2658|2558/2658|853/885||,G|upstream_gene_variant|MODIFIER|gbt|PA14_24290|transcript|ABJ12315.1|protein_coding||c.-547A>G|||||547|,G|upstream_gene_variant|MODIFIER|PA14_24300|PA14_24300|transcript|ABJ12314.1|protein_coding||c.-2570A>G|||||2570|,G|upstream_gene_variant|MODIFIER|PA14_24310|PA14_24310|transcript|ABJ12313.1|protein_coding||c.-4117A>G|||||4117|,G|downstream_gene_variant|MODIFIER|PA14_24230|PA14_24230|transcript|ABJ12319.1|protein_coding||c.*4613A>G|||||4613|,G|downstream_gene_variant|MODIFIER|PA14_24240|PA14_24240|transcript|ABJ12318.1|protein_coding||c.*3756A>G|||||3756|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_24245|PA14_24245|transcript|ABJ15700.1|protein_coding||c.*3409A>G|||||3409|,G|downstream_gene_variant|MODIFIER|PA14_24260|PA14_24260|transcript|ABJ12317.1|protein_coding||c.*2576A>G|||||2576| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,0:9:315:0:0:0,-28.6803 0:5:5,0:5:192:0:0:0,-17.6491 0:9:9,2:7:219:2:37:0,-16.5033 0:7:7,0:7:251:0:0:0,-22.9324 +Chromosome 2117609 . C T 3.68535E-10 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=20;DPB=20;DPRA=1.28571;EPP=3.0103;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=23.1902;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=42;QR=657;RO=18;RPL=0;RPP=7.35324;RPPR=20.3821;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=13;SRP=10.7311;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=T|upstream_gene_variant|MODIFIER|PA14_24340|PA14_24340|transcript|ABJ12311.1|protein_coding||c.-825G>A|||||825|,T|upstream_gene_variant|MODIFIER|PA14_24350|PA14_24350|transcript|ABJ12310.1|protein_coding||c.-157G>A|||||157|,T|upstream_gene_variant|MODIFIER|PA14_24360|PA14_24360|transcript|ABJ12309.1|protein_coding||c.-167C>T|||||167|,T|downstream_gene_variant|MODIFIER|PA14_24310|PA14_24310|transcript|ABJ12313.1|protein_coding||c.*4585C>T|||||4585|,T|downstream_gene_variant|MODIFIER|PA14_24330|PA14_24330|transcript|ABJ12312.1|protein_coding||c.*2192C>T|||||2192|,T|downstream_gene_variant|MODIFIER|PA14_24370|PA14_24370|transcript|ABJ12308.1|protein_coding||c.*3098G>A|||||3098|,T|downstream_gene_variant|MODIFIER|PA14_24380|PA14_24380|transcript|ABJ12307.1|protein_coding||c.*4231G>A|||||4231|,T|intergenic_region|MODIFIER|PA14_24350-PA14_24360|PA14_24350-PA14_24360|intergenic_region|PA14_24350-PA14_24360|||n.2117609C>T|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:152:0:0:0,-14.0492 0:8:8,0:8:301:0:0:0,-27.4456 0:2:2,0:2:52:0:0:0,-4.93673 0:6:6,2:4:152:2:42:0,-10.0633 +Chromosome 2129244 . G T 1.25742E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=23;DPB=23;DPRA=1.05882;EPP=7.35324;EPPR=3.94093;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=33.5778;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=670;RO=21;RPL=2;RPP=7.35324;RPPR=5.59539;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=14;SRP=8.07707;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_24440|PA14_24440|transcript|ABJ12301.1|protein_coding|1/1|c.92G>T|p.Trp31Leu|92/618|92/618|31/205||,T|upstream_gene_variant|MODIFIER|PA14_24390|PA14_24390|transcript|ABJ12306.1|protein_coding||c.-4016C>A|||||4016|,T|upstream_gene_variant|MODIFIER|PA14_24400|PA14_24400|transcript|ABJ12305.1|protein_coding||c.-2997C>A|||||2997|,T|upstream_gene_variant|MODIFIER|PA14_24410|PA14_24410|transcript|ABJ12304.1|protein_coding||c.-2510C>A|||||2510|,T|upstream_gene_variant|MODIFIER|PA14_24420|PA14_24420|transcript|ABJ12303.1|protein_coding||c.-1575C>A|||||1575|,T|upstream_gene_variant|MODIFIER|moxR|PA14_24430|transcript|ABJ12302.1|protein_coding||c.-584C>A|||||584|,T|upstream_gene_variant|MODIFIER|gdhB|PA14_24445|transcript|ABJ15659.1|protein_coding||c.-800G>T|||||800| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:182:0:0:0,-16.734 0:6:6,2:4:144:2:30:0,-10.4613 0:4:4,0:4:104:0:0:0,-9.61579 0:8:8,0:8:240:0:0:0,-21.8846 +Chromosome 2130140 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=65;DPB=65;DPRA=0.482143;EPP=3.0103;EPPR=3.04477;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=60.1431;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=78;QR=2420;RO=63;RPL=1;RPP=3.0103;RPPR=4.69922;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=28;SRP=4.69922;SRR=35;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|gdhB|PA14_24445|transcript|ABJ15659.1|protein_coding|1/1|c.97A>G|p.Thr33Ala|97/4863|97/4863|33/1620||,G|upstream_gene_variant|MODIFIER|PA14_24390|PA14_24390|transcript|ABJ12306.1|protein_coding||c.-4912T>C|||||4912|,G|upstream_gene_variant|MODIFIER|PA14_24400|PA14_24400|transcript|ABJ12305.1|protein_coding||c.-3893T>C|||||3893|,G|upstream_gene_variant|MODIFIER|PA14_24410|PA14_24410|transcript|ABJ12304.1|protein_coding||c.-3406T>C|||||3406|,G|upstream_gene_variant|MODIFIER|PA14_24420|PA14_24420|transcript|ABJ12303.1|protein_coding||c.-2471T>C|||||2471|,G|upstream_gene_variant|MODIFIER|moxR|PA14_24430|transcript|ABJ12302.1|protein_coding||c.-1480T>C|||||1480|,G|downstream_gene_variant|MODIFIER|PA14_24440|PA14_24440|transcript|ABJ12301.1|protein_coding||c.*370A>G|||||370| GT:DP:DPR:RO:QR:AO:QA:GL 0:14:14,0:14:544:0:0:0,-49.3041 0:18:18,0:18:691:0:0:0,-62.5187 0:24:24,0:24:923:0:0:0,-83.3788 0:9:9,2:7:262:2:78:0,-16.533 +Chromosome 2149829 . C G 1.12371E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=27;DPB=27;DPRA=1.25;EPP=9.52472;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=41.586;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=776;RO=24;RPL=0;RPP=9.52472;RPPR=4.45795;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=8;SRP=8.80089;SRR=16;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_24600|PA14_24600|transcript|ABJ12290.1|protein_coding|1/1|c.1243G>C|p.Gly415Arg|1243/1905|1243/1905|415/634||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_24570|PA14_24570|transcript|ABJ12293.1|protein_coding||c.-1895G>C|||||1895|,G|upstream_gene_variant|MODIFIER|PA14_24630|PA14_24630|transcript|ABJ12288.1|protein_coding||c.-3457C>G|||||3457|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|pyrD|PA14_24640|transcript|ABJ12286.1|protein_coding||c.-3795C>G|||||3795|,G|downstream_gene_variant|MODIFIER|pelF|PA14_24550|transcript|ABJ12295.1|protein_coding||c.*3538C>G|||||3538|,G|downstream_gene_variant|MODIFIER|pelG|PA14_24560|transcript|ABJ12294.1|protein_coding||c.*2166C>G|||||2166|,G|downstream_gene_variant|MODIFIER|PA14_24580|PA14_24580|transcript|ABJ12292.1|protein_coding||c.*1293C>G|||||1293|,G|downstream_gene_variant|MODIFIER|PA14_24590|PA14_24590|transcript|ABJ12291.1|protein_coding||c.*779C>G|||||779|,G|downstream_gene_variant|MODIFIER|PA14_24610|PA14_24610|transcript|ABJ12289.1|protein_coding||c.*1410G>C|||||1410|,G|downstream_gene_variant|MODIFIER|PA14_24620|PA14_24620|transcript|ABJ12287.1|protein_coding||c.*2483G>C|||||2483|,G|downstream_gene_variant|MODIFIER|rmf|PA14_24650|transcript|ABJ12285.1|protein_coding||c.*4911G>C|||||4911| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,2:6:190:2:4:0,-17.0228 0:6:6,0:6:237:0:0:0,-21.7037 0:6:6,0:6:210:0:0:0,-19.2329 0:7:7,1:6:139:1:2:0,-12.5333 +Chromosome 2155072 . TGG TG 3092.85 . AB=0;ABP=0;AC=4;AF=1;AN=4;AO=99;CIGAR=1M1D1M;DP=99;DPB=69.6667;DPRA=0;EPP=6.71716;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=4;NUMALT=1;ODDS=183.724;PAIRED=0;PAIREDR=0;PAO=3;PQA=22.5;PQR=22.5;PRO=3;QA=3525;QR=0;RO=0;RPL=42;RPP=7.94546;RPPR=0;RPR=57;RUN=1;SAF=26;SAP=51.4626;SAR=73;SRF=0;SRP=0;SRR=0;TYPE=del;technology.ILLUMINA=1;ANN=TG|upstream_gene_variant|MODIFIER|PA14_24600|PA14_24600|transcript|ABJ12290.1|protein_coding||c.-4003delC|||||4003|WARNING_TRANSCRIPT_NO_START_CODON,TG|upstream_gene_variant|MODIFIER|PA14_24610|PA14_24610|transcript|ABJ12289.1|protein_coding||c.-2834delC|||||2834|,TG|upstream_gene_variant|MODIFIER|PA14_24620|PA14_24620|transcript|ABJ12287.1|protein_coding||c.-1782delC|||||1782|,TG|upstream_gene_variant|MODIFIER|rmf|PA14_24650|transcript|ABJ12285.1|protein_coding||c.-122delC|||||122|,TG|upstream_gene_variant|MODIFIER|PA14_24665|PA14_24665|transcript|ABJ15662.1|protein_coding||c.-340delG|||||340|,TG|upstream_gene_variant|MODIFIER|PA14_24675|PA14_24675|transcript|ABJ15663.1|protein_coding||c.-1487delG|||||1487|,TG|upstream_gene_variant|MODIFIER|PA14_24700|PA14_24700|transcript|ABJ12283.1|protein_coding||c.-4329delG|||||4329|,TG|downstream_gene_variant|MODIFIER|PA14_24630|PA14_24630|transcript|ABJ12288.1|protein_coding||c.*1507delG|||||1507|WARNING_TRANSCRIPT_NO_START_CODON,TG|downstream_gene_variant|MODIFIER|pyrD|PA14_24640|transcript|ABJ12286.1|protein_coding||c.*422delG|||||422|,TG|downstream_gene_variant|MODIFIER|dacB|PA14_24690|transcript|ABJ12284.1|protein_coding||c.*2588delC|||||2588|,TG|intergenic_region|MODIFIER|rmf-PA14_24665|PA14_24650-PA14_24665|intergenic_region|PA14_24650-PA14_24665|||n.2155074delG|||||| GT:DP:DPR:RO:QR:AO:QA:GL 1:26:26,26:0:0:26:947:-85.5238,0 1:23:23,23:0:0:23:761:-68.773,0 1:21:21,21:0:0:21:769:-69.5264,0 1:29:29,29:0:0:29:1048:-94.6024,0 +Chromosome 2172336 . T C 9.98465E-16 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=47;DPB=47;DPRA=1.625;EPP=13.8677;EPPR=3.83753;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=75.5753;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1508;RO=42;RPL=5;RPP=13.8677;RPPR=16.2459;RPR=0;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=20;SRP=3.21711;SRR=22;TYPE=snp;technology.ILLUMINA=1;ANN=C|upstream_gene_variant|MODIFIER|opdQ|PA14_24790|transcript|ABJ12275.1|protein_coding||c.-3663A>G|||||3663|,C|upstream_gene_variant|MODIFIER|PA14_24810|PA14_24810|transcript|ABJ12274.1|protein_coding||c.-2628A>G|||||2628|,C|upstream_gene_variant|MODIFIER|PA14_24820|PA14_24820|transcript|ABJ12273.1|protein_coding||c.-1696A>G|||||1696|,C|upstream_gene_variant|MODIFIER|PA14_24830|PA14_24830|transcript|ABJ12272.1|protein_coding||c.-1083A>G|||||1083|,C|upstream_gene_variant|MODIFIER|snr1|PA14_24860|transcript|ABJ12269.1|protein_coding||c.-292T>C|||||292|,C|upstream_gene_variant|MODIFIER|tRNA|EBG00001225078|transcript|EBT00001793505.1|protein_coding||c.-1756T>C|||||1756|WARNING_TRANSCRIPT_INCOMPLETE,C|upstream_gene_variant|MODIFIER|moaB2|PA14_24900|transcript|ABJ12266.1|protein_coding||c.-2999T>C|||||2999|,C|upstream_gene_variant|MODIFIER|moeA2|PA14_24910|transcript|ABJ12265.1|protein_coding||c.-3535T>C|||||3535|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_24840|PA14_24840|transcript|ABJ12271.1|protein_coding||c.*360T>C|||||360|,C|downstream_gene_variant|MODIFIER|PA14_24850|PA14_24850|transcript|ABJ12270.1|protein_coding||c.*75T>C|||||75|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_24870|PA14_24870|transcript|PA14_24870-1.1|protein_coding||c.*1756A>G|||||1756|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|PA14_24880|PA14_24880|transcript|ABJ12268.1|protein_coding||c.*1983A>G|||||1983|,C|downstream_gene_variant|MODIFIER|mobA|PA14_24890|transcript|ABJ12267.1|protein_coding||c.*2336A>G|||||2336|,C|downstream_gene_variant|MODIFIER|PA14_24920|PA14_24920|transcript|ABJ12264.1|protein_coding||c.*4781A>G|||||4781|,C|intergenic_region|MODIFIER|PA14_24850-snr1|PA14_24850-PA14_24860|intergenic_region|PA14_24850-PA14_24860|||n.2172336T>C|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:281:0:0:0,-25.6222 0:13:13,1:12:435:1:2:0,-39.2776 0:10:10,2:8:316:2:4:0,-28.4267 0:16:16,2:14:476:2:4:0,-42.7664 +Chromosome 2179546 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=42;DPB=42;DPRA=2.46667;EPP=11.6962;EPPR=3.9246;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=43.0692;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1272;RO=38;RPL=4;RPP=11.6962;RPPR=3.9246;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=30;SRP=30.668;SRR=8;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_24940|PA14_24940|transcript|ABJ12263.1|protein_coding|1/1|c.1222A>C|p.Asn408His|1222/1596|1222/1596|408/531||,C|upstream_gene_variant|MODIFIER|mobA|PA14_24890|transcript|ABJ12267.1|protein_coding||c.-4278T>G|||||4278|,C|upstream_gene_variant|MODIFIER|PA14_24920|PA14_24920|transcript|ABJ12264.1|protein_coding||c.-1398T>G|||||1398|,C|upstream_gene_variant|MODIFIER|glpD2|PA14_24950|transcript|ABJ12262.1|protein_coding||c.-575A>C|||||575|,C|upstream_gene_variant|MODIFIER|PA14_24960|PA14_24960|transcript|ABJ12261.1|protein_coding||c.-1981A>C|||||1981|,C|upstream_gene_variant|MODIFIER|yegS|PA14_24970|transcript|ABJ12260.1|protein_coding||c.-3615A>C|||||3615|,C|upstream_gene_variant|MODIFIER|PA14_24980|PA14_24980|transcript|ABJ12259.1|protein_coding||c.-4626A>C|||||4626|,C|downstream_gene_variant|MODIFIER|moaB2|PA14_24900|transcript|ABJ12266.1|protein_coding||c.*3672A>C|||||3672|,C|downstream_gene_variant|MODIFIER|moeA2|PA14_24910|transcript|ABJ12265.1|protein_coding||c.*2458A>C|||||2458|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:199:0:0:0,-18.2889 0:7:7,2:5:128:2:4:0,-11.3875 0:16:16,1:15:495:1:2:0,-44.6409 0:14:14,1:13:450:1:2:0,-40.6115 +Chromosome 2183998 . T C 4.35658E-8 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=1.71429;EPP=7.35324;EPPR=3.25157;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=19.0047;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=332;RO=9;RPL=0;RPP=7.35324;RPPR=3.25157;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=5.18177;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|yegS|PA14_24970|transcript|ABJ12260.1|protein_coding|1/1|c.838T>C|p.Ser280Pro|838/909|838/909|280/302||,C|upstream_gene_variant|MODIFIER|PA14_24980|PA14_24980|transcript|ABJ12259.1|protein_coding||c.-174T>C|||||174|,C|upstream_gene_variant|MODIFIER|uup|PA14_25020|transcript|ABJ12256.1|protein_coding||c.-3621T>C|||||3621|,C|downstream_gene_variant|MODIFIER|PA14_24940|PA14_24940|transcript|ABJ12263.1|protein_coding||c.*4078T>C|||||4078|,C|downstream_gene_variant|MODIFIER|glpD2|PA14_24950|transcript|ABJ12262.1|protein_coding||c.*2492T>C|||||2492|,C|downstream_gene_variant|MODIFIER|PA14_24960|PA14_24960|transcript|ABJ12261.1|protein_coding||c.*912T>C|||||912|,C|downstream_gene_variant|MODIFIER|PA14_24990|PA14_24990|transcript|ABJ12258.1|protein_coding||c.*1024A>G|||||1024|,C|downstream_gene_variant|MODIFIER|slt|PA14_25000|transcript|ABJ12257.1|protein_coding||c.*1467A>G|||||1467| GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:39:0:0:0,-3.89656 0:4:4,2:2:55:2:4:0,-4.84366 0:1:1,0:1:40:0:0:0,-3.99568 0:5:5,0:5:198:0:0:0,-18.1978 +Chromosome 2187765 . C A 2.79231E-10 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=6;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=16.0391;EPPR=18.6449;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=23.4675;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=77;QR=689;RO=20;RPL=0;RPP=16.0391;RPPR=6.91895;RPR=6;RUN=1;SAF=0;SAP=16.0391;SAR=6;SRF=5;SRP=13.8677;SRR=15;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|uup|PA14_25020|transcript|ABJ12256.1|protein_coding|1/1|c.147C>A|p.Val49Val|147/1923|147/1923|49/640||,A|upstream_gene_variant|MODIFIER|PA14_24990|PA14_24990|transcript|ABJ12258.1|protein_coding||c.-2357G>T|||||2357|,A|upstream_gene_variant|MODIFIER|slt|PA14_25000|transcript|ABJ12257.1|protein_coding||c.-372G>T|||||372|,A|upstream_gene_variant|MODIFIER|PA14_25030|PA14_25030|transcript|ABJ12255.1|protein_coding||c.-1927C>A|||||1927|,A|upstream_gene_variant|MODIFIER|PA14_25050|PA14_25050|transcript|ABJ12253.1|protein_coding||c.-3288C>A|||||3288|,A|upstream_gene_variant|MODIFIER|foaA|PA14_25080|transcript|ABJ12251.1|protein_coding||c.-4985C>A|||||4985|,A|downstream_gene_variant|MODIFIER|PA14_24960|PA14_24960|transcript|ABJ12261.1|protein_coding||c.*4679C>A|||||4679|,A|downstream_gene_variant|MODIFIER|yegS|PA14_24970|transcript|ABJ12260.1|protein_coding||c.*3696C>A|||||3696|,A|downstream_gene_variant|MODIFIER|PA14_24980|PA14_24980|transcript|ABJ12259.1|protein_coding||c.*2787C>A|||||2787|,A|downstream_gene_variant|MODIFIER|PA14_25040|PA14_25040|transcript|ABJ12254.1|protein_coding||c.*2643G>T|||||2643|,A|downstream_gene_variant|MODIFIER|PA14_25060|PA14_25060|transcript|ABJ12252.1|protein_coding||c.*3739G>T|||||3739| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,3:2:70:3:45:0,-2.44552 0:9:9,1:8:299:1:2:0,-27.0632 0:6:6,1:5:161:1:15:0,-13.3036 0:6:6,1:5:159:1:15:0,-13.1187 +Chromosome 2187799 . T G 3.66038E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=25;DPB=25;DPRA=0.470588;EPP=9.52472;EPPR=28.2783;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=20.8943;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=768;RO=22;RPL=0;RPP=9.52472;RPPR=9.32731;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=4;SRP=22.3561;SRR=18;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|uup|PA14_25020|transcript|ABJ12256.1|protein_coding|1/1|c.181T>G|p.Trp61Gly|181/1923|181/1923|61/640||,G|upstream_gene_variant|MODIFIER|PA14_24990|PA14_24990|transcript|ABJ12258.1|protein_coding||c.-2391A>C|||||2391|,G|upstream_gene_variant|MODIFIER|slt|PA14_25000|transcript|ABJ12257.1|protein_coding||c.-406A>C|||||406|,G|upstream_gene_variant|MODIFIER|PA14_25030|PA14_25030|transcript|ABJ12255.1|protein_coding||c.-1893T>G|||||1893|,G|upstream_gene_variant|MODIFIER|PA14_25050|PA14_25050|transcript|ABJ12253.1|protein_coding||c.-3254T>G|||||3254|,G|upstream_gene_variant|MODIFIER|foaA|PA14_25080|transcript|ABJ12251.1|protein_coding||c.-4951T>G|||||4951|,G|downstream_gene_variant|MODIFIER|PA14_24960|PA14_24960|transcript|ABJ12261.1|protein_coding||c.*4713T>G|||||4713|,G|downstream_gene_variant|MODIFIER|yegS|PA14_24970|transcript|ABJ12260.1|protein_coding||c.*3730T>G|||||3730|,G|downstream_gene_variant|MODIFIER|PA14_24980|PA14_24980|transcript|ABJ12259.1|protein_coding||c.*2821T>G|||||2821|,G|downstream_gene_variant|MODIFIER|PA14_25040|PA14_25040|transcript|ABJ12254.1|protein_coding||c.*2609A>C|||||2609|,G|downstream_gene_variant|MODIFIER|PA14_25060|PA14_25060|transcript|ABJ12252.1|protein_coding||c.*3705A>C|||||3705| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:231:0:0:0,-21.1566 0:11:11,0:11:377:0:0:0,-34.2453 0:4:4,1:3:118:1:2:0,-10.8027 0:4:4,2:2:42:2:4:0,-3.6059 +Chromosome 2188980 . C A 8.42303E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=38;DPB=38;DPRA=1.23529;EPP=11.6962;EPPR=7.09778;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=35.8235;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1088;RO=34;RPL=0;RPP=11.6962;RPPR=9.39698;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=13;SRP=7.09778;SRR=21;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|uup|PA14_25020|transcript|ABJ12256.1|protein_coding|1/1|c.1362C>A|p.Ser454Arg|1362/1923|1362/1923|454/640||,A|upstream_gene_variant|MODIFIER|PA14_24990|PA14_24990|transcript|ABJ12258.1|protein_coding||c.-3572G>T|||||3572|,A|upstream_gene_variant|MODIFIER|slt|PA14_25000|transcript|ABJ12257.1|protein_coding||c.-1587G>T|||||1587|,A|upstream_gene_variant|MODIFIER|PA14_25030|PA14_25030|transcript|ABJ12255.1|protein_coding||c.-712C>A|||||712|,A|upstream_gene_variant|MODIFIER|PA14_25050|PA14_25050|transcript|ABJ12253.1|protein_coding||c.-2073C>A|||||2073|,A|upstream_gene_variant|MODIFIER|foaA|PA14_25080|transcript|ABJ12251.1|protein_coding||c.-3770C>A|||||3770|,A|downstream_gene_variant|MODIFIER|yegS|PA14_24970|transcript|ABJ12260.1|protein_coding||c.*4911C>A|||||4911|,A|downstream_gene_variant|MODIFIER|PA14_24980|PA14_24980|transcript|ABJ12259.1|protein_coding||c.*4002C>A|||||4002|,A|downstream_gene_variant|MODIFIER|PA14_25040|PA14_25040|transcript|ABJ12254.1|protein_coding||c.*1428G>T|||||1428|,A|downstream_gene_variant|MODIFIER|PA14_25060|PA14_25060|transcript|ABJ12252.1|protein_coding||c.*2524G>T|||||2524| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:195:0:0:0,-17.9228 0:15:15,2:13:457:2:30:0,-38.5974 0:6:6,2:4:94:2:4:0,-8.30782 0:12:12,0:12:342:0:0:0,-31.0435 +Chromosome 2203862 . T G 1.15046E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=26;DPB=26;DPRA=1.33333;EPP=7.35324;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=36.7168;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=795;RO=24;RPL=2;RPP=7.35324;RPPR=8.80089;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=14;SRP=4.45795;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|PA14_25210|PA14_25210|transcript|ABJ12242.1|protein_coding|1/1|c.264T>G|p.Gly88Gly|264/738|264/738|88/245||,G|upstream_gene_variant|MODIFIER|PA14_25150|PA14_25150|transcript|ABJ12245.1|protein_coding||c.-3034A>C|||||3034|,G|upstream_gene_variant|MODIFIER|lexA|PA14_25160|transcript|ABJ12244.1|protein_coding||c.-2408A>C|||||2408|,G|upstream_gene_variant|MODIFIER|gapA|PA14_25250|transcript|ABJ12239.1|protein_coding||c.-4828T>G|||||4828|,G|downstream_gene_variant|MODIFIER|topA|PA14_25110|transcript|ABJ12248.1|protein_coding||c.*4605T>G|||||4605|,G|downstream_gene_variant|MODIFIER|PA14_25130|PA14_25130|transcript|ABJ12247.1|protein_coding||c.*3980T>G|||||3980|,G|downstream_gene_variant|MODIFIER|PA14_25140|PA14_25140|transcript|ABJ12246.1|protein_coding||c.*3541T>G|||||3541|,G|downstream_gene_variant|MODIFIER|psrA|PA14_25180|transcript|ABJ12243.1|protein_coding||c.*1475T>G|||||1475|,G|downstream_gene_variant|MODIFIER|nagZ|PA14_25195|transcript|ABJ15648.1|protein_coding||c.*275T>G|||||275|,G|downstream_gene_variant|MODIFIER|PA14_25220|PA14_25220|transcript|ABJ12241.1|protein_coding||c.*521A>C|||||521|,G|downstream_gene_variant|MODIFIER|mfd|PA14_25230|transcript|ABJ12240.1|protein_coding||c.*1161A>C|||||1161|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:110:0:0:0,-10.1695 0:6:6,0:6:201:0:0:0,-18.4133 0:8:8,2:6:196:2:4:0,-17.5775 0:8:8,0:8:288:0:0:0,-26.2649 +Chromosome 2219200 . A C 2.37362E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=6;CIGAR=1X;DP=40;DPB=40;DPRA=2.33333;EPP=16.0391;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=46.3442;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=1170;RO=34;RPL=6;RPP=16.0391;RPPR=12.2071;RPR=0;RUN=1;SAF=6;SAP=16.0391;SAR=0;SRF=12;SRP=9.39698;SRR=22;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|sth|PA14_25390|transcript|ABJ12230.1|protein_coding|1/1|c.88A>C|p.Lys30Gln|88/1395|88/1395|30/464||,C|upstream_gene_variant|MODIFIER|lolC|PA14_25430|transcript|ABJ12227.1|protein_coding||c.-3089A>C|||||3089|,C|upstream_gene_variant|MODIFIER|lolD|PA14_25440|transcript|ABJ12225.1|protein_coding||c.-4332A>C|||||4332|,C|downstream_gene_variant|MODIFIER|nqrB|PA14_25305|transcript|ABJ15647.1|protein_coding||c.*4803A>C|||||4803|,C|downstream_gene_variant|MODIFIER|nqrC|PA14_25320|transcript|ABJ12236.1|protein_coding||c.*4025A>C|||||4025|,C|downstream_gene_variant|MODIFIER|nqrD|PA14_25330|transcript|ABJ12235.1|protein_coding||c.*3354A>C|||||3354|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|nqrE|PA14_25340|transcript|ABJ12234.1|protein_coding||c.*2746A>C|||||2746|,C|downstream_gene_variant|MODIFIER|nqrF|PA14_25350|transcript|ABJ12233.1|protein_coding||c.*1511A>C|||||1511|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|apbE|PA14_25360|transcript|ABJ12232.1|protein_coding||c.*490A>C|||||490|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_25370|PA14_25370|transcript|ABJ12231.1|protein_coding||c.*266A>C|||||266|,C|downstream_gene_variant|MODIFIER|ugpQ|PA14_25400|transcript|ABJ12229.1|protein_coding||c.*1350T>G|||||1350|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_25410|PA14_25410|transcript|ABJ12228.1|protein_coding||c.*2069T>G|||||2069|,C|downstream_gene_variant|MODIFIER|PA14_25420|PA14_25420|transcript|ABJ12226.1|protein_coding||c.*2387T>G|||||2387| GT:DP:DPR:RO:QR:AO:QA:GL 0:12:12,3:9:324:3:6:0,-28.9363 0:14:14,1:13:455:1:2:0,-41.0683 0:9:9,2:7:259:2:4:0,-23.2821 0:5:5,0:5:132:0:0:0,-12.1335 +Chromosome 2227004 . G T 5.72854E-6 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=1.71429;EPP=3.0103;EPPR=3.25157;GTI=0;LEN=1;MEANALT=1;MQM=57;MQMR=60;NS=4;NUMALT=1;ODDS=13.5528;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=252;RO=9;RPL=1;RPP=3.0103;RPPR=14.8328;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=4;SRP=3.25157;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_25480|PA14_25480|transcript|ABJ12222.1|protein_coding|1/1|c.724G>T|p.Gly242Cys|724/2226|724/2226|242/741||,T|upstream_gene_variant|MODIFIER|PA14_25420|PA14_25420|transcript|ABJ12226.1|protein_coding||c.-4653C>A|||||4653|,T|upstream_gene_variant|MODIFIER|PA14_25470|PA14_25470|transcript|ABJ12223.1|protein_coding||c.-854C>A|||||854|,T|upstream_gene_variant|MODIFIER|PA14_25490|PA14_25490|transcript|ABJ12221.1|protein_coding||c.-1575G>T|||||1575|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|exbD|PA14_25500|transcript|ABJ12220.1|protein_coding||c.-2207G>T|||||2207|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|lpxK|PA14_25510|transcript|ABJ12219.1|protein_coding||c.-2647G>T|||||2647|,T|upstream_gene_variant|MODIFIER|PA14_25520|PA14_25520|transcript|ABJ12218.1|protein_coding||c.-3683G>T|||||3683|,T|upstream_gene_variant|MODIFIER|kdsB|PA14_25530|transcript|ABJ12217.1|protein_coding||c.-3868G>T|||||3868|,T|upstream_gene_variant|MODIFIER|ptpA|PA14_25540|transcript|ABJ12216.1|protein_coding||c.-4632G>T|||||4632|,T|downstream_gene_variant|MODIFIER|lolC|PA14_25430|transcript|ABJ12227.1|protein_coding||c.*3465G>T|||||3465|,T|downstream_gene_variant|MODIFIER|lolD|PA14_25440|transcript|ABJ12225.1|protein_coding||c.*2789G>T|||||2789|,T|downstream_gene_variant|MODIFIER|lolE|PA14_25450|transcript|ABJ12224.1|protein_coding||c.*1475G>T|||||1475|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:83:0:0:0,-7.74473 0:3:3,0:3:91:0:0:0,-8.48801 0:1:1,0:1:35:0:0:0,-3.49863 0:4:4,2:2:43:2:32:0,-1.04486 +Chromosome 2230919 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=38;DPB=38;DPRA=0.931034;EPP=7.35324;EPPR=4.56135;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=61.2221;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=1271;RO=35;RPL=2;RPP=7.35324;RPPR=3.07234;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=41.7866;SRR=30;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|kdsB|PA14_25530|transcript|ABJ12217.1|protein_coding|1/1|c.48T>C|p.Thr16Thr|48/765|48/765|16/254||,C|upstream_gene_variant|MODIFIER|PA14_25470|PA14_25470|transcript|ABJ12223.1|protein_coding||c.-4769A>G|||||4769|,C|upstream_gene_variant|MODIFIER|ptpA|PA14_25540|transcript|ABJ12216.1|protein_coding||c.-717T>C|||||717|,C|upstream_gene_variant|MODIFIER|murB|PA14_25550|transcript|ABJ12215.1|protein_coding||c.-1178T>C|||||1178|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_25480|PA14_25480|transcript|ABJ12222.1|protein_coding||c.*2413T>C|||||2413|,C|downstream_gene_variant|MODIFIER|PA14_25490|PA14_25490|transcript|ABJ12221.1|protein_coding||c.*1705T>C|||||1705|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|exbD|PA14_25500|transcript|ABJ12220.1|protein_coding||c.*1268T>C|||||1268|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|lpxK|PA14_25510|transcript|ABJ12219.1|protein_coding||c.*270T>C|||||270|,C|downstream_gene_variant|MODIFIER|PA14_25520|PA14_25520|transcript|ABJ12218.1|protein_coding||c.*47T>C|||||47|,C|downstream_gene_variant|MODIFIER|rne|PA14_25560|transcript|ABJ12214.1|protein_coding||c.*2355A>G|||||2355| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:255:0:0:0,-23.3002 0:11:11,0:10:357:0:0:0,-32.4116 0:9:9,2:7:259:2:30:0,-20.8107 0:11:11,0:11:400:0:0:0,-36.3401 +Chromosome 2240705 . C G 3.23954E-16 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=70;DPB=70;DPRA=0.842105;EPP=13.8677;EPPR=3.84548;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=107.5;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=2246;RO=65;RPL=0;RPP=13.8677;RPPR=3.84548;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=28;SRP=5.71629;SRR=37;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|PA14_25620|PA14_25620|transcript|ABJ12209.1|protein_coding|1/1|c.297C>G|p.Ala99Ala|297/537|297/537|99/178||,G|upstream_gene_variant|MODIFIER|rne|PA14_25560|transcript|ABJ12214.1|protein_coding||c.-4258G>C|||||4258|,G|upstream_gene_variant|MODIFIER|maf-1|PA14_25610|transcript|ABJ12210.1|protein_coding||c.-406G>C|||||406|,G|upstream_gene_variant|MODIFIER|rpmF|PA14_25630|transcript|ABJ12208.1|protein_coding||c.-254C>G|||||254|,G|upstream_gene_variant|MODIFIER|plsX|PA14_25640|transcript|ABJ12207.1|protein_coding||c.-470C>G|||||470|,G|upstream_gene_variant|MODIFIER|fabD|PA14_25650|transcript|ABJ12206.1|protein_coding||c.-1556C>G|||||1556|,G|upstream_gene_variant|MODIFIER|fabG|PA14_25660|transcript|ABJ12205.1|protein_coding||c.-2517C>G|||||2517|,G|upstream_gene_variant|MODIFIER|acpP|PA14_25670|transcript|ABJ12204.1|protein_coding||c.-3456C>G|||||3456|,G|upstream_gene_variant|MODIFIER|fabF1|PA14_25690|transcript|ABJ12203.1|protein_coding||c.-3821C>G|||||3821|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|rluC|PA14_25580|transcript|ABJ12213.1|protein_coding||c.*2725C>G|||||2725|,G|downstream_gene_variant|MODIFIER|PA14_25590|PA14_25590|transcript|ABJ12212.1|protein_coding||c.*2040C>G|||||2040|,G|downstream_gene_variant|MODIFIER|sppA|PA14_25600|transcript|ABJ12211.1|protein_coding||c.*1067C>G|||||1067| GT:DP:DPR:RO:QR:AO:QA:GL 0:18:18,2:16:573:2:24:0,-49.6114 0:17:17,0:17:560:0:0:0,-50.7017 0:21:21,0:21:705:0:0:0,-63.7375 0:14:14,3:11:408:3:6:0,-36.5061 +Chromosome 2276112 . G C 3.91085E-11 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=23;DPB=23;DPRA=1.6;EPP=7.35324;EPPR=15.5221;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=25.4334;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=789;RO=21;RPL=2;RPP=7.35324;RPPR=8.07707;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=17;SRP=20.4855;SRR=4;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|PA14_26050|PA14_26050|transcript|ABJ12176.1|protein_coding|1/1|c.534G>C|p.Ser178Ser|534/1458|534/1458|178/485||,C|upstream_gene_variant|MODIFIER|PA14_26020|PA14_26020|transcript|ABJ12177.1|protein_coding||c.-1034C>G|||||1034|,C|upstream_gene_variant|MODIFIER|PA14_26080|PA14_26080|transcript|ABJ12173.1|protein_coding||c.-2355G>C|||||2355|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_25990|PA14_25990|transcript|ABJ12180.1|protein_coding||c.*4657G>C|||||4657|,C|downstream_gene_variant|MODIFIER|PA14_26000|PA14_26000|transcript|ABJ12179.1|protein_coding||c.*3992G>C|||||3992|,C|downstream_gene_variant|MODIFIER|phaA|PA14_26010|transcript|ABJ12178.1|protein_coding||c.*2731G>C|||||2731|,C|downstream_gene_variant|MODIFIER|PA14_26060|PA14_26060|transcript|ABJ12175.1|protein_coding||c.*980C>G|||||980|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_26070|PA14_26070|transcript|ABJ12174.1|protein_coding||c.*1384C>G|||||1384|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_26090|PA14_26090|transcript|ABJ12172.1|protein_coding||c.*2575C>G|||||2575|,C|downstream_gene_variant|MODIFIER|PA14_26110|PA14_26110|transcript|ABJ12171.1|protein_coding||c.*3556C>G|||||3556|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|morB|PA14_26130|transcript|ABJ12170.1|protein_coding||c.*4800C>G|||||4800| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,2:6:234:2:17:0,-19.816 0:2:2,0:2:54:0:0:0,-5.12672 0:4:4,0:4:152:0:0:0,-14.0492 0:9:9,0:9:349:0:0:0,-31.7699 +Chromosome 2284705 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=33;DPB=33;DPRA=1.125;EPP=7.35324;EPPR=18.771;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=69.597;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1185;RO=31;RPL=2;RPP=7.35324;RPPR=3.08035;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=13;SRP=4.76149;SRR=18;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_26165|PA14_26165|transcript|ABJ15665.1|protein_coding|1/1|c.283A>C|p.Ser95Arg|283/1563|283/1563|95/520||,C|upstream_gene_variant|MODIFIER|PA14_26110|PA14_26110|transcript|ABJ12171.1|protein_coding||c.-3859T>G|||||3859|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|morB|PA14_26130|transcript|ABJ12170.1|protein_coding||c.-2684T>G|||||2684|,C|upstream_gene_variant|MODIFIER|PA14_26150|PA14_26150|transcript|ABJ12168.1|protein_coding||c.-1031T>G|||||1031|,C|upstream_gene_variant|MODIFIER|PA14_26200|PA14_26200|transcript|ABJ12165.1|protein_coding||c.-2792A>C|||||2792|,C|downstream_gene_variant|MODIFIER|PA14_26140|PA14_26140|transcript|ABJ12169.1|protein_coding||c.*1968A>C|||||1968|,C|downstream_gene_variant|MODIFIER|PA14_26160|PA14_26160|transcript|ABJ12167.1|protein_coding||c.*351A>C|||||351|,C|downstream_gene_variant|MODIFIER|PA14_26190|PA14_26190|transcript|ABJ12166.1|protein_coding||c.*1331T>G|||||1331|,C|downstream_gene_variant|MODIFIER|hisP|PA14_26210|transcript|ABJ12164.1|protein_coding||c.*2984T>G|||||2984|,C|downstream_gene_variant|MODIFIER|hisM|PA14_26220|transcript|ABJ12163.1|protein_coding||c.*3772T>G|||||3772|,C|downstream_gene_variant|MODIFIER|hisQ|PA14_26230|transcript|ABJ12162.1|protein_coding||c.*4482T>G|||||4482| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:304:0:0:0,-27.7169 0:7:7,0:7:272:0:0:0,-24.8465 0:9:9,0:9:345:0:0:0,-31.4068 0:9:9,2:7:264:2:4:0,-23.7374 +Chromosome 2307921 . C A 1.94372E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=38;DPB=38;DPRA=0.931034;EPP=7.35324;EPPR=3.56868;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=62.0295;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1319;RO=35;RPL=0;RPP=7.35324;RPPR=3.56868;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=28;SRP=30.3709;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=A|upstream_gene_variant|MODIFIER|PA14_26420|PA14_26420|transcript|ABJ12149.1|protein_coding||c.-4411G>T|||||4411|,A|upstream_gene_variant|MODIFIER|cobK|PA14_26460|transcript|ABJ12147.1|protein_coding||c.-2423G>T|||||2423|,A|upstream_gene_variant|MODIFIER|cbiD|PA14_26470|transcript|ABJ12146.1|protein_coding||c.-1326G>T|||||1326|,A|upstream_gene_variant|MODIFIER|cobL|PA14_26480|transcript|ABJ12145.1|protein_coding||c.-86G>T|||||86|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|PA14_26485|PA14_26485|transcript|ABJ15672.1|protein_coding||c.-251C>A|||||251|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|cobH|PA14_26500|transcript|ABJ12144.1|protein_coding||c.-1708C>A|||||1708|,A|upstream_gene_variant|MODIFIER|cobI|PA14_26510|transcript|ABJ12143.1|protein_coding||c.-2331C>A|||||2331|,A|upstream_gene_variant|MODIFIER|cobJ|PA14_26530|transcript|ABJ12142.1|protein_coding||c.-3076C>A|||||3076|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|PA14_26540|PA14_26540|transcript|ABJ12141.1|protein_coding||c.-4825C>A|||||4825|,A|downstream_gene_variant|MODIFIER|yebN|PA14_26450|transcript|ABJ12148.1|protein_coding||c.*3205C>A|||||3205|WARNING_TRANSCRIPT_NO_START_CODON,A|intergenic_region|MODIFIER|cobL-PA14_26485|PA14_26480-PA14_26485|intergenic_region|PA14_26480-PA14_26485|||n.2307921C>A|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:225:0:0:0,-20.6105 0:9:9,2:7:264:2:17:0,-22.5023 0:12:12,0:12:448:0:0:0,-40.6643 0:11:11,0:10:382:0:0:0,-34.3804 +Chromosome 2331727 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=47;DPB=47;DPRA=0.740741;EPP=9.52472;EPPR=26.8965;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=47.5015;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=45;QR=1552;RO=44;RPL=0;RPP=9.52472;RPPR=3.20771;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=14;SRP=15.6443;SRR=30;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|PA14_26700|PA14_26700|transcript|ABJ12128.1|protein_coding||c.-4692G>C|||||4692|,G|upstream_gene_variant|MODIFIER|mccB|PA14_26720|transcript|ABJ12127.1|protein_coding||c.-2959G>C|||||2959|,G|upstream_gene_variant|MODIFIER|PA14_26730|PA14_26730|transcript|ABJ12126.1|protein_coding||c.-2079G>C|||||2079|,G|upstream_gene_variant|MODIFIER|PA14_26750|PA14_26750|transcript|ABJ12125.1|protein_coding||c.-204G>C|||||204|,G|upstream_gene_variant|MODIFIER|PA14_26760|PA14_26760|transcript|ABJ12124.1|protein_coding||c.-77C>G|||||77|,G|upstream_gene_variant|MODIFIER|PA14_26810|PA14_26810|transcript|ABJ12121.1|protein_coding||c.-2261C>G|||||2261|,G|upstream_gene_variant|MODIFIER|PA14_26830|PA14_26830|transcript|ABJ12120.1|protein_coding||c.-3378C>G|||||3378|,G|upstream_gene_variant|MODIFIER|hpkR|PA14_26860|transcript|ABJ12118.1|protein_coding||c.-4860C>G|||||4860|,G|downstream_gene_variant|MODIFIER|PA14_26770|PA14_26770|transcript|ABJ12123.1|protein_coding||c.*674G>C|||||674|,G|downstream_gene_variant|MODIFIER|PA14_26780|PA14_26780|transcript|ABJ12122.1|protein_coding||c.*1671G>C|||||1671|,G|downstream_gene_variant|MODIFIER|PA14_26850|PA14_26850|transcript|ABJ12119.1|protein_coding||c.*4298G>C|||||4298|,G|intergenic_region|MODIFIER|PA14_26750-PA14_26760|PA14_26750-PA14_26760|intergenic_region|PA14_26750-PA14_26760|||n.2331727C>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,2:6:174:2:30:0,-13.0894 0:11:11,0:11:370:0:0:0,-33.6113 0:12:12,1:11:394:1:15:0,-34.2922 0:16:16,0:16:614:0:0:0,-55.597 +Chromosome 2338860 . A G 7.90781E-10 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=22;DPB=22;DPRA=0.882353;EPP=7.35324;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=22.4545;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=699;RO=20;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=9;SRP=3.44459;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_26880|PA14_26880|transcript|ABJ12116.1|protein_coding|1/1|c.674A>G|p.Glu225Gly|674/894|674/894|225/297||,G|upstream_gene_variant|MODIFIER|PA14_26850|PA14_26850|transcript|ABJ12119.1|protein_coding||c.-2320T>C|||||2320|,G|upstream_gene_variant|MODIFIER|PA14_26870|PA14_26870|transcript|ABJ12117.1|protein_coding||c.-719T>C|||||719|,G|upstream_gene_variant|MODIFIER|pyrF|PA14_26890|transcript|ABJ12115.1|protein_coding||c.-317A>G|||||317|,G|upstream_gene_variant|MODIFIER|moxR|PA14_26910|transcript|ABJ12114.1|protein_coding||c.-1264A>G|||||1264|,G|upstream_gene_variant|MODIFIER|PA14_26920|PA14_26920|transcript|ABJ12113.1|protein_coding||c.-2181A>G|||||2181|,G|upstream_gene_variant|MODIFIER|PA14_26930|PA14_26930|transcript|ABJ12112.1|protein_coding||c.-3134A>G|||||3134|,G|downstream_gene_variant|MODIFIER|PA14_26810|PA14_26810|transcript|ABJ12121.1|protein_coding||c.*3757A>G|||||3757|,G|downstream_gene_variant|MODIFIER|PA14_26830|PA14_26830|transcript|ABJ12120.1|protein_coding||c.*2844A>G|||||2844|,G|downstream_gene_variant|MODIFIER|hpkR|PA14_26860|transcript|ABJ12118.1|protein_coding||c.*1383A>G|||||1383| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:118:0:0:0,-11.0029 0:5:5,2:3:76:2:18:0,-5.37886 0:1:1,0:1:39:0:0:0,-3.89656 0:13:13,0:13:466:0:0:0,-42.2644 +Chromosome 2349057 . G T 3.86289E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=24;DPB=24;DPRA=0.789474;EPP=7.35324;EPPR=3.40511;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=30.0904;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=719;RO=22;RPL=2;RPP=7.35324;RPPR=22.3561;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=12;SRP=3.40511;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|PA14_27000|PA14_27000|transcript|ABJ12106.1|protein_coding|1/1|c.717C>A|p.Gly239Gly|717/1473|717/1473|239/490||,T|upstream_gene_variant|MODIFIER|PA14_26970|PA14_26970|transcript|ABJ12109.1|protein_coding||c.-1826C>A|||||1826|,T|upstream_gene_variant|MODIFIER|PA14_26980|PA14_26980|transcript|ABJ12108.1|protein_coding||c.-1328C>A|||||1328|,T|upstream_gene_variant|MODIFIER|PA14_26990|PA14_26990|transcript|ABJ12107.1|protein_coding||c.-882C>A|||||882|,T|upstream_gene_variant|MODIFIER|PA14_27050|PA14_27050|transcript|ABJ12104.1|protein_coding||c.-1905G>T|||||1905|,T|upstream_gene_variant|MODIFIER|PA14_27070|PA14_27070|transcript|ABJ12103.1|protein_coding||c.-3434G>T|||||3434|,T|downstream_gene_variant|MODIFIER|PA14_26940|PA14_26940|transcript|ABJ12111.1|protein_coding||c.*4290G>T|||||4290|,T|downstream_gene_variant|MODIFIER|PA14_26960|PA14_26960|transcript|ABJ12110.1|protein_coding||c.*3412G>T|||||3412|,T|downstream_gene_variant|MODIFIER|mttC|PA14_27020|transcript|ABJ12105.1|protein_coding||c.*855C>A|||||855|,T|downstream_gene_variant|MODIFIER|lipH|PA14_27090|transcript|ABJ12102.1|protein_coding||c.*4036C>A|||||4036|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:121:0:0:0,-11.1264 0:5:5,2:3:94:2:30:0,-5.91693 0:5:5,0:5:184:0:0:0,-16.912 0:9:9,0:9:320:0:0:0,-29.1325 +Chromosome 2371925 . C G 6.31357E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=29;DPB=29;DPRA=0.954545;EPP=7.35324;EPPR=12.7417;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=37.2704;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=856;RO=27;RPL=2;RPP=7.35324;RPPR=5.02092;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=13;SRP=3.09072;SRR=14;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_27350|PA14_27350|transcript|ABJ12082.1|protein_coding|1/1|c.9C>G|p.Ser3Arg|9/750|9/750|3/249||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_27250|PA14_27250|transcript|ABJ12088.1|protein_coding||c.-4835G>C|||||4835|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_27280|PA14_27280|transcript|ABJ12086.1|protein_coding||c.-3192G>C|||||3192|,G|upstream_gene_variant|MODIFIER|dhs|PA14_27330|transcript|ABJ12083.1|protein_coding||c.-184G>C|||||184|,G|upstream_gene_variant|MODIFIER|deaD|PA14_27370|transcript|ABJ12080.1|protein_coding||c.-1870C>G|||||1870|,G|downstream_gene_variant|MODIFIER|PA14_27270|PA14_27270|transcript|ABJ12087.1|protein_coding||c.*4048C>G|||||4048|,G|downstream_gene_variant|MODIFIER|PA14_27290|PA14_27290|transcript|ABJ12085.1|protein_coding||c.*2862C>G|||||2862|,G|downstream_gene_variant|MODIFIER|PA14_27310|PA14_27310|transcript|ABJ12084.1|protein_coding||c.*1571C>G|||||1571|,G|downstream_gene_variant|MODIFIER|PA14_27360|PA14_27360|transcript|ABJ12081.1|protein_coding||c.*768G>C|||||768|,G|downstream_gene_variant|MODIFIER|PA14_27390|PA14_27390|transcript|ABJ12079.1|protein_coding||c.*3940G>C|||||3940|,G|downstream_gene_variant|MODIFIER|PA14_27400|PA14_27400|transcript|ABJ12078.1|protein_coding||c.*4801G>C|||||4801| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:106:0:0:0,-9.88511 0:7:7,2:5:157:2:4:0,-14.0559 0:9:9,0:9:274:0:0:0,-24.9491 0:10:10,0:10:319:0:0:0,-29.0139 +Chromosome 2375615 . A G 2.58457E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=47;DPB=47;DPRA=0.516129;EPP=9.52472;EPPR=3.79993;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=61.1047;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1410;RO=44;RPL=0;RPP=9.52472;RPPR=12.6832;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=25;SRP=4.78696;SRR=19;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|dhs|PA14_27330|transcript|ABJ12083.1|protein_coding||c.-3874T>C|||||3874|,G|upstream_gene_variant|MODIFIER|PA14_27360|PA14_27360|transcript|ABJ12081.1|protein_coding||c.-2131T>C|||||2131|,G|downstream_gene_variant|MODIFIER|PA14_27350|PA14_27350|transcript|ABJ12082.1|protein_coding||c.*2949A>G|||||2949|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|deaD|PA14_27370|transcript|ABJ12080.1|protein_coding||c.*117A>G|||||117|,G|downstream_gene_variant|MODIFIER|PA14_27390|PA14_27390|transcript|ABJ12079.1|protein_coding||c.*250T>C|||||250|,G|downstream_gene_variant|MODIFIER|PA14_27400|PA14_27400|transcript|ABJ12078.1|protein_coding||c.*1111T>C|||||1111|,G|downstream_gene_variant|MODIFIER|trpC|PA14_27410|transcript|ABJ12077.1|protein_coding||c.*2119T>C|||||2119|,G|downstream_gene_variant|MODIFIER|trpB|PA14_27420|transcript|ABJ12076.1|protein_coding||c.*3555T>C|||||3555|,G|downstream_gene_variant|MODIFIER|PA14_27430|PA14_27430|transcript|ABJ12075.1|protein_coding||c.*4631T>C|||||4631|,G|intergenic_region|MODIFIER|deaD-PA14_27390|PA14_27370-PA14_27390|intergenic_region|PA14_27370-PA14_27390|||n.2375615A>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,2:6:204:2:4:0,-18.306 0:8:8,1:7:252:1:13:0,-21.7227 0:13:13,0:13:436:0:0:0,-39.546 0:18:18,0:18:518:0:0:0,-46.8741 +Chromosome 2403530 . A G 1.53315E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=32;DPB=32;DPRA=1.36364;EPP=3.0103;EPPR=7.64277;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=40.439;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=40;QR=1057;RO=30;RPL=1;RPP=3.0103;RPPR=17.1973;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=11;SRP=7.64277;SRR=19;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_27720|PA14_27720|transcript|ABJ12051.1|protein_coding|1/1|c.47T>C|p.Leu16Pro|47/381|47/381|16/126||,G|upstream_gene_variant|MODIFIER|PA14_27675|PA14_27675|transcript|ABJ15634.1|protein_coding||c.-3476T>C|||||3476|,G|upstream_gene_variant|MODIFIER|PA14_27680|PA14_27680|transcript|ABJ12055.1|protein_coding||c.-2793T>C|||||2793|,G|upstream_gene_variant|MODIFIER|fecI|PA14_27690|transcript|ABJ12054.1|protein_coding||c.-1858T>C|||||1858|,G|upstream_gene_variant|MODIFIER|PA14_27700|PA14_27700|transcript|ABJ12053.1|protein_coding||c.-1067T>C|||||1067|,G|upstream_gene_variant|MODIFIER|PA14_27710|PA14_27710|transcript|ABJ12052.1|protein_coding||c.-393T>C|||||393|,G|upstream_gene_variant|MODIFIER|PA14_27740|PA14_27740|transcript|ABJ12049.1|protein_coding||c.-2775A>G|||||2775|,G|upstream_gene_variant|MODIFIER|yliJ|PA14_27755|transcript|ABJ15676.1|protein_coding||c.-3561A>G|||||3561|,G|upstream_gene_variant|MODIFIER|yadG|PA14_27770|transcript|ABJ12048.1|protein_coding||c.-4257A>G|||||4257|,G|downstream_gene_variant|MODIFIER|yafH|PA14_27730|transcript|ABJ12050.1|protein_coding||c.*175T>C|||||175| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:115:0:0:0,-10.7245 0:10:10,2:8:276:2:40:0,-21.3744 0:8:8,0:8:268:0:0:0,-24.4371 0:11:11,0:11:398:0:0:0,-36.1524 +Chromosome 2414264 . T C 5.29721E-17 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=23;DPB=23;DPRA=1.92857;EPP=7.35324;EPPR=11.386;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=41.9301;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=40;QR=805;RO=21;RPL=1;RPP=3.0103;RPPR=3.94093;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=14;SRP=8.07707;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_27880|PA14_27880|transcript|ABJ12040.1|protein_coding|1/1|c.329A>G|p.Asp110Gly|329/582|329/582|110/193||,C|upstream_gene_variant|MODIFIER|PA14_27800|PA14_27800|transcript|ABJ12046.1|protein_coding||c.-3388A>G|||||3388|,C|upstream_gene_variant|MODIFIER|copR|PA14_27810|transcript|ABJ12045.1|protein_coding||c.-2711A>G|||||2711|,C|upstream_gene_variant|MODIFIER|PA14_27870|PA14_27870|transcript|ABJ12041.1|protein_coding||c.-327A>G|||||327|,C|upstream_gene_variant|MODIFIER|PA14_27900|PA14_27900|transcript|ABJ12038.1|protein_coding||c.-1202T>C|||||1202|,C|upstream_gene_variant|MODIFIER|vacJ|PA14_27920|transcript|ABJ12036.1|protein_coding||c.-2430T>C|||||2430|,C|upstream_gene_variant|MODIFIER|PA14_27940|PA14_27940|transcript|ABJ12034.1|protein_coding||c.-3737T>C|||||3737|,C|upstream_gene_variant|MODIFIER|PA14_27950|PA14_27950|transcript|ABJ12033.1|protein_coding||c.-4918T>C|||||4918|,C|downstream_gene_variant|MODIFIER|yadH|PA14_27780|transcript|ABJ12047.1|protein_coding||c.*4769T>C|||||4769|,C|downstream_gene_variant|MODIFIER|PA14_27830|PA14_27830|transcript|ABJ12044.1|protein_coding||c.*2394T>C|||||2394|,C|downstream_gene_variant|MODIFIER|PA14_27840|PA14_27840|transcript|ABJ12043.1|protein_coding||c.*1605T>C|||||1605|,C|downstream_gene_variant|MODIFIER|folE|PA14_27850|transcript|ABJ12042.1|protein_coding||c.*657T>C|||||657|,C|downstream_gene_variant|MODIFIER|PA14_27890|PA14_27890|transcript|ABJ12039.1|protein_coding||c.*325A>G|||||325|,C|downstream_gene_variant|MODIFIER|PA14_27910|PA14_27910|transcript|ABJ12037.1|protein_coding||c.*1923A>G|||||1923|,C|downstream_gene_variant|MODIFIER|PA14_27930|PA14_27930|transcript|ABJ12035.1|protein_coding||c.*3192A>G|||||3192| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:142:0:0:0,-13.126 0:4:4,0:4:157:0:0:0,-14.5088 0:6:6,0:6:238:0:0:0,-21.7945 0:9:9,2:7:268:2:40:0,-20.6837 +Chromosome 2439770 . A G 5.2134E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=6;CIGAR=1X;DP=74;DPB=74;DPRA=0;EPP=16.0391;EPPR=15.7837;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=100.116;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=50;QR=2383;RO=68;RPL=0;RPP=16.0391;RPPR=31.7504;RPR=6;RUN=1;SAF=0;SAP=16.0391;SAR=6;SRF=49;SRP=31.7504;SRR=19;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|ordL|PA14_28180|transcript|ABJ12012.1|protein_coding|1/1|c.791T>C|p.Leu264Pro|791/1284|791/1284|264/427||,G|upstream_gene_variant|MODIFIER|PA14_28110|PA14_28110|transcript|ABJ12018.1|protein_coding||c.-4510T>C|||||4510|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_28120|PA14_28120|transcript|ABJ12017.1|protein_coding||c.-3691T>C|||||3691|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_28130|PA14_28130|transcript|ABJ12016.1|protein_coding||c.-3350T>C|||||3350|,G|upstream_gene_variant|MODIFIER|PA14_28190|PA14_28190|transcript|PA14_28190-1.1|protein_coding||c.-974A>G|||||974|WARNING_TRANSCRIPT_INCOMPLETE,G|upstream_gene_variant|MODIFIER|PA14_28200|PA14_28200|transcript|ABJ12011.1|protein_coding||c.-1242A>G|||||1242|,G|upstream_gene_variant|MODIFIER|PA14_28210|PA14_28210|transcript|ABJ12010.1|protein_coding||c.-1684A>G|||||1684|,G|upstream_gene_variant|MODIFIER|PA14_28220|PA14_28220|transcript|ABJ12009.1|protein_coding||c.-2470A>G|||||2470|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_28240|PA14_28240|transcript|ABJ12007.1|protein_coding||c.-3342A>G|||||3342|,G|upstream_gene_variant|MODIFIER|PA14_28260|PA14_28260|transcript|ABJ12005.1|protein_coding||c.-4746A>G|||||4746|,G|downstream_gene_variant|MODIFIER|PA14_28140|PA14_28140|transcript|ABJ12015.1|protein_coding||c.*2544A>G|||||2544|,G|downstream_gene_variant|MODIFIER|PA14_28150|PA14_28150|transcript|ABJ12014.1|protein_coding||c.*1582A>G|||||1582|,G|downstream_gene_variant|MODIFIER|yfdC|PA14_28170|transcript|ABJ12013.1|protein_coding||c.*544A>G|||||544|,G|downstream_gene_variant|MODIFIER|tRNA|EBG00001225035|transcript|EBT00001793471.1|protein_coding||c.*974T>C|||||974|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,G|downstream_gene_variant|MODIFIER|PA14_28230|PA14_28230|transcript|ABJ12008.1|protein_coding||c.*3011T>C|||||3011|,G|downstream_gene_variant|MODIFIER|PA14_28250|PA14_28250|transcript|ABJ12006.1|protein_coding||c.*3600T>C|||||3600| GT:DP:DPR:RO:QR:AO:QA:GL 0:21:21,1:20:688:1:2:0,-62.0157 0:19:19,1:18:660:1:2:0,-59.5155 0:15:15,3:12:419:3:44:0,-33.9292 0:19:19,1:18:616:1:2:0,-55.5349 +Chromosome 2455513 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=33;DPB=33;DPRA=0.666667;EPP=7.35324;EPPR=23.254;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=45.1035;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1129;RO=31;RPL=0;RPP=7.35324;RPPR=8.68415;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=15;SRP=3.08035;SRR=16;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_28420|PA14_28420|transcript|ABJ11990.1|protein_coding|1/1|c.166G>C|p.Glu56Gln|166/888|166/888|56/295||,G|upstream_gene_variant|MODIFIER|PA14_28390|PA14_28390|transcript|ABJ11993.1|protein_coding||c.-3001G>C|||||3001|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|oprQ|PA14_28400|transcript|ABJ11992.1|protein_coding||c.-1612G>C|||||1612|,G|upstream_gene_variant|MODIFIER|PA14_28430|PA14_28430|transcript|ABJ11989.1|protein_coding||c.-268C>G|||||268|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_28440|PA14_28440|transcript|ABJ11988.1|protein_coding||c.-850C>G|||||850|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_28470|PA14_28470|transcript|ABJ11985.1|protein_coding||c.-2564C>G|||||2564|,G|upstream_gene_variant|MODIFIER|PA14_28510|PA14_28510|transcript|ABJ11982.1|protein_coding||c.-3776C>G|||||3776|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_28520|PA14_28520|transcript|ABJ11981.1|protein_coding||c.-4267C>G|||||4267|,G|downstream_gene_variant|MODIFIER|PA14_28360|PA14_28360|transcript|ABJ11996.1|protein_coding||c.*4599C>G|||||4599|,G|downstream_gene_variant|MODIFIER|PA14_28370|PA14_28370|transcript|ABJ11995.1|protein_coding||c.*3916C>G|||||3916|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_28380|PA14_28380|transcript|ABJ11994.1|protein_coding||c.*3460C>G|||||3460|,G|downstream_gene_variant|MODIFIER|PA14_28410|PA14_28410|transcript|ABJ11991.1|protein_coding||c.*933C>G|||||933|,G|downstream_gene_variant|MODIFIER|eco|PA14_28450|transcript|ABJ11987.1|protein_coding||c.*1336G>C|||||1336|,G|downstream_gene_variant|MODIFIER|PA14_28460|PA14_28460|transcript|ABJ11986.1|protein_coding||c.*2155G>C|||||2155|,G|downstream_gene_variant|MODIFIER|PA14_28490|PA14_28490|transcript|ABJ11984.1|protein_coding||c.*2827G>C|||||2827|,G|downstream_gene_variant|MODIFIER|PA14_28500|PA14_28500|transcript|ABJ11983.1|protein_coding||c.*3267G>C|||||3267|,G|downstream_gene_variant|MODIFIER|PA14_28530|PA14_28530|transcript|ABJ11980.1|protein_coding||c.*4682G>C|||||4682| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,2:4:148:2:4:0,-13.3016 0:6:6,0:6:193:0:0:0,-17.6778 0:9:9,0:9:337:0:0:0,-30.6795 0:12:12,0:12:451:0:0:0,-40.9332 +Chromosome 2458482 . T C 2.52433E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=26;DPB=26;DPRA=0.62963;EPP=3.44459;EPPR=3.1137;GTI=0;LEN=1;MEANALT=1;MQM=56.8;MQMR=59.7143;NS=4;NUMALT=1;ODDS=21.339;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=576;RO=21;RPL=3;RPP=3.44459;RPPR=26.2761;RPR=2;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=12;SRP=3.94093;SRR=9;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_28490|PA14_28490|transcript|ABJ11984.1|protein_coding|1/1|c.188A>G|p.Glu63Gly|188/330|188/330|63/109||,C|upstream_gene_variant|MODIFIER|oprQ|PA14_28400|transcript|ABJ11992.1|protein_coding||c.-4581A>G|||||4581|,C|upstream_gene_variant|MODIFIER|PA14_28420|PA14_28420|transcript|ABJ11990.1|protein_coding||c.-2804A>G|||||2804|,C|upstream_gene_variant|MODIFIER|eco|PA14_28450|transcript|ABJ11987.1|protein_coding||c.-1163A>G|||||1163|,C|upstream_gene_variant|MODIFIER|PA14_28460|PA14_28460|transcript|ABJ11986.1|protein_coding||c.-584A>G|||||584|,C|upstream_gene_variant|MODIFIER|PA14_28510|PA14_28510|transcript|ABJ11982.1|protein_coding||c.-807T>C|||||807|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_28520|PA14_28520|transcript|ABJ11981.1|protein_coding||c.-1298T>C|||||1298|,C|upstream_gene_variant|MODIFIER|PA14_28540|PA14_28540|transcript|ABJ11979.1|protein_coding||c.-2835T>C|||||2835|,C|upstream_gene_variant|MODIFIER|PA14_28580|PA14_28580|transcript|ABJ11976.1|protein_coding||c.-4746T>C|||||4746|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|mapB|PA14_28590|transcript|ABJ11975.1|protein_coding||c.-4964T>C|||||4964|,C|downstream_gene_variant|MODIFIER|PA14_28410|PA14_28410|transcript|ABJ11991.1|protein_coding||c.*3902T>C|||||3902|,C|downstream_gene_variant|MODIFIER|PA14_28430|PA14_28430|transcript|ABJ11989.1|protein_coding||c.*2258T>C|||||2258|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_28440|PA14_28440|transcript|ABJ11988.1|protein_coding||c.*1685T>C|||||1685|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_28470|PA14_28470|transcript|ABJ11985.1|protein_coding||c.*208T>C|||||208|,C|downstream_gene_variant|MODIFIER|PA14_28500|PA14_28500|transcript|ABJ11983.1|protein_coding||c.*298A>G|||||298|,C|downstream_gene_variant|MODIFIER|PA14_28530|PA14_28530|transcript|ABJ11980.1|protein_coding||c.*1713A>G|||||1713|,C|downstream_gene_variant|MODIFIER|PA14_28560|PA14_28560|transcript|ABJ11978.1|protein_coding||c.*3339A>G|||||3339|,C|downstream_gene_variant|MODIFIER|endA|PA14_28570|transcript|ABJ11977.1|protein_coding||c.*3876A>G|||||3876| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,2:3:42:2:4:0,-3.53997 0:8:8,1:7:221:1:2:0,-19.9914 0:4:4,2:2:57:2:4:0,-5.03438 0:9:9,0:9:256:0:0:0,-23.3093 +Chromosome 2461525 . T G 2.16432E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=21;DPB=21;DPRA=1.2;EPP=7.35324;EPPR=3.12459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=37.7634;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=680;RO=19;RPL=0;RPP=7.35324;RPPR=3.12459;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=13;SRP=8.61041;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_28540|PA14_28540|transcript|ABJ11979.1|protein_coding|1/1|c.209T>G|p.Met70Arg|209/234|209/234|70/77||,G|upstream_gene_variant|MODIFIER|eco|PA14_28450|transcript|ABJ11987.1|protein_coding||c.-4206A>C|||||4206|,G|upstream_gene_variant|MODIFIER|PA14_28460|PA14_28460|transcript|ABJ11986.1|protein_coding||c.-3627A>C|||||3627|,G|upstream_gene_variant|MODIFIER|PA14_28490|PA14_28490|transcript|ABJ11984.1|protein_coding||c.-2856A>C|||||2856|,G|upstream_gene_variant|MODIFIER|PA14_28500|PA14_28500|transcript|ABJ11983.1|protein_coding||c.-2371A>C|||||2371|,G|upstream_gene_variant|MODIFIER|PA14_28530|PA14_28530|transcript|ABJ11980.1|protein_coding||c.-431A>C|||||431|,G|upstream_gene_variant|MODIFIER|PA14_28580|PA14_28580|transcript|ABJ11976.1|protein_coding||c.-1703T>G|||||1703|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|mapB|PA14_28590|transcript|ABJ11975.1|protein_coding||c.-1921T>G|||||1921|,G|upstream_gene_variant|MODIFIER|PA14_28600|PA14_28600|transcript|ABJ11974.1|protein_coding||c.-3189T>G|||||3189|,G|upstream_gene_variant|MODIFIER|PA14_28630|PA14_28630|transcript|ABJ11971.1|protein_coding||c.-4581T>G|||||4581|,G|downstream_gene_variant|MODIFIER|PA14_28440|PA14_28440|transcript|ABJ11988.1|protein_coding||c.*4728T>G|||||4728|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_28470|PA14_28470|transcript|ABJ11985.1|protein_coding||c.*3251T>G|||||3251|,G|downstream_gene_variant|MODIFIER|PA14_28510|PA14_28510|transcript|ABJ11982.1|protein_coding||c.*1793T>G|||||1793|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_28520|PA14_28520|transcript|ABJ11981.1|protein_coding||c.*1320T>G|||||1320|,G|downstream_gene_variant|MODIFIER|PA14_28560|PA14_28560|transcript|ABJ11978.1|protein_coding||c.*296A>C|||||296|,G|downstream_gene_variant|MODIFIER|endA|PA14_28570|transcript|ABJ11977.1|protein_coding||c.*833A>C|||||833|,G|downstream_gene_variant|MODIFIER|PA14_28610|PA14_28610|transcript|ABJ11973.1|protein_coding||c.*3802A>C|||||3802|,G|downstream_gene_variant|MODIFIER|PA14_28620|PA14_28620|transcript|ABJ11972.1|protein_coding||c.*4063A>C|||||4063| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:185:0:0:0,-17.0083 0:4:4,0:4:153:0:0:0,-14.1409 0:6:6,0:6:233:0:0:0,-21.3383 0:6:6,2:4:109:2:4:0,-9.6953 +Chromosome 2461786 . C G 2.22777E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=37;DPB=37;DPRA=0.85;EPP=9.52472;EPPR=12.2071;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=37.0322;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=988;RO=34;RPL=0;RPP=9.52472;RPPR=3.26577;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=7;SRP=28.557;SRR=27;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|eco|PA14_28450|transcript|ABJ11987.1|protein_coding||c.-4467G>C|||||4467|,G|upstream_gene_variant|MODIFIER|PA14_28460|PA14_28460|transcript|ABJ11986.1|protein_coding||c.-3888G>C|||||3888|,G|upstream_gene_variant|MODIFIER|PA14_28490|PA14_28490|transcript|ABJ11984.1|protein_coding||c.-3117G>C|||||3117|,G|upstream_gene_variant|MODIFIER|PA14_28500|PA14_28500|transcript|ABJ11983.1|protein_coding||c.-2632G>C|||||2632|,G|upstream_gene_variant|MODIFIER|PA14_28530|PA14_28530|transcript|ABJ11980.1|protein_coding||c.-692G>C|||||692|,G|upstream_gene_variant|MODIFIER|PA14_28580|PA14_28580|transcript|ABJ11976.1|protein_coding||c.-1442C>G|||||1442|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|mapB|PA14_28590|transcript|ABJ11975.1|protein_coding||c.-1660C>G|||||1660|,G|upstream_gene_variant|MODIFIER|PA14_28600|PA14_28600|transcript|ABJ11974.1|protein_coding||c.-2928C>G|||||2928|,G|upstream_gene_variant|MODIFIER|PA14_28630|PA14_28630|transcript|ABJ11971.1|protein_coding||c.-4320C>G|||||4320|,G|downstream_gene_variant|MODIFIER|PA14_28440|PA14_28440|transcript|ABJ11988.1|protein_coding||c.*4989C>G|||||4989|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_28470|PA14_28470|transcript|ABJ11985.1|protein_coding||c.*3512C>G|||||3512|,G|downstream_gene_variant|MODIFIER|PA14_28510|PA14_28510|transcript|ABJ11982.1|protein_coding||c.*2054C>G|||||2054|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_28520|PA14_28520|transcript|ABJ11981.1|protein_coding||c.*1581C>G|||||1581|,G|downstream_gene_variant|MODIFIER|PA14_28540|PA14_28540|transcript|ABJ11979.1|protein_coding||c.*236C>G|||||236|,G|downstream_gene_variant|MODIFIER|PA14_28560|PA14_28560|transcript|ABJ11978.1|protein_coding||c.*35G>C|||||35|,G|downstream_gene_variant|MODIFIER|endA|PA14_28570|transcript|ABJ11977.1|protein_coding||c.*572G>C|||||572|,G|downstream_gene_variant|MODIFIER|PA14_28610|PA14_28610|transcript|ABJ11973.1|protein_coding||c.*3541G>C|||||3541|,G|downstream_gene_variant|MODIFIER|PA14_28620|PA14_28620|transcript|ABJ11972.1|protein_coding||c.*3802G>C|||||3802|,G|intergenic_region|MODIFIER|PA14_28540-PA14_28560|PA14_28540-PA14_28560|intergenic_region|PA14_28540-PA14_28560|||n.2461786C>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:11:11,0:11:292:0:0:0,-26.534 0:9:9,0:9:264:0:0:0,-24.0459 0:11:11,1:10:324:1:15:0,-27.9718 0:6:6,2:4:108:2:4:0,-9.60778 +Chromosome 2463495 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=53;DPB=53;DPRA=1.40909;EPP=6.91895;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=87.5349;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=1582;RO=48;RPL=4;RPP=6.91895;RPPR=4.6389;RPR=1;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=27;SRP=4.6389;SRR=21;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|mapB|PA14_28590|transcript|ABJ11975.1|protein_coding|1/1|c.50T>C|p.Leu17Pro|50/783|50/783|17/260||,C|upstream_gene_variant|MODIFIER|PA14_28490|PA14_28490|transcript|ABJ11984.1|protein_coding||c.-4826A>G|||||4826|,C|upstream_gene_variant|MODIFIER|PA14_28500|PA14_28500|transcript|ABJ11983.1|protein_coding||c.-4341A>G|||||4341|,C|upstream_gene_variant|MODIFIER|PA14_28530|PA14_28530|transcript|ABJ11980.1|protein_coding||c.-2401A>G|||||2401|,C|upstream_gene_variant|MODIFIER|PA14_28560|PA14_28560|transcript|ABJ11978.1|protein_coding||c.-1156A>G|||||1156|,C|upstream_gene_variant|MODIFIER|endA|PA14_28570|transcript|ABJ11977.1|protein_coding||c.-424A>G|||||424|,C|upstream_gene_variant|MODIFIER|PA14_28600|PA14_28600|transcript|ABJ11974.1|protein_coding||c.-1219T>C|||||1219|,C|upstream_gene_variant|MODIFIER|PA14_28630|PA14_28630|transcript|ABJ11971.1|protein_coding||c.-2611T>C|||||2611|,C|upstream_gene_variant|MODIFIER|thrS|PA14_28650|transcript|ABJ11970.1|protein_coding||c.-3724T>C|||||3724|,C|downstream_gene_variant|MODIFIER|PA14_28510|PA14_28510|transcript|ABJ11982.1|protein_coding||c.*3763T>C|||||3763|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_28520|PA14_28520|transcript|ABJ11981.1|protein_coding||c.*3290T>C|||||3290|,C|downstream_gene_variant|MODIFIER|PA14_28540|PA14_28540|transcript|ABJ11979.1|protein_coding||c.*1945T>C|||||1945|,C|downstream_gene_variant|MODIFIER|PA14_28580|PA14_28580|transcript|ABJ11976.1|protein_coding||c.*46T>C|||||46|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_28610|PA14_28610|transcript|ABJ11973.1|protein_coding||c.*1832A>G|||||1832|,C|downstream_gene_variant|MODIFIER|PA14_28620|PA14_28620|transcript|ABJ11972.1|protein_coding||c.*2093A>G|||||2093|,C|downstream_gene_variant|MODIFIER|P13|EBG00001225032|transcript|EBT00001793341.1|sRNA||n.*3482A>G|||||3482| GT:DP:DPR:RO:QR:AO:QA:GL 0:17:17,4:13:409:4:57:0,-31.834 0:14:14,1:13:435:1:14:0,-38.062 0:11:11,0:11:400:0:0:0,-36.3396 0:11:11,0:11:338:0:0:0,-30.7093 +Chromosome 2472396 . A G 7.09852E-12 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=17;DPB=17;DPRA=3.375;EPP=7.35324;EPPR=10.1038;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=58.5333;NS=4;NUMALT=1;ODDS=27.8228;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=53;QR=533;RO=15;RPL=0;RPP=7.35324;RPPR=3.15506;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=7;SRP=3.15506;SRR=8;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|pheT|PA14_28710|transcript|ABJ11965.1|protein_coding|1/1|c.920A>G|p.Gln307Arg|920/2379|920/2379|307/792||,G|upstream_gene_variant|MODIFIER|himA|PA14_28720|transcript|ABJ11964.1|protein_coding||c.-1463A>G|||||1463|,G|upstream_gene_variant|MODIFIER|PA14_28730|PA14_28730|transcript|ABJ11963.1|protein_coding||c.-1746A>G|||||1746|,G|upstream_gene_variant|MODIFIER|PA14_28740|PA14_28740|transcript|PA14_28740-1.1|protein_coding||c.-2192A>G|||||2192|WARNING_TRANSCRIPT_INCOMPLETE,G|upstream_gene_variant|MODIFIER|PA14_28770|PA14_28770|transcript|ABJ11960.1|protein_coding||c.-4275A>G|||||4275|,G|downstream_gene_variant|MODIFIER|thrS|PA14_28650|transcript|ABJ11970.1|protein_coding||c.*3255A>G|||||3255|,G|downstream_gene_variant|MODIFIER|infC|PA14_28660|transcript|ABJ11969.1|protein_coding||c.*2704A>G|||||2704|,G|downstream_gene_variant|MODIFIER|rpmI|PA14_28670|transcript|ABJ11968.1|protein_coding||c.*2448A>G|||||2448|,G|downstream_gene_variant|MODIFIER|rplT|PA14_28680|transcript|ABJ11967.1|protein_coding||c.*2068A>G|||||2068|,G|downstream_gene_variant|MODIFIER|pheS|PA14_28690|transcript|ABJ11966.1|protein_coding||c.*954A>G|||||954|,G|downstream_gene_variant|MODIFIER|tRNA|EBG00001225160|transcript|EBT00001793388.1|protein_coding||c.*2192T>C|||||2192|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|PA14_28750|PA14_28750|transcript|ABJ11962.1|protein_coding||c.*2429T>C|||||2429|,G|downstream_gene_variant|MODIFIER|PA14_28760|PA14_28760|transcript|ABJ11961.1|protein_coding||c.*3078T>C|||||3078| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:75:0:0:0,-7.1201 0:4:4,0:4:148:0:0:0,-13.6805 0:2:2,0:2:72:0:0:0,-6.83637 0:9:9,2:7:238:2:53:0,-16.7138 +Chromosome 2503923 . T C 6.06519E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=28;DPB=28;DPRA=1.33333;EPP=9.52472;EPPR=13.5202;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=42.3279;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=69;QR=875;RO=25;RPL=3;RPP=9.52472;RPPR=3.09716;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=14;SRP=3.79203;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_28950|PA14_28950|transcript|ABJ11945.1|protein_coding|1/1|c.245A>G|p.Glu82Gly|245/393|245/393|82/130||,C|upstream_gene_variant|MODIFIER|PA14_28895|PA14_28895|transcript|ABJ15701.1|protein_coding||c.-3688A>G|||||3688|,C|upstream_gene_variant|MODIFIER|PA14_28910|PA14_28910|transcript|ABJ11949.1|protein_coding||c.-3035A>G|||||3035|,C|upstream_gene_variant|MODIFIER|PA14_28920|PA14_28920|transcript|ABJ11948.1|protein_coding||c.-1150A>G|||||1150|,C|upstream_gene_variant|MODIFIER|PA14_28930|PA14_28930|transcript|ABJ11947.1|protein_coding||c.-531A>G|||||531|,C|upstream_gene_variant|MODIFIER|PA14_28940|PA14_28940|transcript|ABJ11946.1|protein_coding||c.-178A>G|||||178|,C|upstream_gene_variant|MODIFIER|PA14_28970|PA14_28970|transcript|ABJ11943.1|protein_coding||c.-924T>C|||||924|,C|upstream_gene_variant|MODIFIER|PA14_28980|PA14_28980|transcript|ABJ11942.1|protein_coding||c.-1451T>C|||||1451|,C|upstream_gene_variant|MODIFIER|PA14_28990|PA14_28990|transcript|ABJ11941.1|protein_coding||c.-2830T>C|||||2830|,C|downstream_gene_variant|MODIFIER|PA14_28960|PA14_28960|transcript|ABJ11944.1|protein_coding||c.*276A>G|||||276|,C|downstream_gene_variant|MODIFIER|PA14_29000|PA14_29000|transcript|ABJ11940.1|protein_coding||c.*3628A>G|||||3628|,C|downstream_gene_variant|MODIFIER|PA14_29010|PA14_29010|transcript|ABJ11939.1|protein_coding||c.*4414A>G|||||4414| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:188:0:0:0,-17.2837 0:8:8,1:7:250:1:15:0,-21.3375 0:7:7,0:7:253:0:0:0,-23.1144 0:8:8,2:6:184:2:54:0,-11.7348 +Chromosome 2504896 . G T 8.43857E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=38;DPB=38;DPRA=0.933333;EPP=11.6962;EPPR=3.26577;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=40.1449;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=47;QR=1111;RO=34;RPL=4;RPP=11.6962;RPPR=3.0103;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=11;SRP=12.2071;SRR=23;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_28970|PA14_28970|transcript|ABJ11943.1|protein_coding|1/1|c.50G>T|p.Cys17Phe|50/540|50/540|17/179||,T|upstream_gene_variant|MODIFIER|PA14_28895|PA14_28895|transcript|ABJ15701.1|protein_coding||c.-4661C>A|||||4661|,T|upstream_gene_variant|MODIFIER|PA14_28910|PA14_28910|transcript|ABJ11949.1|protein_coding||c.-4008C>A|||||4008|,T|upstream_gene_variant|MODIFIER|PA14_28920|PA14_28920|transcript|ABJ11948.1|protein_coding||c.-2123C>A|||||2123|,T|upstream_gene_variant|MODIFIER|PA14_28930|PA14_28930|transcript|ABJ11947.1|protein_coding||c.-1504C>A|||||1504|,T|upstream_gene_variant|MODIFIER|PA14_28940|PA14_28940|transcript|ABJ11946.1|protein_coding||c.-1151C>A|||||1151|,T|upstream_gene_variant|MODIFIER|PA14_28950|PA14_28950|transcript|ABJ11945.1|protein_coding||c.-729C>A|||||729|,T|upstream_gene_variant|MODIFIER|PA14_28960|PA14_28960|transcript|ABJ11944.1|protein_coding||c.-218C>A|||||218|,T|upstream_gene_variant|MODIFIER|PA14_28980|PA14_28980|transcript|ABJ11942.1|protein_coding||c.-478G>T|||||478|,T|upstream_gene_variant|MODIFIER|PA14_28990|PA14_28990|transcript|ABJ11941.1|protein_coding||c.-1857G>T|||||1857|,T|upstream_gene_variant|MODIFIER|cpo|PA14_29020|transcript|ABJ11938.1|protein_coding||c.-4162G>T|||||4162|,T|downstream_gene_variant|MODIFIER|PA14_29000|PA14_29000|transcript|ABJ11940.1|protein_coding||c.*2655C>A|||||2655|,T|downstream_gene_variant|MODIFIER|PA14_29010|PA14_29010|transcript|ABJ11939.1|protein_coding||c.*3441C>A|||||3441| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,0:10:381:0:0:0,-34.641 0:12:12,1:11:335:1:15:0,-28.9326 0:9:9,2:7:262:2:17:0,-22.3225 0:7:7,1:6:133:1:15:0,-10.6833 +Chromosome 2521123 . T G 6.87844E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=36;DPB=36;DPRA=0.724138;EPP=7.35324;EPPR=23.7032;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=32.4035;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=839;RO=34;RPL=0;RPP=7.35324;RPPR=19.3602;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=53.0819;SRR=31;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_29130|PA14_29130|transcript|ABJ11928.1|protein_coding|1/1|c.725T>G|p.Val242Gly|725/846|725/846|242/281||,G|upstream_gene_variant|MODIFIER|potF4|PA14_29090|transcript|ABJ11932.1|protein_coding||c.-3939A>C|||||3939|,G|upstream_gene_variant|MODIFIER|PA14_29100|PA14_29100|transcript|ABJ11931.1|protein_coding||c.-3126A>C|||||3126|,G|upstream_gene_variant|MODIFIER|cysK|PA14_29110|transcript|ABJ11930.1|protein_coding||c.-2093A>C|||||2093|,G|upstream_gene_variant|MODIFIER|PA14_29150|PA14_29150|transcript|ABJ11927.1|protein_coding||c.-186T>G|||||186|,G|upstream_gene_variant|MODIFIER|PA14_29160|PA14_29160|transcript|ABJ11926.1|protein_coding||c.-630T>G|||||630|,G|upstream_gene_variant|MODIFIER|PA14_29180|PA14_29180|transcript|ABJ11925.1|protein_coding||c.-1925T>G|||||1925|,G|downstream_gene_variant|MODIFIER|PA14_29120|PA14_29120|transcript|ABJ11929.1|protein_coding||c.*887T>G|||||887|,G|downstream_gene_variant|MODIFIER|PA14_29190|PA14_29190|transcript|ABJ11924.1|protein_coding||c.*3226A>C|||||3226|,G|downstream_gene_variant|MODIFIER|PA14_29200|PA14_29200|transcript|ABJ11923.1|protein_coding||c.*3469A>C|||||3469|,G|downstream_gene_variant|MODIFIER|tetV|PA14_29210|transcript|ABJ11922.1|protein_coding||c.*4092A>C|||||4092| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:103:0:0:0,-9.47526 0:13:13,0:13:361:0:0:0,-32.751 0:7:7,2:5:94:2:4:0,-8.26301 0:11:11,0:11:281:0:0:0,-25.5303 +Chromosome 2532358 . C A 6.40421E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=51;DPB=51;DPRA=1.04;EPP=11.6962;EPPR=6.75262;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=86.659;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=72;QR=1541;RO=47;RPL=0;RPP=11.6962;RPPR=8.60069;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=13;SRP=23.3852;SRR=34;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|PA14_29260|PA14_29260|transcript|ABJ11917.1|protein_coding|1/1|c.562C>A|p.Gln188Lys|562/894|562/894|188/297||,A|upstream_gene_variant|MODIFIER|opdB|PA14_29220|transcript|ABJ11921.1|protein_coding||c.-4244G>T|||||4244|,A|upstream_gene_variant|MODIFIER|PA14_29230|PA14_29230|transcript|ABJ11920.1|protein_coding||c.-2357G>T|||||2357|,A|upstream_gene_variant|MODIFIER|yaiW|PA14_29270|transcript|ABJ11916.1|protein_coding||c.-446C>A|||||446|,A|upstream_gene_variant|MODIFIER|trxA|PA14_29280|transcript|ABJ11915.1|protein_coding||c.-1630C>A|||||1630|,A|upstream_gene_variant|MODIFIER|PA14_29320|PA14_29320|transcript|ABJ11912.1|protein_coding||c.-3447C>A|||||3447|,A|downstream_gene_variant|MODIFIER|PA14_29240|PA14_29240|transcript|ABJ11919.1|protein_coding||c.*1069C>A|||||1069|,A|downstream_gene_variant|MODIFIER|PA14_29250|PA14_29250|transcript|ABJ11918.1|protein_coding||c.*731C>A|||||731|,A|downstream_gene_variant|MODIFIER|PA14_29290|PA14_29290|transcript|ABJ11914.1|protein_coding||c.*1984G>T|||||1984|,A|downstream_gene_variant|MODIFIER|PA14_29300|PA14_29300|transcript|ABJ11913.1|protein_coding||c.*2654G>T|||||2654|,A|downstream_gene_variant|MODIFIER|PA14_29330|PA14_29330|transcript|ABJ11911.1|protein_coding||c.*4687G>T|||||4687| GT:DP:DPR:RO:QR:AO:QA:GL 0:15:15,3:12:402:3:57:0,-31.1737 0:14:14,0:14:443:0:0:0,-40.1647 0:11:11,1:10:337:1:15:0,-29.1481 0:11:11,0:11:359:0:0:0,-32.6208 +Chromosome 2541658 . C G 2.48639E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=38;DPB=38;DPRA=1.11111;EPP=9.52472;EPPR=3.56868;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=57.6611;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=1154;RO=35;RPL=1;RPP=3.73412;RPPR=4.56135;RPR=2;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=14;SRP=6.05036;SRR=21;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|pfeA|PA14_29350|transcript|ABJ11909.1|protein_coding|1/1|c.13G>C|p.Ala5Pro|13/2241|13/2241|5/746||,G|upstream_gene_variant|MODIFIER|PA14_29330|PA14_29330|transcript|ABJ11911.1|protein_coding||c.-3621G>C|||||3621|,G|upstream_gene_variant|MODIFIER|PA14_29340|PA14_29340|transcript|ABJ11910.1|protein_coding||c.-2248G>C|||||2248|,G|upstream_gene_variant|MODIFIER|PA14_29390|PA14_29390|transcript|ABJ11907.1|protein_coding||c.-2425C>G|||||2425|,G|upstream_gene_variant|MODIFIER|rhs|PA14_29400|transcript|ABJ11906.1|protein_coding||c.-4544C>G|||||4544|,G|downstream_gene_variant|MODIFIER|PA14_29320|PA14_29320|transcript|ABJ11912.1|protein_coding||c.*4648C>G|||||4648|,G|downstream_gene_variant|MODIFIER|pfeS|PA14_29360|transcript|ABJ11908.1|protein_coding||c.*111G>C|||||111| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:198:0:0:0,-18.1364 0:10:10,2:8:292:2:4:0,-26.2474 0:10:10,1:9:301:1:2:0,-27.2082 0:12:12,0:12:363:0:0:0,-32.9514 +Chromosome 2562347 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=52;DPB=52;DPRA=1.83333;EPP=11.6962;EPPR=4.6389;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=47.994;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=109;QR=1571;RO=48;RPL=4;RPP=11.6962;RPPR=3.73412;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=25;SRP=3.19126;SRR=23;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_29550|PA14_29550|transcript|ABJ11893.1|protein_coding|1/1|c.370G>T|p.Ala124Ser|370/1080|370/1080|124/359||,T|upstream_gene_variant|MODIFIER|PA14_29560|PA14_29560|transcript|ABJ11892.1|protein_coding||c.-754G>T|||||754|,T|upstream_gene_variant|MODIFIER|PA14_29570|PA14_29570|transcript|ABJ11891.1|protein_coding||c.-1740G>T|||||1740|,T|upstream_gene_variant|MODIFIER|PA14_29575|PA14_29575|transcript|ABJ15664.1|protein_coding||c.-2567G>T|||||2567|,T|downstream_gene_variant|MODIFIER|hplR|PA14_29490|transcript|ABJ11899.1|protein_coding||c.*3430G>T|||||3430|,T|downstream_gene_variant|MODIFIER|hplS|PA14_29500|transcript|ABJ11898.1|protein_coding||c.*2238G>T|||||2238|,T|downstream_gene_variant|MODIFIER|hplT|PA14_29510|transcript|ABJ11897.1|protein_coding||c.*1750G>T|||||1750|,T|downstream_gene_variant|MODIFIER|hplU|PA14_29520|transcript|ABJ11896.1|protein_coding||c.*1371G>T|||||1371|,T|downstream_gene_variant|MODIFIER|hplV|PA14_29530|transcript|ABJ11895.1|protein_coding||c.*946G>T|||||946|,T|downstream_gene_variant|MODIFIER|hplW|PA14_29540|transcript|ABJ11894.1|protein_coding||c.*359G>T|||||359|,T|downstream_gene_variant|MODIFIER|PA14_29590|PA14_29590|transcript|ABJ11890.1|protein_coding||c.*2960C>A|||||2960|,T|downstream_gene_variant|MODIFIER|ptpS|PA14_29600|transcript|ABJ11889.1|protein_coding||c.*3621C>A|||||3621|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|norR|PA14_29620|transcript|ABJ11888.1|protein_coding||c.*4078C>A|||||4078| GT:DP:DPR:RO:QR:AO:QA:GL 0:16:16,1:15:482:1:27:0,-40.9816 0:8:8,0:8:228:0:0:0,-20.7941 0:7:7,2:5:182:2:51:0,-11.888 0:21:21,1:20:679:1:31:0,-58.3164 +Chromosome 2566242 . T G 7.33769E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=36;DPB=36;DPRA=1;EPP=13.8677;EPPR=18.771;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=54.1377;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=63;QR=1042;RO=31;RPL=0;RPP=13.8677;RPPR=3.08035;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=10;SRP=11.486;SRR=21;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|ptpS|PA14_29600|transcript|ABJ11889.1|protein_coding|1/1|c.83A>C|p.His28Pro|83/357|83/357|28/118||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_29590|PA14_29590|transcript|ABJ11890.1|protein_coding||c.-582A>C|||||582|,G|upstream_gene_variant|MODIFIER|fhp|PA14_29640|transcript|ABJ11887.1|protein_coding||c.-1891T>G|||||1891|,G|upstream_gene_variant|MODIFIER|PA14_29650|PA14_29650|transcript|ABJ11886.1|protein_coding||c.-3126T>G|||||3126|,G|upstream_gene_variant|MODIFIER|PA14_29660|PA14_29660|transcript|ABJ11885.1|protein_coding||c.-3370T>G|||||3370|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|hplV|PA14_29530|transcript|ABJ11895.1|protein_coding||c.*4841T>G|||||4841|,G|downstream_gene_variant|MODIFIER|hplW|PA14_29540|transcript|ABJ11894.1|protein_coding||c.*4254T>G|||||4254|,G|downstream_gene_variant|MODIFIER|PA14_29550|PA14_29550|transcript|ABJ11893.1|protein_coding||c.*3185T>G|||||3185|,G|downstream_gene_variant|MODIFIER|PA14_29560|PA14_29560|transcript|ABJ11892.1|protein_coding||c.*2155T>G|||||2155|,G|downstream_gene_variant|MODIFIER|PA14_29570|PA14_29570|transcript|ABJ11891.1|protein_coding||c.*1571T>G|||||1571|,G|downstream_gene_variant|MODIFIER|PA14_29575|PA14_29575|transcript|ABJ15664.1|protein_coding||c.*1011T>G|||||1011|,G|downstream_gene_variant|MODIFIER|norR|PA14_29620|transcript|ABJ11888.1|protein_coding||c.*183A>C|||||183|,G|downstream_gene_variant|MODIFIER|PA14_29680|PA14_29680|transcript|ABJ11884.1|protein_coding||c.*4814A>C|||||4814| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,1:8:258:1:15:0,-22.0253 0:9:9,0:9:335:0:0:0,-30.4993 0:9:9,1:8:218:1:15:0,-18.3773 0:9:9,3:6:231:3:33:0,-18.0779 +Chromosome 2569544 . G T 1.96114E-16 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=35;DPB=35;DPRA=1.2;EPP=7.35324;EPPR=3.0761;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=48.5296;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=45;QR=1120;RO=33;RPL=2;RPP=7.35324;RPPR=3.0761;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=18;SRP=3.60252;SRR=15;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_29650|PA14_29650|transcript|ABJ11886.1|protein_coding|1/1|c.177G>T|p.Leu59Phe|177/258|177/258|59/85||,T|upstream_gene_variant|MODIFIER|PA14_29590|PA14_29590|transcript|ABJ11890.1|protein_coding||c.-3884C>A|||||3884|,T|upstream_gene_variant|MODIFIER|ptpS|PA14_29600|transcript|ABJ11889.1|protein_coding||c.-3220C>A|||||3220|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|norR|PA14_29620|transcript|ABJ11888.1|protein_coding||c.-1566C>A|||||1566|,T|upstream_gene_variant|MODIFIER|PA14_29660|PA14_29660|transcript|ABJ11885.1|protein_coding||c.-68G>T|||||68|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|PA14_29710|PA14_29710|transcript|ABJ11882.1|protein_coding||c.-3729G>T|||||3729|,T|upstream_gene_variant|MODIFIER|PA14_29720|PA14_29720|transcript|ABJ11881.1|protein_coding||c.-4037G>T|||||4037|,T|upstream_gene_variant|MODIFIER|PA14_29730|PA14_29730|transcript|ABJ11880.1|protein_coding||c.-4351G>T|||||4351|,T|downstream_gene_variant|MODIFIER|PA14_29570|PA14_29570|transcript|ABJ11891.1|protein_coding||c.*4873G>T|||||4873|,T|downstream_gene_variant|MODIFIER|PA14_29575|PA14_29575|transcript|ABJ15664.1|protein_coding||c.*4313G>T|||||4313|,T|downstream_gene_variant|MODIFIER|fhp|PA14_29640|transcript|ABJ11887.1|protein_coding||c.*230G>T|||||230|,T|downstream_gene_variant|MODIFIER|PA14_29680|PA14_29680|transcript|ABJ11884.1|protein_coding||c.*1512C>A|||||1512|,T|downstream_gene_variant|MODIFIER|PA14_29690|PA14_29690|transcript|ABJ11883.1|protein_coding||c.*2432C>A|||||2432| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:152:0:0:0,-14.0492 0:10:10,2:8:241:2:45:0,-17.7015 0:12:12,0:12:420:0:0:0,-38.1267 0:9:9,0:9:307:0:0:0,-27.9479 +Chromosome 2577866 . A C 1.56703E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=43;DPB=43;DPRA=0.583333;EPP=7.35324;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=52.2843;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=29;QR=1451;RO=41;RPL=2;RPP=7.35324;RPPR=14.9269;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=22;SRP=3.48696;SRR=19;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_29760|PA14_29760|transcript|ABJ11877.1|protein_coding|1/1|c.583T>G|p.Cys195Gly|583/2145|583/2145|195/714||,C|upstream_gene_variant|MODIFIER|PA14_29690|PA14_29690|transcript|ABJ11883.1|protein_coding||c.-4808T>G|||||4808|,C|upstream_gene_variant|MODIFIER|PA14_29770|PA14_29770|transcript|ABJ11876.1|protein_coding||c.-841A>C|||||841|,C|upstream_gene_variant|MODIFIER|PA14_29800|PA14_29800|transcript|ABJ11875.1|protein_coding||c.-2280A>C|||||2280|,C|upstream_gene_variant|MODIFIER|PA14_29820|PA14_29820|transcript|ABJ11874.1|protein_coding||c.-4125A>C|||||4125|,C|downstream_gene_variant|MODIFIER|PA14_29710|PA14_29710|transcript|ABJ11882.1|protein_coding||c.*4285A>C|||||4285|,C|downstream_gene_variant|MODIFIER|PA14_29720|PA14_29720|transcript|ABJ11881.1|protein_coding||c.*3971A>C|||||3971|,C|downstream_gene_variant|MODIFIER|PA14_29730|PA14_29730|transcript|ABJ11880.1|protein_coding||c.*3300A>C|||||3300|,C|downstream_gene_variant|MODIFIER|PA14_29740|PA14_29740|transcript|ABJ11879.1|protein_coding||c.*1966A>C|||||1966|,C|downstream_gene_variant|MODIFIER|PA14_29750|PA14_29750|transcript|ABJ11878.1|protein_coding||c.*1567A>C|||||1567| GT:DP:DPR:RO:QR:AO:QA:GL 0:14:14,0:14:484:0:0:0,-43.8766 0:10:10,0:10:357:0:0:0,-32.4548 0:12:12,0:12:417:0:0:0,-37.8448 0:7:7,2:5:193:2:29:0,-14.9857 +Chromosome 2596651 . A G 1.85355E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=9;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=14.8328;EPPR=30.3709;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=52.4821;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=964;RO=35;RPL=0;RPP=22.5536;RPPR=35.8306;RPR=9;RUN=1;SAF=1;SAP=14.8328;SAR=8;SRF=9;SRP=20.9405;SRR=26;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|nuoD|PA14_29990|transcript|ABJ11862.1|protein_coding|1/1|c.1295T>C|p.Leu432Pro|1295/1782|1295/1782|432/593||,G|upstream_gene_variant|MODIFIER|nuoG|PA14_29940|transcript|ABJ11865.1|protein_coding||c.-2467T>C|||||2467|,G|upstream_gene_variant|MODIFIER|nuoF|PA14_29970|transcript|ABJ11864.1|protein_coding||c.-986T>C|||||986|,G|upstream_gene_variant|MODIFIER|nuoE|PA14_29980|transcript|ABJ11863.1|protein_coding||c.-489T>C|||||489|,G|downstream_gene_variant|MODIFIER|nuoB|PA14_30010|transcript|ABJ11861.1|protein_coding||c.*1375T>C|||||1375|,G|downstream_gene_variant|MODIFIER|nuoA|PA14_30020|transcript|ABJ11860.1|protein_coding||c.*2063T>C|||||2063|,G|downstream_gene_variant|MODIFIER|PA14_30030|PA14_30030|transcript|ABJ11859.1|protein_coding||c.*3076T>C|||||3076|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_30040|PA14_30040|transcript|ABJ11858.1|protein_coding||c.*3709T>C|||||3709|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:12:12,3:9:275:3:26:0,-22.6177 0:11:11,1:10:251:1:2:0,-22.6259 0:12:12,4:8:184:4:8:0,-16.0427 0:9:9,1:8:254:1:40:0,-19.1651 +Chromosome 2606092 . G T 1.45341E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=16;DPB=16;DPRA=3;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=21.9992;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=448;RO=14;RPL=2;RPP=7.35324;RPPR=3.0103;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=10;SRP=8.59409;SRR=4;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_30080|PA14_30080|transcript|ABJ11855.1|protein_coding|1/1|c.95C>A|p.Ala32Glu|95/621|95/621|32/206||,T|upstream_gene_variant|MODIFIER|PA14_30040|PA14_30040|transcript|ABJ11858.1|protein_coding||c.-3714C>A|||||3714|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|aceA|PA14_30050|transcript|ABJ11857.1|protein_coding||c.-1939C>A|||||1939|,T|upstream_gene_variant|MODIFIER|PA14_30070|PA14_30070|transcript|ABJ11856.1|protein_coding||c.-523C>A|||||523|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|PA14_30090|PA14_30090|transcript|ABJ11854.1|protein_coding||c.*101C>A|||||101|,T|downstream_gene_variant|MODIFIER|PA14_30100|PA14_30100|transcript|ABJ11853.1|protein_coding||c.*519C>A|||||519|,T|downstream_gene_variant|MODIFIER|purB|PA14_30110|transcript|ABJ11852.1|protein_coding||c.*1748C>A|||||1748|,T|downstream_gene_variant|MODIFIER|PA14_30130|PA14_30130|transcript|ABJ11851.1|protein_coding||c.*3194C>A|||||3194|,T|downstream_gene_variant|MODIFIER|PA14_30140|PA14_30140|transcript|ABJ11850.1|protein_coding||c.*4087C>A|||||4087|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|trmU|PA14_30150|transcript|ABJ11849.1|protein_coding||c.*4704C>A|||||4704| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:52:0:0:0,-4.93835 0:2:2,0:2:55:0:0:0,-5.22088 0:8:8,2:6:221:2:32:0,-17.205 0:4:4,0:4:120:0:0:0,-11.0896 +Chromosome 2611555 . G C 1.20564E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=13.8677;EPPR=4.25114;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=49.5168;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=910;RO=28;RPL=5;RPP=13.8677;RPPR=3.32051;RPR=0;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=15;SRP=3.32051;SRR=13;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|trmU|PA14_30150|transcript|ABJ11849.1|protein_coding|1/1|c.369C>G|p.Leu123Leu|369/1128|369/1128|123/375||,C|upstream_gene_variant|MODIFIER|PA14_30090|PA14_30090|transcript|ABJ11854.1|protein_coding||c.-4937C>G|||||4937|,C|upstream_gene_variant|MODIFIER|PA14_30100|PA14_30100|transcript|ABJ11853.1|protein_coding||c.-3775C>G|||||3775|,C|upstream_gene_variant|MODIFIER|purB|PA14_30110|transcript|ABJ11852.1|protein_coding||c.-2345C>G|||||2345|,C|upstream_gene_variant|MODIFIER|PA14_30130|PA14_30130|transcript|ABJ11851.1|protein_coding||c.-1379C>G|||||1379|,C|upstream_gene_variant|MODIFIER|PA14_30140|PA14_30140|transcript|ABJ11850.1|protein_coding||c.-756C>G|||||756|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|icd|PA14_30190|transcript|ABJ11846.1|protein_coding||c.-3553G>C|||||3553|,C|downstream_gene_variant|MODIFIER|mutT|PA14_30160|transcript|ABJ11848.1|protein_coding||c.*412C>G|||||412|,C|downstream_gene_variant|MODIFIER|idh|PA14_30180|transcript|ABJ11847.1|protein_coding||c.*969C>G|||||969|,C|downstream_gene_variant|MODIFIER|cspD|PA14_30200|transcript|ABJ11845.1|protein_coding||c.*4883C>G|||||4883| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,1:6:169:1:2:0,-15.2801 0:9:9,2:7:264:2:4:0,-23.74 0:9:9,1:8:220:1:2:0,-19.8637 0:8:8,1:7:257:1:2:0,-23.2817 +Chromosome 2617933 . A G 9.22162E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=27;DPB=27;DPRA=1.76471;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=40.2743;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=696;RO=25;RPL=0;RPP=7.35324;RPPR=3.79203;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=9;SRP=7.26639;SRR=16;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|clpA|PA14_30230|transcript|ABJ11843.1|protein_coding|1/1|c.602A>G|p.Glu201Gly|602/2277|602/2277|201/758||,G|upstream_gene_variant|MODIFIER|idh|PA14_30180|transcript|ABJ11847.1|protein_coding||c.-3184T>C|||||3184|,G|upstream_gene_variant|MODIFIER|cspD|PA14_30200|transcript|ABJ11845.1|protein_coding||c.-1223T>C|||||1223|,G|upstream_gene_variant|MODIFIER|ftsK|PA14_30290|transcript|ABJ11838.1|protein_coding||c.-4738A>G|||||4738|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|icd|PA14_30190|transcript|ABJ11846.1|protein_coding||c.*1569A>G|||||1569|,G|downstream_gene_variant|MODIFIER|clpS|PA14_30210|transcript|ABJ11844.1|protein_coding||c.*629A>G|||||629|,G|downstream_gene_variant|MODIFIER|infA|PA14_30240|transcript|ABJ11842.1|protein_coding||c.*1757T>C|||||1757|,G|downstream_gene_variant|MODIFIER|ate1|PA14_30260|transcript|ABJ11841.1|protein_coding||c.*2080T>C|||||2080|,G|downstream_gene_variant|MODIFIER|aat|PA14_30270|transcript|ABJ11840.1|protein_coding||c.*2842T>C|||||2842|,G|downstream_gene_variant|MODIFIER|trxB1|PA14_30280|transcript|ABJ11839.1|protein_coding||c.*3560T>C|||||3560| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,2:8:223:2:27:0,-17.7713 0:5:5,0:5:128:0:0:0,-11.7716 0:5:5,0:5:148:0:0:0,-13.6112 0:7:7,0:7:197:0:0:0,-17.9965 +Chromosome 2623845 . T G 7.7982E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=43;DPB=43;DPRA=0.307692;EPP=7.35324;EPPR=9.41879;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=35.5985;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1475;RO=41;RPL=0;RPP=7.35324;RPPR=3.48696;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=25;SRP=7.30028;SRR=16;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|ftsK|PA14_30290|transcript|ABJ11838.1|protein_coding|1/1|c.1175T>G|p.Leu392Trp|1175/2436|1175/2436|392/811||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|infA|PA14_30240|transcript|ABJ11842.1|protein_coding||c.-3937A>C|||||3937|,G|upstream_gene_variant|MODIFIER|ate1|PA14_30260|transcript|ABJ11841.1|protein_coding||c.-3125A>C|||||3125|,G|upstream_gene_variant|MODIFIER|aat|PA14_30270|transcript|ABJ11840.1|protein_coding||c.-2390A>C|||||2390|,G|upstream_gene_variant|MODIFIER|trxB1|PA14_30280|transcript|ABJ11839.1|protein_coding||c.-1402A>C|||||1402|,G|upstream_gene_variant|MODIFIER|lolA|PA14_30310|transcript|ABJ11837.1|protein_coding||c.-1287T>G|||||1287|,G|upstream_gene_variant|MODIFIER|ycaJ|PA14_30320|transcript|ABJ11836.1|protein_coding||c.-1923T>G|||||1923|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|serS|PA14_30330|transcript|ABJ11835.1|protein_coding||c.-3370T>G|||||3370|,G|upstream_gene_variant|MODIFIER|cysG|PA14_30340|transcript|ABJ11834.1|protein_coding||c.-4652T>G|||||4652|,G|downstream_gene_variant|MODIFIER|clpA|PA14_30230|transcript|ABJ11843.1|protein_coding||c.*4237T>G|||||4237| GT:DP:DPR:RO:QR:AO:QA:GL 0:13:13,0:13:430:0:0:0,-38.9974 0:12:12,0:12:457:0:0:0,-41.4755 0:14:14,0:14:508:0:0:0,-46.0448 0:4:4,2:2:80:2:4:0,-7.21179 +Chromosome 2626839 . T C 2.09744E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=35;DPB=35;DPRA=1.1875;EPP=9.52472;EPPR=48.8827;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=37.6608;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=41;QR=724;RO=32;RPL=3;RPP=9.52472;RPPR=20.3821;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=27;SRP=35.8538;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|ycaJ|PA14_30320|transcript|ABJ11836.1|protein_coding|1/1|c.1072T>C|p.Ser358Pro|1072/1326|1072/1326|358/441||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|trxB1|PA14_30280|transcript|ABJ11839.1|protein_coding||c.-4396A>G|||||4396|,C|upstream_gene_variant|MODIFIER|serS|PA14_30330|transcript|ABJ11835.1|protein_coding||c.-376T>C|||||376|,C|upstream_gene_variant|MODIFIER|cysG|PA14_30340|transcript|ABJ11834.1|protein_coding||c.-1658T>C|||||1658|,C|downstream_gene_variant|MODIFIER|ftsK|PA14_30290|transcript|ABJ11838.1|protein_coding||c.*1733T>C|||||1733|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|lolA|PA14_30310|transcript|ABJ11837.1|protein_coding||c.*1081T>C|||||1081|,C|downstream_gene_variant|MODIFIER|yqjG|PA14_30350|transcript|ABJ11833.1|protein_coding||c.*3060A>G|||||3060|,C|downstream_gene_variant|MODIFIER|PA14_30360|PA14_30360|transcript|ABJ11832.1|protein_coding||c.*4122A>G|||||4122| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:137:0:0:0,-12.5232 0:9:9,0:9:192:0:0:0,-17.4907 0:8:8,2:6:160:2:28:0,-12.0024 0:11:11,1:10:235:1:13:0,-20.0801 +Chromosome 2645249 . T G 3.80688E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=27;DPB=27;DPRA=1.26316;EPP=7.35324;EPPR=7.26639;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=32.5403;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=762;RO=25;RPL=0;RPP=7.35324;RPPR=10.0459;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=13;SRP=3.09716;SRR=12;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|ssuA|PA14_30550|transcript|ABJ11817.1|protein_coding|1/1|c.767T>G|p.Leu256Arg|767/960|767/960|256/319||,G|upstream_gene_variant|MODIFIER|PA14_30580|PA14_30580|transcript|ABJ11814.1|protein_coding||c.-2298T>G|||||2298|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_30590|PA14_30590|transcript|ABJ11813.1|protein_coding||c.-3224T>G|||||3224|,G|downstream_gene_variant|MODIFIER|PA14_30490|PA14_30490|transcript|ABJ11821.1|protein_coding||c.*4140T>G|||||4140|,G|downstream_gene_variant|MODIFIER|PA14_30500|PA14_30500|transcript|ABJ11820.1|protein_coding||c.*2984T>G|||||2984|,G|downstream_gene_variant|MODIFIER|PA14_30520|PA14_30520|transcript|ABJ11819.1|protein_coding||c.*1890T>G|||||1890|,G|downstream_gene_variant|MODIFIER|PA14_30540|PA14_30540|transcript|ABJ11818.1|protein_coding||c.*922T>G|||||922|,G|downstream_gene_variant|MODIFIER|PA14_30560|PA14_30560|transcript|ABJ11816.1|protein_coding||c.*260A>C|||||260|,G|downstream_gene_variant|MODIFIER|potF|PA14_30570|transcript|ABJ11815.1|protein_coding||c.*1042A>C|||||1042| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:92:0:0:0,-8.50472 0:8:8,0:8:245:0:0:0,-22.3444 0:7:7,0:7:258:0:0:0,-23.5715 0:8:8,2:6:167:2:4:0,-14.9167 +Chromosome 2648442 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=51;DPB=51;DPRA=1.04;EPP=3.73412;EPPR=3.0565;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=65.9498;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=115;QR=1803;RO=47;RPL=3;RPP=9.52472;RPPR=8.60069;RPR=0;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=13;SRP=23.3852;SRR=34;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|PA14_30560|PA14_30560|transcript|ABJ11816.1|protein_coding||c.-2361T>C|||||2361|,G|upstream_gene_variant|MODIFIER|potF|PA14_30570|transcript|ABJ11815.1|protein_coding||c.-1048T>C|||||1048|,G|upstream_gene_variant|MODIFIER|PA14_30590|PA14_30590|transcript|ABJ11813.1|protein_coding||c.-31A>G|||||31|,G|upstream_gene_variant|MODIFIER|PA14_30600|PA14_30600|transcript|ABJ11812.1|protein_coding||c.-2696A>G|||||2696|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_30540|PA14_30540|transcript|ABJ11818.1|protein_coding||c.*4115A>G|||||4115|,G|downstream_gene_variant|MODIFIER|ssuA|PA14_30550|transcript|ABJ11817.1|protein_coding||c.*3000A>G|||||3000|,G|downstream_gene_variant|MODIFIER|PA14_30580|PA14_30580|transcript|ABJ11814.1|protein_coding||c.*89A>G|||||89|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_30620|PA14_30620|transcript|ABJ11811.1|protein_coding||c.*3926T>C|||||3926|,G|intergenic_region|MODIFIER|PA14_30580-PA14_30590|PA14_30580-PA14_30590|intergenic_region|PA14_30580-PA14_30590|||n.2648442A>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:14:14,0:13:484:0:0:0,-43.8528 0:10:10,2:8:316:2:75:0,-21.6857 0:11:11,0:11:429:0:0:0,-38.9638 0:16:16,1:15:574:1:40:0,-48.0037 +Chromosome 2652896 . G C 6.3437E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=49;DPB=49;DPRA=1.22727;EPP=6.91895;EPPR=22.751;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=62.586;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=49;QR=1476;RO=44;RPL=4;RPP=6.91895;RPPR=19.0002;RPR=1;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=19;SRP=4.78696;SRR=25;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|PA14_30620|PA14_30620|transcript|ABJ11811.1|protein_coding|1/1|c.501C>G|p.Gly167Gly|501/1029|501/1029|167/342||,C|upstream_gene_variant|MODIFIER|pqsH|PA14_30630|transcript|ABJ11810.1|protein_coding||c.-1118G>C|||||1118|,C|upstream_gene_variant|MODIFIER|gacA|PA14_30650|transcript|ABJ11809.1|protein_coding||c.-2608G>C|||||2608|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|uvrC|PA14_30660|transcript|ABJ11808.1|protein_coding||c.-3253G>C|||||3253|,C|downstream_gene_variant|MODIFIER|PA14_30580|PA14_30580|transcript|ABJ11814.1|protein_coding||c.*4543G>C|||||4543|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_30590|PA14_30590|transcript|ABJ11813.1|protein_coding||c.*1769G>C|||||1769|,C|downstream_gene_variant|MODIFIER|PA14_30600|PA14_30600|transcript|ABJ11812.1|protein_coding||c.*544G>C|||||544|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:206:0:0:0,-18.8226 0:15:15,3:12:426:3:32:0,-35.6804 0:15:15,0:15:545:0:0:0,-49.3737 0:12:12,2:10:299:2:17:0,-25.5764 +Chromosome 2674649 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=32;DPB=32;DPRA=1.17391;EPP=7.35324;EPPR=3.08518;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=51.971;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=1004;RO=29;RPL=0;RPP=7.35324;RPPR=3.08518;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=14;SRP=3.08518;SRR=15;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_30820|PA14_30820|transcript|ABJ11795.1|protein_coding|1/1|c.1556T>G|p.Leu519Arg|1556/1608|1556/1608|519/535||,G|upstream_gene_variant|MODIFIER|PA14_30770|PA14_30770|transcript|ABJ11799.1|protein_coding||c.-4862A>C|||||4862|,G|upstream_gene_variant|MODIFIER|PA14_30800|PA14_30800|transcript|ABJ11797.1|protein_coding||c.-3162A>C|||||3162|,G|upstream_gene_variant|MODIFIER|PA14_30840|PA14_30840|transcript|ABJ11793.1|protein_coding||c.-1483T>G|||||1483|,G|downstream_gene_variant|MODIFIER|PA14_30790|PA14_30790|transcript|ABJ11798.1|protein_coding||c.*3830T>G|||||3830|,G|downstream_gene_variant|MODIFIER|alkB1|PA14_30810|transcript|ABJ11796.1|protein_coding||c.*1667T>G|||||1667|,G|downstream_gene_variant|MODIFIER|PA14_30830|PA14_30830|transcript|ABJ11794.1|protein_coding||c.*63A>C|||||63|,G|downstream_gene_variant|MODIFIER|trbI|PA14_30850|transcript|ABJ11792.1|protein_coding||c.*3786A>C|||||3786| GT:DP:DPR:RO:QR:AO:QA:GL 0:11:11,0:11:379:0:0:0,-34.4283 0:6:6,0:6:220:0:0:0,-20.152 0:9:9,2:6:206:2:32:0,-15.8295 0:6:6,0:6:199:0:0:0,-18.2287 +Chromosome 2685925 . A G 1.47818E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=31;DPB=31;DPRA=1.04348;EPP=7.35324;EPPR=24.6501;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=41.4535;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=42;QR=948;RO=29;RPL=0;RPP=7.35324;RPPR=4.88226;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=8;SRP=15.6647;SRR=21;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|trbE|PA14_30910|transcript|ABJ11786.1|protein_coding|1/1|c.362T>C|p.Leu121Pro|362/2454|362/2454|121/817||,G|upstream_gene_variant|MODIFIER|trbF|PA14_30870|transcript|ABJ11790.1|protein_coding||c.-4526T>C|||||4526|,G|upstream_gene_variant|MODIFIER|trbL|PA14_30880|transcript|ABJ11789.1|protein_coding||c.-3143T>C|||||3143|,G|upstream_gene_variant|MODIFIER|trbJ|PA14_30900|transcript|ABJ11787.1|protein_coding||c.-2089T>C|||||2089|,G|downstream_gene_variant|MODIFIER|PA14_30890|PA14_30890|transcript|ABJ11788.1|protein_coding||c.*2802A>G|||||2802|,G|downstream_gene_variant|MODIFIER|trbC|PA14_30930|transcript|ABJ11785.1|protein_coding||c.*643T>C|||||643|,G|downstream_gene_variant|MODIFIER|trbB|PA14_30940|transcript|ABJ11784.1|protein_coding||c.*1032T>C|||||1032|,G|downstream_gene_variant|MODIFIER|PA14_30950|PA14_30950|transcript|ABJ11783.1|protein_coding||c.*2099T>C|||||2099|,G|downstream_gene_variant|MODIFIER|traG|PA14_30960|transcript|ABJ11782.1|protein_coding||c.*2560T>C|||||2560| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:214:0:0:0,-19.5527 0:9:9,0:9:314:0:0:0,-28.5865 0:8:8,2:6:174:2:42:0,-11.9565 0:7:7,0:7:246:0:0:0,-22.4729 +Chromosome 2695752 . G C 6.23846E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=8;CIGAR=1X;DP=68;DPB=68;DPRA=0.925926;EPP=20.3821;EPPR=13.6468;GTI=0;LEN=1;MEANALT=1.33333;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=70.2495;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=94;QR=2084;RO=59;RPL=8;RPP=20.3821;RPPR=3.34154;RPR=0;RUN=1;SAF=8;SAP=20.3821;SAR=0;SRF=30;SRP=3.0471;SRR=29;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|PA14_31010|PA14_31010|transcript|ABJ11777.1|protein_coding|1/1|c.1290C>G|p.Arg430Arg|1290/3138|1290/3138|430/1045||,C|upstream_gene_variant|MODIFIER|bphR|PA14_30970|transcript|ABJ11781.1|protein_coding||c.-3752C>G|||||3752|,C|upstream_gene_variant|MODIFIER|PA14_30980|PA14_30980|transcript|ABJ11780.1|protein_coding||c.-3320C>G|||||3320|,C|upstream_gene_variant|MODIFIER|PA14_30990|PA14_30990|transcript|ABJ11779.1|protein_coding||c.-2601C>G|||||2601|,C|upstream_gene_variant|MODIFIER|PA14_31000|PA14_31000|transcript|ABJ11778.1|protein_coding||c.-1845C>G|||||1845|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_31030|PA14_31030|transcript|ABJ11776.1|protein_coding||c.*1300C>G|||||1300|,C|downstream_gene_variant|MODIFIER|PA14_31040|PA14_31040|transcript|ABJ11775.1|protein_coding||c.*2526C>G|||||2526|,C|downstream_gene_variant|MODIFIER|PA14_31050|PA14_31050|transcript|ABJ11774.1|protein_coding||c.*3914C>G|||||3914|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_31060|PA14_31060|transcript|ABJ11773.1|protein_coding||c.*4909C>G|||||4909|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:23:23,6:16:560:6:64:0,-44.8278 0:18:18,0:18:652:0:0:0,-58.9989 0:18:18,1:17:631:1:15:0,-55.615 0:9:9,1:8:241:1:15:0,-20.4768 +Chromosome 2706151 . T G 2.56149E-16 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=40;DPB=40;DPRA=1.57143;EPP=13.8677;EPPR=3.56868;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=69.4329;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1210;RO=35;RPL=0;RPP=13.8677;RPPR=20.9405;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=15;SRP=4.56135;SRR=20;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_31110|PA14_31110|transcript|ABJ11768.1|protein_coding|1/1|c.1081A>C|p.Ile361Leu|1081/1329|1081/1329|361/442||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_31060|PA14_31060|transcript|ABJ11773.1|protein_coding||c.-4873A>C|||||4873|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_31070|PA14_31070|transcript|ABJ11772.1|protein_coding||c.-2621A>C|||||2621|,G|upstream_gene_variant|MODIFIER|PA14_31080|PA14_31080|transcript|ABJ11771.1|protein_coding||c.-1972A>C|||||1972|,G|upstream_gene_variant|MODIFIER|PA14_31090|PA14_31090|transcript|ABJ11770.1|protein_coding||c.-1058A>C|||||1058|,G|upstream_gene_variant|MODIFIER|PA14_31100|PA14_31100|transcript|ABJ11769.1|protein_coding||c.-502A>C|||||502|,G|upstream_gene_variant|MODIFIER|PA14_31160|PA14_31160|transcript|ABJ11765.1|protein_coding||c.-2709T>G|||||2709|,G|upstream_gene_variant|MODIFIER|PA14_31170|PA14_31170|transcript|ABJ11764.1|protein_coding||c.-3079T>G|||||3079|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_31130|PA14_31130|transcript|ABJ11767.1|protein_coding||c.*1029A>C|||||1029|,G|downstream_gene_variant|MODIFIER|PA14_31150|PA14_31150|transcript|ABJ11766.1|protein_coding||c.*2143A>C|||||2143|,G|downstream_gene_variant|MODIFIER|PA14_31180|PA14_31180|transcript|ABJ11763.1|protein_coding||c.*3426A>C|||||3426|,G|downstream_gene_variant|MODIFIER|PA14_31190|PA14_31190|transcript|ABJ11762.1|protein_coding||c.*4794A>C|||||4794| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,1:8:258:1:2:0,-23.3283 0:7:7,0:7:277:0:0:0,-25.3005 0:14:14,2:12:381:2:4:0,-34.2098 0:10:10,2:8:294:2:4:0,-26.4275 +Chromosome 2719363 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=30;DPB=30;DPRA=1.09091;EPP=7.35324;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=50.8944;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1028;RO=28;RPL=0;RPP=7.35324;RPPR=3.32051;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=10;SRP=7.97367;SRR=18;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_31270|PA14_31270|transcript|ABJ11755.1|protein_coding|1/1|c.649A>C|p.Ile217Leu|649/1164|649/1164|217/387||,G|upstream_gene_variant|MODIFIER|PA14_31220|PA14_31220|transcript|ABJ11760.1|protein_coding||c.-4460A>C|||||4460|,G|upstream_gene_variant|MODIFIER|PA14_31230|PA14_31230|transcript|ABJ11759.1|protein_coding||c.-3867A>C|||||3867|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_31240|PA14_31240|transcript|ABJ11758.1|protein_coding||c.-2420A>C|||||2420|,G|upstream_gene_variant|MODIFIER|PA14_31250|PA14_31250|transcript|ABJ11757.1|protein_coding||c.-1625A>C|||||1625|,G|upstream_gene_variant|MODIFIER|PA14_31260|PA14_31260|transcript|ABJ11756.1|protein_coding||c.-842A>C|||||842|,G|upstream_gene_variant|MODIFIER|pa1L|PA14_31290|transcript|ABJ11753.1|protein_coding||c.-2498T>G|||||2498|,G|upstream_gene_variant|MODIFIER|PA14_31300|PA14_31300|transcript|ABJ11752.1|protein_coding||c.-3140T>G|||||3140|,G|upstream_gene_variant|MODIFIER|PA14_31310|PA14_31310|transcript|ABJ11751.1|protein_coding||c.-3600T>G|||||3600|,G|downstream_gene_variant|MODIFIER|PA14_31280|PA14_31280|transcript|ABJ11754.1|protein_coding||c.*645A>C|||||645|,G|downstream_gene_variant|MODIFIER|PA14_31330|PA14_31330|transcript|ABJ11750.1|protein_coding||c.*4066A>C|||||4066|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:245:0:0:0,-22.3825 0:8:8,2:6:230:2:4:0,-20.6855 0:10:10,0:10:381:0:0:0,-34.643 0:5:5,0:5:172:0:0:0,-15.8105 +Chromosome 2720205 . A G 3.66167E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=39;DPB=39;DPRA=1.03448;EPP=7.35324;EPPR=16.2152;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=58.9727;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1192;RO=37;RPL=0;RPP=7.35324;RPPR=7.76406;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=21;SRP=4.47751;SRR=16;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_31280|PA14_31280|transcript|ABJ11754.1|protein_coding|1/1|c.1009T>C|p.Ser337Pro|1009/1206|1009/1206|337/401||,G|upstream_gene_variant|MODIFIER|PA14_31230|PA14_31230|transcript|ABJ11759.1|protein_coding||c.-4709T>C|||||4709|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_31240|PA14_31240|transcript|ABJ11758.1|protein_coding||c.-3262T>C|||||3262|,G|upstream_gene_variant|MODIFIER|PA14_31250|PA14_31250|transcript|ABJ11757.1|protein_coding||c.-2467T>C|||||2467|,G|upstream_gene_variant|MODIFIER|PA14_31260|PA14_31260|transcript|ABJ11756.1|protein_coding||c.-1684T>C|||||1684|,G|upstream_gene_variant|MODIFIER|PA14_31270|PA14_31270|transcript|ABJ11755.1|protein_coding||c.-194T>C|||||194|,G|upstream_gene_variant|MODIFIER|pa1L|PA14_31290|transcript|ABJ11753.1|protein_coding||c.-1656A>G|||||1656|,G|upstream_gene_variant|MODIFIER|PA14_31300|PA14_31300|transcript|ABJ11752.1|protein_coding||c.-2298A>G|||||2298|,G|upstream_gene_variant|MODIFIER|PA14_31310|PA14_31310|transcript|ABJ11751.1|protein_coding||c.-2758A>G|||||2758|,G|downstream_gene_variant|MODIFIER|PA14_31330|PA14_31330|transcript|ABJ11750.1|protein_coding||c.*3224T>C|||||3224|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,2:8:228:2:17:0,-19.1826 0:10:10,0:10:352:0:0:0,-32.0141 0:9:9,0:9:280:0:0:0,-25.4956 0:10:10,0:10:332:0:0:0,-30.1894 +Chromosome 2726940 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=43;DPB=43;DPRA=0.909091;EPP=7.35324;EPPR=3.87889;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=49.3712;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1458;RO=40;RPL=0;RPP=7.35324;RPPR=3.22745;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=29;SRP=20.5992;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|PA14_31350|PA14_31350|transcript|ABJ11748.1|protein_coding|1/1|c.940C>A|p.His314Asn|940/1038|940/1038|314/345||,A|upstream_gene_variant|MODIFIER|PA14_31330|PA14_31330|transcript|ABJ11750.1|protein_coding||c.-2012G>T|||||2012|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|PA14_31360|PA14_31360|transcript|ABJ11747.1|protein_coding||c.-121C>A|||||121|,A|upstream_gene_variant|MODIFIER|tam|PA14_31370|transcript|ABJ11746.1|protein_coding||c.-536C>A|||||536|,A|upstream_gene_variant|MODIFIER|PA14_31390|PA14_31390|transcript|ABJ11744.1|protein_coding||c.-3210C>A|||||3210|,A|downstream_gene_variant|MODIFIER|pa1L|PA14_31290|transcript|ABJ11753.1|protein_coding||c.*4711C>A|||||4711|,A|downstream_gene_variant|MODIFIER|PA14_31300|PA14_31300|transcript|ABJ11752.1|protein_coding||c.*4096C>A|||||4096|,A|downstream_gene_variant|MODIFIER|PA14_31310|PA14_31310|transcript|ABJ11751.1|protein_coding||c.*3570C>A|||||3570|,A|downstream_gene_variant|MODIFIER|PA14_31340|PA14_31340|transcript|ABJ11749.1|protein_coding||c.*1283C>A|||||1283|,A|downstream_gene_variant|MODIFIER|sfpA|PA14_31380|transcript|ABJ11745.1|protein_coding||c.*1373G>T|||||1373|,A|downstream_gene_variant|MODIFIER|ctpH|PA14_31400|transcript|ABJ11743.1|protein_coding||c.*3837G>T|||||3837| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,2:8:283:2:4:0,-25.4231 0:13:13,0:13:454:0:0:0,-41.1848 0:15:15,0:15:566:0:0:0,-51.2748 0:5:5,0:4:155:0:0:0,-14.1193 +Chromosome 2726942 . C G 6.05059E-17 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=8;CIGAR=1X;DP=60;DPB=60;DPRA=0;EPP=20.3821;EPPR=11.1951;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=61.3327;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=1538;RO=52;RPL=0;RPP=20.3821;RPPR=11.1951;RPR=8;RUN=1;SAF=0;SAP=20.3821;SAR=8;SRF=28;SRP=3.67845;SRR=24;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_31350|PA14_31350|transcript|ABJ11748.1|protein_coding|1/1|c.942C>G|p.His314Gln|942/1038|942/1038|314/345||,G|upstream_gene_variant|MODIFIER|PA14_31330|PA14_31330|transcript|ABJ11750.1|protein_coding||c.-2014G>C|||||2014|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_31360|PA14_31360|transcript|ABJ11747.1|protein_coding||c.-119C>G|||||119|,G|upstream_gene_variant|MODIFIER|tam|PA14_31370|transcript|ABJ11746.1|protein_coding||c.-534C>G|||||534|,G|upstream_gene_variant|MODIFIER|PA14_31390|PA14_31390|transcript|ABJ11744.1|protein_coding||c.-3208C>G|||||3208|,G|downstream_gene_variant|MODIFIER|pa1L|PA14_31290|transcript|ABJ11753.1|protein_coding||c.*4713C>G|||||4713|,G|downstream_gene_variant|MODIFIER|PA14_31300|PA14_31300|transcript|ABJ11752.1|protein_coding||c.*4098C>G|||||4098|,G|downstream_gene_variant|MODIFIER|PA14_31310|PA14_31310|transcript|ABJ11751.1|protein_coding||c.*3572C>G|||||3572|,G|downstream_gene_variant|MODIFIER|PA14_31340|PA14_31340|transcript|ABJ11749.1|protein_coding||c.*1285C>G|||||1285|,G|downstream_gene_variant|MODIFIER|sfpA|PA14_31380|transcript|ABJ11745.1|protein_coding||c.*1371G>C|||||1371|,G|downstream_gene_variant|MODIFIER|ctpH|PA14_31400|transcript|ABJ11743.1|protein_coding||c.*3835G>C|||||3835| GT:DP:DPR:RO:QR:AO:QA:GL 0:17:17,5:12:326:5:10:0,-28.668 0:17:17,1:16:467:1:2:0,-42.0922 0:17:17,1:16:544:1:2:0,-49.0561 0:9:9,1:8:201:1:2:0,-18.1247 +Chromosome 2740769 . C A 4.02835E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=21;DPB=21;DPRA=1.84615;EPP=7.35324;EPPR=4.03889;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=32.4236;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=636;RO=19;RPL=0;RPP=7.35324;RPPR=12.2676;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=10;SRP=3.12459;SRR=9;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|PA14_31510|PA14_31510|transcript|ABJ11734.1|protein_coding|1/1|c.717C>A|p.Leu239Leu|717/768|717/768|239/255||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|PA14_31530|PA14_31530|transcript|ABJ11733.1|protein_coding||c.-69C>A|||||69|,A|upstream_gene_variant|MODIFIER|acdA|PA14_31540|transcript|ABJ11732.1|protein_coding||c.-1288C>A|||||1288|,A|upstream_gene_variant|MODIFIER|PA14_31580|PA14_31580|transcript|ABJ11730.1|protein_coding||c.-3638C>A|||||3638|,A|downstream_gene_variant|MODIFIER|PA14_31470|PA14_31470|transcript|ABJ11737.1|protein_coding||c.*3734C>A|||||3734|,A|downstream_gene_variant|MODIFIER|PA14_31480|PA14_31480|transcript|ABJ11736.1|protein_coding||c.*2580C>A|||||2580|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_31500|PA14_31500|transcript|ABJ11735.1|protein_coding||c.*736C>A|||||736|,A|downstream_gene_variant|MODIFIER|PA14_31560|PA14_31560|transcript|ABJ11731.1|protein_coding||c.*2532G>T|||||2532| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:144:0:0:0,-13.3109 0:6:6,0:6:187:0:0:0,-17.128 0:3:3,0:3:87:0:0:0,-8.11515 0:8:8,2:6:218:2:32:0,-16.9276 +Chromosome 2745523 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=39;DPB=39;DPRA=1.03448;EPP=7.35324;EPPR=4.47751;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=63.5203;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=78;QR=1407;RO=37;RPL=2;RPP=7.35324;RPPR=3.5385;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=15;SRP=5.88603;SRR=22;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_31580|PA14_31580|transcript|ABJ11730.1|protein_coding|1/1|c.1117A>G|p.Met373Val|1117/1230|1117/1230|373/409||,G|upstream_gene_variant|MODIFIER|PA14_31560|PA14_31560|transcript|ABJ11731.1|protein_coding||c.-1290T>C|||||1290|,G|upstream_gene_variant|MODIFIER|PA14_31640|PA14_31640|transcript|ABJ11726.1|protein_coding||c.-3960A>G|||||3960|,G|downstream_gene_variant|MODIFIER|PA14_31510|PA14_31510|transcript|ABJ11734.1|protein_coding||c.*4703A>G|||||4703|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_31530|PA14_31530|transcript|ABJ11733.1|protein_coding||c.*3495A>G|||||3495|,G|downstream_gene_variant|MODIFIER|acdA|PA14_31540|transcript|ABJ11732.1|protein_coding||c.*2339A>G|||||2339|,G|downstream_gene_variant|MODIFIER|PA14_31610|PA14_31610|transcript|ABJ11729.1|protein_coding||c.*304T>C|||||304|,G|downstream_gene_variant|MODIFIER|PA14_31620|PA14_31620|transcript|ABJ11728.1|protein_coding||c.*1497T>C|||||1497|,G|downstream_gene_variant|MODIFIER|PA14_31630|PA14_31630|transcript|ABJ11727.1|protein_coding||c.*2951T>C|||||2951|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|xthA|PA14_31650|transcript|ABJ11725.1|protein_coding||c.*4498T>C|||||4498| GT:DP:DPR:RO:QR:AO:QA:GL 0:13:13,0:13:481:0:0:0,-43.6218 0:6:6,0:6:220:0:0:0,-20.1504 0:10:10,0:10:386:0:0:0,-35.0961 0:10:10,2:8:320:2:78:0,-21.765 +Chromosome 2762024 . AACAACA GACGACG 1389.15 . AB=0;ABP=0;AC=4;AF=1;AN=4;AO=41;CIGAR=1X2M1X2M1X;DP=42;DPB=43.2857;DPRA=0;EPP=3.48696;EPPR=0;GTI=0;LEN=7;MEANALT=1.25;MQM=59.7073;MQMR=0;NS=4;NUMALT=1;ODDS=67.0705;PAIRED=0;PAIREDR=0;PAO=2;PQA=62;PQR=0;PRO=0;QA=1532;QR=0;RO=0;RPL=10;RPP=26.3669;RPPR=0;RPR=31;RUN=1;SAF=16;SAP=7.30028;SAR=25;SRF=0;SRP=0;SRR=0;TYPE=complex;technology.ILLUMINA=1;ANN=GACGACG|missense_variant|MODERATE|PA14_31750|PA14_31750|transcript|ABJ11717.1|protein_coding|1/1|c.373_379delAACAACAinsGACGACG|p.AsnAsnLys125AspAspGlu|373/630|373/630|125/209||,GACGACG|upstream_gene_variant|MODIFIER|cdsA|PA14_31760|transcript|ABJ11716.1|protein_coding||c.-259_-253delAACAACAinsGACGACG|||||259|,GACGACG|upstream_gene_variant|MODIFIER|PA14_31780|PA14_31780|transcript|ABJ11714.1|protein_coding||c.-2497_-2491delAACAACAinsGACGACG|||||2497|,GACGACG|upstream_gene_variant|MODIFIER|PA14_31800|PA14_31800|transcript|ABJ11713.1|protein_coding||c.-3564_-3558delAACAACAinsGACGACG|||||3564|,GACGACG|downstream_gene_variant|MODIFIER|PA14_31690|PA14_31690|transcript|ABJ11722.1|protein_coding||c.*4798_*4804delAACAACAinsGACGACG|||||4798|WARNING_TRANSCRIPT_NO_START_CODON,GACGACG|downstream_gene_variant|MODIFIER|pgsA|PA14_31700|transcript|ABJ11721.1|protein_coding||c.*4028_*4034delAACAACAinsGACGACG|||||4028|,GACGACG|downstream_gene_variant|MODIFIER|PA14_31720|PA14_31720|transcript|ABJ11720.1|protein_coding||c.*2178_*2184delAACAACAinsGACGACG|||||2178|,GACGACG|downstream_gene_variant|MODIFIER|PA14_31730|PA14_31730|transcript|ABJ11719.1|protein_coding||c.*829_*835delAACAACAinsGACGACG|||||829|WARNING_TRANSCRIPT_NO_START_CODON,GACGACG|downstream_gene_variant|MODIFIER|PA14_31740|PA14_31740|transcript|ABJ11718.1|protein_coding||c.*384_*390delAACAACAinsGACGACG|||||384|,GACGACG|downstream_gene_variant|MODIFIER|PA14_31770|PA14_31770|transcript|ABJ11715.1|protein_coding||c.*1377_*1383delTGTTGTTinsCGTCGTC|||||1383| GT:DP:DPR:RO:QR:AO:QA:GL 1:7:7,7:0:0:7:241:-22.0194,0 1:7:7,7:0:0:7:276:-30.768,0 1:14:14,14:0:0:14:521:-47.2206,0 1:14:14,13:0:0:13:494:-44.4828,0 +Chromosome 2770532 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=32;DPB=32;DPRA=1.17391;EPP=7.35324;EPPR=7.64277;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=60.8164;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=1042;RO=30;RPL=0;RPP=7.35324;RPPR=3.29983;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=15;SRP=3.0103;SRR=15;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_31850|PA14_31850|transcript|ABJ11709.1|protein_coding|1/1|c.1267T>C|p.Ser423Pro|1267/1434|1267/1434|423/477||,G|upstream_gene_variant|MODIFIER|hisC|PA14_31820|transcript|ABJ11711.1|protein_coding||c.-1689T>C|||||1689|,G|upstream_gene_variant|MODIFIER|PA14_31840|PA14_31840|transcript|ABJ11710.1|protein_coding||c.-167T>C|||||167|,G|upstream_gene_variant|MODIFIER|PA14_31870|PA14_31870|transcript|ABJ11708.1|protein_coding||c.-1523A>G|||||1523|,G|upstream_gene_variant|MODIFIER|PA14_31890|PA14_31890|transcript|ABJ11707.1|protein_coding||c.-2800A>G|||||2800|,G|downstream_gene_variant|MODIFIER|PA14_31800|PA14_31800|transcript|ABJ11713.1|protein_coding||c.*3595A>G|||||3595|,G|downstream_gene_variant|MODIFIER|tpx|PA14_31810|transcript|ABJ11712.1|protein_coding||c.*2963A>G|||||2963| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,2:7:260:2:30:0,-20.9039 0:8:8,0:8:275:0:0:0,-25.0763 0:8:8,0:8:283:0:0:0,-25.8036 0:7:7,0:7:224:0:0:0,-20.4667 +Chromosome 2791195 . C A 1.46161E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=32;DPB=32;DPRA=1.19048;EPP=13.8677;EPPR=30.0702;GTI=0;LEN=1;MEANALT=1.33333;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=36.3987;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=50;QR=806;RO=26;RPL=0;RPP=13.8677;RPPR=3.34437;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=14;SRP=3.34437;SRR=12;TYPE=snp;technology.ILLUMINA=1;ANN=A|upstream_gene_variant|MODIFIER|xylX|PA14_32080|transcript|ABJ11698.1|protein_coding||c.-97C>A|||||97|,A|upstream_gene_variant|MODIFIER|xylY|PA14_32100|transcript|ABJ11697.1|protein_coding||c.-1461C>A|||||1461|,A|upstream_gene_variant|MODIFIER|xylZ|PA14_32110|transcript|ABJ11696.1|protein_coding||c.-1983C>A|||||1983|,A|upstream_gene_variant|MODIFIER|xylL|PA14_32130|transcript|ABJ11695.1|protein_coding||c.-3022C>A|||||3022|,A|downstream_gene_variant|MODIFIER|czcB|PA14_31990|transcript|ABJ11700.1|protein_coding||c.*4361C>A|||||4361|,A|downstream_gene_variant|MODIFIER|xylS|PA14_32060|transcript|ABJ11699.1|protein_coding||c.*20C>A|||||20|,A|downstream_gene_variant|MODIFIER|antC|PA14_32140|transcript|ABJ11694.1|protein_coding||c.*3789G>T|||||3789|,A|downstream_gene_variant|MODIFIER|antB|PA14_32150|transcript|ABJ11693.1|protein_coding||c.*4830G>T|||||4830|,A|intergenic_region|MODIFIER|xylS-xylX|PA14_32060-PA14_32080|intergenic_region|PA14_32060-PA14_32080|||n.2791195C>A|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,1:5:118:1:16:0,-9.25313 0:7:7,0:7:211:0:0:0,-19.2816 0:9:9,2:7:238:2:17:0,-20.1293 0:10:10,2:7:239:2:17:0,-20.1263 +Chromosome 2835395 . C G 2.9588E-8 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=17;DPB=17;DPRA=1.25;EPP=9.52472;EPPR=5.49198;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=18.8045;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=28;QR=522;RO=14;RPL=0;RPP=9.52472;RPPR=8.59409;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=13;SRP=25.3454;SRR=1;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|PA14_32640|PA14_32640|transcript|ABJ11654.1|protein_coding|1/1|c.72G>C|p.Ala24Ala|72/912|72/912|24/303||,G|upstream_gene_variant|MODIFIER|PA14_32700|PA14_32700|transcript|ABJ11649.1|protein_coding||c.-4091C>G|||||4091|,G|downstream_gene_variant|MODIFIER|dipZ2|PA14_32590|transcript|ABJ11658.1|protein_coding||c.*3832C>G|||||3832|,G|downstream_gene_variant|MODIFIER|PA14_32600|PA14_32600|transcript|ABJ11657.1|protein_coding||c.*2996C>G|||||2996|,G|downstream_gene_variant|MODIFIER|dsbG|PA14_32610|transcript|ABJ11656.1|protein_coding||c.*2229C>G|||||2229|,G|downstream_gene_variant|MODIFIER|PA14_32630|PA14_32630|transcript|ABJ11655.1|protein_coding||c.*822C>G|||||822|,G|downstream_gene_variant|MODIFIER|PA14_32650|PA14_32650|transcript|ABJ11653.1|protein_coding||c.*113G>C|||||113|,G|downstream_gene_variant|MODIFIER|PA14_32660|PA14_32660|transcript|ABJ11652.1|protein_coding||c.*770G>C|||||770|,G|downstream_gene_variant|MODIFIER|PA14_32670|PA14_32670|transcript|ABJ11651.1|protein_coding||c.*2194G>C|||||2194|,G|downstream_gene_variant|MODIFIER|gtdA|PA14_32690|transcript|ABJ11650.1|protein_coding||c.*2905G>C|||||2905| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:197:0:0:0,-18.1066 0:1:1,0:1:36:0:0:0,-3.59827 0:6:6,0:6:209:0:0:0,-19.1415 0:5:5,3:2:80:3:28:0,-4.97856 +Chromosome 2837980 . TCG CCC 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X1M1X;DP=34;DPB=34.6667;DPRA=0.923077;EPP=7.35324;EPPR=8.68415;GTI=0;LEN=3;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=48.8827;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=20;PRO=1;QA=26;QR=1077;RO=31;RPL=2;RPP=7.35324;RPPR=11.486;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=20;SRP=8.68415;SRR=11;TYPE=complex;technology.ILLUMINA=1;ANN=CCC|missense_variant|MODERATE|PA14_32670|PA14_32670|transcript|ABJ11651.1|protein_coding|1/1|c.306_308delCGAinsGGG|p.AlaGlu102AlaGly|308/699|306/699|102/232||,CCC|upstream_gene_variant|MODIFIER|PA14_32640|PA14_32640|transcript|ABJ11654.1|protein_coding||c.-2516_-2514delCGAinsGGG|||||2514|,CCC|upstream_gene_variant|MODIFIER|PA14_32650|PA14_32650|transcript|ABJ11653.1|protein_coding||c.-1830_-1828delCGAinsGGG|||||1828|,CCC|upstream_gene_variant|MODIFIER|PA14_32660|PA14_32660|transcript|ABJ11652.1|protein_coding||c.-471_-469delCGAinsGGG|||||469|,CCC|upstream_gene_variant|MODIFIER|PA14_32700|PA14_32700|transcript|ABJ11649.1|protein_coding||c.-1506_-1504delTCGinsCCC|||||1506|,CCC|upstream_gene_variant|MODIFIER|PA14_32710|PA14_32710|transcript|ABJ11648.1|protein_coding||c.-2509_-2507delTCGinsCCC|||||2509|,CCC|upstream_gene_variant|MODIFIER|PA14_32720|PA14_32720|transcript|ABJ11647.1|protein_coding||c.-3036_-3034delTCGinsCCC|||||3036|WARNING_TRANSCRIPT_NO_START_CODON,CCC|upstream_gene_variant|MODIFIER|optS|PA14_32740|transcript|ABJ11646.1|protein_coding||c.-4166_-4164delTCGinsCCC|||||4166|,CCC|downstream_gene_variant|MODIFIER|dsbG|PA14_32610|transcript|ABJ11656.1|protein_coding||c.*4814_*4816delTCGinsCCC|||||4814|,CCC|downstream_gene_variant|MODIFIER|PA14_32630|PA14_32630|transcript|ABJ11655.1|protein_coding||c.*3407_*3409delTCGinsCCC|||||3407|,CCC|downstream_gene_variant|MODIFIER|gtdA|PA14_32690|transcript|ABJ11650.1|protein_coding||c.*318_*320delCGAinsGGG|||||320| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:5:172:0:0:0,-15.625 0:11:11,0:11:364:0:0:0,-33.0677 0:8:8,2:6:224:2:26:0,-18.0497 0:9:9,0:9:317:0:0:0,-30.647 +Chromosome 2840424 . G T 1.70626E-11 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=17;DPB=17;DPRA=1.42857;EPP=11.6962;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=26.5134;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=42;QR=412;RO=13;RPL=4;RPP=11.6962;RPPR=16.5402;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=8;SRP=4.51363;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=T|upstream_gene_variant|MODIFIER|PA14_32640|PA14_32640|transcript|ABJ11654.1|protein_coding||c.-4958C>A|||||4958|,T|upstream_gene_variant|MODIFIER|PA14_32650|PA14_32650|transcript|ABJ11653.1|protein_coding||c.-4272C>A|||||4272|,T|upstream_gene_variant|MODIFIER|PA14_32660|PA14_32660|transcript|ABJ11652.1|protein_coding||c.-2913C>A|||||2913|,T|upstream_gene_variant|MODIFIER|PA14_32670|PA14_32670|transcript|ABJ11651.1|protein_coding||c.-2137C>A|||||2137|,T|upstream_gene_variant|MODIFIER|gtdA|PA14_32690|transcript|ABJ11650.1|protein_coding||c.-1063C>A|||||1063|,T|upstream_gene_variant|MODIFIER|PA14_32710|PA14_32710|transcript|ABJ11648.1|protein_coding||c.-65G>T|||||65|,T|upstream_gene_variant|MODIFIER|PA14_32720|PA14_32720|transcript|ABJ11647.1|protein_coding||c.-592G>T|||||592|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|optS|PA14_32740|transcript|ABJ11646.1|protein_coding||c.-1722G>T|||||1722|,T|upstream_gene_variant|MODIFIER|PA14_32750|PA14_32750|transcript|ABJ11645.1|protein_coding||c.-4302G>T|||||4302|,T|downstream_gene_variant|MODIFIER|PA14_32700|PA14_32700|transcript|ABJ11649.1|protein_coding||c.*24G>T|||||24|,T|intergenic_region|MODIFIER|PA14_32700-PA14_32710|PA14_32700-PA14_32710|intergenic_region|PA14_32700-PA14_32710|||n.2840424G>T|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,1:2:73:1:2:0,-6.7307 0:7:7,3:4:126:3:40:0,-7.91389 0:5:5,0:5:135:0:0:0,-12.4105 0:2:2,0:2:78:0:0:0,-7.40347 +Chromosome 2846785 . G T 8.7816E-16 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=37;DPB=37;DPRA=0.947368;EPP=9.52472;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=66.5191;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=1249;RO=34;RPL=3;RPP=9.52472;RPPR=7.09778;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=10;SRP=15.5282;SRR=24;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_32780|PA14_32780|transcript|ABJ11643.1|protein_coding|1/1|c.28G>T|p.Val10Phe|28/1698|28/1698|10/565||,T|upstream_gene_variant|MODIFIER|PA14_32790|PA14_32790|transcript|ABJ11642.1|protein_coding||c.-1783G>T|||||1783|,T|downstream_gene_variant|MODIFIER|PA14_32720|PA14_32720|transcript|ABJ11647.1|protein_coding||c.*4783G>T|||||4783|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|optS|PA14_32740|transcript|ABJ11646.1|protein_coding||c.*2177G>T|||||2177|,T|downstream_gene_variant|MODIFIER|PA14_32750|PA14_32750|transcript|ABJ11645.1|protein_coding||c.*911G>T|||||911|,T|downstream_gene_variant|MODIFIER|PA14_32770|PA14_32770|transcript|ABJ11644.1|protein_coding||c.*340G>T|||||340| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:319:0:0:0,-29.078 0:11:11,0:11:365:0:0:0,-33.1558 0:9:9,1:8:310:1:2:0,-28.062 0:9:9,2:7:255:2:17:0,-21.6819 +Chromosome 2853613 . T C 3.1642E-16 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=57;DPB=57;DPRA=0.571429;EPP=11.6962;EPPR=17.8009;GTI=0;LEN=1;MEANALT=1;MQM=57.75;MQMR=60;NS=4;NUMALT=1;ODDS=76.2948;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=1928;RO=53;RPL=4;RPP=11.6962;RPPR=12.2288;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=25;SRP=3.37904;SRR=28;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|PA14_32790|PA14_32790|transcript|ABJ11642.1|protein_coding|1/1|c.5046T>C|p.Ala1682Ala|5046/15639|5046/15639|1682/5212|| GT:DP:DPR:RO:QR:AO:QA:GL 0:12:12,1:11:352:1:14:0,-30.577 0:21:21,0:21:774:0:0:0,-69.9723 0:15:15,1:14:538:1:2:0,-48.5618 0:9:9,2:7:264:2:4:0,-23.7373 +Chromosome 2876651 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=46;DPB=46;DPRA=1.42105;EPP=11.6962;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=64.8756;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=1504;RO=42;RPL=0;RPP=11.6962;RPPR=10.4553;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=12;SRP=19.7617;SRR=30;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_32860|PA14_32860|transcript|ABJ11636.1|protein_coding|1/1|c.419A>C|p.Gln140Pro|419/537|419/537|140/178||,G|upstream_gene_variant|MODIFIER|PA14_32830|PA14_32830|transcript|ABJ11639.1|protein_coding||c.-3401A>C|||||3401|,G|upstream_gene_variant|MODIFIER|PA14_32840|PA14_32840|transcript|ABJ11638.1|protein_coding||c.-2433A>C|||||2433|,G|upstream_gene_variant|MODIFIER|PA14_32850|PA14_32850|transcript|ABJ11637.1|protein_coding||c.-648A>C|||||648|,G|upstream_gene_variant|MODIFIER|PA14_32905|PA14_32905|transcript|ABJ15666.1|protein_coding||c.-1698T>G|||||1698|,G|upstream_gene_variant|MODIFIER|PA14_32930|PA14_32930|transcript|ABJ11633.1|protein_coding||c.-3481T>G|||||3481|,G|upstream_gene_variant|MODIFIER|PA14_32940|PA14_32940|transcript|ABJ11632.1|protein_coding||c.-4480T>G|||||4480|,G|downstream_gene_variant|MODIFIER|PA14_32880|PA14_32880|transcript|ABJ11635.1|protein_coding||c.*415A>C|||||415|,G|downstream_gene_variant|MODIFIER|PA14_32890|PA14_32890|transcript|ABJ11634.1|protein_coding||c.*1320A>C|||||1320| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:229:0:0:0,-20.9194 0:12:12,0:12:442:0:0:0,-40.1129 0:14:14,1:13:458:1:2:0,-41.3391 0:13:13,3:10:375:3:19:0,-32.3258 +Chromosome 2912131 . G T 3.62281E-11 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=30;DPB=30;DPRA=3.28571;EPP=9.52472;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=25.5098;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=998;RO=27;RPL=3;RPP=9.52472;RPPR=21.1059;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=7;SRP=16.6021;SRR=20;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|pvdL|PA14_33280|transcript|ABJ11607.1|protein_coding|1/1|c.33G>T|p.Leu11Leu|33/13029|33/13029|11/4342||,T|upstream_gene_variant|MODIFIER|PA14_33230|PA14_33230|transcript|ABJ11612.1|protein_coding||c.-3824C>A|||||3824|,T|upstream_gene_variant|MODIFIER|pvdS|PA14_33260|transcript|ABJ11609.1|protein_coding||c.-1514C>A|||||1514|,T|downstream_gene_variant|MODIFIER|PA14_33220|PA14_33220|transcript|ABJ11613.1|protein_coding||c.*4106G>T|||||4106|,T|downstream_gene_variant|MODIFIER|PA14_33240|PA14_33240|transcript|ABJ11611.1|protein_coding||c.*2648G>T|||||2648|,T|downstream_gene_variant|MODIFIER|PA14_33250|PA14_33250|transcript|ABJ11610.1|protein_coding||c.*2094G>T|||||2094|,T|downstream_gene_variant|MODIFIER|pvdG|PA14_33270|transcript|ABJ11608.1|protein_coding||c.*106G>T|||||106|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:219:0:0:0,-20.0596 0:1:1,0:1:40:0:0:0,-3.99568 0:7:7,2:5:172:2:17:0,-14.1951 0:16:16,1:15:567:1:15:0,-49.8587 +Chromosome 2940268 . T C 4.75E-11 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=7;CIGAR=1X;DP=27;DPB=27;DPRA=0.952381;EPP=10.7656;EPPR=18.6449;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=25.2389;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=69;QR=558;RO=20;RPL=6;RPP=10.7656;RPPR=13.8677;RPR=1;RUN=1;SAF=7;SAP=18.2106;SAR=0;SRF=5;SRP=13.8677;SRR=15;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|opdJ|PA14_33410|transcript|ABJ11596.1|protein_coding|1/1|c.600A>G|p.Glu200Glu|600/1419|600/1419|200/472||,C|upstream_gene_variant|MODIFIER|PA14_33350|PA14_33350|transcript|ABJ11600.1|protein_coding||c.-4612A>G|||||4612|,C|upstream_gene_variant|MODIFIER|PA14_33370|PA14_33370|transcript|ABJ11598.1|protein_coding||c.-2478A>G|||||2478|,C|upstream_gene_variant|MODIFIER|PA14_33380|PA14_33380|transcript|ABJ11597.1|protein_coding||c.-853A>G|||||853|,C|upstream_gene_variant|MODIFIER|PA14_33440|PA14_33440|transcript|ABJ11593.1|protein_coding||c.-2420T>C|||||2420|,C|downstream_gene_variant|MODIFIER|PA14_33360|PA14_33360|transcript|ABJ11599.1|protein_coding||c.*2977T>C|||||2977|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225089|transcript|EBT00001793434.1|pseudogene||n.*4324T>C|||||4324|,C|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225162|transcript|EBT00001793465.1|pseudogene||n.*4264T>C|||||4264|,C|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225173|transcript|EBT00001793509.1|pseudogene||n.*4204T>C|||||4204|,C|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225020|transcript|EBT00001793405.1|pseudogene||n.*4144T>C|||||4144|,C|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225068|transcript|EBT00001793459.1|pseudogene||n.*4084T>C|||||4084|,C|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225029|transcript|EBT00001793517.1|pseudogene||n.*4024T>C|||||4024|,C|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225082|transcript|EBT00001793457.1|pseudogene||n.*3964T>C|||||3964|,C|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225095|transcript|EBT00001793418.1|pseudogene||n.*3904T>C|||||3904|,C|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225017|transcript|EBT00001793443.1|pseudogene||n.*3844T>C|||||3844|,C|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225065|transcript|EBT00001793427.1|pseudogene||n.*3784T>C|||||3784|,C|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225077|transcript|EBT00001793429.1|pseudogene||n.*3724T>C|||||3724|,C|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225161|transcript|EBT00001793454.1|pseudogene||n.*3664T>C|||||3664|,C|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225056|transcript|EBT00001793487.1|pseudogene||n.*3604T>C|||||3604|,C|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225019|transcript|EBT00001793432.1|pseudogene||n.*3544T>C|||||3544|,C|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225122|transcript|EBT00001793380.1|pseudogene||n.*3484T>C|||||3484|,C|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225158|transcript|EBT00001793449.1|pseudogene||n.*3424T>C|||||3424|,C|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225144|transcript|EBT00001793461.1|pseudogene||n.*3364T>C|||||3364|,C|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225113|transcript|EBT00001793483.1|pseudogene||n.*3304T>C|||||3304|,C|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225070|transcript|EBT00001793515.1|pseudogene||n.*3244T>C|||||3244|,C|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225073|transcript|EBT00001793433.1|pseudogene||n.*3184T>C|||||3184|,C|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225155|transcript|EBT00001793364.1|pseudogene||n.*3123T>C|||||3123|,C|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225090|transcript|EBT00001793428.1|pseudogene||n.*3063T>C|||||3063|,C|downstream_gene_variant|MODIFIER|PA14_33420|PA14_33420|transcript|ABJ11595.1|protein_coding||c.*681A>G|||||681|,C|downstream_gene_variant|MODIFIER|PA14_33430|PA14_33430|transcript|ABJ11594.1|protein_coding||c.*1459A>G|||||1459|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|treA|PA14_33450|transcript|ABJ11592.1|protein_coding||c.*3362A>G|||||3362| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,3:3:93:3:34:0,-5.49945 0:7:7,0:7:207:0:0:0,-18.9166 0:8:8,2:6:139:2:31:0,-9.78963 0:6:6,2:4:119:2:4:0,-10.6178 +Chromosome 2941466 . A G 6.05059E-17 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=73;DPB=73;DPRA=1.08571;EPP=13.8677;EPPR=4.1599;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=99.0293;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=2455;RO=68;RPL=0;RPP=13.8677;RPPR=3.13803;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=24;SRP=15.7837;SRR=44;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_33420|PA14_33420|transcript|ABJ11595.1|protein_coding|1/1|c.164T>C|p.Leu55Pro|164/681|164/681|55/226||,G|upstream_gene_variant|MODIFIER|PA14_33370|PA14_33370|transcript|ABJ11598.1|protein_coding||c.-3676T>C|||||3676|,G|upstream_gene_variant|MODIFIER|PA14_33380|PA14_33380|transcript|ABJ11597.1|protein_coding||c.-2051T>C|||||2051|,G|upstream_gene_variant|MODIFIER|opdJ|PA14_33410|transcript|ABJ11596.1|protein_coding||c.-599T>C|||||599|,G|upstream_gene_variant|MODIFIER|PA14_33440|PA14_33440|transcript|ABJ11593.1|protein_coding||c.-1222A>G|||||1222|,G|upstream_gene_variant|MODIFIER|PA14_33460|PA14_33460|transcript|ABJ11591.1|protein_coding||c.-4160A>G|||||4160|,G|upstream_gene_variant|MODIFIER|sndH|PA14_33480|transcript|ABJ11590.1|protein_coding||c.-4578A>G|||||4578|,G|downstream_gene_variant|MODIFIER|PA14_33360|PA14_33360|transcript|ABJ11599.1|protein_coding||c.*4175A>G|||||4175|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225065|transcript|EBT00001793427.1|pseudogene||n.*4982A>G|||||4982|,G|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225077|transcript|EBT00001793429.1|pseudogene||n.*4922A>G|||||4922|,G|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225161|transcript|EBT00001793454.1|pseudogene||n.*4862A>G|||||4862|,G|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225056|transcript|EBT00001793487.1|pseudogene||n.*4802A>G|||||4802|,G|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225019|transcript|EBT00001793432.1|pseudogene||n.*4742A>G|||||4742|,G|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225122|transcript|EBT00001793380.1|pseudogene||n.*4682A>G|||||4682|,G|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225158|transcript|EBT00001793449.1|pseudogene||n.*4622A>G|||||4622|,G|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225144|transcript|EBT00001793461.1|pseudogene||n.*4562A>G|||||4562|,G|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225113|transcript|EBT00001793483.1|pseudogene||n.*4502A>G|||||4502|,G|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225070|transcript|EBT00001793515.1|pseudogene||n.*4442A>G|||||4442|,G|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225073|transcript|EBT00001793433.1|pseudogene||n.*4382A>G|||||4382|,G|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225155|transcript|EBT00001793364.1|pseudogene||n.*4321A>G|||||4321|,G|downstream_gene_variant|MODIFIER|CRISPR-DR4|EBG00001225090|transcript|EBT00001793428.1|pseudogene||n.*4261A>G|||||4261|,G|downstream_gene_variant|MODIFIER|PA14_33430|PA14_33430|transcript|ABJ11594.1|protein_coding||c.*261T>C|||||261|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|treA|PA14_33450|transcript|ABJ11592.1|protein_coding||c.*2164T>C|||||2164| GT:DP:DPR:RO:QR:AO:QA:GL 0:11:11,0:11:421:0:0:0,-38.2411 0:24:24,0:24:858:0:0:0,-77.5112 0:15:15,3:12:377:3:6:0,-33.661 0:23:23,2:21:799:2:26:0,-69.7529 +Chromosome 2943838 . T C 8.09178E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=25;DPB=25;DPRA=1.16667;EPP=7.35324;EPPR=10.6577;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=41.4748;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=776;RO=23;RPL=0;RPP=7.35324;RPPR=7.63648;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=30.2953;SRR=20;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|treA|PA14_33450|transcript|ABJ11592.1|protein_coding|1/1|c.1430A>G|p.Asp477Gly|1430/1638|1430/1638|477/545||,C|upstream_gene_variant|MODIFIER|PA14_33380|PA14_33380|transcript|ABJ11597.1|protein_coding||c.-4423A>G|||||4423|,C|upstream_gene_variant|MODIFIER|opdJ|PA14_33410|transcript|ABJ11596.1|protein_coding||c.-2971A>G|||||2971|,C|upstream_gene_variant|MODIFIER|PA14_33420|PA14_33420|transcript|ABJ11595.1|protein_coding||c.-2209A>G|||||2209|,C|upstream_gene_variant|MODIFIER|PA14_33430|PA14_33430|transcript|ABJ11594.1|protein_coding||c.-1251A>G|||||1251|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_33460|PA14_33460|transcript|ABJ11591.1|protein_coding||c.-1788T>C|||||1788|,C|upstream_gene_variant|MODIFIER|sndH|PA14_33480|transcript|ABJ11590.1|protein_coding||c.-2206T>C|||||2206|,C|upstream_gene_variant|MODIFIER|pvdH|PA14_33500|transcript|ABJ11589.1|protein_coding||c.-3704T>C|||||3704|,C|downstream_gene_variant|MODIFIER|PA14_33440|PA14_33440|transcript|ABJ11593.1|protein_coding||c.*212T>C|||||212| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:154:0:0:0,-14.1567 0:8:8,0:8:279:0:0:0,-25.4387 0:7:7,2:5:193:2:4:0,-17.3603 0:5:5,0:5:150:0:0:0,-13.7906 +Chromosome 2955423 . A G 5.95171E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=52;DPB=52;DPRA=1.08;EPP=9.52472;EPPR=15.8176;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=65.1104;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=40;QR=1794;RO=49;RPL=0;RPP=9.52472;RPPR=5.18177;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=36;SRP=26.4533;SRR=13;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_33600|PA14_33600|transcript|ABJ11579.1|protein_coding|1/1|c.874T>C|p.Trp292Arg|874/1212|874/1212|292/403||,G|upstream_gene_variant|MODIFIER|PA14_33530|PA14_33530|transcript|ABJ11586.1|protein_coding||c.-4394T>C|||||4394|,G|upstream_gene_variant|MODIFIER|PA14_33540|PA14_33540|transcript|ABJ11585.1|protein_coding||c.-3492T>C|||||3492|,G|upstream_gene_variant|MODIFIER|PA14_33550|PA14_33550|transcript|ABJ11584.1|protein_coding||c.-2740T>C|||||2740|,G|upstream_gene_variant|MODIFIER|PA14_33560|PA14_33560|transcript|ABJ11583.1|protein_coding||c.-1790T>C|||||1790|,G|upstream_gene_variant|MODIFIER|PA14_33570|PA14_33570|transcript|ABJ11582.1|protein_coding||c.-1197T>C|||||1197|,G|upstream_gene_variant|MODIFIER|PA14_33580|PA14_33580|transcript|ABJ11581.1|protein_coding||c.-871T>C|||||871|,G|upstream_gene_variant|MODIFIER|PA14_33590|PA14_33590|transcript|ABJ11580.1|protein_coding||c.-335T>C|||||335|,G|upstream_gene_variant|MODIFIER|PA14_33610|PA14_33610|transcript|ABJ11578.1|protein_coding||c.-1192A>G|||||1192| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,2:7:235:2:38:0,-17.8642 0:10:10,0:10:373:0:0:0,-33.9181 0:18:18,1:17:660:1:2:0,-59.534 0:15:15,0:15:526:0:0:0,-47.651 +Chromosome 2955468 . A G 1379.07 . AB=0;ABP=0;AC=4;AF=1;AN=4;AO=41;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=9.41879;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=4;NUMALT=1;ODDS=64.741;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1557;QR=0;RO=0;RPL=23;RPP=4.33437;RPPR=0;RPR=18;RUN=1;SAF=23;SAP=4.33437;SAR=18;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|PA14_33600|PA14_33600|transcript|ABJ11579.1|protein_coding|1/1|c.829T>C|p.Leu277Leu|829/1212|829/1212|277/403||,G|upstream_gene_variant|MODIFIER|PA14_33530|PA14_33530|transcript|ABJ11586.1|protein_coding||c.-4439T>C|||||4439|,G|upstream_gene_variant|MODIFIER|PA14_33540|PA14_33540|transcript|ABJ11585.1|protein_coding||c.-3537T>C|||||3537|,G|upstream_gene_variant|MODIFIER|PA14_33550|PA14_33550|transcript|ABJ11584.1|protein_coding||c.-2785T>C|||||2785|,G|upstream_gene_variant|MODIFIER|PA14_33560|PA14_33560|transcript|ABJ11583.1|protein_coding||c.-1835T>C|||||1835|,G|upstream_gene_variant|MODIFIER|PA14_33570|PA14_33570|transcript|ABJ11582.1|protein_coding||c.-1242T>C|||||1242|,G|upstream_gene_variant|MODIFIER|PA14_33580|PA14_33580|transcript|ABJ11581.1|protein_coding||c.-916T>C|||||916|,G|upstream_gene_variant|MODIFIER|PA14_33590|PA14_33590|transcript|ABJ11580.1|protein_coding||c.-380T>C|||||380|,G|upstream_gene_variant|MODIFIER|PA14_33610|PA14_33610|transcript|ABJ11578.1|protein_coding||c.-1147A>G|||||1147| GT:DP:DPR:RO:QR:AO:QA:GL 1:6:6,6:0:0:6:225:-20.6093,0 1:11:11,11:0:0:11:415:-37.6947,0 1:14:14,14:0:0:14:532:-48.2114,0 1:10:10,10:0:0:10:385:-35.0042,0 +Chromosome 2979718 . T G 7.31533E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=6;CIGAR=1X;DP=51;DPB=51;DPRA=2;EPP=16.0391;EPPR=4.21667;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=15.6444;NS=4;NUMALT=1;ODDS=35.518;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=25;QR=1489;RO=45;RPL=0;RPP=16.0391;RPPR=4.21667;RPR=6;RUN=1;SAF=0;SAP=16.0391;SAR=6;SRF=15;SRP=13.8677;SRR=30;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|pvdD|PA14_33650|transcript|ABJ11576.1|protein_coding|1/1|c.1070T>G|p.Leu357Arg|1070/7347|1070/7347|357/2448||WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|pvdJ|PA14_33630|transcript|ABJ11577.1|protein_coding||c.*1081T>G|||||1081| GT:DP:DPR:RO:QR:AO:QA:GL 0:11:11,0:11:358:0:0:0,-15.3126 0:6:6,0:6:187:0:0:0,-7.45385 0:14:14,3:11:387:3:6:0,-11.3288 0:20:20,3:17:557:3:19:0,-20.1148 +Chromosome 3000510 . C G 5.39191E-5 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=1.125;EPP=3.0103;EPPR=3.25157;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=11.2967;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=41;QR=280;RO=9;RPL=2;RPP=7.35324;RPPR=9.04217;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=2;SRP=9.04217;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_33770|PA14_33770|transcript|ABJ11566.1|protein_coding|1/1|c.1153G>C|p.Ala385Pro|1153/1176|1153/1176|385/391||,G|upstream_gene_variant|MODIFIER|opmQ|PA14_33750|transcript|ABJ11568.1|protein_coding||c.-2020G>C|||||2020|,G|upstream_gene_variant|MODIFIER|PA14_33760|PA14_33760|transcript|ABJ11567.1|protein_coding||c.-23G>C|||||23|,G|upstream_gene_variant|MODIFIER|PA14_33800|PA14_33800|transcript|ABJ11564.1|protein_coding||c.-2412C>G|||||2412|,G|upstream_gene_variant|MODIFIER|pvdA|PA14_33810|transcript|ABJ11563.1|protein_coding||c.-3024C>G|||||3024|,G|upstream_gene_variant|MODIFIER|pvdQ|PA14_33820|transcript|ABJ11562.1|protein_coding||c.-4478C>G|||||4478|,G|downstream_gene_variant|MODIFIER|pvdP|PA14_33740|transcript|ABJ11569.1|protein_coding||c.*3493C>G|||||3493|,G|downstream_gene_variant|MODIFIER|PA14_33780|PA14_33780|transcript|ABJ11565.1|protein_coding||c.*1253G>C|||||1253| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:79:0:0:0,-7.49763 0:4:4,0:4:120:0:0:0,-11.0896 0:3:3,2:1:40:2:41:0,-0.103943 0:2:2,0:2:41:0:0:0,-3.89478 +Chromosome 3005128 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=25;DPB=25;DPRA=1.41176;EPP=3.0103;EPPR=30.2953;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=42.6628;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=812;RO=23;RPL=1;RPP=3.0103;RPPR=14.4341;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=7;SRP=10.6577;SRR=16;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|pvdQ|PA14_33820|transcript|ABJ11562.1|protein_coding|1/1|c.141C>A|p.Ala47Ala|141/2289|141/2289|47/762||,A|upstream_gene_variant|MODIFIER|PA14_33760|PA14_33760|transcript|ABJ11567.1|protein_coding||c.-4641G>T|||||4641|,A|upstream_gene_variant|MODIFIER|PA14_33770|PA14_33770|transcript|ABJ11566.1|protein_coding||c.-3466G>T|||||3466|,A|upstream_gene_variant|MODIFIER|PA14_33780|PA14_33780|transcript|ABJ11565.1|protein_coding||c.-2370G>T|||||2370|,A|upstream_gene_variant|MODIFIER|PA14_33830|PA14_33830|transcript|ABJ11561.1|protein_coding||c.-2329C>A|||||2329|,A|upstream_gene_variant|MODIFIER|PA14_33840|PA14_33840|transcript|ABJ11560.1|protein_coding||c.-2694C>A|||||2694|,A|upstream_gene_variant|MODIFIER|lldA|PA14_33860|transcript|ABJ11559.1|protein_coding||c.-3711C>A|||||3711|,A|downstream_gene_variant|MODIFIER|PA14_33800|PA14_33800|transcript|ABJ11564.1|protein_coding||c.*1727C>A|||||1727|,A|downstream_gene_variant|MODIFIER|pvdA|PA14_33810|transcript|ABJ11563.1|protein_coding||c.*263C>A|||||263|,A|downstream_gene_variant|MODIFIER|PA14_33870|PA14_33870|transcript|ABJ11558.1|protein_coding||c.*4929G>T|||||4929| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:176:0:0:0,-16.1839 0:5:5,0:5:167:0:0:0,-15.359 0:7:7,0:7:263:0:0:0,-24.0267 0:8:8,2:6:206:2:31:0,-15.9288 +Chromosome 3009905 . T C 1.35839E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=39;DPB=39;DPRA=2.91667;EPP=11.6962;EPPR=8.03571;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=40.6121;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=47;QR=1226;RO=35;RPL=4;RPP=11.6962;RPPR=6.05036;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=20;SRP=4.56135;SRR=15;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|lldA|PA14_33860|transcript|ABJ11559.1|protein_coding|1/1|c.1067T>C|p.Leu356Pro|1067/1152|1067/1152|356/383||,C|upstream_gene_variant|MODIFIER|PA14_33880|PA14_33880|transcript|ABJ11557.1|protein_coding||c.-689T>C|||||689|,C|upstream_gene_variant|MODIFIER|aldG|PA14_33890|transcript|ABJ11556.1|protein_coding||c.-1191T>C|||||1191|,C|upstream_gene_variant|MODIFIER|PA14_33900|PA14_33900|transcript|ABJ11555.1|protein_coding||c.-1658T>C|||||1658|,C|downstream_gene_variant|MODIFIER|pvdQ|PA14_33820|transcript|ABJ11562.1|protein_coding||c.*2629T>C|||||2629|,C|downstream_gene_variant|MODIFIER|PA14_33830|PA14_33830|transcript|ABJ11561.1|protein_coding||c.*2125T>C|||||2125|,C|downstream_gene_variant|MODIFIER|PA14_33840|PA14_33840|transcript|ABJ11560.1|protein_coding||c.*1163T>C|||||1163|,C|downstream_gene_variant|MODIFIER|PA14_33870|PA14_33870|transcript|ABJ11558.1|protein_coding||c.*152A>G|||||152|,C|downstream_gene_variant|MODIFIER|PA14_33910|PA14_33910|transcript|ABJ11554.1|protein_coding||c.*4390A>G|||||4390| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:118:0:0:0,-10.9058 0:10:10,2:8:297:2:30:0,-24.2309 0:7:7,1:6:182:1:2:0,-16.4712 0:18:18,1:17:629:1:15:0,-55.4336 +Chromosome 3015416 . A T 7.20609E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=27;DPB=27;DPRA=1.5;EPP=7.35324;EPPR=17.6895;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=42.0855;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=828;RO=25;RPL=0;RPP=7.35324;RPPR=5.18177;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=17;SRP=10.0459;SRR=8;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_33910|PA14_33910|transcript|ABJ11554.1|protein_coding|1/1|c.154T>A|p.Leu52Met|154/1275|154/1275|52/424||,T|upstream_gene_variant|MODIFIER|PA14_33930|PA14_33930|transcript|ABJ11552.1|protein_coding||c.-1203A>T|||||1203|,T|downstream_gene_variant|MODIFIER|PA14_33880|PA14_33880|transcript|ABJ11557.1|protein_coding||c.*4586A>T|||||4586|,T|downstream_gene_variant|MODIFIER|aldG|PA14_33890|transcript|ABJ11556.1|protein_coding||c.*3850A>T|||||3850|,T|downstream_gene_variant|MODIFIER|PA14_33900|PA14_33900|transcript|ABJ11555.1|protein_coding||c.*1538A>T|||||1538|,T|downstream_gene_variant|MODIFIER|PA14_33920|PA14_33920|transcript|ABJ11553.1|protein_coding||c.*285T>A|||||285|,T|downstream_gene_variant|MODIFIER|PA14_33940|PA14_33940|transcript|ABJ11551.1|protein_coding||c.*1621T>A|||||1621|,T|downstream_gene_variant|MODIFIER|PA14_33960|PA14_33960|transcript|ABJ11550.1|protein_coding||c.*2168T>A|||||2168|,T|downstream_gene_variant|MODIFIER|PA14_33970|PA14_33970|transcript|ABJ11549.1|protein_coding||c.*4211T>A|||||4211| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:223:0:0:0,-20.427 0:9:9,2:7:264:2:4:0,-23.7357 0:5:5,0:5:138:0:0:0,-12.6886 0:7:7,0:7:203:0:0:0,-18.5466 +Chromosome 3015837 . A G 2.44509E-10 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=24;DPB=24;DPRA=0.789474;EPP=3.0103;EPPR=12.8806;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=23.6004;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=810;RO=22;RPL=1;RPP=3.0103;RPPR=6.56362;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=8;SRP=6.56362;SRR=14;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_33920|PA14_33920|transcript|ABJ11553.1|protein_coding|1/1|c.506T>C|p.Leu169Pro|506/642|506/642|169/213||,G|upstream_gene_variant|MODIFIER|PA14_33910|PA14_33910|transcript|ABJ11554.1|protein_coding||c.-268T>C|||||268|,G|upstream_gene_variant|MODIFIER|PA14_33930|PA14_33930|transcript|ABJ11552.1|protein_coding||c.-782A>G|||||782|,G|downstream_gene_variant|MODIFIER|aldG|PA14_33890|transcript|ABJ11556.1|protein_coding||c.*4271A>G|||||4271|,G|downstream_gene_variant|MODIFIER|PA14_33900|PA14_33900|transcript|ABJ11555.1|protein_coding||c.*1959A>G|||||1959|,G|downstream_gene_variant|MODIFIER|PA14_33940|PA14_33940|transcript|ABJ11551.1|protein_coding||c.*1200T>C|||||1200|,G|downstream_gene_variant|MODIFIER|PA14_33960|PA14_33960|transcript|ABJ11550.1|protein_coding||c.*1747T>C|||||1747|,G|downstream_gene_variant|MODIFIER|PA14_33970|PA14_33970|transcript|ABJ11549.1|protein_coding||c.*3790T>C|||||3790|,G|downstream_gene_variant|MODIFIER|PA14_33980|PA14_33980|transcript|ABJ11548.1|protein_coding||c.*4896T>C|||||4896| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:189:0:0:0,-17.3752 0:5:5,2:3:91:2:39:0,-4.78556 0:3:3,0:3:117:0:0:0,-10.9102 0:11:11,0:11:413:0:0:0,-37.5171 +Chromosome 3022790 . A C 4.57364E-10 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=29;DPB=29;DPRA=0.346154;EPP=7.35324;EPPR=6.01695;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=22.9741;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=873;RO=26;RPL=2;RPP=7.35324;RPPR=3.0103;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=17;SRP=8.35546;SRR=9;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_33990|PA14_33990|transcript|ABJ11547.1|protein_coding|1/1|c.1100T>G|p.Leu367Arg|1100/2550|1100/2550|367/849||,C|upstream_gene_variant|MODIFIER|PA14_33960|PA14_33960|transcript|ABJ11550.1|protein_coding||c.-3200T>G|||||3200|,C|upstream_gene_variant|MODIFIER|PA14_33970|PA14_33970|transcript|ABJ11549.1|protein_coding||c.-2096T>G|||||2096|,C|upstream_gene_variant|MODIFIER|PA14_33980|PA14_33980|transcript|ABJ11548.1|protein_coding||c.-1524T>G|||||1524|,C|downstream_gene_variant|MODIFIER|PA14_34000|PA14_34000|transcript|ABJ11546.1|protein_coding||c.*1101T>G|||||1101|,C|downstream_gene_variant|MODIFIER|PA14_34010|PA14_34010|transcript|ABJ11545.1|protein_coding||c.*2081T>G|||||2081|,C|downstream_gene_variant|MODIFIER|PA14_34020|PA14_34020|transcript|ABJ11544.1|protein_coding||c.*3858T>G|||||3858|,C|downstream_gene_variant|MODIFIER|PA14_34030|PA14_34030|transcript|ABJ11543.1|protein_coding||c.*4296T>G|||||4296|,C|downstream_gene_variant|MODIFIER|PA14_34050|PA14_34050|transcript|ABJ11542.1|protein_coding||c.*4867T>G|||||4867| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,2:1:35:2:4:0,-3.11863 0:8:8,0:8:255:0:0:0,-23.2533 0:13:13,0:12:401:0:0:0,-36.2399 0:5:5,0:5:182:0:0:0,-16.7345 +Chromosome 3048214 . G C 2.34019E-16 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=34;DPB=34;DPRA=1.08;EPP=7.35324;EPPR=3.28173;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=50.3419;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1143;RO=32;RPL=2;RPP=7.35324;RPPR=3.28173;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=22;SRP=12.7819;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|metQ-l|PA14_34280|transcript|ABJ11525.1|protein_coding|1/1|c.403C>G|p.Arg135Gly|403/795|403/795|135/264||,C|upstream_gene_variant|MODIFIER|PA14_34250|PA14_34250|transcript|ABJ11528.1|protein_coding||c.-2313C>G|||||2313|,C|upstream_gene_variant|MODIFIER|metI-1|PA14_34260|transcript|ABJ11527.1|protein_coding||c.-1482C>G|||||1482|,C|upstream_gene_variant|MODIFIER|metN-1|PA14_34270|transcript|ABJ11526.1|protein_coding||c.-389C>G|||||389|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_34330|PA14_34330|transcript|ABJ11521.1|protein_coding||c.-4722G>C|||||4722|,C|downstream_gene_variant|MODIFIER|sfnR|PA14_34210|transcript|ABJ11530.1|protein_coding||c.*4832G>C|||||4832|,C|downstream_gene_variant|MODIFIER|PA14_34230|PA14_34230|transcript|ABJ11529.1|protein_coding||c.*3506G>C|||||3506|,C|downstream_gene_variant|MODIFIER|PA14_34290|PA14_34290|transcript|ABJ11524.1|protein_coding||c.*434C>G|||||434|,C|downstream_gene_variant|MODIFIER|PA14_34300|PA14_34300|transcript|ABJ11523.1|protein_coding||c.*1840C>G|||||1840|,C|downstream_gene_variant|MODIFIER|PA14_34320|PA14_34320|transcript|ABJ11522.1|protein_coding||c.*3068C>G|||||3068| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:163:0:0:0,-14.9323 0:9:9,0:9:331:0:0:0,-30.1361 0:10:10,0:10:379:0:0:0,-34.4607 0:9:9,2:7:270:2:4:0,-24.285 +Chromosome 3053005 . G C 1.61841E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=6;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=16.0391;EPPR=26.1727;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=31.5288;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=24;QR=683;RO=24;RPL=6;RPP=16.0391;RPPR=8.80089;RPR=0;RUN=1;SAF=6;SAP=16.0391;SAR=0;SRF=14;SRP=4.45795;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_34330|PA14_34330|transcript|ABJ11521.1|protein_coding|1/1|c.70G>C|p.Gly24Arg|70/1236|70/1236|24/411||,C|upstream_gene_variant|MODIFIER|metQ-l|PA14_34280|transcript|ABJ11525.1|protein_coding||c.-4389C>G|||||4389|,C|upstream_gene_variant|MODIFIER|PA14_34290|PA14_34290|transcript|ABJ11524.1|protein_coding||c.-2969C>G|||||2969|,C|upstream_gene_variant|MODIFIER|PA14_34300|PA14_34300|transcript|ABJ11523.1|protein_coding||c.-1734C>G|||||1734|,C|upstream_gene_variant|MODIFIER|PA14_34320|PA14_34320|transcript|ABJ11522.1|protein_coding||c.-488C>G|||||488|,C|downstream_gene_variant|MODIFIER|mtlZ|PA14_34340|transcript|ABJ11520.1|protein_coding||c.*1197C>G|||||1197|,C|downstream_gene_variant|MODIFIER|mtlY|PA14_34350|transcript|ABJ11519.1|protein_coding||c.*2171C>G|||||2171|,C|downstream_gene_variant|MODIFIER|mtlD|PA14_34360|transcript|ABJ11518.1|protein_coding||c.*3676C>G|||||3676| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,2:3:91:2:4:0,-8.10757 0:6:6,1:5:95:1:2:0,-8.53475 0:5:5,1:4:107:1:2:0,-9.69255 0:14:14,2:12:390:2:16:0,-33.8839 +Chromosome 3063969 . A G 2.65484E-8 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=1.5;EPP=7.35324;EPPR=6.48466;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=18.9406;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=328;RO=10;RPL=0;RPP=7.35324;RPPR=6.48466;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=6;SRP=3.87889;SRR=4;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_34450|PA14_34450|transcript|ABJ11512.1|protein_coding|1/1|c.716T>C|p.Leu239Pro|716/906|716/906|239/301||,G|upstream_gene_variant|MODIFIER|mtlk|PA14_34370|transcript|ABJ11517.1|protein_coding||c.-4678T>C|||||4678|,G|upstream_gene_variant|MODIFIER|mtlG|PA14_34390|transcript|ABJ11516.1|protein_coding||c.-3805T>C|||||3805|,G|upstream_gene_variant|MODIFIER|mtlF|PA14_34410|transcript|ABJ11515.1|protein_coding||c.-2862T>C|||||2862|,G|upstream_gene_variant|MODIFIER|mtlE|PA14_34420|transcript|ABJ11514.1|protein_coding||c.-1476T>C|||||1476|,G|upstream_gene_variant|MODIFIER|mtlR|PA14_34440|transcript|ABJ11513.1|protein_coding||c.-413T>C|||||413|,G|upstream_gene_variant|MODIFIER|PA14_34460|PA14_34460|transcript|ABJ11511.1|protein_coding||c.-820A>G|||||820|,G|upstream_gene_variant|MODIFIER|PA14_34490|PA14_34490|transcript|ABJ11510.1|protein_coding||c.-1430A>G|||||1430|,G|upstream_gene_variant|MODIFIER|PA14_34500|PA14_34500|transcript|ABJ11509.1|protein_coding||c.-2494A>G|||||2494|,G|upstream_gene_variant|MODIFIER|srpL|PA14_34510|transcript|ABJ11508.1|protein_coding||c.-3296A>G|||||3296|,G|upstream_gene_variant|MODIFIER|srpM|PA14_34520|transcript|ABJ11507.1|protein_coding||c.-4492A>G|||||4492|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,2:2:42:2:4:0,-3.60978 0:1:1,0:1:40:0:0:0,-3.99568 0:4:4,0:4:156:0:0:0,-14.4171 0:3:3,0:3:90:0:0:0,-8.39541 +Chromosome 3068762 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=33;DPB=33;DPRA=0.736842;EPP=9.52472;EPPR=3.29983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=50.2236;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=45;QR=1032;RO=30;RPL=3;RPP=9.52472;RPPR=7.64277;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=11;SRP=7.64277;SRR=19;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|srpM|PA14_34520|transcript|ABJ11507.1|protein_coding|1/1|c.302A>C|p.Gln101Pro|302/765|302/765|101/254||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_34450|PA14_34450|transcript|ABJ11512.1|protein_coding||c.-4078T>G|||||4078|,C|upstream_gene_variant|MODIFIER|PA14_34540|PA14_34540|transcript|ABJ11506.1|protein_coding||c.-689A>C|||||689|,C|downstream_gene_variant|MODIFIER|PA14_34460|PA14_34460|transcript|ABJ11511.1|protein_coding||c.*3413A>C|||||3413|,C|downstream_gene_variant|MODIFIER|PA14_34490|PA14_34490|transcript|ABJ11510.1|protein_coding||c.*2296A>C|||||2296|,C|downstream_gene_variant|MODIFIER|PA14_34500|PA14_34500|transcript|ABJ11509.1|protein_coding||c.*1463A>C|||||1463|,C|downstream_gene_variant|MODIFIER|srpL|PA14_34510|transcript|ABJ11508.1|protein_coding||c.*298A>C|||||298|,C|downstream_gene_variant|MODIFIER|PA14_34550|PA14_34550|transcript|ABJ11505.1|protein_coding||c.*2158T>G|||||2158|,C|downstream_gene_variant|MODIFIER|PA14_34580|PA14_34580|transcript|ABJ11504.1|protein_coding||c.*3424T>G|||||3424|,C|downstream_gene_variant|MODIFIER|gapB|PA14_34600|transcript|ABJ11503.1|protein_coding||c.*4901T>G|||||4901| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,1:6:234:1:15:0,-19.9305 0:7:7,2:5:196:2:30:0,-15.1649 0:12:12,0:12:357:0:0:0,-32.4017 0:7:7,0:7:245:0:0:0,-22.3826 +Chromosome 3075312 . T G 7.44317E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=47;DPB=47;DPRA=0.711111;EPP=13.8677;EPPR=37.9607;GTI=0;LEN=1;MEANALT=1;MQM=54.4;MQMR=60;NS=4;NUMALT=1;ODDS=62.7955;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1469;RO=42;RPL=5;RPP=13.8677;RPPR=8.18047;RPR=0;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=18;SRP=4.87156;SRR=24;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|PA14_34550|PA14_34550|transcript|ABJ11505.1|protein_coding||c.-3157A>C|||||3157|,G|upstream_gene_variant|MODIFIER|PA14_34580|PA14_34580|transcript|ABJ11504.1|protein_coding||c.-1867A>C|||||1867|,G|upstream_gene_variant|MODIFIER|gapB|PA14_34600|transcript|ABJ11503.1|protein_coding||c.-24A>C|||||24|,G|upstream_gene_variant|MODIFIER|gntR|PA14_34660|transcript|ABJ11499.1|protein_coding||c.-2475T>G|||||2475|,G|downstream_gene_variant|MODIFIER|PA14_34540|PA14_34540|transcript|ABJ11506.1|protein_coding||c.*4452T>G|||||4452|,G|downstream_gene_variant|MODIFIER|PA14_34610|PA14_34610|transcript|ABJ11502.1|protein_coding||c.*141A>C|||||141|,G|downstream_gene_variant|MODIFIER|gnuT|PA14_34630|transcript|ABJ11501.1|protein_coding||c.*310A>C|||||310|,G|downstream_gene_variant|MODIFIER|gntK|PA14_34640|transcript|ABJ11500.1|protein_coding||c.*1759A>C|||||1759|,G|downstream_gene_variant|MODIFIER|PA14_34670|PA14_34670|transcript|ABJ11498.1|protein_coding||c.*3860A>C|||||3860|,G|downstream_gene_variant|MODIFIER|PA14_34680|PA14_34680|transcript|ABJ11497.1|protein_coding||c.*4258A>C|||||4258|,G|intergenic_region|MODIFIER|gapB-PA14_34610|PA14_34600-PA14_34610|intergenic_region|PA14_34600-PA14_34610|||n.3075312T>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,1:9:355:1:14:0,-30.9129 0:13:13,1:12:396:1:2:0,-35.7412 0:9:9,3:6:231:3:18:0,-19.4765 0:15:15,0:15:487:0:0:0,-44.1254 +Chromosome 3103618 . G T 0.0227988 . AB=0;ABP=0;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=1;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=2;NUMALT=1;ODDS=5.74083;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=54;RO=2;RPL=0;RPP=7.35324;RPPR=7.35324;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_34850|PA14_34850|transcript|ABJ11481.1|protein_coding|1/1|c.387G>T|p.Leu129Phe|387/543|387/543|129/180||,T|upstream_gene_variant|MODIFIER|chiC|PA14_34870|transcript|ABJ11480.1|protein_coding||c.-375G>T|||||375|,T|upstream_gene_variant|MODIFIER|PA14_34880|PA14_34880|transcript|ABJ11479.1|protein_coding||c.-2003G>T|||||2003|,T|upstream_gene_variant|MODIFIER|PA14_34900|PA14_34900|transcript|ABJ11478.1|protein_coding||c.-2749G>T|||||2749|,T|upstream_gene_variant|MODIFIER|PA14_34920|PA14_34920|transcript|ABJ11477.1|protein_coding||c.-4559G>T|||||4559|,T|downstream_gene_variant|MODIFIER|PA14_34840|PA14_34840|transcript|ABJ11482.1|protein_coding||c.*454G>T|||||454| GT:DP:DPR:RO:QR:AO:QA:GL 1:2:2,2:0:0:2:32:-3.03997,0 . 0:2:2,0:2:54:0:0:0,-5.12589 . +Chromosome 3113966 . G C 3.45917E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=18;DPB=18;DPRA=1.25;EPP=9.52472;EPPR=3.15506;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=33.4378;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=565;RO=15;RPL=3;RPP=9.52472;RPPR=3.15506;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=5;SRP=6.62942;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|gcd|PA14_34970|transcript|ABJ11473.1|protein_coding|1/1|c.2111G>C|p.Arg704Pro|2111/2412|2111/2412|704/803||,C|upstream_gene_variant|MODIFIER|PA14_34990|PA14_34990|transcript|ABJ11472.1|protein_coding||c.-433G>C|||||433|,C|upstream_gene_variant|MODIFIER|PA14_35000|PA14_35000|transcript|ABJ11471.1|protein_coding||c.-2674G>C|||||2674|,C|downstream_gene_variant|MODIFIER|PA14_34930|PA14_34930|transcript|ABJ11476.1|protein_coding||c.*4241G>C|||||4241|,C|downstream_gene_variant|MODIFIER|PA14_34940|PA14_34940|transcript|ABJ11475.1|protein_coding||c.*3963G>C|||||3963|,C|downstream_gene_variant|MODIFIER|opbA|PA14_34960|transcript|ABJ11474.1|protein_coding||c.*2264G>C|||||2264|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_35010|PA14_35010|transcript|ABJ11470.1|protein_coding||c.*2974C>G|||||2974|,C|downstream_gene_variant|MODIFIER|PA14_35020|PA14_35020|transcript|ABJ11469.1|protein_coding||c.*3596C>G|||||3596|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:102:0:0:0,-9.51498 0:5:5,0:5:195:0:0:0,-17.9239 0:4:4,1:3:116:1:15:0,-9.31741 0:6:6,2:4:152:2:4:0,-13.6692 +Chromosome 3122289 . G C 1.55973E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=37;DPB=37;DPRA=1.11111;EPP=7.35324;EPPR=10.5174;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=60.6656;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=1264;RO=35;RPL=2;RPP=7.35324;RPPR=30.3709;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=24;SRP=13.4954;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_35060|PA14_35060|transcript|ABJ11465.1|protein_coding|1/1|c.38C>G|p.Ala13Gly|38/429|38/429|13/142||,C|upstream_gene_variant|MODIFIER|PA14_35010|PA14_35010|transcript|ABJ11470.1|protein_coding||c.-4714C>G|||||4714|,C|upstream_gene_variant|MODIFIER|PA14_35020|PA14_35020|transcript|ABJ11469.1|protein_coding||c.-3183C>G|||||3183|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_35030|PA14_35030|transcript|ABJ11468.1|protein_coding||c.-2520C>G|||||2520|,C|upstream_gene_variant|MODIFIER|PA14_35040|PA14_35040|transcript|ABJ11467.1|protein_coding||c.-1852C>G|||||1852|,C|upstream_gene_variant|MODIFIER|PA14_35050|PA14_35050|transcript|ABJ11466.1|protein_coding||c.-398C>G|||||398|,C|upstream_gene_variant|MODIFIER|PA14_35070|PA14_35070|transcript|ABJ11464.1|protein_coding||c.-325G>C|||||325|,C|downstream_gene_variant|MODIFIER|arsH|PA14_35080|transcript|ABJ11463.1|protein_coding||c.*1192C>G|||||1192|,C|downstream_gene_variant|MODIFIER|arsC|PA14_35100|transcript|ABJ11462.1|protein_coding||c.*1896C>G|||||1896|,C|downstream_gene_variant|MODIFIER|arsB|PA14_35110|transcript|ABJ11461.1|protein_coding||c.*2398C>G|||||2398|,C|downstream_gene_variant|MODIFIER|arsR|PA14_35130|transcript|ABJ11460.1|protein_coding||c.*3695C>G|||||3695|,C|downstream_gene_variant|MODIFIER|PA14_35140|PA14_35140|transcript|ABJ11459.1|protein_coding||c.*4124C>G|||||4124| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:236:0:0:0,-21.5634 0:12:12,0:12:467:0:0:0,-42.3813 0:10:10,2:8:296:2:16:0,-25.4688 0:8:8,0:8:265:0:0:0,-24.1605 +Chromosome 3126485 . C G 5.12534E-16 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=37;DPB=37;DPRA=0.85;EPP=11.6962;EPPR=4.65535;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=51.7529;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=1195;RO=33;RPL=0;RPP=11.6962;RPPR=8.34028;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=13;SRP=6.23461;SRR=20;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|PA14_35140|PA14_35140|transcript|ABJ11459.1|protein_coding|1/1|c.819G>C|p.Ser273Ser|819/891|819/891|273/296||,G|upstream_gene_variant|MODIFIER|PA14_35050|PA14_35050|transcript|ABJ11466.1|protein_coding||c.-4594G>C|||||4594|,G|upstream_gene_variant|MODIFIER|PA14_35060|PA14_35060|transcript|ABJ11465.1|protein_coding||c.-4159G>C|||||4159|,G|upstream_gene_variant|MODIFIER|arsH|PA14_35080|transcript|ABJ11463.1|protein_coding||c.-2312G>C|||||2312|,G|upstream_gene_variant|MODIFIER|arsC|PA14_35100|transcript|ABJ11462.1|protein_coding||c.-1830G>C|||||1830|,G|upstream_gene_variant|MODIFIER|arsB|PA14_35110|transcript|ABJ11461.1|protein_coding||c.-515G>C|||||515|,G|upstream_gene_variant|MODIFIER|arsR|PA14_35130|transcript|ABJ11460.1|protein_coding||c.-151G>C|||||151|,G|upstream_gene_variant|MODIFIER|PA14_35150|PA14_35150|transcript|ABJ11458.1|protein_coding||c.-1027C>G|||||1027|,G|upstream_gene_variant|MODIFIER|soxR|PA14_35170|transcript|ABJ11456.1|protein_coding||c.-2568C>G|||||2568|,G|downstream_gene_variant|MODIFIER|PA14_35070|PA14_35070|transcript|ABJ11464.1|protein_coding||c.*3017C>G|||||3017|,G|downstream_gene_variant|MODIFIER|PA14_35160|PA14_35160|transcript|ABJ11457.1|protein_coding||c.*2113G>C|||||2113|,G|downstream_gene_variant|MODIFIER|pbpC|PA14_35190|transcript|ABJ11455.1|protein_coding||c.*3046G>C|||||3046|,G|downstream_gene_variant|MODIFIER|PA14_35200|PA14_35200|transcript|ABJ11454.1|protein_coding||c.*4865G>C|||||4865| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:160:0:0:0,-14.784 0:7:7,1:6:188:1:2:0,-17.0217 0:10:10,3:7:267:3:19:0,-22.6177 0:16:16,0:16:580:0:0:0,-52.5234 +Chromosome 3140690 . C A 8.90416E-7 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=3.6;EPP=7.35324;EPPR=14.8328;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=15.6007;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=29;QR=247;RO=9;RPL=0;RPP=7.35324;RPPR=14.8328;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=22.5536;SRR=9;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|kguD|PA14_35320|transcript|ABJ11446.1|protein_coding|1/1|c.222G>T|p.Val74Val|222/987|222/987|74/328||,A|upstream_gene_variant|MODIFIER|PA14_35270|PA14_35270|transcript|ABJ11449.1|protein_coding||c.-3439G>T|||||3439|,A|upstream_gene_variant|MODIFIER|gnd|PA14_35290|transcript|ABJ11448.1|protein_coding||c.-1652G>T|||||1652|,A|upstream_gene_variant|MODIFIER|PA14_35300|PA14_35300|transcript|ABJ11447.1|protein_coding||c.-933G>T|||||933|,A|upstream_gene_variant|MODIFIER|ptxR|PA14_35380|transcript|ABJ11441.1|protein_coding||c.-4991C>A|||||4991|,A|downstream_gene_variant|MODIFIER|PA14_35250|PA14_35250|transcript|ABJ11450.1|protein_coding||c.*4858C>A|||||4858|,A|downstream_gene_variant|MODIFIER|kguT|PA14_35330|transcript|ABJ11445.1|protein_coding||c.*240G>T|||||240|,A|downstream_gene_variant|MODIFIER|kguK|PA14_35340|transcript|ABJ11444.1|protein_coding||c.*1610G>T|||||1610|,A|downstream_gene_variant|MODIFIER|kguE|PA14_35360|transcript|ABJ11443.1|protein_coding||c.*2553G>T|||||2553|,A|downstream_gene_variant|MODIFIER|ptxS|PA14_35370|transcript|ABJ11442.1|protein_coding||c.*3407G>T|||||3407|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:38:0:0:0,-3.79727 0:6:6,2:4:92:2:29:0,-5.75374 0:1:1,0:1:31:0:0:0,-3.09945 0:3:3,0:3:86:0:0:0,-8.0257 +Chromosome 3154052 . C A 3.12677E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=31;DPB=31;DPRA=1.42857;EPP=7.35324;EPPR=19.8579;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=44.706;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=1074;RO=29;RPL=0;RPP=7.35324;RPPR=19.8579;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=25;SRP=36.0317;SRR=4;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|PA14_35470|PA14_35470|transcript|ABJ11434.1|protein_coding|1/1|c.342C>A|p.Ala114Ala|342/819|342/819|114/272||,A|upstream_gene_variant|MODIFIER|pvcB|PA14_35420|transcript|ABJ11438.1|protein_coding||c.-4261G>T|||||4261|,A|upstream_gene_variant|MODIFIER|pvcA|PA14_35430|transcript|ABJ11437.1|protein_coding||c.-3257G>T|||||3257|,A|upstream_gene_variant|MODIFIER|ansA|PA14_35440|transcript|ABJ11436.1|protein_coding||c.-2055G>T|||||2055|,A|upstream_gene_variant|MODIFIER|PA14_35460|PA14_35460|transcript|ABJ11435.1|protein_coding||c.-510G>T|||||510|,A|downstream_gene_variant|MODIFIER|lpdV|PA14_35490|transcript|ABJ11433.1|protein_coding||c.*610G>T|||||610|,A|downstream_gene_variant|MODIFIER|bkdB|PA14_35500|transcript|ABJ11432.1|protein_coding||c.*2008G>T|||||2008|,A|downstream_gene_variant|MODIFIER|bkdA2|PA14_35520|transcript|ABJ11431.1|protein_coding||c.*3295G>T|||||3295|,A|downstream_gene_variant|MODIFIER|bkdA1|PA14_35530|transcript|ABJ11430.1|protein_coding||c.*4344G>T|||||4344| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,2:8:300:2:31:0,-24.4077 0:11:11,0:11:394:0:0:0,-35.789 0:4:4,0:4:151:0:0:0,-13.9568 0:6:6,0:6:229:0:0:0,-20.975 +Chromosome 3154070 . A G 5.40174E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=34;DPB=34;DPRA=1.25;EPP=3.0103;EPPR=16.3106;GTI=0;LEN=1;MEANALT=1;MQM=49.5;MQMR=60;NS=4;NUMALT=1;ODDS=61.4076;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=42;QR=1195;RO=32;RPL=0;RPP=7.35324;RPPR=16.3106;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=26;SRP=30.1537;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|PA14_35470|PA14_35470|transcript|ABJ11434.1|protein_coding|1/1|c.360A>G|p.Pro120Pro|360/819|360/819|120/272||,G|upstream_gene_variant|MODIFIER|pvcB|PA14_35420|transcript|ABJ11438.1|protein_coding||c.-4279T>C|||||4279|,G|upstream_gene_variant|MODIFIER|pvcA|PA14_35430|transcript|ABJ11437.1|protein_coding||c.-3275T>C|||||3275|,G|upstream_gene_variant|MODIFIER|ansA|PA14_35440|transcript|ABJ11436.1|protein_coding||c.-2073T>C|||||2073|,G|upstream_gene_variant|MODIFIER|PA14_35460|PA14_35460|transcript|ABJ11435.1|protein_coding||c.-528T>C|||||528|,G|downstream_gene_variant|MODIFIER|lpdV|PA14_35490|transcript|ABJ11433.1|protein_coding||c.*592T>C|||||592|,G|downstream_gene_variant|MODIFIER|bkdB|PA14_35500|transcript|ABJ11432.1|protein_coding||c.*1990T>C|||||1990|,G|downstream_gene_variant|MODIFIER|bkdA2|PA14_35520|transcript|ABJ11431.1|protein_coding||c.*3277T>C|||||3277|,G|downstream_gene_variant|MODIFIER|bkdA1|PA14_35530|transcript|ABJ11430.1|protein_coding||c.*4326T>C|||||4326| GT:DP:DPR:RO:QR:AO:QA:GL 0:11:11,0:11:413:0:0:0,-37.5086 0:10:10,2:8:298:2:42:0,-23.188 0:7:7,0:7:251:0:0:0,-22.933 0:6:6,0:6:233:0:0:0,-21.3389 +Chromosome 3169992 . G T 6.83831E-12 . AB=0;ABP=0;AC=0;AF=0;AN=3;AO=3;CIGAR=1X;DP=18;DPB=18;DPRA=1.27273;EPP=3.73412;EPPR=27.4756;GTI=0;LEN=1;MEANALT=1;MQM=53.6667;MQMR=60;NS=3;NUMALT=1;ODDS=27.2184;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=344;RO=15;RPL=2;RPP=3.73412;RPPR=4.31318;RPR=1;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=7;SRP=3.15506;SRR=8;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|pslH|PA14_35650|transcript|ABJ11421.1|protein_coding|1/1|c.54C>A|p.Gly18Gly|54/1209|54/1209|18/402||,T|upstream_gene_variant|MODIFIER|pslK|PA14_35620|transcript|ABJ11424.1|protein_coding||c.-3690C>A|||||3690|,T|upstream_gene_variant|MODIFIER|pslJ|PA14_35630|transcript|ABJ11423.1|protein_coding||c.-2252C>A|||||2252|,T|upstream_gene_variant|MODIFIER|pslI|PA14_35640|transcript|ABJ11422.1|protein_coding||c.-1146C>A|||||1146|,T|upstream_gene_variant|MODIFIER|PA14_35700|PA14_35700|transcript|ABJ11417.1|protein_coding||c.-4611G>T|||||4611|,T|downstream_gene_variant|MODIFIER|pslG|PA14_35670|transcript|ABJ11420.1|protein_coding||c.*62C>A|||||62|,T|downstream_gene_variant|MODIFIER|pslF|PA14_35680|transcript|ABJ11419.1|protein_coding||c.*1380C>A|||||1380|,T|downstream_gene_variant|MODIFIER|pslE|PA14_35690|transcript|ABJ11418.1|protein_coding||c.*2567C>A|||||2567| GT:DP:DPR:RO:QR:AO:QA:GL . 0:4:4,0:4:89:0:0:0,-8.22947 0:7:7,3:4:83:3:6:0,-7.11034 0:7:7,0:7:172:0:0:0,-15.7137 +Chromosome 3190037 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=15;CIGAR=1X;DP=125;DPB=125;DPRA=0;EPP=35.5824;EPPR=3.08926;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=128.479;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=169;QR=3609;RO=110;RPL=15;RPP=35.5824;RPPR=23.2247;RPR=0;RUN=1;SAF=15;SAP=35.5824;SAR=0;SRF=71;SRP=23.2247;SRR=39;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_35850|PA14_35850|transcript|ABJ11402.1|protein_coding|1/1|c.111G>T|p.Leu37Phe|111/480|111/480|37/159||,T|upstream_gene_variant|MODIFIER|PA14_35800|PA14_35800|transcript|ABJ11407.1|protein_coding||c.-3722C>A|||||3722|,T|upstream_gene_variant|MODIFIER|PA14_35810|PA14_35810|transcript|ABJ11406.1|protein_coding||c.-2990C>A|||||2990|,T|upstream_gene_variant|MODIFIER|tnpS|PA14_35820|transcript|ABJ11405.1|protein_coding||c.-1956C>A|||||1956|,T|upstream_gene_variant|MODIFIER|PA14_35860|PA14_35860|transcript|ABJ11401.1|protein_coding||c.-951G>T|||||951|,T|upstream_gene_variant|MODIFIER|PA14_35880|PA14_35880|transcript|ABJ11400.1|protein_coding||c.-2319G>T|||||2319|,T|upstream_gene_variant|MODIFIER|PA14_35890|PA14_35890|transcript|ABJ11399.1|protein_coding||c.-3804G>T|||||3804|,T|downstream_gene_variant|MODIFIER|tnpT|PA14_35830|transcript|ABJ11404.1|protein_coding||c.*774G>T|||||774|,T|downstream_gene_variant|MODIFIER|PA14_35840|PA14_35840|transcript|ABJ11403.1|protein_coding||c.*91G>T|||||91| GT:DP:DPR:RO:QR:AO:QA:GL 0:35:35,2:33:991:2:39:0,-85.7277 0:37:37,3:34:1209:3:19:0,-107.303 0:23:23,5:18:544:5:75:0,-42.328 0:30:30,5:25:865:5:36:0,-74.8232 +Chromosome 3229665 . G C 3.2095E-8 . AB=0;ABP=0;AC=0;AF=0;AN=3;AO=2;CIGAR=1X;DP=8;DPB=8;DPRA=2;EPP=7.35324;EPPR=8.80089;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=18.7233;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=229;RO=6;RPL=2;RPP=7.35324;RPPR=4.45795;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=3.0103;SRR=3;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_36260|PA14_36260|transcript|ABJ11369.1|protein_coding|1/1|c.539C>G|p.Ser180Trp|539/1596|539/1596|180/531||,C|upstream_gene_variant|MODIFIER|PA14_36250|PA14_36250|transcript|ABJ11370.1|protein_coding||c.-1183C>G|||||1183|,C|downstream_gene_variant|MODIFIER|PA14_36190|PA14_36190|transcript|ABJ11374.1|protein_coding||c.*4664G>C|||||4664|,C|downstream_gene_variant|MODIFIER|PA14_36200|PA14_36200|transcript|ABJ11373.1|protein_coding||c.*3559G>C|||||3559|,C|downstream_gene_variant|MODIFIER|gltJ|PA14_36220|transcript|ABJ11372.1|protein_coding||c.*2762G>C|||||2762|,C|downstream_gene_variant|MODIFIER|glnP|PA14_36230|transcript|ABJ11371.1|protein_coding||c.*2083G>C|||||2083|,C|downstream_gene_variant|MODIFIER|PA14_36270|PA14_36270|transcript|ABJ11368.1|protein_coding||c.*627C>G|||||627|,C|downstream_gene_variant|MODIFIER|PA14_36280|PA14_36280|transcript|ABJ11367.1|protein_coding||c.*1508C>G|||||1508|,C|downstream_gene_variant|MODIFIER|yncB|PA14_36290|transcript|ABJ11366.1|protein_coding||c.*1849C>G|||||1849|,C|downstream_gene_variant|MODIFIER|PA14_36300|PA14_36300|transcript|ABJ11365.1|protein_coding||c.*3017C>G|||||3017|,C|downstream_gene_variant|MODIFIER|hcnC|PA14_36310|transcript|ABJ11364.1|protein_coding||c.*3754C>G|||||3754| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:112:0:0:0,-10.4459 . 0:1:1,0:1:40:0:0:0,-3.99568 0:4:4,2:2:77:2:4:0,-6.92914 +Chromosome 3241259 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=41;DPB=41;DPRA=2.41667;EPP=13.8677;EPPR=18.4519;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=55.913;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=62;QR=1174;RO=36;RPL=0;RPP=13.8677;RPPR=22.5536;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=7;SRP=32.2045;SRR=29;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|PA14_36375|PA14_36375|transcript|ABJ15684.1|protein_coding|1/1|c.762C>A|p.Arg254Arg|762/1425|762/1425|254/474||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|hcnA|PA14_36330|transcript|ABJ11362.1|protein_coding||c.-4879G>T|||||4879|,A|upstream_gene_variant|MODIFIER|PA14_36350|PA14_36350|transcript|ABJ11361.1|protein_coding||c.-2720G>T|||||2720|,A|upstream_gene_variant|MODIFIER|PA14_36360|PA14_36360|transcript|ABJ11360.1|protein_coding||c.-2141G>T|||||2141|,A|upstream_gene_variant|MODIFIER|PA14_36370|PA14_36370|transcript|ABJ11359.1|protein_coding||c.-899G>T|||||899|,A|upstream_gene_variant|MODIFIER|PA14_36390|PA14_36390|transcript|ABJ11358.1|protein_coding||c.-647C>A|||||647|,A|upstream_gene_variant|MODIFIER|PA14_36410|PA14_36410|transcript|ABJ11356.1|protein_coding||c.-1964C>A|||||1964|,A|upstream_gene_variant|MODIFIER|PA14_36450|PA14_36450|transcript|ABJ11354.1|protein_coding||c.-4758C>A|||||4758|,A|downstream_gene_variant|MODIFIER|exoY|PA14_36345|transcript|ABJ15697.1|protein_coding||c.*3271C>A|||||3271|,A|downstream_gene_variant|MODIFIER|PA14_36400|PA14_36400|transcript|ABJ11357.1|protein_coding||c.*1581G>T|||||1581|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_36420|PA14_36420|transcript|ABJ11355.1|protein_coding||c.*2576G>T|||||2576| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:201:0:0:0,-18.4134 0:6:6,0:6:209:0:0:0,-19.1491 0:14:14,4:10:293:4:47:0,-22.3037 0:15:15,1:14:471:1:15:0,-41.2073 +Chromosome 3247096 . G T 1.50676E-16 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=30;CIGAR=1X;DP=124;DPB=124;DPRA=0;EPP=68.1545;EPPR=3.1027;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=130.782;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=413;QR=3035;RO=94;RPL=30;RPP=68.1545;RPPR=12.2506;RPR=0;RUN=1;SAF=30;SAP=68.1545;SAR=0;SRF=61;SRP=21.1213;SRR=33;TYPE=snp;technology.ILLUMINA=1;ANN=T|upstream_gene_variant|MODIFIER|PA14_36400|PA14_36400|transcript|ABJ11357.1|protein_coding||c.-3936C>A|||||3936|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|PA14_36420|PA14_36420|transcript|ABJ11355.1|protein_coding||c.-1162C>A|||||1162|,T|upstream_gene_variant|MODIFIER|PA14_36470|PA14_36470|transcript|ABJ11352.1|protein_coding||c.-156G>T|||||156|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|PA14_36390|PA14_36390|transcript|ABJ11358.1|protein_coding||c.*4240G>T|||||4240|,T|downstream_gene_variant|MODIFIER|PA14_36410|PA14_36410|transcript|ABJ11356.1|protein_coding||c.*3265G>T|||||3265|,T|downstream_gene_variant|MODIFIER|PA14_36450|PA14_36450|transcript|ABJ11354.1|protein_coding||c.*489G>T|||||489|,T|downstream_gene_variant|MODIFIER|PA14_36460|PA14_36460|transcript|ABJ11353.1|protein_coding||c.*129G>T|||||129|,T|downstream_gene_variant|MODIFIER|PA14_36480|PA14_36480|transcript|ABJ11351.1|protein_coding||c.*495C>A|||||495|,T|downstream_gene_variant|MODIFIER|PA14_36490|PA14_36490|transcript|ABJ11350.1|protein_coding||c.*772C>A|||||772|,T|downstream_gene_variant|MODIFIER|PA14_36500|PA14_36500|transcript|ABJ11349.1|protein_coding||c.*1149C>A|||||1149|,T|downstream_gene_variant|MODIFIER|PA14_36520|PA14_36520|transcript|ABJ11348.1|protein_coding||c.*2229C>A|||||2229|,T|downstream_gene_variant|MODIFIER|PA14_36530|PA14_36530|transcript|ABJ11347.1|protein_coding||c.*2901C>A|||||2901|,T|downstream_gene_variant|MODIFIER|PA14_36540|PA14_36540|transcript|ABJ11346.1|protein_coding||c.*3479C>A|||||3479|,T|downstream_gene_variant|MODIFIER|PA14_36550|PA14_36550|transcript|ABJ11345.1|protein_coding||c.*4252C>A|||||4252|,T|intergenic_region|MODIFIER|PA14_36460-PA14_36470|PA14_36460-PA14_36470|intergenic_region|PA14_36460-PA14_36470|||n.3247096G>T|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:22:22,6:16:558:6:77:0,-43.4729 0:36:36,9:27:853:9:122:0,-65.9126 0:29:29,7:22:665:7:108:0,-50.2363 0:37:37,8:29:959:8:106:0,-76.9131 +Chromosome 3254740 . T G 6.40291E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=22;DPB=22;DPRA=2.5;EPP=7.35324;EPPR=5.8675;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=29.5484;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=687;RO=19;RPL=0;RPP=7.35324;RPPR=4.03889;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=13;SRP=8.61041;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|glgA|PA14_36570|transcript|ABJ11343.1|protein_coding|1/1|c.1234T>G|p.Cys412Gly|1234/1542|1234/1542|412/513||,G|upstream_gene_variant|MODIFIER|PA14_36520|PA14_36520|transcript|ABJ11348.1|protein_coding||c.-4945A>C|||||4945|,G|upstream_gene_variant|MODIFIER|PA14_36530|PA14_36530|transcript|ABJ11347.1|protein_coding||c.-4291A>C|||||4291|,G|upstream_gene_variant|MODIFIER|PA14_36540|PA14_36540|transcript|ABJ11346.1|protein_coding||c.-3389A>C|||||3389|,G|upstream_gene_variant|MODIFIER|PA14_36550|PA14_36550|transcript|ABJ11345.1|protein_coding||c.-2295A>C|||||2295|,G|upstream_gene_variant|MODIFIER|PA14_36560|PA14_36560|transcript|ABJ11344.1|protein_coding||c.-1601A>C|||||1601|,G|upstream_gene_variant|MODIFIER|glgB|PA14_36580|transcript|ABJ11342.1|protein_coding||c.-308T>G|||||308|,G|upstream_gene_variant|MODIFIER|malQ|PA14_36590|transcript|ABJ11341.1|protein_coding||c.-2052T>G|||||2052|,G|upstream_gene_variant|MODIFIER|PA14_36605|PA14_36605|transcript|ABJ15692.1|protein_coding||c.-4099T>G|||||4099| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:190:0:0:0,-17.4665 0:2:2,0:2:79:0:0:0,-7.49763 0:5:5,0:5:197:0:0:0,-18.1066 0:10:10,2:7:221:2:4:0,-19.774 +Chromosome 3262389 . C T 1.07002E-6 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=28;DPB=28;DPRA=1;EPP=7.35324;EPPR=4.34659;GTI=0;LEN=1;MEANALT=1;MQM=43.5;MQMR=58;NS=4;NUMALT=1;ODDS=15.2164;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=716;RO=26;RPL=0;RPP=7.35324;RPPR=3.34437;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=7;SRP=15.0369;SRR=19;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|glgX|PA14_36630|transcript|ABJ11339.1|protein_coding|1/1|c.456C>T|p.Ala152Ala|456/2151|456/2151|152/716||,T|upstream_gene_variant|MODIFIER|PA14_36650|PA14_36650|transcript|ABJ11338.1|protein_coding||c.-1795C>T|||||1795|,T|upstream_gene_variant|MODIFIER|PA14_36660|PA14_36660|transcript|ABJ11337.1|protein_coding||c.-2278C>T|||||2278|,T|upstream_gene_variant|MODIFIER|PA14_36670|PA14_36670|transcript|ABJ11336.1|protein_coding||c.-3529C>T|||||3529|,T|upstream_gene_variant|MODIFIER|PA14_36680|PA14_36680|transcript|ABJ11335.1|protein_coding||c.-4464C>T|||||4464|,T|downstream_gene_variant|MODIFIER|malQ|PA14_36590|transcript|ABJ11341.1|protein_coding||c.*3543C>T|||||3543|,T|downstream_gene_variant|MODIFIER|PA14_36605|PA14_36605|transcript|ABJ15692.1|protein_coding||c.*770C>T|||||770|,T|downstream_gene_variant|MODIFIER|PA14_36620|PA14_36620|transcript|ABJ11340.1|protein_coding||c.*468C>T|||||468| GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:2:0:0:0,-0.2 0:6:6,0:6:213:0:0:0,-19.5076 0:7:7,2:5:137:2:32:0,-9.58073 0:14:14,0:14:364:0:0:0,-32.9919 +Chromosome 3265119 . C A 1.64407E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=24;DPB=24;DPRA=1.8;EPP=7.35324;EPPR=4.58955;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=30.9244;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=752;RO=22;RPL=0;RPP=7.35324;RPPR=3.40511;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=9;SRP=4.58955;SRR=13;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|PA14_36660|PA14_36660|transcript|ABJ11337.1|protein_coding|1/1|c.453C>A|p.Ser151Arg|453/1248|453/1248|151/415||,A|upstream_gene_variant|MODIFIER|PA14_36670|PA14_36670|transcript|ABJ11336.1|protein_coding||c.-799C>A|||||799|,A|upstream_gene_variant|MODIFIER|PA14_36680|PA14_36680|transcript|ABJ11335.1|protein_coding||c.-1734C>A|||||1734|,A|upstream_gene_variant|MODIFIER|ybhO|PA14_36690|transcript|ABJ11334.1|protein_coding||c.-2468C>A|||||2468|,A|upstream_gene_variant|MODIFIER|PA14_36700|PA14_36700|transcript|ABJ11333.1|protein_coding||c.-3670C>A|||||3670|,A|downstream_gene_variant|MODIFIER|PA14_36605|PA14_36605|transcript|ABJ15692.1|protein_coding||c.*3500C>A|||||3500|,A|downstream_gene_variant|MODIFIER|PA14_36620|PA14_36620|transcript|ABJ11340.1|protein_coding||c.*3198C>A|||||3198|,A|downstream_gene_variant|MODIFIER|glgX|PA14_36630|transcript|ABJ11339.1|protein_coding||c.*1035C>A|||||1035|,A|downstream_gene_variant|MODIFIER|PA14_36650|PA14_36650|transcript|ABJ11338.1|protein_coding||c.*519C>A|||||519|,A|downstream_gene_variant|MODIFIER|glgB|PA14_36710|transcript|ABJ11332.1|protein_coding||c.*4667G>T|||||4667| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:79:0:0:0,-7.36758 0:6:6,0:6:236:0:0:0,-21.6125 0:9:9,2:7:235:2:31:0,-18.5278 0:6:6,0:6:202:0:0:0,-18.5031 +Chromosome 3269595 . C G 1.13031E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=32;DPB=32;DPRA=1;EPP=7.35324;EPPR=4.16842;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=61.0332;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1087;RO=30;RPL=0;RPP=7.35324;RPPR=10.2485;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=13;SRP=4.16842;SRR=17;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|PA14_36700|PA14_36700|transcript|ABJ11333.1|protein_coding|1/1|c.807C>G|p.Leu269Leu|807/996|807/996|269/331||,G|downstream_gene_variant|MODIFIER|PA14_36650|PA14_36650|transcript|ABJ11338.1|protein_coding||c.*4995C>G|||||4995|,G|downstream_gene_variant|MODIFIER|PA14_36660|PA14_36660|transcript|ABJ11337.1|protein_coding||c.*3681C>G|||||3681|,G|downstream_gene_variant|MODIFIER|PA14_36670|PA14_36670|transcript|ABJ11336.1|protein_coding||c.*2739C>G|||||2739|,G|downstream_gene_variant|MODIFIER|PA14_36680|PA14_36680|transcript|ABJ11335.1|protein_coding||c.*2005C>G|||||2005|,G|downstream_gene_variant|MODIFIER|ybhO|PA14_36690|transcript|ABJ11334.1|protein_coding||c.*803C>G|||||803|,G|downstream_gene_variant|MODIFIER|glgB|PA14_36710|transcript|ABJ11332.1|protein_coding||c.*191G>C|||||191|,G|downstream_gene_variant|MODIFIER|PA14_36730|PA14_36730|transcript|ABJ11331.1|protein_coding||c.*2386G>C|||||2386| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,2:6:223:2:4:0,-20.0471 0:9:9,0:9:312:0:0:0,-28.4096 0:8:8,0:8:306:0:0:0,-27.8977 0:7:7,0:7:246:0:0:0,-22.4789 +Chromosome 3280467 . T C 3.20187E-16 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=55;DPB=55;DPRA=1.71429;EPP=11.6962;EPPR=8.16222;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=102.163;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1879;RO=51;RPL=4;RPP=11.6962;RPPR=5.09662;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=35;SRP=18.3809;SRR=16;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|katE|PA14_36810|transcript|ABJ11325.1|protein_coding|1/1|c.974A>G|p.Glu325Gly|974/2130|974/2130|325/709||,C|upstream_gene_variant|MODIFIER|PA14_36740|PA14_36740|transcript|ABJ11330.1|protein_coding||c.-3179A>G|||||3179|,C|upstream_gene_variant|MODIFIER|PA14_36760|PA14_36760|transcript|ABJ11329.1|protein_coding||c.-2154A>G|||||2154|,C|upstream_gene_variant|MODIFIER|PA14_36770|PA14_36770|transcript|ABJ11328.1|protein_coding||c.-1889A>G|||||1889|,C|upstream_gene_variant|MODIFIER|PA14_36780|PA14_36780|transcript|ABJ11327.1|protein_coding||c.-1384A>G|||||1384|,C|upstream_gene_variant|MODIFIER|PA14_36790|PA14_36790|transcript|ABJ11326.1|protein_coding||c.-1253A>G|||||1253|,C|upstream_gene_variant|MODIFIER|PA14_36830|PA14_36830|transcript|ABJ11323.1|protein_coding||c.-1720T>C|||||1720|,C|downstream_gene_variant|MODIFIER|PA14_36820|PA14_36820|transcript|ABJ11324.1|protein_coding||c.*1054A>G|||||1054|,C|downstream_gene_variant|MODIFIER|glgP|PA14_36840|transcript|ABJ11322.1|protein_coding||c.*2125A>G|||||2125|,C|downstream_gene_variant|MODIFIER|PA14_36850|PA14_36850|transcript|ABJ11321.1|protein_coding||c.*4616A>G|||||4616| GT:DP:DPR:RO:QR:AO:QA:GL 0:12:12,0:12:448:0:0:0,-40.6619 0:12:12,0:12:450:0:0:0,-40.8417 0:20:20,4:16:574:4:8:0,-51.2365 0:11:11,0:11:407:0:0:0,-36.9723 +Chromosome 3284923 . C G 2.17202E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=34;DPB=34;DPRA=3.25;EPP=13.8677;EPPR=12.0706;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=33.5244;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=36;QR=957;RO=29;RPL=0;RPP=13.8677;RPPR=4.88226;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=10;SRP=9.07545;SRR=19;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|glgP|PA14_36840|transcript|ABJ11322.1|protein_coding|1/1|c.108G>C|p.Pro36Pro|108/2439|108/2439|36/812||,G|upstream_gene_variant|MODIFIER|katE|PA14_36810|transcript|ABJ11325.1|protein_coding||c.-3483G>C|||||3483|,G|upstream_gene_variant|MODIFIER|PA14_36820|PA14_36820|transcript|ABJ11324.1|protein_coding||c.-3235G>C|||||3235|,G|upstream_gene_variant|MODIFIER|PA14_36860|PA14_36860|transcript|ABJ11320.1|protein_coding||c.-691C>G|||||691|,G|downstream_gene_variant|MODIFIER|PA14_36830|PA14_36830|transcript|ABJ11323.1|protein_coding||c.*2338C>G|||||2338|,G|downstream_gene_variant|MODIFIER|PA14_36850|PA14_36850|transcript|ABJ11321.1|protein_coding||c.*160G>C|||||160|,G|downstream_gene_variant|MODIFIER|PA14_36870|PA14_36870|transcript|ABJ11319.1|protein_coding||c.*899G>C|||||899|,G|downstream_gene_variant|MODIFIER|PA14_36880|PA14_36880|transcript|ABJ11318.1|protein_coding||c.*1785G>C|||||1785|,G|downstream_gene_variant|MODIFIER|PA14_36890|PA14_36890|transcript|ABJ11317.1|protein_coding||c.*2314G>C|||||2314|,G|downstream_gene_variant|MODIFIER|PA14_36900|PA14_36900|transcript|ABJ11316.1|protein_coding||c.*2573G>C|||||2573|,G|downstream_gene_variant|MODIFIER|PA14_36910|PA14_36910|transcript|ABJ11315.1|protein_coding||c.*2864G>C|||||2864| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:119:0:0:0,-10.9978 0:4:4,0:4:91:0:0:0,-8.41248 0:15:15,1:14:478:1:15:0,-41.8257 0:11:11,4:7:269:4:21:0,-22.6303 +Chromosome 3310254 . C A 1.37394E-11 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=18;DPB=18;DPRA=1.15385;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=26.5068;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=565;RO=16;RPL=0;RPP=7.35324;RPPR=5.18177;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=14;SRP=22.5536;SRR=2;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|PA14_37140|PA14_37140|transcript|ABJ11297.1|protein_coding|1/1|c.732C>A|p.Gly244Gly|732/906|732/906|244/301||,A|upstream_gene_variant|MODIFIER|gbsA|PA14_37090|transcript|ABJ11301.1|protein_coding||c.-4726G>T|||||4726|,A|upstream_gene_variant|MODIFIER|PA14_37100|PA14_37100|transcript|ABJ11300.1|protein_coding||c.-3067G>T|||||3067|,A|upstream_gene_variant|MODIFIER|PA14_37120|PA14_37120|transcript|ABJ11299.1|protein_coding||c.-2030G>T|||||2030|,A|upstream_gene_variant|MODIFIER|PA14_37130|PA14_37130|transcript|ABJ11298.1|protein_coding||c.-857G>T|||||857|,A|upstream_gene_variant|MODIFIER|PA14_37150|PA14_37150|transcript|ABJ11296.1|protein_coding||c.-322C>A|||||322|,A|upstream_gene_variant|MODIFIER|PA14_37170|PA14_37170|transcript|ABJ11295.1|protein_coding||c.-767C>A|||||767|,A|upstream_gene_variant|MODIFIER|PA14_37200|PA14_37200|transcript|ABJ11293.1|protein_coding||c.-3682C>A|||||3682|,A|downstream_gene_variant|MODIFIER|ada|PA14_37190|transcript|ABJ11294.1|protein_coding||c.*2414G>T|||||2414|,A|downstream_gene_variant|MODIFIER|PA14_37210|PA14_37210|transcript|ABJ11292.1|protein_coding||c.*4650G>T|||||4650| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:75:0:0:0,-7.11959 0:5:5,2:3:82:2:4:0,-7.26527 0:6:6,0:6:213:0:0:0,-19.5124 0:5:5,0:5:195:0:0:0,-17.9236 +Chromosome 3314622 . G A 3.21188E-10 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=13;DPB=13;DPRA=1.875;EPP=7.35324;EPPR=4.78696;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=23.3737;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=364;RO=11;RPL=2;RPP=7.35324;RPPR=4.78696;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=9;SRP=12.6832;SRR=2;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|PA14_37200|PA14_37200|transcript|ABJ11293.1|protein_coding|1/1|c.687G>A|p.Lys229Lys|687/984|687/984|229/327||,A|upstream_gene_variant|MODIFIER|ada|PA14_37190|transcript|ABJ11294.1|protein_coding||c.-878C>T|||||878|,A|upstream_gene_variant|MODIFIER|PA14_37250|PA14_37250|transcript|ABJ11290.1|protein_coding||c.-2394G>A|||||2394|,A|upstream_gene_variant|MODIFIER|opdO|PA14_37260|transcript|ABJ11289.1|protein_coding||c.-3690G>A|||||3690|,A|upstream_gene_variant|MODIFIER|PA14_37270|PA14_37270|transcript|ABJ11288.1|protein_coding||c.-4952G>A|||||4952|,A|downstream_gene_variant|MODIFIER|PA14_37140|PA14_37140|transcript|ABJ11297.1|protein_coding||c.*4194G>A|||||4194|,A|downstream_gene_variant|MODIFIER|PA14_37150|PA14_37150|transcript|ABJ11296.1|protein_coding||c.*3618G>A|||||3618|,A|downstream_gene_variant|MODIFIER|PA14_37170|PA14_37170|transcript|ABJ11295.1|protein_coding||c.*2489G>A|||||2489|,A|downstream_gene_variant|MODIFIER|PA14_37210|PA14_37210|transcript|ABJ11292.1|protein_coding||c.*282C>T|||||282|,A|downstream_gene_variant|MODIFIER|PA14_37220|PA14_37220|transcript|ABJ11291.1|protein_coding||c.*1186C>T|||||1186| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:63:0:0:0,-5.98315 0:2:2,0:2:77:0:0:0,-7.30914 0:5:5,2:3:113:2:4:0,-10.1593 0:4:4,0:4:111:0:0:0,-10.2617 +Chromosome 3317174 . G T 4.32464E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=63;DPB=63;DPRA=0.436364;EPP=7.35324;EPPR=3.90025;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=59.5437;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=2178;RO=61;RPL=2;RPP=7.35324;RPPR=18.709;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=31;SRP=3.0459;SRR=30;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|PA14_37250|PA14_37250|transcript|ABJ11290.1|protein_coding|1/1|c.159G>T|p.Leu53Leu|159/1272|159/1272|53/423||,T|upstream_gene_variant|MODIFIER|ada|PA14_37190|transcript|ABJ11294.1|protein_coding||c.-3430C>A|||||3430|,T|upstream_gene_variant|MODIFIER|PA14_37210|PA14_37210|transcript|ABJ11292.1|protein_coding||c.-1473C>A|||||1473|,T|upstream_gene_variant|MODIFIER|PA14_37220|PA14_37220|transcript|ABJ11291.1|protein_coding||c.-413C>A|||||413|,T|upstream_gene_variant|MODIFIER|opdO|PA14_37260|transcript|ABJ11289.1|protein_coding||c.-1138G>T|||||1138|,T|upstream_gene_variant|MODIFIER|PA14_37270|PA14_37270|transcript|ABJ11288.1|protein_coding||c.-2400G>T|||||2400|,T|upstream_gene_variant|MODIFIER|PA14_37290|PA14_37290|transcript|ABJ11287.1|protein_coding||c.-3140G>T|||||3140|,T|upstream_gene_variant|MODIFIER|PA14_37310|PA14_37310|transcript|ABJ11286.1|protein_coding||c.-3850G>T|||||3850|,T|upstream_gene_variant|MODIFIER|PA14_37320|PA14_37320|transcript|ABJ11285.1|protein_coding||c.-4859G>T|||||4859|,T|downstream_gene_variant|MODIFIER|PA14_37200|PA14_37200|transcript|ABJ11293.1|protein_coding||c.*2255G>T|||||2255| GT:DP:DPR:RO:QR:AO:QA:GL 0:20:20,0:20:727:0:0:0,-65.7381 0:8:8,2:6:209:2:31:0,-16.1975 0:20:20,0:20:737:0:0:0,-66.6425 0:15:15,0:15:505:0:0:0,-45.7524 +Chromosome 3320408 . T G 3.17047E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=13;DPB=13;DPRA=2.25;EPP=9.52472;EPPR=6.48466;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=21.1158;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=334;RO=10;RPL=0;RPP=9.52472;RPPR=3.87889;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=7;SRP=6.48466;SRR=3;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_37290|PA14_37290|transcript|ABJ11287.1|protein_coding|1/1|c.95T>G|p.Leu32Arg|95/714|95/714|32/237||,G|upstream_gene_variant|MODIFIER|PA14_37210|PA14_37210|transcript|ABJ11292.1|protein_coding||c.-4707A>C|||||4707|,G|upstream_gene_variant|MODIFIER|PA14_37220|PA14_37220|transcript|ABJ11291.1|protein_coding||c.-3647A>C|||||3647|,G|upstream_gene_variant|MODIFIER|PA14_37310|PA14_37310|transcript|ABJ11286.1|protein_coding||c.-616T>G|||||616|,G|upstream_gene_variant|MODIFIER|PA14_37320|PA14_37320|transcript|ABJ11285.1|protein_coding||c.-1625T>G|||||1625|,G|upstream_gene_variant|MODIFIER|PA14_37350|PA14_37350|transcript|ABJ11283.1|protein_coding||c.-4063T>G|||||4063|,G|downstream_gene_variant|MODIFIER|PA14_37250|PA14_37250|transcript|ABJ11290.1|protein_coding||c.*2121T>G|||||2121|,G|downstream_gene_variant|MODIFIER|opdO|PA14_37260|transcript|ABJ11289.1|protein_coding||c.*867T>G|||||867|,G|downstream_gene_variant|MODIFIER|PA14_37270|PA14_37270|transcript|ABJ11288.1|protein_coding||c.*91T>G|||||91|,G|downstream_gene_variant|MODIFIER|PA14_37340|PA14_37340|transcript|ABJ11284.1|protein_coding||c.*2120A>C|||||2120|,G|downstream_gene_variant|MODIFIER|PA14_37360|PA14_37360|transcript|ABJ11282.1|protein_coding||c.*4860A>C|||||4860|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:64:0:0:0,-6.07855 0:2:2,0:2:75:0:0:0,-7.1201 0:4:4,2:2:42:2:4:0,-3.6059 0:5:5,1:4:153:1:2:0,-13.9413 +Chromosome 3331493 . A T 1.93923E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=26;DPB=26;DPRA=0.857143;EPP=9.52472;EPPR=10.6577;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=35.0927;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=41;QR=732;RO=23;RPL=0;RPP=9.52472;RPPR=3.86001;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=12;SRP=3.10471;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_37420|PA14_37420|transcript|ABJ11277.1|protein_coding|1/1|c.67T>A|p.Ser23Thr|67/957|67/957|23/318||,T|upstream_gene_variant|MODIFIER|PA14_37370|PA14_37370|transcript|ABJ11281.1|protein_coding||c.-4553T>A|||||4553|,T|upstream_gene_variant|MODIFIER|PA14_37380|PA14_37380|transcript|ABJ11280.1|protein_coding||c.-3067T>A|||||3067|,T|downstream_gene_variant|MODIFIER|PA14_37400|PA14_37400|transcript|ABJ11279.1|protein_coding||c.*1886A>T|||||1886|,T|downstream_gene_variant|MODIFIER|PA14_37410|PA14_37410|transcript|ABJ11278.1|protein_coding||c.*892A>T|||||892|,T|downstream_gene_variant|MODIFIER|PA14_37430|PA14_37430|transcript|ABJ11276.1|protein_coding||c.*63T>A|||||63|,T|downstream_gene_variant|MODIFIER|PA14_37440|PA14_37440|transcript|ABJ11275.1|protein_coding||c.*675T>A|||||675|,T|downstream_gene_variant|MODIFIER|PA14_37460|PA14_37460|transcript|ABJ11274.1|protein_coding||c.*1858T>A|||||1858|,T|downstream_gene_variant|MODIFIER|PA14_37470|PA14_37470|transcript|ABJ11273.1|protein_coding||c.*3138T>A|||||3138|,T|downstream_gene_variant|MODIFIER|PA14_37490|PA14_37490|transcript|ABJ11272.1|protein_coding||c.*4230T>A|||||4230| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:256:0:0:0,-23.3439 0:6:6,0:6:205:0:0:0,-18.779 0:6:6,1:5:160:1:24:0,-12.3096 0:6:6,2:4:111:2:17:0,-8.64449 +Chromosome 3341478 . T C 3.87046E-7 . AB=0;ABP=0;AC=0;AF=0;AN=3;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=7;EPP=7.35324;EPPR=18.2106;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=16.9264;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=256;RO=7;RPL=2;RPP=7.35324;RPPR=18.2106;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=18.2106;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|asnB|PA14_37560|transcript|ABJ11267.1|protein_coding|1/1|c.1756A>G|p.Ser586Gly|1756/1833|1756/1833|586/610||,C|upstream_gene_variant|MODIFIER|PA14_37490|PA14_37490|transcript|ABJ11272.1|protein_coding||c.-3104A>G|||||3104|,C|upstream_gene_variant|MODIFIER|PA14_37510|PA14_37510|transcript|ABJ11271.1|protein_coding||c.-2164A>G|||||2164|,C|upstream_gene_variant|MODIFIER|PA14_37520|PA14_37520|transcript|ABJ11270.1|protein_coding||c.-1524A>G|||||1524|,C|upstream_gene_variant|MODIFIER|PA14_37530|PA14_37530|transcript|ABJ11269.1|protein_coding||c.-625A>G|||||625|,C|upstream_gene_variant|MODIFIER|PA14_37550|PA14_37550|transcript|ABJ11268.1|protein_coding||c.-105A>G|||||105|,C|upstream_gene_variant|MODIFIER|kynB|PA14_37590|transcript|ABJ11264.1|protein_coding||c.-3928T>C|||||3928|,C|upstream_gene_variant|MODIFIER|PA14_37610|PA14_37610|transcript|ABJ11263.1|protein_coding||c.-4573T>C|||||4573|,C|downstream_gene_variant|MODIFIER|PA14_37570|PA14_37570|transcript|ABJ11266.1|protein_coding||c.*1843A>G|||||1843|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|lrp|PA14_37580|transcript|ABJ11265.1|protein_coding||c.*3319A>G|||||3319| GT:DP:DPR:RO:QR:AO:QA:GL . 0:1:1,0:1:39:0:0:0,-3.89656 0:1:1,0:1:39:0:0:0,-3.89656 0:7:7,2:5:178:2:4:0,-15.9853 +Chromosome 3348378 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=31;DPB=31;DPRA=1.22727;EPP=7.35324;EPPR=49.8093;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=52.3649;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=1091;RO=29;RPL=0;RPP=7.35324;RPPR=42.621;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=42.621;SRR=26;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|PA14_37630|PA14_37630|transcript|ABJ11262.1|protein_coding|1/1|c.922C>A|p.Gln308Lys|922/1407|922/1407|308/468||,A|upstream_gene_variant|MODIFIER|PA14_37570|PA14_37570|transcript|ABJ11266.1|protein_coding||c.-3783G>T|||||3783|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|lrp|PA14_37580|transcript|ABJ11265.1|protein_coding||c.-3105G>T|||||3105|,A|upstream_gene_variant|MODIFIER|PA14_37640|PA14_37640|transcript|ABJ11261.1|protein_coding||c.-771C>A|||||771|,A|upstream_gene_variant|MODIFIER|PA14_37650|PA14_37650|transcript|ABJ11260.1|protein_coding||c.-2685C>A|||||2685|,A|downstream_gene_variant|MODIFIER|kynB|PA14_37590|transcript|ABJ11264.1|protein_coding||c.*2331C>A|||||2331|,A|downstream_gene_variant|MODIFIER|PA14_37610|PA14_37610|transcript|ABJ11263.1|protein_coding||c.*1077C>A|||||1077|,A|downstream_gene_variant|MODIFIER|PA14_37660|PA14_37660|transcript|ABJ11259.1|protein_coding||c.*4626G>T|||||4626| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:229:0:0:0,-20.9751 0:9:9,2:7:261:2:30:0,-20.9947 0:6:6,0:6:229:0:0:0,-20.9745 0:10:10,0:10:372:0:0:0,-33.828 +Chromosome 3350430 . G C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=34;DPB=34;DPRA=1;EPP=9.52472;EPPR=28.2974;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=53.1266;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=1058;RO=31;RPL=3;RPP=9.52472;RPPR=14.8483;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=13;SRP=4.76149;SRR=18;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_37640|PA14_37640|transcript|ABJ11261.1|protein_coding|1/1|c.1282G>C|p.Gly428Arg|1282/1875|1282/1875|428/624||,C|upstream_gene_variant|MODIFIER|PA14_37650|PA14_37650|transcript|ABJ11260.1|protein_coding||c.-633G>C|||||633|,C|upstream_gene_variant|MODIFIER|PA14_37670|PA14_37670|transcript|ABJ11258.1|protein_coding||c.-3933G>C|||||3933|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_37680|PA14_37680|transcript|ABJ11257.1|protein_coding||c.-4376G>C|||||4376|,C|downstream_gene_variant|MODIFIER|kynB|PA14_37590|transcript|ABJ11264.1|protein_coding||c.*4383G>C|||||4383|,C|downstream_gene_variant|MODIFIER|PA14_37610|PA14_37610|transcript|ABJ11263.1|protein_coding||c.*3129G>C|||||3129|,C|downstream_gene_variant|MODIFIER|PA14_37630|PA14_37630|transcript|ABJ11262.1|protein_coding||c.*1567G>C|||||1567|,C|downstream_gene_variant|MODIFIER|PA14_37660|PA14_37660|transcript|ABJ11259.1|protein_coding||c.*2574C>G|||||2574| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:310:0:0:0,-28.2622 0:10:10,1:9:286:1:2:0,-25.8421 0:9:9,0:9:264:0:0:0,-24.0365 0:7:7,2:5:198:2:4:0,-17.8178 +Chromosome 3352265 . G C 6.82671E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=23;DPB=23;DPRA=2.28571;EPP=11.6962;EPPR=4.03889;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=29.4843;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=642;RO=19;RPL=4;RPP=11.6962;RPPR=5.8675;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=11;SRP=4.03889;SRR=8;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|PA14_37650|PA14_37650|transcript|ABJ11260.1|protein_coding|1/1|c.1203G>C|p.Ala401Ala|1203/1905|1203/1905|401/634||,C|upstream_gene_variant|MODIFIER|PA14_37670|PA14_37670|transcript|ABJ11258.1|protein_coding||c.-2098G>C|||||2098|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_37680|PA14_37680|transcript|ABJ11257.1|protein_coding||c.-2541G>C|||||2541|,C|downstream_gene_variant|MODIFIER|PA14_37610|PA14_37610|transcript|ABJ11263.1|protein_coding||c.*4964G>C|||||4964|,C|downstream_gene_variant|MODIFIER|PA14_37630|PA14_37630|transcript|ABJ11262.1|protein_coding||c.*3402G>C|||||3402|,C|downstream_gene_variant|MODIFIER|PA14_37640|PA14_37640|transcript|ABJ11261.1|protein_coding||c.*1242G>C|||||1242|,C|downstream_gene_variant|MODIFIER|PA14_37660|PA14_37660|transcript|ABJ11259.1|protein_coding||c.*739C>G|||||739|,C|downstream_gene_variant|MODIFIER|PA14_37690|PA14_37690|transcript|ABJ11256.1|protein_coding||c.*4601C>G|||||4601| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:192:0:0:0,-17.6493 0:2:2,0:2:74:0:0:0,-7.02486 0:9:9,2:7:199:2:4:0,-17.8036 0:7:7,2:5:177:2:4:0,-15.895 +Chromosome 3358567 . C A 3.87968E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=34;DPB=34;DPRA=1;EPP=3.73412;EPPR=8.68415;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=55.8655;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=47;QR=1077;RO=31;RPL=2;RPP=3.73412;RPPR=11.486;RPR=1;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=16;SRP=3.08035;SRR=15;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|PA14_37690|PA14_37690|transcript|ABJ11256.1|protein_coding|1/1|c.894G>T|p.Leu298Leu|894/2595|894/2595|298/864||,A|upstream_gene_variant|MODIFIER|PA14_37660|PA14_37660|transcript|ABJ11259.1|protein_coding||c.-4661G>T|||||4661|,A|upstream_gene_variant|MODIFIER|PA14_37730|PA14_37730|transcript|ABJ11254.1|protein_coding||c.-3449C>A|||||3449|,A|downstream_gene_variant|MODIFIER|PA14_37670|PA14_37670|transcript|ABJ11258.1|protein_coding||c.*3938C>A|||||3938|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_37680|PA14_37680|transcript|ABJ11257.1|protein_coding||c.*2094C>A|||||2094|,A|downstream_gene_variant|MODIFIER|fusA2|PA14_37710|transcript|ABJ11255.1|protein_coding||c.*1065G>T|||||1065| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,1:7:217:1:15:0,-18.3286 0:7:7,0:7:255:0:0:0,-23.2982 0:10:10,0:10:376:0:0:0,-34.189 0:9:9,2:7:229:2:32:0,-17.879 +Chromosome 3367245 . T C 5.59385E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=20;DPB=20;DPRA=1.61538;EPP=7.35324;EPPR=3.49285;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=36.6776;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=29;QR=659;RO=18;RPL=2;RPP=7.35324;RPPR=10.7311;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=11;SRP=4.9405;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_37760|PA14_37760|transcript|ABJ11253.1|protein_coding|1/1|c.640T>C|p.Ser214Pro|640/1164|640/1164|214/387||,C|upstream_gene_variant|MODIFIER|PA14_37770|PA14_37770|transcript|ABJ11252.1|protein_coding||c.-526T>C|||||526|,C|upstream_gene_variant|MODIFIER|PA14_37780|PA14_37780|transcript|ABJ11251.1|protein_coding||c.-1191T>C|||||1191|,C|upstream_gene_variant|MODIFIER|pcoA|PA14_37790|transcript|ABJ11250.1|protein_coding||c.-1978T>C|||||1978|,C|upstream_gene_variant|MODIFIER|pcoB|PA14_37810|transcript|ABJ11249.1|protein_coding||c.-3795T>C|||||3795|,C|downstream_gene_variant|MODIFIER|PA14_37730|PA14_37730|transcript|ABJ11254.1|protein_coding||c.*2587T>C|||||2587|,C|downstream_gene_variant|MODIFIER|PA14_37745|PA14_37745|transcript|ABJ15683.1|protein_coding||c.*683T>C|||||683|,C|downstream_gene_variant|MODIFIER|PA14_37820|PA14_37820|transcript|ABJ11248.1|protein_coding||c.*4870A>G|||||4870| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,2:5:167:2:29:0,-12.6019 0:4:4,0:4:155:0:0:0,-14.3242 0:3:3,0:3:114:0:0:0,-10.6315 0:6:6,0:6:223:0:0:0,-20.4271 +Chromosome 3387056 . G C 1.42585E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=35;DPB=35;DPRA=0.62069;EPP=9.52472;EPPR=5.45321;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=31.0784;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=45;QR=1066;RO=32;RPL=3;RPP=9.52472;RPPR=5.45321;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=16;SRP=3.0103;SRR=16;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|cynT|PA14_37950|transcript|ABJ11239.1|protein_coding|1/1|c.16G>C|p.Asp6His|16/663|16/663|6/220||,C|upstream_gene_variant|MODIFIER|PA14_37900|PA14_37900|transcript|ABJ11242.1|protein_coding||c.-4131C>G|||||4131|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_37910|PA14_37910|transcript|ABJ11241.1|protein_coding||c.-2550C>G|||||2550|,C|upstream_gene_variant|MODIFIER|cynR|PA14_37940|transcript|ABJ11240.1|protein_coding||c.-130C>G|||||130|,C|upstream_gene_variant|MODIFIER|cynS|PA14_37965|transcript|ABJ15651.1|protein_coding||c.-687G>C|||||687|,C|upstream_gene_variant|MODIFIER|PA14_38000|PA14_38000|transcript|ABJ11236.1|protein_coding||c.-2979G>C|||||2979|,C|upstream_gene_variant|MODIFIER|PA14_38010|PA14_38010|transcript|ABJ11235.1|protein_coding||c.-3542G>C|||||3542|,C|downstream_gene_variant|MODIFIER|PA14_37915|PA14_37915|transcript|ABJ15682.1|protein_coding||c.*1024G>C|||||1024|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_37980|PA14_37980|transcript|ABJ11238.1|protein_coding||c.*1195C>G|||||1195|,C|downstream_gene_variant|MODIFIER|PA14_37990|PA14_37990|transcript|ABJ11237.1|protein_coding||c.*2145C>G|||||2145| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:250:0:0:0,-22.7949 0:6:6,3:3:106:3:45:0,-5.68593 0:8:8,0:8:264:0:0:0,-24.0755 0:13:13,0:13:446:0:0:0,-40.4527 +Chromosome 3392756 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=46;DPB=46;DPRA=0.942857;EPP=9.52472;EPPR=4.27278;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=52.2374;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=1590;RO=43;RPL=3;RPP=9.52472;RPPR=4.27278;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=32;SRP=25.2805;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|PA14_37980|PA14_37980|transcript|ABJ11238.1|protein_coding||c.-3552T>C|||||3552|,G|upstream_gene_variant|MODIFIER|PA14_37990|PA14_37990|transcript|ABJ11237.1|protein_coding||c.-3049T>C|||||3049|,G|upstream_gene_variant|MODIFIER|PA14_38020|PA14_38020|transcript|ABJ11234.1|protein_coding||c.-260T>C|||||260|,G|upstream_gene_variant|MODIFIER|PA14_38040|PA14_38040|transcript|ABJ11233.1|protein_coding||c.-154A>G|||||154|,G|upstream_gene_variant|MODIFIER|PA14_38050|PA14_38050|transcript|ABJ11232.1|protein_coding||c.-2179A>G|||||2179|,G|upstream_gene_variant|MODIFIER|PA14_38060|PA14_38060|transcript|ABJ11231.1|protein_coding||c.-2645A>G|||||2645|,G|upstream_gene_variant|MODIFIER|PA14_38080|PA14_38080|transcript|ABJ11230.1|protein_coding||c.-3080A>G|||||3080|,G|downstream_gene_variant|MODIFIER|cynS|PA14_37965|transcript|ABJ15651.1|protein_coding||c.*4543A>G|||||4543|,G|downstream_gene_variant|MODIFIER|PA14_38000|PA14_38000|transcript|ABJ11236.1|protein_coding||c.*2257A>G|||||2257|,G|downstream_gene_variant|MODIFIER|PA14_38010|PA14_38010|transcript|ABJ11235.1|protein_coding||c.*725A>G|||||725|,G|intergenic_region|MODIFIER|PA14_38020-PA14_38040|PA14_38020-PA14_38040|intergenic_region|PA14_38020-PA14_38040|||n.3392756A>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:158:0:0:0,-14.6007 0:12:12,0:12:446:0:0:0,-40.4734 0:11:11,3:8:274:3:6:0,-24.4193 0:19:19,0:19:712:0:0:0,-64.392 +Chromosome 3396304 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=46;DPB=46;DPRA=1;EPP=13.8677;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=65.8986;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1412;RO=41;RPL=0;RPP=13.8677;RPPR=3.48696;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=38;SRP=67.8897;SRR=3;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_38080|PA14_38080|transcript|ABJ11230.1|protein_coding|1/1|c.469A>G|p.Ser157Gly|469/1875|469/1875|157/624||,G|upstream_gene_variant|MODIFIER|PA14_38020|PA14_38020|transcript|ABJ11234.1|protein_coding||c.-3808T>C|||||3808|,G|downstream_gene_variant|MODIFIER|PA14_38010|PA14_38010|transcript|ABJ11235.1|protein_coding||c.*4273A>G|||||4273|,G|downstream_gene_variant|MODIFIER|PA14_38040|PA14_38040|transcript|ABJ11233.1|protein_coding||c.*2405A>G|||||2405|,G|downstream_gene_variant|MODIFIER|PA14_38050|PA14_38050|transcript|ABJ11232.1|protein_coding||c.*962A>G|||||962|,G|downstream_gene_variant|MODIFIER|PA14_38060|PA14_38060|transcript|ABJ11231.1|protein_coding||c.*643A>G|||||643|,G|downstream_gene_variant|MODIFIER|PA14_38090|PA14_38090|transcript|ABJ11229.1|protein_coding||c.*1564T>C|||||1564|,G|downstream_gene_variant|MODIFIER|ygjU|PA14_38110|transcript|ABJ11228.1|protein_coding||c.*2587T>C|||||2587|,G|downstream_gene_variant|MODIFIER|ycjJ|PA14_38130|transcript|ABJ11227.1|protein_coding||c.*4304T>C|||||4304| GT:DP:DPR:RO:QR:AO:QA:GL 0:11:11,0:11:391:0:0:0,-35.5203 0:12:12,1:11:377:1:2:0,-34.0498 0:12:12,0:12:412:0:0:0,-37.4008 0:11:11,4:7:232:4:8:0,-20.4531 +Chromosome 3400039 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=46;DPB=46;DPRA=0.642857;EPP=9.52472;EPPR=17.6046;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=57.8134;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=1432;RO=43;RPL=0;RPP=9.52472;RPPR=7.10075;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=12;SRP=21.2406;SRR=31;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|ygjU|PA14_38110|transcript|ABJ11228.1|protein_coding|1/1|c.82G>C|p.Gly28Arg|82/1230|82/1230|28/409||,G|upstream_gene_variant|MODIFIER|PA14_38090|PA14_38090|transcript|ABJ11229.1|protein_coding||c.-1269G>C|||||1269|,G|upstream_gene_variant|MODIFIER|azlC|PA14_38160|transcript|ABJ11225.1|protein_coding||c.-3978C>G|||||3978|,G|upstream_gene_variant|MODIFIER|PA14_38170|PA14_38170|transcript|ABJ11224.1|protein_coding||c.-4721C>G|||||4721|,G|downstream_gene_variant|MODIFIER|PA14_38050|PA14_38050|transcript|ABJ11232.1|protein_coding||c.*4697C>G|||||4697|,G|downstream_gene_variant|MODIFIER|PA14_38060|PA14_38060|transcript|ABJ11231.1|protein_coding||c.*4378C>G|||||4378|,G|downstream_gene_variant|MODIFIER|PA14_38080|PA14_38080|transcript|ABJ11230.1|protein_coding||c.*2329C>G|||||2329|,G|downstream_gene_variant|MODIFIER|ycjJ|PA14_38130|transcript|ABJ11227.1|protein_coding||c.*569G>C|||||569|,G|downstream_gene_variant|MODIFIER|PA14_38140|PA14_38140|transcript|ABJ11226.1|protein_coding||c.*2096G>C|||||2096| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,2:6:214:2:16:0,-18.084 0:10:10,1:9:325:1:2:0,-29.3889 0:10:10,0:10:315:0:0:0,-28.6442 0:18:18,0:18:578:0:0:0,-52.3023 +Chromosome 3409471 . G A 9.54279E-10 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=17;DPB=17;DPRA=0.923077;EPP=3.0103;EPPR=6.62942;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=22.2386;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=584;RO=15;RPL=2;RPP=7.35324;RPPR=14.7363;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=2;SRP=20.5268;SRR=13;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|ilvG|PA14_38200|transcript|ABJ11221.1|protein_coding|1/1|c.1417G>A|p.Gly473Ser|1417/1659|1417/1659|473/552||,A|upstream_gene_variant|MODIFIER|PA14_38180|PA14_38180|transcript|ABJ11223.1|protein_coding||c.-2812C>T|||||2812|,A|upstream_gene_variant|MODIFIER|PA14_38190|PA14_38190|transcript|ABJ11222.1|protein_coding||c.-2151C>T|||||2151|,A|upstream_gene_variant|MODIFIER|PA14_38260|PA14_38260|transcript|ABJ11217.1|protein_coding||c.-3571G>A|||||3571|,A|upstream_gene_variant|MODIFIER|PA14_38270|PA14_38270|transcript|ABJ11216.1|protein_coding||c.-3822G>A|||||3822|,A|downstream_gene_variant|MODIFIER|azlC|PA14_38160|transcript|ABJ11225.1|protein_coding||c.*4696G>A|||||4696|,A|downstream_gene_variant|MODIFIER|PA14_38170|PA14_38170|transcript|ABJ11224.1|protein_coding||c.*4397G>A|||||4397|,A|downstream_gene_variant|MODIFIER|PA14_38210|PA14_38210|transcript|ABJ11220.1|protein_coding||c.*250C>T|||||250|,A|downstream_gene_variant|MODIFIER|PA14_38220|PA14_38220|transcript|ABJ11219.1|protein_coding||c.*924C>T|||||924|,A|downstream_gene_variant|MODIFIER|yjiR|PA14_38250|transcript|ABJ11218.1|protein_coding||c.*1967C>T|||||1967|,A|downstream_gene_variant|MODIFIER|PA14_38290|PA14_38290|transcript|ABJ11215.1|protein_coding||c.*4154C>T|||||4154|,A|downstream_gene_variant|MODIFIER|grp|PA14_38300|transcript|ABJ11214.1|protein_coding||c.*4477C>T|||||4477| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:120:0:0:0,-11.1879 0:3:3,0:3:120:0:0:0,-11.1879 0:4:4,2:2:79:2:32:0,-4.45766 0:7:7,0:7:265:0:0:0,-24.2093 +Chromosome 3420536 . T C 3.82741E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=34;DPB=34;DPRA=1.25;EPP=7.35324;EPPR=5.45321;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=48.7657;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=1012;RO=32;RPL=2;RPP=7.35324;RPPR=3.28173;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=24;SRP=20.3821;SRR=8;TYPE=snp;technology.ILLUMINA=1;ANN=C|upstream_gene_variant|MODIFIER|gor|PA14_38330|transcript|ABJ11211.1|protein_coding||c.-3026A>G|||||3026|,C|upstream_gene_variant|MODIFIER|galU|PA14_38350|transcript|ABJ11209.1|protein_coding||c.-1438A>G|||||1438|,C|upstream_gene_variant|MODIFIER|ugd|PA14_38360|transcript|ABJ11208.1|protein_coding||c.-29A>G|||||29|,C|upstream_gene_variant|MODIFIER|PA14_38370|PA14_38370|transcript|ABJ11207.1|protein_coding||c.-123T>C|||||123|,C|upstream_gene_variant|MODIFIER|PA14_38395|PA14_38395|transcript|ABJ15633.1|protein_coding||c.-1150T>C|||||1150|,C|upstream_gene_variant|MODIFIER|amrB|PA14_38410|transcript|ABJ11205.1|protein_coding||c.-2356T>C|||||2356|,C|downstream_gene_variant|MODIFIER|yfeH|PA14_38320|transcript|ABJ11212.1|protein_coding||c.*4436T>C|||||4436|,C|downstream_gene_variant|MODIFIER|PA14_38340|PA14_38340|transcript|ABJ11210.1|protein_coding||c.*2459T>C|||||2459|,C|downstream_gene_variant|MODIFIER|amrR|PA14_38380|transcript|ABJ11206.1|protein_coding||c.*353A>G|||||353|WARNING_TRANSCRIPT_NO_START_CODON,C|intergenic_region|MODIFIER|ugd-PA14_38370|PA14_38360-PA14_38370|intergenic_region|PA14_38360-PA14_38370|||n.3420536T>C|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:195:0:0:0,-17.8667 0:5:5,0:5:164:0:0:0,-15.0813 0:10:10,2:8:220:2:30:0,-17.2132 0:13:13,0:13:433:0:0:0,-39.277 +Chromosome 3420560 . C G 5.48108E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=27;DPB=27;DPRA=2.375;EPP=13.8677;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=37.4912;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=23;QR=782;RO=22;RPL=0;RPP=13.8677;RPPR=4.58955;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=14;SRP=6.56362;SRR=8;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|gor|PA14_38330|transcript|ABJ11211.1|protein_coding||c.-3050G>C|||||3050|,G|upstream_gene_variant|MODIFIER|galU|PA14_38350|transcript|ABJ11209.1|protein_coding||c.-1462G>C|||||1462|,G|upstream_gene_variant|MODIFIER|ugd|PA14_38360|transcript|ABJ11208.1|protein_coding||c.-53G>C|||||53|,G|upstream_gene_variant|MODIFIER|PA14_38370|PA14_38370|transcript|ABJ11207.1|protein_coding||c.-99C>G|||||99|,G|upstream_gene_variant|MODIFIER|PA14_38395|PA14_38395|transcript|ABJ15633.1|protein_coding||c.-1126C>G|||||1126|,G|upstream_gene_variant|MODIFIER|amrB|PA14_38410|transcript|ABJ11205.1|protein_coding||c.-2332C>G|||||2332|,G|downstream_gene_variant|MODIFIER|yfeH|PA14_38320|transcript|ABJ11212.1|protein_coding||c.*4460C>G|||||4460|,G|downstream_gene_variant|MODIFIER|PA14_38340|PA14_38340|transcript|ABJ11210.1|protein_coding||c.*2483C>G|||||2483|,G|downstream_gene_variant|MODIFIER|amrR|PA14_38380|transcript|ABJ11206.1|protein_coding||c.*329G>C|||||329|WARNING_TRANSCRIPT_NO_START_CODON,G|intergenic_region|MODIFIER|ugd-PA14_38370|PA14_38360-PA14_38370|intergenic_region|PA14_38360-PA14_38370|||n.3420560C>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:183:0:0:0,-16.8232 0:3:3,0:3:115:0:0:0,-10.724 0:6:6,1:5:194:1:2:0,-17.6311 0:13:13,4:9:290:4:21:0,-24.4568 +Chromosome 3426130 . TCC TC 117.909 . AB=0;ABP=0;AC=3;AF=1;AN=3;AO=4;CIGAR=1M1D1M;DP=5;DPB=6.33333;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1.33333;MQM=60;MQMR=0;NS=3;NUMALT=1;ODDS=15.3215;PAIRED=0;PAIREDR=0;PAO=1.5;PQA=18.5;PQR=18.5;PRO=1.5;QA=142;QR=0;RO=0;RPL=1;RPP=5.18177;RPPR=0;RPR=3;RUN=1;SAF=3;SAP=5.18177;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=del;technology.ILLUMINA=1;ANN=TC|upstream_gene_variant|MODIFIER|amrR|PA14_38380|transcript|ABJ11206.1|protein_coding||c.-4611delG|||||4611|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|gnyR|PA14_38430|transcript|ABJ11203.1|protein_coding||c.-1261delC|||||1261|,TC|upstream_gene_variant|MODIFIER|gnyD|PA14_38440|transcript|ABJ11202.1|protein_coding||c.-1714delC|||||1714|,TC|upstream_gene_variant|MODIFIER|gnyB|PA14_38460|transcript|ABJ11201.1|protein_coding||c.-3000delC|||||3000|,TC|upstream_gene_variant|MODIFIER|gnyH|PA14_38470|transcript|ABJ11200.1|protein_coding||c.-4621delC|||||4621|,TC|downstream_gene_variant|MODIFIER|PA14_38395|PA14_38395|transcript|ABJ15633.1|protein_coding||c.*3256delC|||||3256|,TC|downstream_gene_variant|MODIFIER|amrB|PA14_38410|transcript|ABJ11205.1|protein_coding||c.*103delC|||||103|,TC|downstream_gene_variant|MODIFIER|PA14_38420|PA14_38420|transcript|ABJ11204.1|protein_coding||c.*139delG|||||139|,TC|intergenic_region|MODIFIER|amrB-PA14_38420|PA14_38410-PA14_38420|intergenic_region|PA14_38410-PA14_38420|||n.3426132delC|||||| GT:DP:DPR:RO:QR:AO:QA:GL 1:2:2,2:0:0:2:75:-7.1201,0 1:1:1,1:0:0:1:27:-2.69978,0 . 1:2:2,1:0:0:1:40:-3.60107,0 +Chromosome 3436181 . T C 3.19045E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=19;DPB=19;DPRA=3.75;EPP=9.52472;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=21.3057;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=79;QR=519;RO=16;RPL=3;RPP=9.52472;RPPR=7.89611;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=11;SRP=7.89611;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|hmgA|PA14_38510|transcript|ABJ11196.1|protein_coding|1/1|c.713T>C|p.Leu238Pro|713/1299|713/1299|238/432||,C|upstream_gene_variant|MODIFIER|PA14_38500|PA14_38500|transcript|ABJ11197.1|protein_coding||c.-873A>G|||||873|,C|upstream_gene_variant|MODIFIER|fahA|PA14_38530|transcript|ABJ11195.1|protein_coding||c.-591T>C|||||591|,C|upstream_gene_variant|MODIFIER|maiA|PA14_38550|transcript|ABJ11194.1|protein_coding||c.-1886T>C|||||1886|,C|upstream_gene_variant|MODIFIER|pcaK|PA14_38560|transcript|ABJ11193.1|protein_coding||c.-2609T>C|||||2609|,C|upstream_gene_variant|MODIFIER|PA14_38570|PA14_38570|transcript|ABJ11192.1|protein_coding||c.-4090T>C|||||4090|,C|downstream_gene_variant|MODIFIER|gnyH|PA14_38470|transcript|ABJ11200.1|protein_coding||c.*4631T>C|||||4631|,C|downstream_gene_variant|MODIFIER|gnyA|PA14_38480|transcript|ABJ11199.1|protein_coding||c.*2667T>C|||||2667|,C|downstream_gene_variant|MODIFIER|gnyL|PA14_38490|transcript|ABJ11198.1|protein_coding||c.*1744T>C|||||1744| GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:40:0:0:0,-3.99568 0:10:10,1:9:298:1:13:0,-25.8357 0:3:3,0:3:86:0:0:0,-8.02244 0:5:5,2:3:95:2:66:0,-2.59288 +Chromosome 3438805 . G C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=43;DPB=43;DPRA=0.535714;EPP=9.52472;EPPR=3.87889;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=49.7153;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=1512;RO=40;RPL=3;RPP=9.52472;RPPR=20.5992;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=29;SRP=20.5992;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|pcaK|PA14_38560|transcript|ABJ11193.1|protein_coding|1/1|c.16G>C|p.Ala6Pro|16/1353|16/1353|6/450||,C|upstream_gene_variant|MODIFIER|PA14_38500|PA14_38500|transcript|ABJ11197.1|protein_coding||c.-3497C>G|||||3497|,C|upstream_gene_variant|MODIFIER|PA14_38570|PA14_38570|transcript|ABJ11192.1|protein_coding||c.-1466G>C|||||1466|,C|upstream_gene_variant|MODIFIER|PA14_38580|PA14_38580|transcript|ABJ11191.1|protein_coding||c.-3113G>C|||||3113|,C|upstream_gene_variant|MODIFIER|bdhA|PA14_38590|transcript|ABJ11190.1|protein_coding||c.-4538G>C|||||4538|,C|downstream_gene_variant|MODIFIER|gnyL|PA14_38490|transcript|ABJ11198.1|protein_coding||c.*4368G>C|||||4368|,C|downstream_gene_variant|MODIFIER|hmgA|PA14_38510|transcript|ABJ11196.1|protein_coding||c.*2038G>C|||||2038|,C|downstream_gene_variant|MODIFIER|fahA|PA14_38530|transcript|ABJ11195.1|protein_coding||c.*735G>C|||||735|,C|downstream_gene_variant|MODIFIER|maiA|PA14_38550|transcript|ABJ11194.1|protein_coding||c.*100G>C|||||100| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,1:4:155:1:2:0,-14.1254 0:12:12,0:12:446:0:0:0,-40.4789 0:16:16,0:16:616:0:0:0,-55.7774 0:10:10,2:8:295:2:4:0,-26.518 +Chromosome 3451979 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=38;DPB=38;DPRA=1.92308;EPP=9.52472;EPPR=3.07234;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=62.8371;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=45;QR=1312;RO=35;RPL=0;RPP=9.52472;RPPR=10.5174;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=12;SRP=10.5174;SRR=23;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|ppiC1|PA14_38700|transcript|ABJ11183.1|protein_coding|1/1|c.186C>A|p.Asp62Glu|186/279|186/279|62/92||,A|upstream_gene_variant|MODIFIER|atoB|PA14_38630|transcript|ABJ11188.1|protein_coding||c.-4857G>T|||||4857|,A|upstream_gene_variant|MODIFIER|scoB|PA14_38640|transcript|ABJ11187.1|protein_coding||c.-4051G>T|||||4051|,A|upstream_gene_variant|MODIFIER|scoA|PA14_38660|transcript|ABJ11186.1|protein_coding||c.-3318G>T|||||3318|,A|upstream_gene_variant|MODIFIER|PA14_38710|PA14_38710|transcript|ABJ11182.1|protein_coding||c.-112C>A|||||112|,A|upstream_gene_variant|MODIFIER|PA14_38720|PA14_38720|transcript|ABJ11181.1|protein_coding||c.-465C>A|||||465|,A|upstream_gene_variant|MODIFIER|yhhS|PA14_38730|transcript|ABJ11180.1|protein_coding||c.-1153C>A|||||1153|,A|downstream_gene_variant|MODIFIER|PA14_38680|PA14_38680|transcript|ABJ11185.1|protein_coding||c.*2266C>A|||||2266|,A|downstream_gene_variant|MODIFIER|acsA|PA14_38690|transcript|ABJ11184.1|protein_coding||c.*243C>A|||||243|,A|downstream_gene_variant|MODIFIER|PA14_38740|PA14_38740|transcript|ABJ11179.1|protein_coding||c.*2306G>T|||||2306|,A|downstream_gene_variant|MODIFIER|PA14_38750|PA14_38750|transcript|ABJ11178.1|protein_coding||c.*4074G>T|||||4074| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:221:0:0:0,-20.2423 0:9:9,2:7:270:2:30:0,-21.8147 0:7:7,0:7:265:0:0:0,-24.2101 0:16:16,1:15:556:1:15:0,-48.8749 +Chromosome 3456360 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=55;DPB=55;DPRA=0.4375;EPP=7.35324;EPPR=5.01789;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=48.3968;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=28;QR=1860;RO=53;RPL=0;RPP=7.35324;RPPR=3.37904;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=35;SRP=14.851;SRR=18;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|PA14_38750|PA14_38750|transcript|ABJ11178.1|protein_coding|1/1|c.857C>T|p.Ala286Val|857/1164|857/1164|286/387||,A|upstream_gene_variant|MODIFIER|PA14_38740|PA14_38740|transcript|ABJ11179.1|protein_coding||c.-291C>T|||||291|,A|downstream_gene_variant|MODIFIER|acsA|PA14_38690|transcript|ABJ11184.1|protein_coding||c.*4624G>A|||||4624|,A|downstream_gene_variant|MODIFIER|ppiC1|PA14_38700|transcript|ABJ11183.1|protein_coding||c.*4288G>A|||||4288|,A|downstream_gene_variant|MODIFIER|PA14_38710|PA14_38710|transcript|ABJ11182.1|protein_coding||c.*3913G>A|||||3913|,A|downstream_gene_variant|MODIFIER|PA14_38720|PA14_38720|transcript|ABJ11181.1|protein_coding||c.*3353G>A|||||3353|,A|downstream_gene_variant|MODIFIER|yhhS|PA14_38730|transcript|ABJ11180.1|protein_coding||c.*2020G>A|||||2020|,A|downstream_gene_variant|MODIFIER|PA14_38770|PA14_38770|transcript|ABJ11177.1|protein_coding||c.*942C>T|||||942|,A|downstream_gene_variant|MODIFIER|pqqE|PA14_38780|transcript|ABJ11176.1|protein_coding||c.*2773C>T|||||2773|,A|downstream_gene_variant|MODIFIER|pqqD|PA14_38790|transcript|ABJ11175.1|protein_coding||c.*3890C>T|||||3890|,A|downstream_gene_variant|MODIFIER|pqqC|PA14_38800|transcript|ABJ11174.1|protein_coding||c.*4165C>T|||||4165|,A|downstream_gene_variant|MODIFIER|pqqB|PA14_38820|transcript|ABJ11173.1|protein_coding||c.*4927C>T|||||4927| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,2:5:155:2:28:0,-11.5906 0:16:16,0:16:605:0:0:0,-54.7843 0:19:19,0:19:627:0:0:0,-56.7171 0:13:13,0:13:473:0:0:0,-42.9025 +Chromosome 3487576 . C G 1.00977E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=34;DPB=34;DPRA=1.42857;EPP=13.8677;EPPR=19.8579;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=53.0206;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=929;RO=29;RPL=0;RPP=13.8677;RPPR=9.07545;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=7;SRP=19.8579;SRR=22;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_39140|PA14_39140|transcript|ABJ11150.1|protein_coding|1/1|c.31G>C|p.Ala11Pro|31/267|31/267|11/88||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_39070|PA14_39070|transcript|ABJ11156.1|protein_coding||c.-4203G>C|||||4203|,G|upstream_gene_variant|MODIFIER|PA14_39080|PA14_39080|transcript|ABJ11155.1|protein_coding||c.-3923G>C|||||3923|,G|upstream_gene_variant|MODIFIER|PA14_39100|PA14_39100|transcript|ABJ11153.1|protein_coding||c.-2846G>C|||||2846|,G|upstream_gene_variant|MODIFIER|PA14_39110|PA14_39110|transcript|ABJ11152.1|protein_coding||c.-2216G>C|||||2216|,G|upstream_gene_variant|MODIFIER|PA14_39160|PA14_39160|transcript|ABJ11148.1|protein_coding||c.-893C>G|||||893|,G|upstream_gene_variant|MODIFIER|PA14_39200|PA14_39200|transcript|ABJ11145.1|protein_coding||c.-3743C>G|||||3743|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|nadR|PA14_39210|transcript|ABJ11144.1|protein_coding||c.-4315C>G|||||4315|,G|downstream_gene_variant|MODIFIER|PA14_39060|PA14_39060|transcript|ABJ11157.1|protein_coding||c.*4662C>G|||||4662|,G|downstream_gene_variant|MODIFIER|PA14_39090|PA14_39090|transcript|ABJ11154.1|protein_coding||c.*3238C>G|||||3238|,G|downstream_gene_variant|MODIFIER|ybiT|PA14_39130|transcript|ABJ11151.1|protein_coding||c.*323C>G|||||323|,G|downstream_gene_variant|MODIFIER|acpD|PA14_39150|transcript|ABJ11149.1|protein_coding||c.*137G>C|||||137|,G|downstream_gene_variant|MODIFIER|PA14_39180|PA14_39180|transcript|ABJ11147.1|protein_coding||c.*1839G>C|||||1839|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|bacA|PA14_39190|transcript|ABJ11146.1|protein_coding||c.*2628G>C|||||2628| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:167:0:0:0,-15.3524 0:9:9,0:9:318:0:0:0,-28.9451 0:11:11,3:8:240:3:6:0,-21.3223 0:9:9,2:7:204:2:4:0,-18.2617 +Chromosome 3506304 . A C 3.38292E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=76;DPB=76;DPRA=0.677419;EPP=9.52472;EPPR=30.1537;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=103.472;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=2422;RO=72;RPL=3;RPP=9.52472;RPPR=8.92153;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=36;SRP=3.0103;SRR=36;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_39390|PA14_39390|transcript|ABJ11131.1|protein_coding|1/1|c.224T>G|p.Val75Gly|224/1488|224/1488|75/495||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|rbsA|PA14_39330|transcript|ABJ11134.1|protein_coding||c.-3928T>G|||||3928|,C|upstream_gene_variant|MODIFIER|rbsB|PA14_39350|transcript|ABJ11133.1|protein_coding||c.-2947T>G|||||2947|,C|upstream_gene_variant|MODIFIER|PA14_39360|PA14_39360|transcript|ABJ11132.1|protein_coding||c.-1400T>G|||||1400|,C|upstream_gene_variant|MODIFIER|PA14_39410|PA14_39410|transcript|ABJ11130.1|protein_coding||c.-414A>C|||||414|,C|upstream_gene_variant|MODIFIER|PA14_39420|PA14_39420|transcript|ABJ11129.1|protein_coding||c.-1573A>C|||||1573|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_39440|PA14_39440|transcript|ABJ11128.1|protein_coding||c.-2114A>C|||||2114|,C|upstream_gene_variant|MODIFIER|PA14_39460|PA14_39460|transcript|ABJ11127.1|protein_coding||c.-4188A>C|||||4188| GT:DP:DPR:RO:QR:AO:QA:GL 0:21:21,0:20:662:0:0:0,-59.7237 0:15:15,0:15:539:0:0:0,-48.8261 0:14:14,3:11:392:3:6:0,-35.0535 0:26:26,0:26:829:0:0:0,-74.8625 +Chromosome 3506964 . A C 2.21536E-8 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=2.14286;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=19.1028;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=282;RO=10;RPL=2;RPP=7.35324;RPPR=24.725;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=3.0103;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_39410|PA14_39410|transcript|ABJ11130.1|protein_coding|1/1|c.247A>C|p.Ile83Leu|247/1098|247/1098|83/365||,C|upstream_gene_variant|MODIFIER|rbsA|PA14_39330|transcript|ABJ11134.1|protein_coding||c.-4588T>G|||||4588|,C|upstream_gene_variant|MODIFIER|rbsB|PA14_39350|transcript|ABJ11133.1|protein_coding||c.-3607T>G|||||3607|,C|upstream_gene_variant|MODIFIER|PA14_39360|PA14_39360|transcript|ABJ11132.1|protein_coding||c.-2060T>G|||||2060|,C|upstream_gene_variant|MODIFIER|PA14_39390|PA14_39390|transcript|ABJ11131.1|protein_coding||c.-437T>G|||||437|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_39420|PA14_39420|transcript|ABJ11129.1|protein_coding||c.-913A>C|||||913|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_39440|PA14_39440|transcript|ABJ11128.1|protein_coding||c.-1454A>C|||||1454|,C|upstream_gene_variant|MODIFIER|PA14_39460|PA14_39460|transcript|ABJ11127.1|protein_coding||c.-3528A>C|||||3528| GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:40:0:0:0,-3.99568 0:3:3,0:3:80:0:0:0,-7.46025 0:3:3,0:3:81:0:0:0,-7.55276 0:5:5,2:3:81:2:17:0,-5.93777 +Chromosome 3509870 . A T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=27;DPB=27;DPRA=1.76471;EPP=7.35324;EPPR=18.9659;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=42.6503;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=790;RO=23;RPL=0;RPP=7.35324;RPPR=3.10471;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=12;SRP=3.10471;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_39440|PA14_39440|transcript|ABJ11128.1|protein_coding|1/1|c.1453A>T|p.Ile485Phe|1453/1896|1453/1896|485/631||,T|upstream_gene_variant|MODIFIER|PA14_39360|PA14_39360|transcript|ABJ11132.1|protein_coding||c.-4966T>A|||||4966|,T|upstream_gene_variant|MODIFIER|PA14_39390|PA14_39390|transcript|ABJ11131.1|protein_coding||c.-3343T>A|||||3343|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|PA14_39460|PA14_39460|transcript|ABJ11127.1|protein_coding||c.-622A>T|||||622|,T|upstream_gene_variant|MODIFIER|PA14_39470|PA14_39470|transcript|ABJ11126.1|protein_coding||c.-2206A>T|||||2206|,T|upstream_gene_variant|MODIFIER|PA14_39480|PA14_39480|transcript|ABJ11125.1|protein_coding||c.-3223A>T|||||3223|,T|downstream_gene_variant|MODIFIER|PA14_39410|PA14_39410|transcript|ABJ11130.1|protein_coding||c.*2055A>T|||||2055|,T|downstream_gene_variant|MODIFIER|PA14_39420|PA14_39420|transcript|ABJ11129.1|protein_coding||c.*1763A>T|||||1763|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:146:0:0:0,-13.4936 0:10:10,2:7:185:2:4:0,-16.4907 0:8:8,0:8:313:0:0:0,-28.5345 0:5:5,0:4:146:0:0:0,-13.4047 +Chromosome 3523628 . T C 3.44976E-12 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=30;DPB=30;DPRA=1.30769;EPP=9.52472;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=27.8657;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=701;RO=26;RPL=3;RPP=9.52472;RPPR=3.34437;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=21;SRP=24.391;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|metE|PA14_39590|transcript|ABJ11117.1|protein_coding|1/1|c.2125A>G|p.Ser709Gly|2125/2301|2125/2301|709/766||,C|upstream_gene_variant|MODIFIER|PA14_39520|PA14_39520|transcript|ABJ11123.1|protein_coding||c.-4419A>G|||||4419|,C|upstream_gene_variant|MODIFIER|PA14_39530|PA14_39530|transcript|ABJ11122.1|protein_coding||c.-3433A>G|||||3433|,C|upstream_gene_variant|MODIFIER|PA14_39540|PA14_39540|transcript|ABJ11121.1|protein_coding||c.-2924A>G|||||2924|,C|upstream_gene_variant|MODIFIER|PA14_39560|PA14_39560|transcript|ABJ11120.1|protein_coding||c.-1459A>G|||||1459|,C|downstream_gene_variant|MODIFIER|PA14_39570|PA14_39570|transcript|ABJ11119.1|protein_coding||c.*854T>C|||||854|,C|downstream_gene_variant|MODIFIER|rimJ|PA14_39580|transcript|ABJ11118.1|protein_coding||c.*238T>C|||||238|,C|downstream_gene_variant|MODIFIER|PA14_39610|PA14_39610|transcript|ABJ11116.1|protein_coding||c.*2257A>G|||||2257|,C|downstream_gene_variant|MODIFIER|PA14_39620|PA14_39620|transcript|ABJ11115.1|protein_coding||c.*4608A>G|||||4608|,C|downstream_gene_variant|MODIFIER|PA14_39630|PA14_39630|transcript|ABJ11114.1|protein_coding||c.*4934A>G|||||4934| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:4:93:0:0:0,-8.53581 0:10:10,1:9:265:1:13:0,-22.8341 0:7:7,2:5:94:2:26:0,-6.17464 0:8:8,0:8:249:0:0:0,-22.7105 +Chromosome 3546081 . T G 5.44718E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=54;DPB=54;DPRA=1.45455;EPP=11.6962;EPPR=11.5225;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=53.8527;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=1360;RO=50;RPL=0;RPP=11.6962;RPPR=17.0814;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=12;SRP=32.3686;SRR=38;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_39790|PA14_39790|transcript|ABJ11101.1|protein_coding|1/1|c.451T>G|p.Trp151Gly|451/681|451/681|151/226||,G|upstream_gene_variant|MODIFIER|PA14_39800|PA14_39800|transcript|ABJ11100.1|protein_coding||c.-322T>G|||||322|,G|upstream_gene_variant|MODIFIER|PA14_39810|PA14_39810|transcript|ABJ11099.1|protein_coding||c.-825T>G|||||825|,G|upstream_gene_variant|MODIFIER|ufrA|PA14_39820|transcript|ABJ11098.1|protein_coding||c.-1983T>G|||||1983|,G|upstream_gene_variant|MODIFIER|PA14_39830|PA14_39830|transcript|ABJ11097.1|protein_coding||c.-4438T>G|||||4438|,G|downstream_gene_variant|MODIFIER|PA14_39750|PA14_39750|transcript|ABJ11104.1|protein_coding||c.*3962T>G|||||3962|,G|downstream_gene_variant|MODIFIER|PA14_39770|PA14_39770|transcript|ABJ11103.1|protein_coding||c.*2351T>G|||||2351|,G|downstream_gene_variant|MODIFIER|hvn|PA14_39780|transcript|ABJ11102.1|protein_coding||c.*557T>G|||||557| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:151:0:0:0,-13.9571 0:13:13,3:10:284:3:6:0,-25.2693 0:19:19,1:18:381:1:13:0,-33.186 0:18:18,0:18:544:0:0:0,-49.2301 +Chromosome 3554773 . T C 4.58079E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=45;DPB=45;DPRA=0.648649;EPP=3.0103;EPPR=3.0608;GTI=0;LEN=1;MEANALT=1;MQM=47;MQMR=60;NS=4;NUMALT=1;ODDS=64.8329;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1597;RO=43;RPL=1;RPP=3.0103;RPPR=21.2406;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=34;SRP=34.5724;SRR=9;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|apaH|PA14_39870|transcript|ABJ11094.1|protein_coding|1/1|c.26T>C|p.Ile9Thr|26/537|26/537|9/178||,C|downstream_gene_variant|MODIFIER|ufrA|PA14_39820|transcript|ABJ11098.1|protein_coding||c.*4295T>C|||||4295|,C|downstream_gene_variant|MODIFIER|PA14_39830|PA14_39830|transcript|ABJ11097.1|protein_coding||c.*3103T>C|||||3103|,C|downstream_gene_variant|MODIFIER|PA14_39850|PA14_39850|transcript|ABJ11096.1|protein_coding||c.*1705T>C|||||1705|,C|downstream_gene_variant|MODIFIER|PA14_39860|PA14_39860|transcript|ABJ11095.1|protein_coding||c.*68T>C|||||68|,C|downstream_gene_variant|MODIFIER|phzG2|PA14_39880|transcript|ABJ11093.1|protein_coding||c.*686A>G|||||686|,C|downstream_gene_variant|MODIFIER|phzF2|PA14_39890|transcript|ABJ11092.1|protein_coding||c.*1356A>G|||||1356|,C|downstream_gene_variant|MODIFIER|phzE2|PA14_39910|transcript|ABJ11091.1|protein_coding||c.*2206A>G|||||2206|,C|downstream_gene_variant|MODIFIER|phzD2|PA14_39925|transcript|ABJ15681.1|protein_coding||c.*4086A>G|||||4086|,C|downstream_gene_variant|MODIFIER|phzC2|PA14_39945|transcript|ABJ15680.1|protein_coding||c.*4706A>G|||||4706| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,2:6:239:2:4:0,-21.5055 0:10:10,0:10:333:0:0:0,-30.282 0:11:11,0:11:412:0:0:0,-37.4177 0:16:16,0:16:613:0:0:0,-55.5047 +Chromosome 3566749 . AAA GAG 530.521 . AB=0;ABP=0;AC=4;AF=1;AN=4;AO=16;CIGAR=1X1M1X;DP=16;DPB=16.3333;DPRA=0;EPP=7.89611;EPPR=0;GTI=0;LEN=3;MEANALT=1;MQM=59.625;MQMR=0;NS=4;NUMALT=1;ODDS=27.5831;PAIRED=0;PAIREDR=0;PAO=1;PQA=35;PQR=0;PRO=0;QA=573;QR=0;RO=0;RPL=11;RPP=7.89611;RPPR=0;RPR=5;RUN=1;SAF=8;SAP=3.0103;SAR=8;SRF=0;SRP=0;SRR=0;TYPE=complex;technology.ILLUMINA=1;ANN=GAG|missense_variant|MODERATE|PA14_40020|PA14_40020|transcript|ABJ11085.1|protein_coding|1/1|c.1100_1102delAAAinsGAG|p.GlnAsn367ArgAsp|1100/1275|1100/1275|367/424||,GAG|upstream_gene_variant|MODIFIER|qscR|PA14_39980|transcript|ABJ11088.1|protein_coding||c.-3824_-3822delTTTinsCTC|||||3822|,GAG|upstream_gene_variant|MODIFIER|PA14_40030|PA14_40030|transcript|ABJ11084.1|protein_coding||c.-123_-121delAAAinsGAG|||||123|,GAG|upstream_gene_variant|MODIFIER|PA14_40040|PA14_40040|transcript|ABJ11083.1|protein_coding||c.-841_-839delAAAinsGAG|||||841|,GAG|upstream_gene_variant|MODIFIER|PA14_40050|PA14_40050|transcript|ABJ11082.1|protein_coding||c.-3267_-3265delAAAinsGAG|||||3267|,GAG|upstream_gene_variant|MODIFIER|PA14_40060|PA14_40060|transcript|ABJ11081.1|protein_coding||c.-4001_-3999delAAAinsGAG|||||4001|WARNING_TRANSCRIPT_NO_START_CODON,GAG|upstream_gene_variant|MODIFIER|PA14_40070|PA14_40070|transcript|ABJ11080.1|protein_coding||c.-4479_-4477delAAAinsGAG|||||4479|,GAG|downstream_gene_variant|MODIFIER|PA14_39990|PA14_39990|transcript|ABJ11087.1|protein_coding||c.*2293_*2295delAAAinsGAG|||||2293|,GAG|downstream_gene_variant|MODIFIER|PA14_40010|PA14_40010|transcript|ABJ11086.1|protein_coding||c.*1118_*1120delAAAinsGAG|||||1118| GT:DP:DPR:RO:QR:AO:QA:GL 1:2:2,2:0:0:2:70:-6.6474,0 1:3:3,3:0:0:3:110:-10.2558,0 1:7:7,7:0:0:7:255:-23.2993,0 1:4:4,4:0:0:4:138:-15.9089,0 +Chromosome 3569024 . A G 1.62859E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=16;DPB=16;DPRA=2.33333;EPP=3.0103;EPPR=8.59409;GTI=0;LEN=1;MEANALT=1;MQM=58.5;MQMR=60;NS=4;NUMALT=1;ODDS=21.7041;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=516;RO=14;RPL=1;RPP=3.0103;RPPR=8.59409;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=8;SRP=3.63072;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_40040|PA14_40040|transcript|ABJ11083.1|protein_coding|1/1|c.1435A>G|p.Ser479Gly|1435/2430|1435/2430|479/809||,G|upstream_gene_variant|MODIFIER|PA14_40050|PA14_40050|transcript|ABJ11082.1|protein_coding||c.-992A>G|||||992|,G|upstream_gene_variant|MODIFIER|PA14_40060|PA14_40060|transcript|ABJ11081.1|protein_coding||c.-1726A>G|||||1726|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_40070|PA14_40070|transcript|ABJ11080.1|protein_coding||c.-2204A>G|||||2204|,G|upstream_gene_variant|MODIFIER|PA14_40100|PA14_40100|transcript|ABJ11078.1|protein_coding||c.-4054A>G|||||4054|,G|downstream_gene_variant|MODIFIER|PA14_39990|PA14_39990|transcript|ABJ11087.1|protein_coding||c.*4568A>G|||||4568|,G|downstream_gene_variant|MODIFIER|PA14_40010|PA14_40010|transcript|ABJ11086.1|protein_coding||c.*3393A>G|||||3393|,G|downstream_gene_variant|MODIFIER|PA14_40020|PA14_40020|transcript|ABJ11085.1|protein_coding||c.*2100A>G|||||2100|,G|downstream_gene_variant|MODIFIER|PA14_40030|PA14_40030|transcript|ABJ11084.1|protein_coding||c.*1460A>G|||||1460|,G|downstream_gene_variant|MODIFIER|PA14_40080|PA14_40080|transcript|ABJ11079.1|protein_coding||c.*2841T>C|||||2841|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:39:0:0:0,-3.89656 0:5:5,0:5:184:0:0:0,-16.9165 0:3:3,0:3:100:0:0:0,-9.32891 0:7:7,2:5:193:2:16:0,-16.2199 +Chromosome 3572682 . T C 6.52428E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=12;CIGAR=1X;DP=80;DPB=80;DPRA=0;EPP=29.068;EPPR=11.1853;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=98.0358;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=2021;RO=68;RPL=12;RPP=29.068;RPPR=3.13803;RPR=0;RUN=1;SAF=12;SAP=29.068;SAR=0;SRF=39;SRP=6.20364;SRR=29;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_40080|PA14_40080|transcript|ABJ11079.1|protein_coding|1/1|c.167A>G|p.Glu56Gly|167/984|167/984|56/327||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_40100|PA14_40100|transcript|ABJ11078.1|protein_coding||c.-396T>C|||||396|,C|upstream_gene_variant|MODIFIER|PA14_40110|PA14_40110|transcript|ABJ11077.1|protein_coding||c.-1789T>C|||||1789|,C|downstream_gene_variant|MODIFIER|PA14_40040|PA14_40040|transcript|ABJ11083.1|protein_coding||c.*2663T>C|||||2663|,C|downstream_gene_variant|MODIFIER|PA14_40050|PA14_40050|transcript|ABJ11082.1|protein_coding||c.*1929T>C|||||1929|,C|downstream_gene_variant|MODIFIER|PA14_40060|PA14_40060|transcript|ABJ11081.1|protein_coding||c.*1543T>C|||||1543|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_40070|PA14_40070|transcript|ABJ11080.1|protein_coding||c.*831T>C|||||831|,C|downstream_gene_variant|MODIFIER|polB|PA14_40120|transcript|ABJ11076.1|protein_coding||c.*2461A>G|||||2461|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_40130|PA14_40130|transcript|ABJ11075.1|protein_coding||c.*4893A>G|||||4893| GT:DP:DPR:RO:QR:AO:QA:GL 0:16:16,4:12:384:4:33:0,-31.804 0:22:22,2:20:588:2:4:0,-52.7917 0:23:23,3:20:577:3:33:0,-49.1015 0:19:19,3:16:472:3:6:0,-42.1926 +Chromosome 3586486 . T C 7.64729E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=38;DPB=38;DPRA=0.8;EPP=7.35324;EPPR=27.1378;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=56.8416;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=29;QR=1358;RO=36;RPL=2;RPP=7.35324;RPPR=9.04217;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=17;SRP=3.25157;SRR=19;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_40240|PA14_40240|transcript|ABJ11066.1|protein_coding|1/1|c.818A>G|p.Glu273Gly|818/2172|818/2172|273/723||,C|upstream_gene_variant|MODIFIER|PA14_40230|PA14_40230|transcript|ABJ11067.1|protein_coding||c.-1344A>G|||||1344|,C|downstream_gene_variant|MODIFIER|PA14_40200|PA14_40200|transcript|ABJ11070.1|protein_coding||c.*4018T>C|||||4018|,C|downstream_gene_variant|MODIFIER|PA14_40210|PA14_40210|transcript|ABJ11069.1|protein_coding||c.*3306T>C|||||3306|,C|downstream_gene_variant|MODIFIER|PA14_40220|PA14_40220|transcript|ABJ11068.1|protein_coding||c.*2640T>C|||||2640|,C|downstream_gene_variant|MODIFIER|opmL|PA14_40250|transcript|ABJ11065.1|protein_coding||c.*807A>G|||||807|,C|downstream_gene_variant|MODIFIER|PA14_40260|PA14_40260|transcript|ABJ11064.1|protein_coding||c.*2084A>G|||||2084|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:199:0:0:0,-18.2889 0:8:8,2:6:224:2:29:0,-17.7626 0:8:8,0:8:293:0:0:0,-26.716 0:17:17,0:17:642:0:0:0,-58.1085 +Chromosome 3610820 . G C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=41;DPB=41;DPRA=0.967742;EPP=7.35324;EPPR=7.52028;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=67.7024;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=1437;RO=39;RPL=2;RPP=7.35324;RPPR=12.42;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=12;SRP=15.538;SRR=27;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|modB|PA14_40410|transcript|ABJ11051.1|protein_coding|1/1|c.52G>C|p.Glu18Gln|52/687|52/687|18/228||,C|upstream_gene_variant|MODIFIER|PA14_40350|PA14_40350|transcript|ABJ11055.1|protein_coding||c.-3388C>G|||||3388|,C|upstream_gene_variant|MODIFIER|PA14_40370|PA14_40370|transcript|ABJ11054.1|protein_coding||c.-1719C>G|||||1719|,C|upstream_gene_variant|MODIFIER|modC|PA14_40420|transcript|ABJ11050.1|protein_coding||c.-637G>C|||||637|,C|upstream_gene_variant|MODIFIER|PA14_40440|PA14_40440|transcript|ABJ11048.1|protein_coding||c.-2657G>C|||||2657|,C|upstream_gene_variant|MODIFIER|str|PA14_40450|transcript|ABJ11047.1|protein_coding||c.-3553G>C|||||3553|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_40380|PA14_40380|transcript|ABJ11053.1|protein_coding||c.*935G>C|||||935|,C|downstream_gene_variant|MODIFIER|modA|PA14_40390|transcript|ABJ11052.1|protein_coding||c.*64G>C|||||64|,C|downstream_gene_variant|MODIFIER|PA14_40430|PA14_40430|transcript|ABJ11049.1|protein_coding||c.*1744C>G|||||1744|,C|downstream_gene_variant|MODIFIER|PA14_40470|PA14_40470|transcript|ABJ11046.1|protein_coding||c.*4375C>G|||||4375| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:266:0:0:0,-24.3016 0:13:13,0:13:471:0:0:0,-42.7232 0:11:11,0:11:425:0:0:0,-38.602 0:10:10,2:8:275:2:30:0,-22.2264 +Chromosome 3612508 . G T 5.80146E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=25;DPB=25;DPRA=1.6875;EPP=7.35324;EPPR=3.86001;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=32.0164;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=739;RO=23;RPL=2;RPP=7.35324;RPPR=5.3706;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=15;SRP=7.63648;SRR=8;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|modC|PA14_40420|transcript|ABJ11050.1|protein_coding|1/1|c.1052G>T|p.Trp351Leu|1052/1086|1052/1086|351/361||,T|upstream_gene_variant|MODIFIER|PA14_40370|PA14_40370|transcript|ABJ11054.1|protein_coding||c.-3407C>A|||||3407|,T|upstream_gene_variant|MODIFIER|PA14_40440|PA14_40440|transcript|ABJ11048.1|protein_coding||c.-969G>T|||||969|,T|upstream_gene_variant|MODIFIER|str|PA14_40450|transcript|ABJ11047.1|protein_coding||c.-1865G>T|||||1865|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|yedI|PA14_40490|transcript|ABJ11045.1|protein_coding||c.-4319G>T|||||4319|,T|downstream_gene_variant|MODIFIER|PA14_40380|PA14_40380|transcript|ABJ11053.1|protein_coding||c.*2623G>T|||||2623|,T|downstream_gene_variant|MODIFIER|modA|PA14_40390|transcript|ABJ11052.1|protein_coding||c.*1752G>T|||||1752|,T|downstream_gene_variant|MODIFIER|modB|PA14_40410|transcript|ABJ11051.1|protein_coding||c.*1053G>T|||||1053|,T|downstream_gene_variant|MODIFIER|PA14_40430|PA14_40430|transcript|ABJ11049.1|protein_coding||c.*56C>A|||||56|,T|downstream_gene_variant|MODIFIER|PA14_40470|PA14_40470|transcript|ABJ11046.1|protein_coding||c.*2687C>A|||||2687| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:175:0:0:0,-16.0909 0:3:3,0:3:86:0:0:0,-8.02211 0:9:9,2:7:215:2:18:0,-17.9375 0:8:8,0:8:263:0:0:0,-23.9834 +Chromosome 3613654 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=36;DPB=36;DPRA=1.15385;EPP=7.35324;EPPR=15.5282;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=53.2901;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=79;QR=1299;RO=34;RPL=0;RPP=7.35324;RPPR=12.2071;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=5;SRP=39.7976;SRR=29;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_40440|PA14_40440|transcript|ABJ11048.1|protein_coding|1/1|c.178A>G|p.Thr60Ala|178/888|178/888|60/295||,G|upstream_gene_variant|MODIFIER|PA14_40370|PA14_40370|transcript|ABJ11054.1|protein_coding||c.-4553T>C|||||4553|,G|upstream_gene_variant|MODIFIER|PA14_40430|PA14_40430|transcript|ABJ11049.1|protein_coding||c.-263T>C|||||263|,G|upstream_gene_variant|MODIFIER|str|PA14_40450|transcript|ABJ11047.1|protein_coding||c.-719A>G|||||719|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|yedI|PA14_40490|transcript|ABJ11045.1|protein_coding||c.-3173A>G|||||3173|,G|upstream_gene_variant|MODIFIER|ccoN-2|PA14_40510|transcript|ABJ11044.1|protein_coding||c.-4443A>G|||||4443|,G|downstream_gene_variant|MODIFIER|PA14_40380|PA14_40380|transcript|ABJ11053.1|protein_coding||c.*3769A>G|||||3769|,G|downstream_gene_variant|MODIFIER|modA|PA14_40390|transcript|ABJ11052.1|protein_coding||c.*2898A>G|||||2898|,G|downstream_gene_variant|MODIFIER|modB|PA14_40410|transcript|ABJ11051.1|protein_coding||c.*2199A>G|||||2199|,G|downstream_gene_variant|MODIFIER|modC|PA14_40420|transcript|ABJ11050.1|protein_coding||c.*1112A>G|||||1112|,G|downstream_gene_variant|MODIFIER|PA14_40470|PA14_40470|transcript|ABJ11046.1|protein_coding||c.*1541T>C|||||1541| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:234:0:0:0,-21.4298 0:5:5,0:5:184:0:0:0,-16.917 0:15:15,0:15:567:0:0:0,-51.3655 0:10:10,2:8:314:2:79:0,-21.1268 +Chromosome 3614805 . T C 3.53667E-11 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=14;DPB=14;DPRA=2.25;EPP=7.35324;EPPR=5.9056;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=26.2257;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=29;QR=452;RO=12;RPL=2;RPP=7.35324;RPPR=3.0103;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=6;SRP=3.0103;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|str|PA14_40450|transcript|ABJ11047.1|protein_coding|1/1|c.433T>C|p.Cys145Arg|433/822|433/822|145/273||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_40430|PA14_40430|transcript|ABJ11049.1|protein_coding||c.-1414A>G|||||1414|,C|upstream_gene_variant|MODIFIER|yedI|PA14_40490|transcript|ABJ11045.1|protein_coding||c.-2022T>C|||||2022|,C|upstream_gene_variant|MODIFIER|ccoN-2|PA14_40510|transcript|ABJ11044.1|protein_coding||c.-3292T>C|||||3292|,C|upstream_gene_variant|MODIFIER|PA14_40520|PA14_40520|transcript|ABJ11043.1|protein_coding||c.-4737T>C|||||4737|,C|downstream_gene_variant|MODIFIER|PA14_40380|PA14_40380|transcript|ABJ11053.1|protein_coding||c.*4920T>C|||||4920|,C|downstream_gene_variant|MODIFIER|modA|PA14_40390|transcript|ABJ11052.1|protein_coding||c.*4049T>C|||||4049|,C|downstream_gene_variant|MODIFIER|modB|PA14_40410|transcript|ABJ11051.1|protein_coding||c.*3350T>C|||||3350|,C|downstream_gene_variant|MODIFIER|modC|PA14_40420|transcript|ABJ11050.1|protein_coding||c.*2263T>C|||||2263|,C|downstream_gene_variant|MODIFIER|PA14_40440|PA14_40440|transcript|ABJ11048.1|protein_coding||c.*441T>C|||||441|,C|downstream_gene_variant|MODIFIER|PA14_40470|PA14_40470|transcript|ABJ11046.1|protein_coding||c.*390A>G|||||390| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:70:0:0:0,-6.64622 0:4:4,0:4:157:0:0:0,-14.509 0:6:6,2:4:155:2:29:0,-11.5706 0:2:2,0:2:70:0:0:0,-6.6474 +Chromosome 3619369 . T C 7.86534E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=33;DPB=33;DPRA=0.583333;EPP=11.6962;EPPR=6.67934;GTI=0;LEN=1;MEANALT=1;MQM=49.25;MQMR=59.6207;NS=4;NUMALT=1;ODDS=31.7347;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=45;QR=976;RO=29;RPL=4;RPP=11.6962;RPPR=3.68421;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=6;SRP=24.6501;SRR=23;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|ccoN-2|PA14_40510|transcript|ABJ11044.1|protein_coding|1/1|c.1273T>C|p.Tyr425His|1273/1443|1273/1443|425/480||,C|upstream_gene_variant|MODIFIER|PA14_40470|PA14_40470|transcript|ABJ11046.1|protein_coding||c.-2720A>G|||||2720|,C|upstream_gene_variant|MODIFIER|PA14_40520|PA14_40520|transcript|ABJ11043.1|protein_coding||c.-173T>C|||||173|,C|upstream_gene_variant|MODIFIER|PA14_40540|PA14_40540|transcript|ABJ11042.1|protein_coding||c.-486T>C|||||486|,C|upstream_gene_variant|MODIFIER|PA14_40560|PA14_40560|transcript|ABJ11040.1|protein_coding||c.-2779T>C|||||2779|,C|upstream_gene_variant|MODIFIER|PA14_40600|PA14_40600|transcript|ABJ11038.1|protein_coding||c.-4557T>C|||||4557|,C|downstream_gene_variant|MODIFIER|str|PA14_40450|transcript|ABJ11047.1|protein_coding||c.*4175T>C|||||4175|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|yedI|PA14_40490|transcript|ABJ11045.1|protein_coding||c.*1619T>C|||||1619|,C|downstream_gene_variant|MODIFIER|PA14_40550|PA14_40550|transcript|ABJ11041.1|protein_coding||c.*1631A>G|||||1631|,C|downstream_gene_variant|MODIFIER|PA14_40570|PA14_40570|transcript|ABJ11039.1|protein_coding||c.*3103A>G|||||3103| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,2:3:90:2:15:0,-6.97666 0:8:8,1:7:227:1:15:0,-19.239 0:8:8,1:7:273:1:15:0,-23.4367 0:12:12,0:12:386:0:0:0,-35.0388 +Chromosome 3629669 . C A 7.64729E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=25;DPB=25;DPRA=1.16667;EPP=7.35324;EPPR=7.63648;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=42.3216;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=760;RO=23;RPL=0;RPP=7.35324;RPPR=3.10471;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=6;SRP=14.4341;SRR=17;TYPE=snp;technology.ILLUMINA=1;ANN=A|upstream_gene_variant|MODIFIER|yhgI|PA14_40630|transcript|ABJ11035.1|protein_coding||c.-2657G>T|||||2657|,A|upstream_gene_variant|MODIFIER|cti|PA14_40640|transcript|ABJ11034.1|protein_coding||c.-246G>T|||||246|,A|upstream_gene_variant|MODIFIER|PA14_40650|PA14_40650|transcript|ABJ11033.1|protein_coding||c.-116C>A|||||116|,A|upstream_gene_variant|MODIFIER|PA14_40660|PA14_40660|transcript|ABJ11032.1|protein_coding||c.-676C>A|||||676|,A|upstream_gene_variant|MODIFIER|metH|PA14_40670|transcript|ABJ11031.1|protein_coding||c.-1415C>A|||||1415|,A|downstream_gene_variant|MODIFIER|PA14_40600|PA14_40600|transcript|ABJ11038.1|protein_coding||c.*4739C>A|||||4739|,A|downstream_gene_variant|MODIFIER|PA14_40610|PA14_40610|transcript|ABJ11037.1|protein_coding||c.*4474C>A|||||4474|,A|downstream_gene_variant|MODIFIER|PA14_40620|PA14_40620|transcript|ABJ11036.1|protein_coding||c.*3300C>A|||||3300|,A|intergenic_region|MODIFIER|cti-PA14_40650|PA14_40640-PA14_40650|intergenic_region|PA14_40640-PA14_40650|||n.3629669C>A|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:189:0:0:0,-17.3173 0:7:7,2:5:169:2:32:0,-12.5007 0:6:6,0:6:195:0:0:0,-17.8685 0:6:6,0:6:207:0:0:0,-18.9641 +Chromosome 3629927 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=42;DPB=42;DPRA=0.75;EPP=9.52472;EPPR=3.51141;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=62.0116;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=45;QR=1448;RO=39;RPL=0;RPP=9.52472;RPPR=7.52028;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=21;SRP=3.51141;SRR=18;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_40650|PA14_40650|transcript|ABJ11033.1|protein_coding|1/1|c.143T>G|p.Val48Gly|143/519|143/519|48/172||,G|upstream_gene_variant|MODIFIER|yhgI|PA14_40630|transcript|ABJ11035.1|protein_coding||c.-2915A>C|||||2915|,G|upstream_gene_variant|MODIFIER|cti|PA14_40640|transcript|ABJ11034.1|protein_coding||c.-504A>C|||||504|,G|upstream_gene_variant|MODIFIER|PA14_40660|PA14_40660|transcript|ABJ11032.1|protein_coding||c.-418T>G|||||418|,G|upstream_gene_variant|MODIFIER|metH|PA14_40670|transcript|ABJ11031.1|protein_coding||c.-1157T>G|||||1157|,G|upstream_gene_variant|MODIFIER|PA14_40690|PA14_40690|transcript|ABJ11030.1|protein_coding||c.-4876T>G|||||4876|,G|downstream_gene_variant|MODIFIER|PA14_40600|PA14_40600|transcript|ABJ11038.1|protein_coding||c.*4997T>G|||||4997|,G|downstream_gene_variant|MODIFIER|PA14_40610|PA14_40610|transcript|ABJ11037.1|protein_coding||c.*4732T>G|||||4732|,G|downstream_gene_variant|MODIFIER|PA14_40620|PA14_40620|transcript|ABJ11036.1|protein_coding||c.*3558T>G|||||3558| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,1:9:343:1:15:0,-29.7257 0:8:8,2:6:238:2:30:0,-18.9445 0:12:12,0:12:430:0:0:0,-39.0263 0:12:12,0:12:437:0:0:0,-39.6622 +Chromosome 3631525 . T C 2.8223E-8 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=1.71429;EPP=7.35324;EPPR=9.04217;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=18.8557;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=329;RO=9;RPL=2;RPP=7.35324;RPPR=3.25157;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=3.25157;SRR=4;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|metH|PA14_40670|transcript|ABJ11031.1|protein_coding|1/1|c.442T>C|p.Ser148Pro|442/3705|442/3705|148/1234||,C|upstream_gene_variant|MODIFIER|yhgI|PA14_40630|transcript|ABJ11035.1|protein_coding||c.-4513A>G|||||4513|,C|upstream_gene_variant|MODIFIER|cti|PA14_40640|transcript|ABJ11034.1|protein_coding||c.-2102A>G|||||2102|,C|upstream_gene_variant|MODIFIER|PA14_40690|PA14_40690|transcript|ABJ11030.1|protein_coding||c.-3278T>C|||||3278|,C|upstream_gene_variant|MODIFIER|PA14_40730|PA14_40730|transcript|ABJ11027.1|protein_coding||c.-4603T>C|||||4603|,C|downstream_gene_variant|MODIFIER|PA14_40650|PA14_40650|transcript|ABJ11033.1|protein_coding||c.*1222T>C|||||1222|,C|downstream_gene_variant|MODIFIER|PA14_40660|PA14_40660|transcript|ABJ11032.1|protein_coding||c.*716T>C|||||716|,C|downstream_gene_variant|MODIFIER|PA14_40700|PA14_40700|transcript|ABJ11029.1|protein_coding||c.*3692A>G|||||3692|,C|downstream_gene_variant|MODIFIER|PA14_40710|PA14_40710|transcript|ABJ11028.1|protein_coding||c.*4203A>G|||||4203| GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:40:0:0:0,-3.99568 0:4:4,2:2:74:2:18:0,-5.31578 0:2:2,0:2:74:0:0:0,-7.02486 0:4:4,0:4:141:0:0:0,-13.036 +Chromosome 3663153 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=8;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=20.3821;EPPR=28.2974;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=43.0384;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=868;RO=31;RPL=8;RPP=20.3821;RPPR=40.0654;RPR=0;RUN=1;SAF=8;SAP=20.3821;SAR=0;SRF=27;SRP=40.0654;SRR=4;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_41080|PA14_41080|transcript|ABJ10999.1|protein_coding|1/1|c.275T>C|p.Leu92Pro|275/483|275/483|92/160||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|adi|PA14_41020|transcript|ABJ11004.1|protein_coding||c.-3296A>G|||||3296|,C|upstream_gene_variant|MODIFIER|dnaQ|PA14_41050|transcript|ABJ11002.1|protein_coding||c.-1945A>G|||||1945|,C|upstream_gene_variant|MODIFIER|rnhA|PA14_41060|transcript|ABJ11001.1|protein_coding||c.-1434A>G|||||1434|,C|upstream_gene_variant|MODIFIER|PA14_41070|PA14_41070|transcript|ABJ11000.1|protein_coding||c.-670A>G|||||670|,C|upstream_gene_variant|MODIFIER|mltD|PA14_41090|transcript|ABJ10998.1|protein_coding||c.-286T>C|||||286|,C|upstream_gene_variant|MODIFIER|PA14_41110|PA14_41110|transcript|ABJ10997.1|protein_coding||c.-2081T>C|||||2081|,C|upstream_gene_variant|MODIFIER|PA14_41130|PA14_41130|transcript|ABJ10996.1|protein_coding||c.-3907T>C|||||3907|,C|downstream_gene_variant|MODIFIER|PA14_41030|PA14_41030|transcript|ABJ11003.1|protein_coding||c.*2713T>C|||||2713| GT:DP:DPR:RO:QR:AO:QA:GL 0:12:12,2:10:195:2:4:0,-17.361 0:6:6,1:5:191:1:2:0,-17.3581 0:8:8,1:7:225:1:2:0,-20.3621 0:13:13,4:9:257:4:19:0,-21.6427 +Chromosome 3665832 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=41;DPB=41;DPRA=0.84375;EPP=7.35324;EPPR=3.9246;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=53.0081;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1181;RO=38;RPL=2;RPP=7.35324;RPPR=11.239;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=12;SRP=14.2105;SRR=26;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_41110|PA14_41110|transcript|ABJ10997.1|protein_coding|1/1|c.599A>C|p.Glu200Ala|599/1830|599/1830|200/609||,C|upstream_gene_variant|MODIFIER|dnaQ|PA14_41050|transcript|ABJ11002.1|protein_coding||c.-4624T>G|||||4624|,C|upstream_gene_variant|MODIFIER|rnhA|PA14_41060|transcript|ABJ11001.1|protein_coding||c.-4113T>G|||||4113|,C|upstream_gene_variant|MODIFIER|PA14_41070|PA14_41070|transcript|ABJ11000.1|protein_coding||c.-3349T>G|||||3349|,C|upstream_gene_variant|MODIFIER|PA14_41130|PA14_41130|transcript|ABJ10996.1|protein_coding||c.-1228A>C|||||1228|,C|upstream_gene_variant|MODIFIER|PA14_41140|PA14_41140|transcript|ABJ10995.1|protein_coding||c.-3082A>C|||||3082|,C|upstream_gene_variant|MODIFIER|PA14_41150|PA14_41150|transcript|ABJ10994.1|protein_coding||c.-4169A>C|||||4169|,C|downstream_gene_variant|MODIFIER|PA14_41080|PA14_41080|transcript|ABJ10999.1|protein_coding||c.*2471A>C|||||2471|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|mltD|PA14_41090|transcript|ABJ10998.1|protein_coding||c.*789A>C|||||789| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,0:10:351:0:0:0,-31.9195 0:11:11,0:11:335:0:0:0,-30.4344 0:11:11,0:10:318:0:0:0,-28.7476 0:9:9,2:7:177:2:4:0,-15.797 +Chromosome 3690320 . G T 3.4053E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=6;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=16.0391;EPPR=4.34659;GTI=0;LEN=1;MEANALT=1.25;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=38.8488;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=83;QR=934;RO=26;RPL=6;RPP=16.0391;RPPR=3.34437;RPR=0;RUN=1;SAF=6;SAP=16.0391;SAR=0;SRF=19;SRP=15.0369;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|glnS|PA14_41380|transcript|ABJ10978.1|protein_coding|1/1|c.1290C>A|p.Gly430Gly|1290/1671|1290/1671|430/556||,T|upstream_gene_variant|MODIFIER|PA14_41300|PA14_41300|transcript|ABJ10981.1|protein_coding||c.-3637C>A|||||3637|,T|upstream_gene_variant|MODIFIER|PA14_41320|PA14_41320|transcript|PA14_41320-1.1|protein_coding||c.-3222C>A|||||3222|WARNING_TRANSCRIPT_INCOMPLETE,T|upstream_gene_variant|MODIFIER|PA14_41330|PA14_41330|transcript|PA14_41330-1.1|protein_coding||c.-3092C>A|||||3092|WARNING_TRANSCRIPT_INCOMPLETE,T|upstream_gene_variant|MODIFIER|PA14_41340|PA14_41340|transcript|PA14_41340-1.1|protein_coding||c.-2964C>A|||||2964|WARNING_TRANSCRIPT_INCOMPLETE,T|upstream_gene_variant|MODIFIER|cysS|PA14_41360|transcript|ABJ10979.1|protein_coding||c.-391C>A|||||391|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ppiB|PA14_41390|transcript|ABJ10977.1|protein_coding||c.-1412G>T|||||1412|,T|upstream_gene_variant|MODIFIER|PA14_41400|PA14_41400|transcript|ABJ10976.1|protein_coding||c.-1914G>T|||||1914|,T|upstream_gene_variant|MODIFIER|PA14_41420|PA14_41420|transcript|ABJ10975.1|protein_coding||c.-2768G>T|||||2768|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|uspA|PA14_41440|transcript|ABJ10973.1|protein_coding||c.-4942G>T|||||4942|,T|downstream_gene_variant|MODIFIER|PA14_41280|PA14_41280|transcript|ABJ10983.1|protein_coding||c.*4145G>T|||||4145|,T|downstream_gene_variant|MODIFIER|PA14_41290|PA14_41290|transcript|ABJ10982.1|protein_coding||c.*4032G>T|||||4032|,T|downstream_gene_variant|MODIFIER|tRNA|EBG00001225080|transcript|EBT00001793350.1|protein_coding||c.*3373G>T|||||3373|WARNING_TRANSCRIPT_INCOMPLETE,T|downstream_gene_variant|MODIFIER|tRNA|EBG00001225081|transcript|EBT00001793377.1|protein_coding||c.*3222G>T|||||3222|WARNING_TRANSCRIPT_INCOMPLETE,T|downstream_gene_variant|MODIFIER|tRNA|EBG00001225148|transcript|EBT00001793452.1|protein_coding||c.*3092G>T|||||3092|WARNING_TRANSCRIPT_INCOMPLETE,T|downstream_gene_variant|MODIFIER|tRNA|EBG00001225051|transcript|EBT00001793420.1|protein_coding||c.*2964G>T|||||2964|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,T|downstream_gene_variant|MODIFIER|folD|PA14_41350|transcript|ABJ10980.1|protein_coding||c.*1831G>T|||||1831|,T|downstream_gene_variant|MODIFIER|miaE|PA14_41430|transcript|ABJ10974.1|protein_coding||c.*4148C>A|||||4148|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,1:6:223:1:2:0,-20.2258 0:8:8,1:7:246:1:15:0,-20.9796 0:8:8,3:5:162:3:51:0,-10.1364 0:10:10,1:8:303:1:15:0,-26.0077 +Chromosome 3690552 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=56;DPB=56;DPRA=1;EPP=11.6962;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=53.0235;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=47;QR=1821;RO=52;RPL=4;RPP=11.6962;RPPR=11.1951;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=35;SRP=16.5402;SRR=17;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|glnS|PA14_41380|transcript|ABJ10978.1|protein_coding|1/1|c.1058T>G|p.Val353Gly|1058/1671|1058/1671|353/556||,C|upstream_gene_variant|MODIFIER|PA14_41300|PA14_41300|transcript|ABJ10981.1|protein_coding||c.-3869T>G|||||3869|,C|upstream_gene_variant|MODIFIER|PA14_41320|PA14_41320|transcript|PA14_41320-1.1|protein_coding||c.-3454T>G|||||3454|WARNING_TRANSCRIPT_INCOMPLETE,C|upstream_gene_variant|MODIFIER|PA14_41330|PA14_41330|transcript|PA14_41330-1.1|protein_coding||c.-3324T>G|||||3324|WARNING_TRANSCRIPT_INCOMPLETE,C|upstream_gene_variant|MODIFIER|PA14_41340|PA14_41340|transcript|PA14_41340-1.1|protein_coding||c.-3196T>G|||||3196|WARNING_TRANSCRIPT_INCOMPLETE,C|upstream_gene_variant|MODIFIER|cysS|PA14_41360|transcript|ABJ10979.1|protein_coding||c.-623T>G|||||623|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ppiB|PA14_41390|transcript|ABJ10977.1|protein_coding||c.-1180A>C|||||1180|,C|upstream_gene_variant|MODIFIER|PA14_41400|PA14_41400|transcript|ABJ10976.1|protein_coding||c.-1682A>C|||||1682|,C|upstream_gene_variant|MODIFIER|PA14_41420|PA14_41420|transcript|ABJ10975.1|protein_coding||c.-2536A>C|||||2536|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|uspA|PA14_41440|transcript|ABJ10973.1|protein_coding||c.-4710A>C|||||4710|,C|downstream_gene_variant|MODIFIER|PA14_41280|PA14_41280|transcript|ABJ10983.1|protein_coding||c.*4377A>C|||||4377|,C|downstream_gene_variant|MODIFIER|PA14_41290|PA14_41290|transcript|ABJ10982.1|protein_coding||c.*4264A>C|||||4264|,C|downstream_gene_variant|MODIFIER|tRNA|EBG00001225080|transcript|EBT00001793350.1|protein_coding||c.*3605A>C|||||3605|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|tRNA|EBG00001225081|transcript|EBT00001793377.1|protein_coding||c.*3454A>C|||||3454|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|tRNA|EBG00001225148|transcript|EBT00001793452.1|protein_coding||c.*3324A>C|||||3324|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|tRNA|EBG00001225051|transcript|EBT00001793420.1|protein_coding||c.*3196A>C|||||3196|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|downstream_gene_variant|MODIFIER|folD|PA14_41350|transcript|ABJ10980.1|protein_coding||c.*2063A>C|||||2063|,C|downstream_gene_variant|MODIFIER|miaE|PA14_41430|transcript|ABJ10974.1|protein_coding||c.*3916T>G|||||3916|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,2:5:185:2:30:0,-14.1569 0:14:14,0:14:521:0:0:0,-47.2254 0:14:14,1:13:423:1:2:0,-38.1652 0:21:21,1:20:692:1:15:0,-61.0756 +Chromosome 3692316 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=7;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=3.32051;EPPR=14.2105;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=43.5417;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=74;QR=1018;RO=38;RPL=3;RPP=3.32051;RPPR=17.6392;RPR=4;RUN=1;SAF=0;SAP=18.2106;SAR=7;SRF=13;SRP=11.239;SRR=25;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_41400|PA14_41400|transcript|ABJ10976.1|protein_coding|1/1|c.83A>G|p.Glu28Gly|83/723|83/723|28/240||,G|upstream_gene_variant|MODIFIER|PA14_41340|PA14_41340|transcript|PA14_41340-1.1|protein_coding||c.-4960T>C|||||4960|WARNING_TRANSCRIPT_INCOMPLETE,G|upstream_gene_variant|MODIFIER|cysS|PA14_41360|transcript|ABJ10979.1|protein_coding||c.-2387T>C|||||2387|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|glnS|PA14_41380|transcript|ABJ10978.1|protein_coding||c.-707T>C|||||707|,G|upstream_gene_variant|MODIFIER|PA14_41420|PA14_41420|transcript|ABJ10975.1|protein_coding||c.-772A>G|||||772|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|uspA|PA14_41440|transcript|ABJ10973.1|protein_coding||c.-2946A>G|||||2946|,G|upstream_gene_variant|MODIFIER|acnB|PA14_41470|transcript|ABJ10971.1|protein_coding||c.-4714A>G|||||4714|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|tRNA|EBG00001225051|transcript|EBT00001793420.1|protein_coding||c.*4960A>G|||||4960|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,G|downstream_gene_variant|MODIFIER|folD|PA14_41350|transcript|ABJ10980.1|protein_coding||c.*3827A>G|||||3827|,G|downstream_gene_variant|MODIFIER|ppiB|PA14_41390|transcript|ABJ10977.1|protein_coding||c.*87A>G|||||87|,G|downstream_gene_variant|MODIFIER|miaE|PA14_41430|transcript|ABJ10974.1|protein_coding||c.*2152T>C|||||2152|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_41450|PA14_41450|transcript|ABJ10972.1|protein_coding||c.*3865T>C|||||3865| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,1:5:146:1:14:0,-12.028 0:13:13,2:11:310:2:4:0,-27.7862 0:12:12,3:9:213:3:42:0,-15.4821 0:14:14,1:13:349:1:14:0,-30.2628 +Chromosome 3696313 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=9;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=22.5536;EPPR=25.8679;GTI=0;LEN=1;MEANALT=1.25;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=52.0708;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=122;QR=1272;RO=38;RPL=0;RPP=22.5536;RPPR=3.9246;RPR=9;RUN=1;SAF=0;SAP=22.5536;SAR=9;SRF=16;SRP=5.06748;SRR=22;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|PA14_41450|PA14_41450|transcript|ABJ10972.1|protein_coding|1/1|c.336A>C|p.Ala112Ala|336/468|336/468|112/155||,G|upstream_gene_variant|MODIFIER|glnS|PA14_41380|transcript|ABJ10978.1|protein_coding||c.-4704A>C|||||4704|,G|upstream_gene_variant|MODIFIER|miaE|PA14_41430|transcript|ABJ10974.1|protein_coding||c.-1222A>C|||||1222|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|acnB|PA14_41470|transcript|ABJ10971.1|protein_coding||c.-717T>G|||||717|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|nasS|PA14_41480|transcript|ABJ10970.1|protein_coding||c.-3504T>G|||||3504|,G|upstream_gene_variant|MODIFIER|nasT|PA14_41490|transcript|ABJ10969.1|protein_coding||c.-4729T>G|||||4729|,G|downstream_gene_variant|MODIFIER|ppiB|PA14_41390|transcript|ABJ10977.1|protein_coding||c.*4084T>G|||||4084|,G|downstream_gene_variant|MODIFIER|PA14_41400|PA14_41400|transcript|ABJ10976.1|protein_coding||c.*3357T>G|||||3357|,G|downstream_gene_variant|MODIFIER|PA14_41420|PA14_41420|transcript|ABJ10975.1|protein_coding||c.*1894T>G|||||1894|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|uspA|PA14_41440|transcript|ABJ10973.1|protein_coding||c.*188T>G|||||188| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,3:6:209:3:45:0,-14.943 0:16:16,1:14:479:1:15:0,-41.9671 0:12:12,2:10:340:2:30:0,-28.0709 0:11:11,3:8:244:3:32:0,-19.2613 +Chromosome 3697193 . C G 1.71394E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=48;DPB=48;DPRA=0.789474;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=66.1794;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1621;RO=46;RPL=0;RPP=7.35324;RPPR=3.76559;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=16;SRP=12.2627;SRR=30;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|acnB|PA14_41470|transcript|ABJ10971.1|protein_coding|1/1|c.164C>G|p.Pro55Arg|164/2610|164/2610|55/869||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|miaE|PA14_41430|transcript|ABJ10974.1|protein_coding||c.-2102G>C|||||2102|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_41450|PA14_41450|transcript|ABJ10972.1|protein_coding||c.-545G>C|||||545|,G|upstream_gene_variant|MODIFIER|nasS|PA14_41480|transcript|ABJ10970.1|protein_coding||c.-2624C>G|||||2624|,G|upstream_gene_variant|MODIFIER|nasT|PA14_41490|transcript|ABJ10969.1|protein_coding||c.-3849C>G|||||3849|,G|upstream_gene_variant|MODIFIER|PA14_41500|PA14_41500|transcript|ABJ10968.1|protein_coding||c.-4657C>G|||||4657|,G|downstream_gene_variant|MODIFIER|ppiB|PA14_41390|transcript|ABJ10977.1|protein_coding||c.*4964C>G|||||4964|,G|downstream_gene_variant|MODIFIER|PA14_41400|PA14_41400|transcript|ABJ10976.1|protein_coding||c.*4237C>G|||||4237|,G|downstream_gene_variant|MODIFIER|PA14_41420|PA14_41420|transcript|ABJ10975.1|protein_coding||c.*2774C>G|||||2774|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|uspA|PA14_41440|transcript|ABJ10973.1|protein_coding||c.*1068C>G|||||1068| GT:DP:DPR:RO:QR:AO:QA:GL 0:19:19,0:19:701:0:0:0,-63.4033 0:11:11,0:11:430:0:0:0,-39.0542 0:10:10,2:8:230:2:4:0,-20.5884 0:8:8,0:8:260:0:0:0,-23.7122 +Chromosome 3711749 . T C 1053.53 . AB=0;ABP=0;AC=4;AF=1;AN=4;AO=33;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=22.0271;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=4;NUMALT=1;ODDS=42.0882;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1223;QR=0;RO=0;RPL=22;RPP=10.9724;RPPR=0;RPR=11;RUN=1;SAF=11;SAP=10.9724;SAR=22;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|cobA|PA14_41563|transcript|ABJ15644.1|protein_coding|1/1|c.109T>C|p.Leu37Leu|109/738|109/738|37/245||,C|downstream_gene_variant|MODIFIER|nirB|PA14_41530|transcript|ABJ10965.1|protein_coding||c.*3252T>C|||||3252|,C|downstream_gene_variant|MODIFIER|nirD|PA14_41540|transcript|ABJ10964.1|protein_coding||c.*2873T>C|||||2873|,C|downstream_gene_variant|MODIFIER|nasA|PA14_41560|transcript|ABJ10963.1|protein_coding||c.*120T>C|||||120|,C|downstream_gene_variant|MODIFIER|oprF|PA14_41570|transcript|ABJ10962.1|protein_coding||c.*698A>G|||||698|,C|downstream_gene_variant|MODIFIER|sigX|PA14_41575|transcript|ABJ15679.1|protein_coding||c.*1859A>G|||||1859|,C|downstream_gene_variant|MODIFIER|cmpX|PA14_41590|transcript|ABJ10961.1|protein_coding||c.*2521A>G|||||2521|,C|downstream_gene_variant|MODIFIER|crfX|PA14_41610|transcript|ABJ10960.1|protein_coding||c.*3348A>G|||||3348|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|cmaX|PA14_41630|transcript|ABJ10959.1|protein_coding||c.*3651A>G|||||3651|,C|downstream_gene_variant|MODIFIER|menG|PA14_41640|transcript|ABJ10958.1|protein_coding||c.*4837A>G|||||4837| GT:DP:DPR:RO:QR:AO:QA:GL 1:4:4,4:0:0:4:131:-12.1087,0 1:13:13,13:0:0:13:480:-43.5327,0 1:7:7,7:0:0:7:268:-24.4827,0 1:9:9,9:0:0:9:344:-31.315,0 +Chromosome 3715971 . G T 1.96414E-6 . AB=0;ABP=0;AC=0;AF=0;AN=3;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=1.14286;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=45;MQMR=60;NS=3;NUMALT=1;ODDS=14.6092;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=282;RO=8;RPL=2;RPP=7.35324;RPPR=7.35324;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=4;SRP=3.0103;SRR=4;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|cmaX|PA14_41630|transcript|ABJ10959.1|protein_coding|1/1|c.428C>A|p.Pro143Gln|428/999|428/999|143/332||,T|upstream_gene_variant|MODIFIER|oprF|PA14_41570|transcript|ABJ10962.1|protein_coding||c.-2472C>A|||||2472|,T|upstream_gene_variant|MODIFIER|sigX|PA14_41575|transcript|ABJ15679.1|protein_coding||c.-1773C>A|||||1773|,T|upstream_gene_variant|MODIFIER|cmpX|PA14_41590|transcript|ABJ10961.1|protein_coding||c.-877C>A|||||877|,T|upstream_gene_variant|MODIFIER|crfX|PA14_41610|transcript|ABJ10960.1|protein_coding||c.-620C>A|||||620|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ydiA|PA14_41680|transcript|ABJ10955.1|protein_coding||c.-4831G>T|||||4831|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|nasA|PA14_41560|transcript|ABJ10963.1|protein_coding||c.*4342G>T|||||4342|,T|downstream_gene_variant|MODIFIER|cobA|PA14_41563|transcript|ABJ15644.1|protein_coding||c.*3593G>T|||||3593|,T|downstream_gene_variant|MODIFIER|menG|PA14_41640|transcript|ABJ10958.1|protein_coding||c.*615C>A|||||615|,T|downstream_gene_variant|MODIFIER|estX|PA14_41650|transcript|ABJ10957.1|protein_coding||c.*1210C>A|||||1210|,T|downstream_gene_variant|MODIFIER|ppsA|PA14_41670|transcript|ABJ10956.1|protein_coding||c.*2290C>A|||||2290| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:1:16:0:0:0,-1.50998 0:4:4,2:2:77:2:31:0,-4.37986 . 0:5:5,0:5:189:0:0:0,-17.3748 +Chromosome 3721382 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=9;CIGAR=1X;DP=73;DPB=73;DPRA=1.28889;EPP=14.8328;EPPR=37.7539;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=103.307;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=77;QR=2290;RO=64;RPL=8;RPP=14.8328;RPPR=16.582;RPR=1;RUN=1;SAF=9;SAP=22.5536;SAR=0;SRF=26;SRP=7.89611;SRR=38;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|ydiA|PA14_41680|transcript|ABJ10955.1|protein_coding|1/1|c.581T>C|p.Leu194Pro|581/825|581/825|194/274||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|cmaX|PA14_41630|transcript|ABJ10959.1|protein_coding||c.-4984A>G|||||4984|,C|upstream_gene_variant|MODIFIER|menG|PA14_41640|transcript|ABJ10958.1|protein_coding||c.-4308A>G|||||4308|,C|upstream_gene_variant|MODIFIER|estX|PA14_41650|transcript|ABJ10957.1|protein_coding||c.-3191A>G|||||3191|,C|upstream_gene_variant|MODIFIER|ppsA|PA14_41670|transcript|ABJ10956.1|protein_coding||c.-746A>G|||||746|,C|upstream_gene_variant|MODIFIER|PA14_41690|PA14_41690|transcript|ABJ10954.1|protein_coding||c.-535T>C|||||535|,C|upstream_gene_variant|MODIFIER|PA14_41710|PA14_41710|transcript|ABJ10953.1|protein_coding||c.-1080T>C|||||1080|,C|upstream_gene_variant|MODIFIER|PA14_41730|PA14_41730|transcript|ABJ10952.1|protein_coding||c.-2610T>C|||||2610|,C|downstream_gene_variant|MODIFIER|PA14_41740|PA14_41740|transcript|ABJ10951.1|protein_coding||c.*3650A>G|||||3650|,C|downstream_gene_variant|MODIFIER|PA14_41750|PA14_41750|transcript|ABJ10950.1|protein_coding||c.*4851A>G|||||4851| GT:DP:DPR:RO:QR:AO:QA:GL 0:13:13,2:11:413:2:4:0,-37.1361 0:20:20,2:18:661:2:4:0,-59.4328 0:25:25,5:20:696:5:69:0,-56.596 0:15:15,0:15:520:0:0:0,-47.111 +Chromosome 3746335 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=43;DPB=43;DPRA=0.909091;EPP=3.0103;EPPR=6.48466;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=65.922;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=1341;RO=40;RPL=1;RPP=3.0103;RPPR=3.22745;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=29;SRP=20.5992;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=T|upstream_gene_variant|MODIFIER|panE|PA14_41900|transcript|ABJ10938.1|protein_coding||c.-4172C>A|||||4172|,T|upstream_gene_variant|MODIFIER|PA14_41910|PA14_41910|transcript|ABJ10937.1|protein_coding||c.-3795C>A|||||3795|,T|upstream_gene_variant|MODIFIER|PA14_41930|PA14_41930|transcript|ABJ10935.1|protein_coding||c.-1858C>A|||||1858|,T|upstream_gene_variant|MODIFIER|PA14_41970|PA14_41970|transcript|ABJ10932.1|protein_coding||c.-69C>A|||||69|,T|upstream_gene_variant|MODIFIER|PA14_41980|PA14_41980|transcript|ABJ10931.1|protein_coding||c.-152G>T|||||152|,T|upstream_gene_variant|MODIFIER|PA14_41990|PA14_41990|transcript|ABJ10930.1|protein_coding||c.-795G>T|||||795|,T|upstream_gene_variant|MODIFIER|PA14_42000|PA14_42000|transcript|ABJ10929.1|protein_coding||c.-1041G>T|||||1041|,T|upstream_gene_variant|MODIFIER|arsC|PA14_42020|transcript|ABJ10927.1|protein_coding||c.-2304G>T|||||2304|,T|upstream_gene_variant|MODIFIER|PA14_42060|PA14_42060|transcript|ABJ10924.1|protein_coding||c.-4827G>T|||||4827|,T|downstream_gene_variant|MODIFIER|aroF-1|PA14_41920|transcript|ABJ10936.1|protein_coding||c.*2401G>T|||||2401|,T|downstream_gene_variant|MODIFIER|PA14_41950|PA14_41950|transcript|ABJ10934.1|protein_coding||c.*985G>T|||||985|,T|downstream_gene_variant|MODIFIER|PA14_41960|PA14_41960|transcript|ABJ10933.1|protein_coding||c.*647G>T|||||647|,T|downstream_gene_variant|MODIFIER|PA14_42010|PA14_42010|transcript|ABJ10928.1|protein_coding||c.*1338C>A|||||1338|,T|downstream_gene_variant|MODIFIER|PA14_42030|PA14_42030|transcript|ABJ10926.1|protein_coding||c.*2684C>A|||||2684|,T|downstream_gene_variant|MODIFIER|PA14_42050|PA14_42050|transcript|ABJ10925.1|protein_coding||c.*3705C>A|||||3705|,T|intergenic_region|MODIFIER|PA14_41970-PA14_41980|PA14_41970-PA14_41980|intergenic_region|PA14_41970-PA14_41980|||n.3746335G>T|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,0:10:336:0:0:0,-30.5591 0:10:10,2:8:277:2:31:0,-22.3133 0:11:11,0:10:360:0:0:0,-32.69 0:12:12,0:12:368:0:0:0,-33.4079 +Chromosome 3757438 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=34;DPB=34;DPRA=1;EPP=11.6962;EPPR=3.29983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=56.7815;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=60;QR=1104;RO=30;RPL=4;RPP=11.6962;RPPR=3.0103;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=7;SRP=21.5402;SRR=23;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_42120|PA14_42120|transcript|ABJ10920.1|protein_coding|1/1|c.44T>C|p.Leu15Pro|44/822|44/822|15/273||,C|upstream_gene_variant|MODIFIER|fadB|PA14_42080|transcript|ABJ10923.1|protein_coding||c.-2833A>G|||||2833|,C|upstream_gene_variant|MODIFIER|PA14_42090|PA14_42090|transcript|ABJ10922.1|protein_coding||c.-1614A>G|||||1614|,C|upstream_gene_variant|MODIFIER|PA14_42100|PA14_42100|transcript|ABJ10921.1|protein_coding||c.-156A>G|||||156|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_42130|PA14_42130|transcript|ABJ10919.1|protein_coding||c.*786A>G|||||786|,C|downstream_gene_variant|MODIFIER|PA14_42140|PA14_42140|transcript|ABJ10918.1|protein_coding||c.*1599A>G|||||1599|,C|downstream_gene_variant|MODIFIER|PA14_42150|PA14_42150|transcript|ABJ10917.1|protein_coding||c.*2396A>G|||||2396|,C|downstream_gene_variant|MODIFIER|PA14_42160|PA14_42160|transcript|ABJ10916.1|protein_coding||c.*3352A>G|||||3352| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,0:10:370:0:0:0,-33.6431 0:7:7,0:7:273:0:0:0,-24.9371 0:8:8,2:6:235:2:30:0,-18.6714 0:9:9,2:7:226:2:30:0,-17.8028 +Chromosome 3761959 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=42;DPB=42;DPRA=1.66667;EPP=9.52472;EPPR=19.1015;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=71.1586;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=45;QR=1243;RO=39;RPL=3;RPP=9.52472;RPPR=3.51141;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=18;SRP=3.51141;SRR=21;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_42160|PA14_42160|transcript|ABJ10916.1|protein_coding|1/1|c.244C>A|p.His82Asn|244/1413|244/1413|82/470||,T|upstream_gene_variant|MODIFIER|PA14_42100|PA14_42100|transcript|ABJ10921.1|protein_coding||c.-4677C>A|||||4677|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|PA14_42130|PA14_42130|transcript|ABJ10919.1|protein_coding||c.-3004C>A|||||3004|,T|upstream_gene_variant|MODIFIER|PA14_42140|PA14_42140|transcript|ABJ10918.1|protein_coding||c.-2122C>A|||||2122|,T|upstream_gene_variant|MODIFIER|PA14_42150|PA14_42150|transcript|ABJ10917.1|protein_coding||c.-1172C>A|||||1172|,T|upstream_gene_variant|MODIFIER|PA14_42220|PA14_42220|transcript|ABJ10913.1|protein_coding||c.-2083G>T|||||2083|,T|upstream_gene_variant|MODIFIER|bglX|PA14_42230|transcript|ABJ10912.1|protein_coding||c.-4311G>T|||||4311|,T|downstream_gene_variant|MODIFIER|PA14_42120|PA14_42120|transcript|ABJ10920.1|protein_coding||c.*3743G>T|||||3743|,T|downstream_gene_variant|MODIFIER|PA14_42180|PA14_42180|transcript|ABJ10915.1|protein_coding||c.*593C>A|||||593|,T|downstream_gene_variant|MODIFIER|PA14_42200|PA14_42200|transcript|ABJ10914.1|protein_coding||c.*1389C>A|||||1389| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,0:9:318:0:0:0,-28.948 0:10:10,0:10:330:0:0:0,-30.0094 0:15:15,3:12:328:3:45:0,-25.5793 0:8:8,0:8:267:0:0:0,-24.3491 +Chromosome 3774198 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=52;DPB=52;DPRA=1.36364;EPP=9.52472;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=63.258;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=45;QR=1648;RO=49;RPL=0;RPP=9.52472;RPPR=8.37251;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=20;SRP=6.59988;SRR=29;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|pscC|PA14_42350|transcript|ABJ10902.1|protein_coding|1/1|c.1109T>C|p.Leu370Pro|1109/1803|1109/1803|370/600||,G|upstream_gene_variant|MODIFIER|pscL|PA14_42250|transcript|ABJ10911.1|protein_coding||c.-4887T>C|||||4887|,G|upstream_gene_variant|MODIFIER|pscK|PA14_42260|transcript|ABJ10910.1|protein_coding||c.-4288T>C|||||4288|,G|upstream_gene_variant|MODIFIER|pscJ|PA14_42270|transcript|ABJ10909.1|protein_coding||c.-3533T>C|||||3533|,G|upstream_gene_variant|MODIFIER|pscI|PA14_42280|transcript|ABJ10908.1|protein_coding||c.-3198T>C|||||3198|,G|upstream_gene_variant|MODIFIER|pscH|PA14_42290|transcript|ABJ10907.1|protein_coding||c.-2767T>C|||||2767|,G|upstream_gene_variant|MODIFIER|pscG|PA14_42300|transcript|ABJ10906.1|protein_coding||c.-2423T>C|||||2423|,G|upstream_gene_variant|MODIFIER|pscF|PA14_42310|transcript|ABJ10905.1|protein_coding||c.-2163T>C|||||2163|,G|upstream_gene_variant|MODIFIER|pscE|PA14_42320|transcript|ABJ10904.1|protein_coding||c.-1957T>C|||||1957|,G|upstream_gene_variant|MODIFIER|pscD|PA14_42340|transcript|ABJ10903.1|protein_coding||c.-696T>C|||||696|,G|downstream_gene_variant|MODIFIER|pscB|PA14_42360|transcript|ABJ10901.1|protein_coding||c.*1108T>C|||||1108|,G|downstream_gene_variant|MODIFIER|exsD|PA14_42380|transcript|ABJ10900.1|protein_coding||c.*1564T>C|||||1564|,G|downstream_gene_variant|MODIFIER|exsA|PA14_42390|transcript|ABJ10899.1|protein_coding||c.*2492T>C|||||2492|,G|downstream_gene_variant|MODIFIER|exsB|PA14_42400|transcript|ABJ10898.1|protein_coding||c.*3626T>C|||||3626|,G|downstream_gene_variant|MODIFIER|PA14_42410|PA14_42410|transcript|ABJ10897.1|protein_coding||c.*4048T>C|||||4048|,G|downstream_gene_variant|MODIFIER|exsC|PA14_42430|transcript|ABJ10896.1|protein_coding||c.*4302T>C|||||4302|,G|downstream_gene_variant|MODIFIER|popD|PA14_42440|transcript|ABJ10895.1|protein_coding||c.*4866T>C|||||4866| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:247:0:0:0,-22.526 0:9:9,2:7:240:2:30:0,-19.0774 0:21:21,1:20:646:1:15:0,-56.9286 0:14:14,0:14:515:0:0:0,-46.6854 +Chromosome 3783473 . A G 2.75408E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=37;DPB=37;DPRA=0.964286;EPP=7.35324;EPPR=3.07234;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=63.5947;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1301;RO=35;RPL=2;RPP=7.35324;RPPR=16.9698;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=20;SRP=4.56135;SRR=15;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|pcrD|PA14_42500|transcript|ABJ10889.1|protein_coding|1/1|c.1928T>C|p.Phe643Ser|1928/2121|1928/2121|643/706||,G|upstream_gene_variant|MODIFIER|PA14_42410|PA14_42410|transcript|ABJ10897.1|protein_coding||c.-4982T>C|||||4982|,G|upstream_gene_variant|MODIFIER|exsC|PA14_42430|transcript|ABJ10896.1|protein_coding||c.-4536T>C|||||4536|,G|upstream_gene_variant|MODIFIER|popD|PA14_42440|transcript|ABJ10895.1|protein_coding||c.-3522T>C|||||3522|,G|upstream_gene_variant|MODIFIER|popB|PA14_42450|transcript|ABJ10894.1|protein_coding||c.-2338T>C|||||2338|,G|upstream_gene_variant|MODIFIER|pcrH|PA14_42460|transcript|ABJ10893.1|protein_coding||c.-1851T>C|||||1851|,G|upstream_gene_variant|MODIFIER|pcrV|PA14_42470|transcript|ABJ10892.1|protein_coding||c.-958T>C|||||958|,G|upstream_gene_variant|MODIFIER|pcrG|PA14_42480|transcript|ABJ10891.1|protein_coding||c.-652T>C|||||652|,G|upstream_gene_variant|MODIFIER|pcrR|PA14_42490|transcript|ABJ10890.1|protein_coding||c.-190T>C|||||190|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|pscN|PA14_42570|transcript|ABJ10883.1|protein_coding||c.-4294A>G|||||4294|,G|downstream_gene_variant|MODIFIER|pcr4|PA14_42510|transcript|ABJ10888.1|protein_coding||c.*1924T>C|||||1924|,G|downstream_gene_variant|MODIFIER|pcr3|PA14_42520|transcript|ABJ10887.1|protein_coding||c.*2258T>C|||||2258|,G|downstream_gene_variant|MODIFIER|pcr2|PA14_42530|transcript|ABJ10886.1|protein_coding||c.*2620T>C|||||2620|,G|downstream_gene_variant|MODIFIER|pcr1|PA14_42540|transcript|ABJ10885.1|protein_coding||c.*2978T>C|||||2978|,G|downstream_gene_variant|MODIFIER|popN|PA14_42550|transcript|ABJ10884.1|protein_coding||c.*3237T>C|||||3237| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,2:7:236:2:4:0,-21.1769 0:10:10,0:10:372:0:0:0,-33.8285 0:9:9,0:9:357:0:0:0,-32.4935 0:9:9,0:9:336:0:0:0,-30.5908 +Chromosome 3798174 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=36;DPB=36;DPRA=0.866667;EPP=11.6962;EPPR=4.09604;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=60.7712;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1140;RO=32;RPL=4;RPP=11.6962;RPPR=3.0103;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=24;SRP=20.3821;SRR=8;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|speE|PA14_42690|transcript|ABJ10873.1|protein_coding|1/1|c.272A>G|p.Glu91Gly|272/861|272/861|91/286||,C|upstream_gene_variant|MODIFIER|PA14_42670|PA14_42670|transcript|ABJ10875.1|protein_coding||c.-1622A>G|||||1622|,C|upstream_gene_variant|MODIFIER|PA14_42680|PA14_42680|transcript|ABJ10874.1|protein_coding||c.-750A>G|||||750|,C|upstream_gene_variant|MODIFIER|alkA|PA14_42700|transcript|ABJ10872.1|protein_coding||c.-420T>C|||||420|,C|downstream_gene_variant|MODIFIER|pscT|PA14_42640|transcript|ABJ10877.1|protein_coding||c.*4876T>C|||||4876|,C|downstream_gene_variant|MODIFIER|pscU|PA14_42660|transcript|ABJ10876.1|protein_coding||c.*3830T>C|||||3830|,C|downstream_gene_variant|MODIFIER|PA14_42710|PA14_42710|transcript|ABJ10871.1|protein_coding||c.*1329A>G|||||1329|,C|downstream_gene_variant|MODIFIER|masA|PA14_42720|transcript|ABJ10870.1|protein_coding||c.*1569A>G|||||1569|,C|downstream_gene_variant|MODIFIER|PA14_42730|PA14_42730|transcript|ABJ10869.1|protein_coding||c.*2319A>G|||||2319|,C|downstream_gene_variant|MODIFIER|PA14_42740|PA14_42740|transcript|ABJ10868.1|protein_coding||c.*2861A>G|||||2861|,C|downstream_gene_variant|MODIFIER|PA14_42750|PA14_42750|transcript|ABJ10867.1|protein_coding||c.*3475A>G|||||3475|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|aroC|PA14_42760|transcript|ABJ10866.1|protein_coding||c.*4670A>G|||||4670| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,1:6:223:1:2:0,-20.2284 0:10:10,0:10:360:0:0:0,-32.7343 0:11:11,1:10:344:1:2:0,-31.0871 0:8:8,2:6:213:2:4:0,-19.1324 +Chromosome 3816795 . A G 1.95879E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=9;CIGAR=1X;DP=43;DPB=43;DPRA=0;EPP=22.5536;EPPR=19.3602;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=42.4735;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=847;RO=34;RPL=0;RPP=22.5536;RPPR=4.03217;RPR=9;RUN=1;SAF=0;SAP=22.5536;SAR=9;SRF=12;SRP=9.39698;SRR=22;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_42920|PA14_42920|transcript|ABJ10852.1|protein_coding|1/1|c.1166T>C|p.Leu389Pro|1166/1332|1166/1332|389/443||,G|upstream_gene_variant|MODIFIER|stp1|PA14_42890|transcript|ABJ10855.1|protein_coding||c.-4581T>C|||||4581|,G|upstream_gene_variant|MODIFIER|PA14_42900|PA14_42900|transcript|ABJ10854.1|protein_coding||c.-1054T>C|||||1054|,G|upstream_gene_variant|MODIFIER|PA14_42910|PA14_42910|transcript|ABJ10853.1|protein_coding||c.-169T>C|||||169|,G|downstream_gene_variant|MODIFIER|PA14_42940|PA14_42940|transcript|ABJ10851.1|protein_coding||c.*1162T>C|||||1162|,G|downstream_gene_variant|MODIFIER|PA14_42950|PA14_42950|transcript|ABJ10850.1|protein_coding||c.*1674T>C|||||1674|,G|downstream_gene_variant|MODIFIER|PA14_42960|PA14_42960|transcript|ABJ10849.1|protein_coding||c.*2885T>C|||||2885|,G|downstream_gene_variant|MODIFIER|PA14_42970|PA14_42970|transcript|ABJ10848.1|protein_coding||c.*3114T>C|||||3114|,G|downstream_gene_variant|MODIFIER|PA14_42980|PA14_42980|transcript|ABJ10847.1|protein_coding||c.*4636T>C|||||4636| GT:DP:DPR:RO:QR:AO:QA:GL 0:14:14,2:12:334:2:4:0,-29.9373 0:9:9,2:7:186:2:4:0,-16.6163 0:9:9,4:5:141:4:28:0,-10.3745 0:11:11,1:10:186:1:2:0,-16.7162 +Chromosome 3820080 . C G 1.75877E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=21;DPB=21;DPRA=1.84615;EPP=7.35324;EPPR=3.12459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=33.6605;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=637;RO=19;RPL=0;RPP=7.35324;RPPR=12.2676;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=11;SRP=4.03889;SRR=8;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|PA14_42970|PA14_42970|transcript|ABJ10848.1|protein_coding|1/1|c.1341G>C|p.Pro447Pro|1341/1512|1341/1512|447/503||,G|upstream_gene_variant|MODIFIER|PA14_42900|PA14_42900|transcript|ABJ10854.1|protein_coding||c.-4339G>C|||||4339|,G|upstream_gene_variant|MODIFIER|PA14_42910|PA14_42910|transcript|ABJ10853.1|protein_coding||c.-3454G>C|||||3454|,G|upstream_gene_variant|MODIFIER|PA14_42920|PA14_42920|transcript|ABJ10852.1|protein_coding||c.-2120G>C|||||2120|,G|upstream_gene_variant|MODIFIER|PA14_42940|PA14_42940|transcript|ABJ10851.1|protein_coding||c.-1617G>C|||||1617|,G|upstream_gene_variant|MODIFIER|PA14_42950|PA14_42950|transcript|ABJ10850.1|protein_coding||c.-418G>C|||||418|,G|upstream_gene_variant|MODIFIER|PA14_42960|PA14_42960|transcript|ABJ10849.1|protein_coding||c.-260G>C|||||260|,G|downstream_gene_variant|MODIFIER|PA14_42980|PA14_42980|transcript|ABJ10847.1|protein_coding||c.*1351G>C|||||1351|,G|downstream_gene_variant|MODIFIER|PA14_42990|PA14_42990|transcript|ABJ10846.1|protein_coding||c.*3991G>C|||||3991|,G|downstream_gene_variant|MODIFIER|PA14_43000|PA14_43000|transcript|ABJ10845.1|protein_coding||c.*4962G>C|||||4962| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:146:0:0:0,-13.4974 0:6:6,0:6:233:0:0:0,-21.3401 0:3:3,0:3:101:0:0:0,-9.42141 0:8:8,2:6:157:2:4:0,-13.9996 +Chromosome 3828507 . C A 1.13914E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=6;CIGAR=1X;DP=89;DPB=89;DPRA=1.15;EPP=16.0391;EPPR=7.43173;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=97.9847;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=107;QR=2442;RO=83;RPL=0;RPP=16.0391;RPPR=3.66436;RPR=6;RUN=1;SAF=0;SAP=16.0391;SAR=6;SRF=23;SRP=38.8265;SRR=60;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|PA14_43030|PA14_43030|transcript|ABJ10843.1|protein_coding|1/1|c.556G>T|p.Ala186Ser|556/1476|556/1476|186/491||,A|upstream_gene_variant|MODIFIER|PA14_42980|PA14_42980|transcript|ABJ10847.1|protein_coding||c.-4443G>T|||||4443|,A|upstream_gene_variant|MODIFIER|PA14_42990|PA14_42990|transcript|ABJ10846.1|protein_coding||c.-3429G>T|||||3429|,A|upstream_gene_variant|MODIFIER|PA14_43000|PA14_43000|transcript|ABJ10845.1|protein_coding||c.-1885G>T|||||1885|,A|upstream_gene_variant|MODIFIER|PA14_43020|PA14_43020|transcript|ABJ10844.1|protein_coding||c.-933G>T|||||933|,A|upstream_gene_variant|MODIFIER|hcpD|PA14_43070|transcript|ABJ10840.1|protein_coding||c.-3379C>A|||||3379|,A|upstream_gene_variant|MODIFIER|PA14_43080|PA14_43080|transcript|ABJ10839.1|protein_coding||c.-4093C>A|||||4093|,A|downstream_gene_variant|MODIFIER|P10|EBG00001225132|transcript|EBT00001793412.1|sRNA||n.*1374C>A|||||1374|,A|downstream_gene_variant|MODIFIER|PA14_43040|PA14_43040|transcript|ABJ10842.1|protein_coding||c.*583G>T|||||583|,A|downstream_gene_variant|MODIFIER|PA14_43050|PA14_43050|transcript|ABJ10841.1|protein_coding||c.*1125G>T|||||1125| GT:DP:DPR:RO:QR:AO:QA:GL 0:20:20,0:20:609:0:0:0,-55.0845 0:14:14,3:11:372:3:46:0,-29.5061 0:30:30,1:29:814:1:15:0,-72.0035 0:25:25,2:23:647:2:46:0,-54.1159 +Chromosome 3849468 . T G 7.28557E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=16;DPB=16;DPRA=1.66667;EPP=9.52472;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=20.2059;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=377;RO=13;RPL=0;RPP=9.52472;RPPR=7.18621;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=8;SRP=4.51363;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_43200|PA14_43200|transcript|ABJ10828.1|protein_coding|1/1|c.710T>G|p.Leu237Arg|710/1722|710/1722|237/573||,G|upstream_gene_variant|MODIFIER|PA14_43170|PA14_43170|transcript|ABJ10831.1|protein_coding||c.-3048A>C|||||3048|,G|upstream_gene_variant|MODIFIER|PA14_43180|PA14_43180|transcript|ABJ10830.1|protein_coding||c.-2128A>C|||||2128|,G|upstream_gene_variant|MODIFIER|PA14_43230|PA14_43230|transcript|ABJ10826.1|protein_coding||c.-3153T>G|||||3153|,G|upstream_gene_variant|MODIFIER|PA14_43250|PA14_43250|transcript|ABJ10824.1|protein_coding||c.-4313T>G|||||4313|,G|downstream_gene_variant|MODIFIER|benE|PA14_43160|transcript|ABJ10832.1|protein_coding||c.*3948T>G|||||3948|,G|downstream_gene_variant|MODIFIER|PA14_43190|PA14_43190|transcript|ABJ10829.1|protein_coding||c.*873T>G|||||873|,G|downstream_gene_variant|MODIFIER|PA14_43220|PA14_43220|transcript|ABJ10827.1|protein_coding||c.*993A>C|||||993|,G|downstream_gene_variant|MODIFIER|PA14_43240|PA14_43240|transcript|ABJ10825.1|protein_coding||c.*3567A>C|||||3567|,G|downstream_gene_variant|MODIFIER|ybbB|PA14_43270|transcript|ABJ10823.1|protein_coding||c.*4639A>C|||||4639| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,1:3:116:1:2:0,-10.6177 0:5:5,0:5:119:0:0:0,-10.9428 0:1:1,0:1:40:0:0:0,-3.99568 0:6:6,2:4:102:2:4:0,-9.05206 +Chromosome 3852268 . T G 9.91496E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=29;DPB=29;DPRA=1.35;EPP=7.35324;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=34.7577;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=1007;RO=27;RPL=0;RPP=7.35324;RPPR=3.09072;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=18;SRP=9.52472;SRR=9;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_43220|PA14_43220|transcript|ABJ10827.1|protein_coding|1/1|c.152A>C|p.Gln51Pro|152/1959|152/1959|51/652||,G|upstream_gene_variant|MODIFIER|PA14_43180|PA14_43180|transcript|ABJ10830.1|protein_coding||c.-4928A>C|||||4928|,G|upstream_gene_variant|MODIFIER|PA14_43230|PA14_43230|transcript|ABJ10826.1|protein_coding||c.-353T>G|||||353|,G|upstream_gene_variant|MODIFIER|PA14_43250|PA14_43250|transcript|ABJ10824.1|protein_coding||c.-1513T>G|||||1513|,G|upstream_gene_variant|MODIFIER|PA14_43300|PA14_43300|transcript|ABJ10820.1|protein_coding||c.-4459T>G|||||4459|,G|downstream_gene_variant|MODIFIER|PA14_43190|PA14_43190|transcript|ABJ10829.1|protein_coding||c.*3673T>G|||||3673|,G|downstream_gene_variant|MODIFIER|PA14_43200|PA14_43200|transcript|ABJ10828.1|protein_coding||c.*1788T>G|||||1788|,G|downstream_gene_variant|MODIFIER|PA14_43240|PA14_43240|transcript|ABJ10825.1|protein_coding||c.*767A>C|||||767|,G|downstream_gene_variant|MODIFIER|ybbB|PA14_43270|transcript|ABJ10823.1|protein_coding||c.*1839A>C|||||1839|,G|downstream_gene_variant|MODIFIER|selD|PA14_43280|transcript|ABJ10822.1|protein_coding||c.*2948A>C|||||2948|,G|downstream_gene_variant|MODIFIER|PA14_43290|PA14_43290|transcript|ABJ10821.1|protein_coding||c.*4066A>C|||||4066| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:91:0:0:0,-8.48768 0:9:9,0:9:348:0:0:0,-31.6782 0:8:8,0:8:308:0:0:0,-28.0793 0:9:9,2:7:260:2:30:0,-20.9056 +Chromosome 3864628 . TCCT CCCC 1.0009E-6 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X2M1X;DP=11;DPB=11.75;DPRA=0.833333;EPP=9.52472;EPPR=12.7819;GTI=0;LEN=4;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=15.3564;PAIRED=0;PAIREDR=0;PAO=1;PQA=11;PQR=0;PRO=0;QA=28;QR=255;RO=8;RPL=3;RPP=9.52472;RPPR=7.35324;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=1;SRP=12.7819;SRR=7;TYPE=complex;technology.ILLUMINA=1;ANN=CCCC|missense_variant|MODERATE|kdpB|PA14_43380|transcript|ABJ10814.1|protein_coding|1/1|c.1118_1121delAGGAinsGGGG|p.GluGlu373GlyGly|1121/2073|1118/2073|373/690||,CCCC|upstream_gene_variant|MODIFIER|kdpE|PA14_43340|transcript|ABJ10817.1|protein_coding||c.-4426_-4423delAGGAinsGGGG|||||4423|,CCCC|upstream_gene_variant|MODIFIER|kdpD|PA14_43350|transcript|ABJ10816.1|protein_coding||c.-1668_-1665delAGGAinsGGGG|||||1665|,CCCC|upstream_gene_variant|MODIFIER|kdpC|PA14_43370|transcript|ABJ10815.1|protein_coding||c.-1009_-1006delAGGAinsGGGG|||||1006|,CCCC|downstream_gene_variant|MODIFIER|kdpA|PA14_43400|transcript|ABJ10813.1|protein_coding||c.*1129_*1132delAGGAinsGGGG|||||1132|,CCCC|downstream_gene_variant|MODIFIER|kdpF|PA14_43405|transcript|ABJ15698.1|protein_coding||c.*2834_*2837delAGGAinsGGGG|||||2837|,CCCC|downstream_gene_variant|MODIFIER|PA14_43420|PA14_43420|transcript|ABJ10812.1|protein_coding||c.*3111_*3114delAGGAinsGGGG|||||3114|,CCCC|downstream_gene_variant|MODIFIER|PA14_43430|PA14_43430|transcript|ABJ10811.1|protein_coding||c.*4320_*4323delAGGAinsGGGG|||||4323| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,2:1:40:2:26:0,-1.52569 0:2:2,1:1:37:1:2:0,-3.49783 0:2:2,0:2:66:0:0:0,-6.26573 0:4:4,0:4:112:0:0:0,-9.25301 +Chromosome 3867932 . A G 3.77656E-15 . AB=0;ABP=0;AC=0;AF=0;AN=3;AO=2;CIGAR=1X;DP=14;DPB=14;DPRA=1.11111;EPP=7.35324;EPPR=5.9056;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=34.81;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=431;RO=12;RPL=0;RPP=7.35324;RPPR=5.9056;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=4;SRP=5.9056;SRR=8;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_43420|PA14_43420|transcript|ABJ10812.1|protein_coding|1/1|c.965T>C|p.Leu322Pro|965/1155|965/1155|322/384||,G|upstream_gene_variant|MODIFIER|kdpD|PA14_43350|transcript|ABJ10816.1|protein_coding||c.-4969T>C|||||4969|,G|upstream_gene_variant|MODIFIER|kdpC|PA14_43370|transcript|ABJ10815.1|protein_coding||c.-4310T>C|||||4310|,G|upstream_gene_variant|MODIFIER|kdpB|PA14_43380|transcript|ABJ10814.1|protein_coding||c.-2184T>C|||||2184|,G|upstream_gene_variant|MODIFIER|kdpA|PA14_43400|transcript|ABJ10813.1|protein_coding||c.-478T>C|||||478|,G|upstream_gene_variant|MODIFIER|kdpF|PA14_43405|transcript|ABJ15698.1|protein_coding||c.-378T>C|||||378|,G|upstream_gene_variant|MODIFIER|PA14_43440|PA14_43440|transcript|ABJ10810.1|protein_coding||c.-2127A>G|||||2127|,G|upstream_gene_variant|MODIFIER|paaH|PA14_43460|transcript|ABJ10809.1|protein_coding||c.-2916A>G|||||2916|,G|upstream_gene_variant|MODIFIER|PA14_43480|PA14_43480|transcript|ABJ10808.1|protein_coding||c.-4583A>G|||||4583|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_43430|PA14_43430|transcript|ABJ10811.1|protein_coding||c.*1019T>C|||||1019| GT:DP:DPR:RO:QR:AO:QA:GL . 0:4:4,0:4:128:0:0:0,-11.8315 0:5:5,0:5:194:0:0:0,-17.8311 0:5:5,2:3:109:2:4:0,-9.78624 +Chromosome 3870259 . T G 4.29473E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=7;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=18.2106;EPPR=4.1599;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=30.248;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=61;QR=570;RO=17;RPL=0;RPP=18.2106;RPPR=3.13803;RPR=7;RUN=1;SAF=0;SAP=18.2106;SAR=7;SRF=3;SRP=18.4661;SRR=14;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|PA14_43440|PA14_43440|transcript|ABJ10810.1|protein_coding|1/1|c.201T>G|p.Ala67Ala|201/786|201/786|67/261||,G|upstream_gene_variant|MODIFIER|kdpB|PA14_43380|transcript|ABJ10814.1|protein_coding||c.-4511A>C|||||4511|,G|upstream_gene_variant|MODIFIER|kdpA|PA14_43400|transcript|ABJ10813.1|protein_coding||c.-2805A>C|||||2805|,G|upstream_gene_variant|MODIFIER|kdpF|PA14_43405|transcript|ABJ15698.1|protein_coding||c.-2705A>C|||||2705|,G|upstream_gene_variant|MODIFIER|PA14_43420|PA14_43420|transcript|ABJ10812.1|protein_coding||c.-1363A>C|||||1363|,G|upstream_gene_variant|MODIFIER|PA14_43430|PA14_43430|transcript|ABJ10811.1|protein_coding||c.-442A>C|||||442|,G|upstream_gene_variant|MODIFIER|paaH|PA14_43460|transcript|ABJ10809.1|protein_coding||c.-589T>G|||||589|,G|upstream_gene_variant|MODIFIER|PA14_43480|PA14_43480|transcript|ABJ10808.1|protein_coding||c.-2256T>G|||||2256|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_43490|PA14_43490|transcript|ABJ10807.1|protein_coding||c.-2919T>G|||||2919|,G|downstream_gene_variant|MODIFIER|PA14_43510|PA14_43510|transcript|ABJ10806.1|protein_coding||c.*4245A>C|||||4245| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,1:3:118:1:24:0,-8.603 0:3:3,1:2:78:1:2:0,-7.2033 0:9:9,3:6:217:3:31:0,-16.9851 0:8:8,2:6:157:2:4:0,-14.0067 +Chromosome 3891150 . C A 2.99116E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=40;DPB=40;DPRA=0.636364;EPP=7.35324;EPPR=3.9246;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=45.6056;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=1342;RO=38;RPL=0;RPP=7.35324;RPPR=17.6392;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=20;SRP=3.23888;SRR=18;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|fabB|PA14_43690|transcript|ABJ10790.1|protein_coding|1/1|c.534C>A|p.Gly178Gly|534/1218|534/1218|178/405||,A|upstream_gene_variant|MODIFIER|PA14_43710|PA14_43710|transcript|ABJ10789.1|protein_coding||c.-838C>A|||||838|,A|upstream_gene_variant|MODIFIER|PA14_43720|PA14_43720|transcript|ABJ10788.1|protein_coding||c.-2568C>A|||||2568|,A|upstream_gene_variant|MODIFIER|PA14_43760|PA14_43760|transcript|ABJ10786.1|protein_coding||c.-4760C>A|||||4760|,A|downstream_gene_variant|MODIFIER|PA14_43650|PA14_43650|transcript|ABJ10794.1|protein_coding||c.*4131C>A|||||4131|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_43660|PA14_43660|transcript|ABJ10793.1|protein_coding||c.*3201C>A|||||3201|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_43670|PA14_43670|transcript|ABJ10792.1|protein_coding||c.*1249C>A|||||1249|,A|downstream_gene_variant|MODIFIER|fabA|PA14_43680|transcript|ABJ10791.1|protein_coding||c.*545C>A|||||545|,A|downstream_gene_variant|MODIFIER|PA14_43730|PA14_43730|transcript|ABJ10787.1|protein_coding||c.*3182G>T|||||3182|,A|downstream_gene_variant|MODIFIER|PA14_43740|PA14_43740|transcript|ABJ10785.1|protein_coding||c.*3727G>T|||||3727| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,2:5:166:2:31:0,-12.3157 0:10:10,0:10:336:0:0:0,-30.5528 0:10:10,0:10:389:0:0:0,-35.3675 0:13:13,0:13:451:0:0:0,-40.9104 +Chromosome 3909632 . TGGGGGT TGGGGT 354.974 . AB=0;ABP=0;AC=4;AF=1;AN=4;AO=14;CIGAR=1M1D5M;DP=14;DPB=13.2857;DPRA=0;EPP=12.937;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=4;NUMALT=1;ODDS=19.4315;PAIRED=0;PAIREDR=0;PAO=1;PQA=35;PQR=35;PRO=1;QA=458;QR=0;RO=0;RPL=1;RPP=25.3454;RPPR=0;RPR=13;RUN=1;SAF=12;SAP=18.5208;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=del;technology.ILLUMINA=1;ANN=TGGGGT|upstream_gene_variant|MODIFIER|htpG|PA14_43850|transcript|ABJ10777.1|protein_coding||c.-3665delC|||||3665|,TGGGGT|upstream_gene_variant|MODIFIER|PA14_43870|PA14_43870|transcript|ABJ10776.1|protein_coding||c.-2318delC|||||2318|,TGGGGT|upstream_gene_variant|MODIFIER|PA14_43880|PA14_43880|transcript|ABJ10775.1|protein_coding||c.-1835delC|||||1835|,TGGGGT|upstream_gene_variant|MODIFIER|PA14_43890|PA14_43890|transcript|ABJ10774.1|protein_coding||c.-1365delC|||||1365|,TGGGGT|upstream_gene_variant|MODIFIER|PA14_43910|PA14_43910|transcript|ABJ10772.1|protein_coding||c.-133delC|||||133|,TGGGGT|downstream_gene_variant|MODIFIER|PA14_43900|PA14_43900|transcript|ABJ10773.1|protein_coding||c.*956delG|||||956|,TGGGGT|downstream_gene_variant|MODIFIER|braB|PA14_43920|transcript|ABJ10771.1|protein_coding||c.*14delC|||||14|,TGGGGT|downstream_gene_variant|MODIFIER|sucD|PA14_43940|transcript|ABJ10770.1|protein_coding||c.*1638delC|||||1638|,TGGGGT|downstream_gene_variant|MODIFIER|sucC|PA14_43950|transcript|ABJ10769.1|protein_coding||c.*2525delC|||||2525|,TGGGGT|downstream_gene_variant|MODIFIER|lpdG|PA14_43970|transcript|ABJ10768.1|protein_coding||c.*4020delC|||||4020|,TGGGGT|intergenic_region|MODIFIER|PA14_43910-braB|PA14_43910-PA14_43920|intergenic_region|PA14_43910-PA14_43920|||n.3909637delG|||||| GT:DP:DPR:RO:QR:AO:QA:GL 1:2:2,2:0:0:2:68:-6.45788,0 1:2:2,2:0:0:2:51:-4.84368,0 1:2:2,2:0:0:2:68:-6.45788,0 1:8:8,8:0:0:8:271:-24.715,0 +Chromosome 3914649 . T A 8.17889E-16 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=30;DPB=30;DPRA=1.5;EPP=3.0103;EPPR=5.80219;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=55.4768;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=1055;RO=28;RPL=1;RPP=3.0103;RPPR=3.32051;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=14;SRP=3.0103;SRR=14;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|lpdG|PA14_43970|transcript|ABJ10768.1|protein_coding|1/1|c.445A>T|p.Ile149Phe|445/1437|445/1437|149/478||,A|upstream_gene_variant|MODIFIER|braB|PA14_43920|transcript|ABJ10771.1|protein_coding||c.-3685A>T|||||3685|,A|upstream_gene_variant|MODIFIER|sucD|PA14_43940|transcript|ABJ10770.1|protein_coding||c.-2487A>T|||||2487|,A|upstream_gene_variant|MODIFIER|sucC|PA14_43950|transcript|ABJ10769.1|protein_coding||c.-1321A>T|||||1321|,A|downstream_gene_variant|MODIFIER|sucB|PA14_44000|transcript|ABJ10767.1|protein_coding||c.*513A>T|||||513|,A|downstream_gene_variant|MODIFIER|sucA|PA14_44010|transcript|ABJ10766.1|protein_coding||c.*1785A>T|||||1785|,A|downstream_gene_variant|MODIFIER|sdhB|PA14_44020|transcript|ABJ10765.1|protein_coding||c.*4873A>T|||||4873| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,2:8:287:2:16:0,-24.6471 0:8:8,0:8:297:0:0:0,-27.0772 0:5:5,0:5:195:0:0:0,-17.9237 0:7:7,0:7:276:0:0:0,-25.2097 +Chromosome 3918686 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=34;DPB=34;DPRA=1.55556;EPP=11.6962;EPPR=10.2485;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=61.7077;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=1129;RO=30;RPL=4;RPP=11.6962;RPPR=7.64277;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=13;SRP=4.16842;SRR=17;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|sucA|PA14_44010|transcript|ABJ10766.1|protein_coding|1/1|c.580A>G|p.Ser194Gly|580/2832|580/2832|194/943||,C|upstream_gene_variant|MODIFIER|lpdG|PA14_43970|transcript|ABJ10768.1|protein_coding||c.-3593A>G|||||3593|,C|upstream_gene_variant|MODIFIER|sucB|PA14_44000|transcript|ABJ10767.1|protein_coding||c.-2295A>G|||||2295|,C|upstream_gene_variant|MODIFIER|gltA|PA14_44070|transcript|ABJ10761.1|protein_coding||c.-4428T>C|||||4428|,C|downstream_gene_variant|MODIFIER|sdhB|PA14_44020|transcript|ABJ10765.1|protein_coding||c.*836A>G|||||836|,C|downstream_gene_variant|MODIFIER|sdhA|PA14_44030|transcript|ABJ10764.1|protein_coding||c.*1555A>G|||||1555|,C|downstream_gene_variant|MODIFIER|sdhD|PA14_44050|transcript|ABJ10763.1|protein_coding||c.*3331A>G|||||3331|,C|downstream_gene_variant|MODIFIER|sdhC|PA14_44060|transcript|ABJ10762.1|protein_coding||c.*3693A>G|||||3693|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,1:9:353:1:2:0,-31.9311 0:9:9,2:7:249:2:16:0,-21.2263 0:6:6,0:6:229:0:0:0,-20.9741 0:9:9,1:8:298:1:2:0,-26.9734 +Chromosome 3919122 . A G 1.41339E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=72;DPB=72;DPRA=0.757576;EPP=6.91895;EPPR=47.3796;GTI=0;LEN=1;MEANALT=1;MQM=58.4;MQMR=60;NS=4;NUMALT=1;ODDS=65.0501;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=79;QR=2252;RO=67;RPL=4;RPP=6.91895;RPPR=6.93191;RPR=1;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=15;SRP=47.3796;SRR=52;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|sucA|PA14_44010|transcript|ABJ10766.1|protein_coding|1/1|c.144T>C|p.Leu48Leu|144/2832|144/2832|48/943||,G|upstream_gene_variant|MODIFIER|lpdG|PA14_43970|transcript|ABJ10768.1|protein_coding||c.-4029T>C|||||4029|,G|upstream_gene_variant|MODIFIER|sucB|PA14_44000|transcript|ABJ10767.1|protein_coding||c.-2731T>C|||||2731|,G|upstream_gene_variant|MODIFIER|gltA|PA14_44070|transcript|ABJ10761.1|protein_coding||c.-3992A>G|||||3992|,G|downstream_gene_variant|MODIFIER|sdhB|PA14_44020|transcript|ABJ10765.1|protein_coding||c.*400T>C|||||400|,G|downstream_gene_variant|MODIFIER|sdhA|PA14_44030|transcript|ABJ10764.1|protein_coding||c.*1119T>C|||||1119|,G|downstream_gene_variant|MODIFIER|sdhD|PA14_44050|transcript|ABJ10763.1|protein_coding||c.*2895T>C|||||2895|,G|downstream_gene_variant|MODIFIER|sdhC|PA14_44060|transcript|ABJ10762.1|protein_coding||c.*3257T>C|||||3257|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:22:22,2:20:733:2:34:0,-63.0463 0:10:10,2:8:219:2:16:0,-18.4507 0:22:22,0:22:731:0:0:0,-66.0694 0:18:18,1:17:569:1:29:0,-48.6029 +Chromosome 3921568 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=28;DPB=28;DPRA=1.2;EPP=7.35324;EPPR=15.0369;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=46.8561;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=949;RO=26;RPL=0;RPP=7.35324;RPPR=4.34659;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=16;SRP=6.01695;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|sdhA|PA14_44030|transcript|ABJ10764.1|protein_coding|1/1|c.446T>C|p.Leu149Pro|446/1773|446/1773|149/590||,G|upstream_gene_variant|MODIFIER|sucA|PA14_44010|transcript|ABJ10766.1|protein_coding||c.-2303T>C|||||2303|,G|upstream_gene_variant|MODIFIER|sdhB|PA14_44020|transcript|ABJ10765.1|protein_coding||c.-1339T>C|||||1339|,G|upstream_gene_variant|MODIFIER|gltA|PA14_44070|transcript|ABJ10761.1|protein_coding||c.-1546A>G|||||1546|,G|upstream_gene_variant|MODIFIER|PA14_44110|PA14_44110|transcript|ABJ10757.1|protein_coding||c.-4915A>G|||||4915|,G|downstream_gene_variant|MODIFIER|sdhD|PA14_44050|transcript|ABJ10763.1|protein_coding||c.*449T>C|||||449|,G|downstream_gene_variant|MODIFIER|sdhC|PA14_44060|transcript|ABJ10762.1|protein_coding||c.*811T>C|||||811|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_44080|PA14_44080|transcript|ABJ10760.1|protein_coding||c.*2947T>C|||||2947|,G|downstream_gene_variant|MODIFIER|PA14_44090|PA14_44090|transcript|ABJ10759.1|protein_coding||c.*3689T>C|||||3689|,G|downstream_gene_variant|MODIFIER|PA14_44100|PA14_44100|transcript|ABJ10758.1|protein_coding||c.*4047T>C|||||4047| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,2:6:219:2:17:0,-18.4479 0:4:4,0:4:154:0:0:0,-14.2326 0:8:8,0:8:278:0:0:0,-25.3473 0:8:8,0:8:298:0:0:0,-27.1722 +Chromosome 3933633 . G C 7.22516E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=31;DPB=31;DPRA=0.576923;EPP=7.35324;EPPR=3.68421;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=37.6038;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1067;RO=29;RPL=2;RPP=7.35324;RPPR=6.67934;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=20;SRP=12.0706;SRR=9;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_44190|PA14_44190|transcript|ABJ10749.1|protein_coding|1/1|c.1319G>C|p.Arg440Pro|1319/1389|1319/1389|440/462||,C|upstream_gene_variant|MODIFIER|yijF|PA14_44150|transcript|ABJ10753.1|protein_coding||c.-4191C>G|||||4191|,C|upstream_gene_variant|MODIFIER|PA14_44160|PA14_44160|transcript|ABJ10752.1|protein_coding||c.-3035C>G|||||3035|,C|upstream_gene_variant|MODIFIER|PA14_44180|PA14_44180|transcript|ABJ10750.1|protein_coding||c.-1696C>G|||||1696|,C|upstream_gene_variant|MODIFIER|PA14_44200|PA14_44200|transcript|ABJ10748.1|protein_coding||c.-123G>C|||||123|,C|upstream_gene_variant|MODIFIER|PA14_44210|PA14_44210|transcript|ABJ10747.1|protein_coding||c.-487G>C|||||487|,C|upstream_gene_variant|MODIFIER|PA14_44230|PA14_44230|transcript|ABJ10746.1|protein_coding||c.-2036G>C|||||2036|,C|upstream_gene_variant|MODIFIER|PA14_44240|PA14_44240|transcript|ABJ10745.1|protein_coding||c.-2352G>C|||||2352|,C|upstream_gene_variant|MODIFIER|PA14_44260|PA14_44260|transcript|ABJ10744.1|protein_coding||c.-3787G>C|||||3787|,C|downstream_gene_variant|MODIFIER|yaiE|PA14_44140|transcript|ABJ10754.1|protein_coding||c.*4905G>C|||||4905|,C|downstream_gene_variant|MODIFIER|PA14_44170|PA14_44170|transcript|ABJ10751.1|protein_coding||c.*2646G>C|||||2646| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:220:0:0:0,-20.151 0:10:10,0:10:384:0:0:0,-34.913 0:5:5,2:3:119:2:17:0,-9.48041 0:10:10,0:10:344:0:0:0,-31.2832 +Chromosome 3971491 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=44;DPB=44;DPRA=0.666667;EPP=7.35324;EPPR=19.7617;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=53.2396;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1512;RO=42;RPL=0;RPP=7.35324;RPPR=16.2459;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=70.0157;SRR=39;TYPE=snp;technology.ILLUMINA=1;ANN=G|stop_lost&splice_region_variant|HIGH|dnaX|PA14_44630|transcript|ABJ10712.1|protein_coding|1/1|c.2104T>C|p.Ter702Argext*?|2104/2106|2104/2106|702/701||,G|upstream_gene_variant|MODIFIER|PA14_44590|PA14_44590|transcript|ABJ10715.1|protein_coding||c.-1172T>C|||||1172|,G|upstream_gene_variant|MODIFIER|recR|PA14_44610|transcript|ABJ10714.1|protein_coding||c.-453T>C|||||453|,G|upstream_gene_variant|MODIFIER|PA14_44620|PA14_44620|transcript|ABJ10713.1|protein_coding||c.-48T>C|||||48|,G|upstream_gene_variant|MODIFIER|PA14_44640|PA14_44640|transcript|ABJ10711.1|protein_coding||c.-2140A>G|||||2140|,G|upstream_gene_variant|MODIFIER|Bacteria_small_SRP|EBG00001225025|transcript|EBT00001793458.1|lincRNA||n.-3053A>G|||||3053|,G|upstream_gene_variant|MODIFIER|Bacteria_small_SRP|EBG00001225177|transcript|EBT00001793464.1|lincRNA||n.-4149A>G|||||4149|,G|downstream_gene_variant|MODIFIER|PA14_44560|PA14_44560|transcript|ABJ10718.1|protein_coding||c.*3830A>G|||||3830|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_44570|PA14_44570|transcript|ABJ10717.1|protein_coding||c.*2946A>G|||||2946|,G|downstream_gene_variant|MODIFIER|PA14_44580|PA14_44580|transcript|ABJ10716.1|protein_coding||c.*2333A>G|||||2333|,G|downstream_gene_variant|MODIFIER|PA14_44650|PA14_44650|transcript|ABJ10710.1|protein_coding||c.*4356T>C|||||4356|,G|downstream_gene_variant|MODIFIER|lig|PA14_44660|transcript|ABJ10709.1|protein_coding||c.*4779T>C|||||4779| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,0:10:369:0:0:0,-33.5528 0:17:17,0:17:624:0:0:0,-56.4815 0:8:8,2:6:195:2:17:0,-16.2483 0:9:9,0:9:324:0:0:0,-29.5019 +Chromosome 4014200 . C G 6.90876E-12 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=20;DPB=20;DPRA=1.61538;EPP=7.35324;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=27.1671;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=610;RO=18;RPL=0;RPP=7.35324;RPPR=3.49285;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=4;SRP=15.074;SRR=14;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|hyi|PA14_45010|transcript|ABJ10681.1|protein_coding|1/1|c.192C>G|p.Gly64Gly|192/783|192/783|64/260||,G|upstream_gene_variant|MODIFIER|moaA2|PA14_44970|transcript|ABJ10685.1|protein_coding||c.-4113G>C|||||4113|,G|upstream_gene_variant|MODIFIER|PA14_44990|PA14_44990|transcript|ABJ10683.1|protein_coding||c.-2391G>C|||||2391|,G|upstream_gene_variant|MODIFIER|glxR|PA14_45020|transcript|ABJ10680.1|protein_coding||c.-666C>G|||||666|,G|upstream_gene_variant|MODIFIER|ttuD|PA14_45030|transcript|ABJ10679.1|protein_coding||c.-1853C>G|||||1853|,G|upstream_gene_variant|MODIFIER|pykF|PA14_45050|transcript|ABJ10678.1|protein_coding||c.-3120C>G|||||3120|,G|upstream_gene_variant|MODIFIER|PA14_45060|PA14_45060|transcript|ABJ10677.1|protein_coding||c.-4920C>G|||||4920|,G|downstream_gene_variant|MODIFIER|PA14_44980|PA14_44980|transcript|ABJ10684.1|protein_coding||c.*3227C>G|||||3227|,G|downstream_gene_variant|MODIFIER|gcl|PA14_45000|transcript|ABJ10682.1|protein_coding||c.*287C>G|||||287| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:67:0:0:0,-6.36284 0:7:7,2:5:166:2:31:0,-12.3223 0:5:5,0:5:176:0:0:0,-16.1818 0:6:6,0:6:201:0:0:0,-18.4189 +Chromosome 4018751 . T G 5.1536E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=32;DPB=32;DPRA=1.66667;EPP=9.52472;EPPR=9.07545;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=48.0728;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=1012;RO=29;RPL=0;RPP=9.52472;RPPR=24.6501;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=23;SRP=24.6501;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=G|stop_lost&splice_region_variant|HIGH|pykF|PA14_45050|transcript|ABJ10678.1|protein_coding|1/1|c.1432T>G|p.Ter478Glyext*?|1432/1434|1432/1434|478/477||,G|upstream_gene_variant|MODIFIER|PA14_45060|PA14_45060|transcript|ABJ10677.1|protein_coding||c.-369T>G|||||369|,G|upstream_gene_variant|MODIFIER|PA14_45070|PA14_45070|transcript|ABJ10676.1|protein_coding||c.-1348T>G|||||1348|,G|upstream_gene_variant|MODIFIER|PA14_45090|PA14_45090|transcript|ABJ10675.1|protein_coding||c.-2186T>G|||||2186|,G|upstream_gene_variant|MODIFIER|muiA|PA14_45100|transcript|ABJ10674.1|protein_coding||c.-2936T>G|||||2936|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|cysP|PA14_45110|transcript|ABJ10673.1|protein_coding||c.-4720T>G|||||4720|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|gcl|PA14_45000|transcript|ABJ10682.1|protein_coding||c.*4838T>G|||||4838|,G|downstream_gene_variant|MODIFIER|hyi|PA14_45010|transcript|ABJ10681.1|protein_coding||c.*3960T>G|||||3960|,G|downstream_gene_variant|MODIFIER|glxR|PA14_45020|transcript|ABJ10680.1|protein_coding||c.*2995T>G|||||2995|,G|downstream_gene_variant|MODIFIER|ttuD|PA14_45030|transcript|ABJ10679.1|protein_coding||c.*1433T>G|||||1433| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:255:0:0:0,-23.2992 0:5:5,0:5:180:0:0:0,-16.5513 0:7:7,2:5:166:2:4:0,-14.8875 0:13:13,1:12:411:1:2:0,-37.1118 +Chromosome 4028093 . A C 2.40557E-11 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=22;DPB=22;DPRA=1.125;EPP=7.35324;EPPR=13.8677;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=25.9346;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=558;RO=20;RPL=2;RPP=7.35324;RPPR=6.91895;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=10;SRP=3.0103;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_45170|PA14_45170|transcript|ABJ10669.1|protein_coding|1/1|c.365A>C|p.His122Pro|365/1191|365/1191|122/396||,C|upstream_gene_variant|MODIFIER|PA14_45120|PA14_45120|transcript|ABJ10672.1|protein_coding||c.-3186T>G|||||3186|,C|upstream_gene_variant|MODIFIER|PA14_45130|PA14_45130|transcript|ABJ10671.1|protein_coding||c.-1891T>G|||||1891|,C|upstream_gene_variant|MODIFIER|PA14_45180|PA14_45180|transcript|ABJ10668.1|protein_coding||c.-813A>C|||||813|,C|upstream_gene_variant|MODIFIER|PA14_45190|PA14_45190|transcript|ABJ10667.1|protein_coding||c.-2072A>C|||||2072|,C|downstream_gene_variant|MODIFIER|muiA|PA14_45100|transcript|ABJ10674.1|protein_coding||c.*4751A>C|||||4751|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|cysP|PA14_45110|transcript|ABJ10673.1|protein_coding||c.*3624A>C|||||3624|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_45150|PA14_45150|transcript|ABJ10670.1|protein_coding||c.*768A>C|||||768|,C|downstream_gene_variant|MODIFIER|PA14_45210|PA14_45210|transcript|ABJ10666.1|protein_coding||c.*3495T>G|||||3495|,C|downstream_gene_variant|MODIFIER|PA14_45240|PA14_45240|transcript|ABJ10665.1|protein_coding||c.*4609T>G|||||4609| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:79:0:0:0,-7.49763 0:4:4,0:4:100:0:0:0,-9.24769 0:10:10,0:10:301:0:0:0,-27.3824 0:6:6,2:4:78:2:18:0,-5.50057 +Chromosome 4028672 . T C 4.22519E-6 . AB=0;ABP=0;AC=0;AF=0;AN=3;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=2.66667;EPP=7.35324;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=14.2236;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=111;RO=5;RPL=2;RPP=7.35324;RPPR=6.91895;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=1;SRP=6.91895;SRR=4;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_45170|PA14_45170|transcript|ABJ10669.1|protein_coding|1/1|c.944T>C|p.Leu315Pro|944/1191|944/1191|315/396||,C|upstream_gene_variant|MODIFIER|PA14_45120|PA14_45120|transcript|ABJ10672.1|protein_coding||c.-3765A>G|||||3765|,C|upstream_gene_variant|MODIFIER|PA14_45130|PA14_45130|transcript|ABJ10671.1|protein_coding||c.-2470A>G|||||2470|,C|upstream_gene_variant|MODIFIER|PA14_45180|PA14_45180|transcript|ABJ10668.1|protein_coding||c.-234T>C|||||234|,C|upstream_gene_variant|MODIFIER|PA14_45190|PA14_45190|transcript|ABJ10667.1|protein_coding||c.-1493T>C|||||1493|,C|downstream_gene_variant|MODIFIER|cysP|PA14_45110|transcript|ABJ10673.1|protein_coding||c.*4203T>C|||||4203|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_45150|PA14_45150|transcript|ABJ10670.1|protein_coding||c.*1347T>C|||||1347|,C|downstream_gene_variant|MODIFIER|PA14_45210|PA14_45210|transcript|ABJ10666.1|protein_coding||c.*2916A>G|||||2916|,C|downstream_gene_variant|MODIFIER|PA14_45240|PA14_45240|transcript|ABJ10665.1|protein_coding||c.*4030A>G|||||4030| GT:DP:DPR:RO:QR:AO:QA:GL . 0:1:1,0:1:30:0:0:0,-2.99957 0:4:4,2:2:27:2:17:0,-0.949995 0:2:2,0:2:54:0:0:0,-5.12672 +Chromosome 4044470 . T C 2.44142E-15 . AB=0;ABP=0;AC=0;AF=0;AN=3;AO=2;CIGAR=1X;DP=17;DPB=17;DPRA=1.09091;EPP=7.35324;EPPR=4.31318;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=44.8648;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=564;RO=15;RPL=2;RPP=7.35324;RPPR=14.7363;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=10;SRP=6.62942;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_45410|PA14_45410|transcript|ABJ10652.1|protein_coding|1/1|c.74T>C|p.Leu25Pro|74/336|74/336|25/111||,C|upstream_gene_variant|MODIFIER|ccmF|PA14_45310|transcript|ABJ10659.1|protein_coding||c.-4743A>G|||||4743|,C|upstream_gene_variant|MODIFIER|ccmE|PA14_45330|transcript|ABJ10658.1|protein_coding||c.-4254A>G|||||4254|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_45340|PA14_45340|transcript|ABJ10657.1|protein_coding||c.-4081A>G|||||4081|,C|upstream_gene_variant|MODIFIER|ccmC|PA14_45350|transcript|ABJ10656.1|protein_coding||c.-3326A>G|||||3326|,C|upstream_gene_variant|MODIFIER|ccmB|PA14_45370|transcript|ABJ10655.1|protein_coding||c.-2532A>G|||||2532|,C|upstream_gene_variant|MODIFIER|ccmA|PA14_45380|transcript|ABJ10654.1|protein_coding||c.-1834A>G|||||1834|,C|upstream_gene_variant|MODIFIER|PA14_45470|PA14_45470|transcript|ABJ10647.1|protein_coding||c.-4026T>C|||||4026|,C|downstream_gene_variant|MODIFIER|PA14_45400|PA14_45400|transcript|ABJ10653.1|protein_coding||c.*70T>C|||||70|,C|downstream_gene_variant|MODIFIER|PA14_45430|PA14_45430|transcript|ABJ10651.1|protein_coding||c.*786A>G|||||786|,C|downstream_gene_variant|MODIFIER|PA14_45440|PA14_45440|transcript|ABJ10650.1|protein_coding||c.*1657A>G|||||1657|,C|downstream_gene_variant|MODIFIER|PA14_45450|PA14_45450|transcript|ABJ10649.1|protein_coding||c.*2439A>G|||||2439|,C|downstream_gene_variant|MODIFIER|PA14_45460|PA14_45460|transcript|ABJ10648.1|protein_coding||c.*2946A>G|||||2946|,C|downstream_gene_variant|MODIFIER|PA14_45480|PA14_45480|transcript|ABJ10646.1|protein_coding||c.*4740A>G|||||4740| GT:DP:DPR:RO:QR:AO:QA:GL . 0:6:6,2:4:144:2:4:0,-12.933 0:5:5,0:5:198:0:0:0,-18.1978 0:6:6,0:6:222:0:0:0,-20.3348 +Chromosome 4045139 . C G 3.16443E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=8;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=20.3821;EPPR=9.04217;GTI=0;LEN=1;MEANALT=1.25;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=53.3348;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=82;QR=1049;RO=36;RPL=0;RPP=20.3821;RPPR=3.25157;RPR=8;RUN=1;SAF=0;SAP=20.3821;SAR=8;SRF=8;SRP=27.1378;SRR=28;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|ccmE|PA14_45330|transcript|ABJ10658.1|protein_coding||c.-4923G>C|||||4923|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_45340|PA14_45340|transcript|ABJ10657.1|protein_coding||c.-4750G>C|||||4750|,G|upstream_gene_variant|MODIFIER|ccmC|PA14_45350|transcript|ABJ10656.1|protein_coding||c.-3995G>C|||||3995|,G|upstream_gene_variant|MODIFIER|ccmB|PA14_45370|transcript|ABJ10655.1|protein_coding||c.-3201G>C|||||3201|,G|upstream_gene_variant|MODIFIER|ccmA|PA14_45380|transcript|ABJ10654.1|protein_coding||c.-2503G>C|||||2503|,G|upstream_gene_variant|MODIFIER|PA14_45470|PA14_45470|transcript|ABJ10647.1|protein_coding||c.-3357C>G|||||3357|,G|downstream_gene_variant|MODIFIER|PA14_45400|PA14_45400|transcript|ABJ10653.1|protein_coding||c.*739C>G|||||739|,G|downstream_gene_variant|MODIFIER|PA14_45410|PA14_45410|transcript|ABJ10652.1|protein_coding||c.*407C>G|||||407|,G|downstream_gene_variant|MODIFIER|PA14_45430|PA14_45430|transcript|ABJ10651.1|protein_coding||c.*117G>C|||||117|,G|downstream_gene_variant|MODIFIER|PA14_45440|PA14_45440|transcript|ABJ10650.1|protein_coding||c.*988G>C|||||988|,G|downstream_gene_variant|MODIFIER|PA14_45450|PA14_45450|transcript|ABJ10649.1|protein_coding||c.*1770G>C|||||1770|,G|downstream_gene_variant|MODIFIER|PA14_45460|PA14_45460|transcript|ABJ10648.1|protein_coding||c.*2277G>C|||||2277|,G|downstream_gene_variant|MODIFIER|PA14_45480|PA14_45480|transcript|ABJ10646.1|protein_coding||c.*4071G>C|||||4071|,G|downstream_gene_variant|MODIFIER|cheW|PA14_45500|transcript|ABJ10645.1|protein_coding||c.*4509G>C|||||4509|,G|intergenic_region|MODIFIER|PA14_45410-PA14_45430|PA14_45410-PA14_45430|intergenic_region|PA14_45410-PA14_45430|||n.4045139C>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,1:7:221:1:15:0,-18.6919 0:13:13,3:9:243:3:33:0,-19.026 0:15:15,1:14:384:1:2:0,-34.6152 0:9:9,3:6:201:3:32:0,-15.4256 +Chromosome 4052714 . T C 5.7586E-11 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=28;DPB=28;DPRA=3;EPP=9.52472;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=25.0608;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=55;QR=761;RO=25;RPL=3;RPP=9.52472;RPPR=5.18177;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=20;SRP=22.5536;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|motD|PA14_45540|transcript|ABJ10642.1|protein_coding|1/1|c.215A>G|p.Glu72Gly|215/891|215/891|72/296||,C|upstream_gene_variant|MODIFIER|PA14_45460|PA14_45460|transcript|ABJ10648.1|protein_coding||c.-4327A>G|||||4327|,C|upstream_gene_variant|MODIFIER|PA14_45480|PA14_45480|transcript|ABJ10646.1|protein_coding||c.-3097A>G|||||3097|,C|upstream_gene_variant|MODIFIER|cheW|PA14_45500|transcript|ABJ10645.1|protein_coding||c.-2587A>G|||||2587|,C|upstream_gene_variant|MODIFIER|PA14_45510|PA14_45510|transcript|ABJ10644.1|protein_coding||c.-1651A>G|||||1651|,C|upstream_gene_variant|MODIFIER|PA14_45520|PA14_45520|transcript|ABJ10643.1|protein_coding||c.-771A>G|||||771|,C|downstream_gene_variant|MODIFIER|PA14_45470|PA14_45470|transcript|ABJ10647.1|protein_coding||c.*3532T>C|||||3532|,C|downstream_gene_variant|MODIFIER|motC|PA14_45560|transcript|ABJ10641.1|protein_coding||c.*227A>G|||||227|,C|downstream_gene_variant|MODIFIER|cheB|PA14_45580|transcript|ABJ10640.1|protein_coding||c.*1056A>G|||||1056|,C|downstream_gene_variant|MODIFIER|cheA|PA14_45590|transcript|ABJ10639.1|protein_coding||c.*2216A>G|||||2216|,C|downstream_gene_variant|MODIFIER|cheZ|PA14_45610|transcript|ABJ10638.1|protein_coding||c.*4678A>G|||||4678| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:52:0:0:0,-4.93673 0:15:15,1:14:401:1:2:0,-36.1497 0:5:5,0:5:184:0:0:0,-16.9152 0:6:6,2:4:124:2:53:0,-6.43306 +Chromosome 4062638 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=52;DPB=52;DPRA=0.857143;EPP=13.8677;EPPR=47.41;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=64.5094;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=49;QR=1601;RO=47;RPL=0;RPP=13.8677;RPPR=4.16534;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=21;SRP=4.16534;SRR=26;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|flhA|PA14_45680|transcript|ABJ10633.1|protein_coding|1/1|c.1256T>C|p.Leu419Pro|1256/2124|1256/2124|419/707||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|cheZ|PA14_45610|transcript|ABJ10638.1|protein_coding||c.-4458T>C|||||4458|,G|upstream_gene_variant|MODIFIER|cheY|PA14_45620|transcript|ABJ10637.1|protein_coding||c.-4064T>C|||||4064|,G|upstream_gene_variant|MODIFIER|fliA|PA14_45630|transcript|ABJ10636.1|protein_coding||c.-3219T>C|||||3219|,G|upstream_gene_variant|MODIFIER|fleN|PA14_45640|transcript|ABJ10635.1|protein_coding||c.-2380T>C|||||2380|,G|upstream_gene_variant|MODIFIER|flhF|PA14_45660|transcript|ABJ10634.1|protein_coding||c.-952T>C|||||952|,G|downstream_gene_variant|MODIFIER|PA14_45700|PA14_45700|transcript|ABJ10632.1|protein_coding||c.*1394T>C|||||1394|,G|downstream_gene_variant|MODIFIER|PA14_45710|PA14_45710|transcript|ABJ10631.1|protein_coding||c.*2788T>C|||||2788|,G|downstream_gene_variant|MODIFIER|flhB|PA14_45720|transcript|ABJ10630.1|protein_coding||c.*4120T>C|||||4120| GT:DP:DPR:RO:QR:AO:QA:GL 0:12:12,1:11:395:1:2:0,-35.6802 0:12:12,4:8:268:4:47:0,-20.0871 0:16:16,0:16:547:0:0:0,-49.5377 0:12:12,0:12:391:0:0:0,-35.4942 +Chromosome 4089858 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=42;DPB=42;DPRA=0.74359;EPP=13.8677;EPPR=3.5385;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=57.4443;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1238;RO=37;RPL=0;RPP=13.8677;RPPR=16.2152;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=23;SRP=7.76406;SRR=14;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|lasI|PA14_45940|transcript|ABJ10613.1|protein_coding||c.-4883T>C|||||4883|,G|upstream_gene_variant|MODIFIER|lasR|PA14_45960|transcript|ABJ10611.1|protein_coding||c.-3800T>C|||||3800|,G|upstream_gene_variant|MODIFIER|PA14_45970|PA14_45970|transcript|ABJ10610.1|protein_coding||c.-641T>C|||||641|,G|upstream_gene_variant|MODIFIER|yjaB|PA14_45980|transcript|ABJ10609.1|protein_coding||c.-44T>C|||||44|,G|upstream_gene_variant|MODIFIER|PA14_46030|PA14_46030|transcript|ABJ10605.1|protein_coding||c.-4781A>G|||||4781|,G|downstream_gene_variant|MODIFIER|rsaL|PA14_45950|transcript|ABJ10612.1|protein_coding||c.*4509A>G|||||4509|,G|downstream_gene_variant|MODIFIER|PA14_46000|PA14_46000|transcript|ABJ10608.1|protein_coding||c.*1374T>C|||||1374|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_46010|PA14_46010|transcript|ABJ10607.1|protein_coding||c.*1771T>C|||||1771|,G|downstream_gene_variant|MODIFIER|PA14_46020|PA14_46020|transcript|ABJ10606.1|protein_coding||c.*3876T>C|||||3876|,G|intergenic_region|MODIFIER|yjaB-PA14_46000|PA14_45980-PA14_46000|intergenic_region|PA14_45980-PA14_46000|||n.4089858A>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,1:6:199:1:2:0,-18.0287 0:10:10,2:8:279:2:4:0,-25.0534 0:12:12,2:10:305:2:4:0,-27.3563 0:13:13,0:13:455:0:0:0,-41.2687 +Chromosome 4091765 . T G 5.90642E-12 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=16;DPB=16;DPRA=2.33333;EPP=11.6962;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=27.6611;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=441;RO=12;RPL=0;RPP=11.6962;RPPR=3.73412;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=4;SRP=5.9056;SRR=8;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_46010|PA14_46010|transcript|ABJ10607.1|protein_coding|1/1|c.1481A>C|p.Gln494Pro|1481/1617|1481/1617|494/538||,G|upstream_gene_variant|MODIFIER|PA14_45970|PA14_45970|transcript|ABJ10610.1|protein_coding||c.-2548A>C|||||2548|,G|upstream_gene_variant|MODIFIER|yjaB|PA14_45980|transcript|ABJ10609.1|protein_coding||c.-1951A>C|||||1951|,G|upstream_gene_variant|MODIFIER|PA14_46000|PA14_46000|transcript|ABJ10608.1|protein_coding||c.-177A>C|||||177|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_46030|PA14_46030|transcript|ABJ10605.1|protein_coding||c.-2874T>G|||||2874|,G|downstream_gene_variant|MODIFIER|PA14_46020|PA14_46020|transcript|ABJ10606.1|protein_coding||c.*1969A>C|||||1969|,G|downstream_gene_variant|MODIFIER|gbuR|PA14_46060|transcript|ABJ10604.1|protein_coding||c.*4131A>C|||||4131|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:78:0:0:0,-7.40347 0:3:3,1:2:78:1:2:0,-7.20347 0:7:7,1:6:210:1:2:0,-19.0333 0:4:4,2:2:75:2:4:0,-6.7401 +Chromosome 4130598 . T C 8.11791E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=29;DPB=29;DPRA=0.782609;EPP=7.35324;EPPR=6.95112;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=40.4094;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=784;RO=27;RPL=2;RPP=7.35324;RPPR=3.09072;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=9;SRP=9.52472;SRR=18;TYPE=snp;technology.ILLUMINA=1;ANN=C|upstream_gene_variant|MODIFIER|PA14_46380|PA14_46380|transcript|ABJ10577.1|protein_coding||c.-3083A>G|||||3083|,C|upstream_gene_variant|MODIFIER|PA14_46390|PA14_46390|transcript|ABJ10576.1|protein_coding||c.-2813A>G|||||2813|,C|upstream_gene_variant|MODIFIER|yqhC|PA14_46400|transcript|ABJ10575.1|protein_coding||c.-1504A>G|||||1504|,C|upstream_gene_variant|MODIFIER|PA14_46430|PA14_46430|transcript|ABJ10573.1|protein_coding||c.-127A>G|||||127|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|aceK|PA14_46450|transcript|ABJ10571.1|protein_coding||c.-685T>C|||||685|,C|downstream_gene_variant|MODIFIER|PA14_46370|PA14_46370|transcript|ABJ10578.1|protein_coding||c.*3526T>C|||||3526|,C|downstream_gene_variant|MODIFIER|PA14_46420|PA14_46420|transcript|ABJ10574.1|protein_coding||c.*579T>C|||||579|,C|downstream_gene_variant|MODIFIER|PA14_46440|PA14_46440|transcript|ABJ10572.1|protein_coding||c.*16A>G|||||16|,C|downstream_gene_variant|MODIFIER|PA14_46460|PA14_46460|transcript|ABJ10570.1|protein_coding||c.*3102A>G|||||3102|,C|downstream_gene_variant|MODIFIER|pdxB|PA14_46470|transcript|ABJ10569.1|protein_coding||c.*4541A>G|||||4541|,C|intergenic_region|MODIFIER|PA14_46430-PA14_46440|PA14_46430-PA14_46440|intergenic_region|PA14_46430-PA14_46440|||n.4130598T>C|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:180:0:0:0,-16.4957 0:7:7,0:7:180:0:0:0,-16.4456 0:6:6,2:4:132:2:17:0,-10.5896 0:10:10,0:10:292:0:0:0,-26.5538 +Chromosome 4138393 . T C 6.46424E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=12;CIGAR=1X;DP=86;DPB=86;DPRA=0;EPP=29.068;EPPR=22.847;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=96.1518;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=24;QR=2670;RO=74;RPL=12;RPP=29.068;RPPR=36.9322;RPR=0;RUN=1;SAF=12;SAP=29.068;SAR=0;SRF=52;SRP=29.4201;SRR=22;TYPE=snp;technology.ILLUMINA=1;ANN=C|upstream_gene_variant|MODIFIER|PA14_46460|PA14_46460|transcript|ABJ10570.1|protein_coding||c.-3503A>G|||||3503|,C|upstream_gene_variant|MODIFIER|pdxB|PA14_46470|transcript|ABJ10569.1|protein_coding||c.-2112A>G|||||2112|,C|upstream_gene_variant|MODIFIER|PA14_46480|PA14_46480|transcript|ABJ10568.1|protein_coding||c.-1391A>G|||||1391|,C|upstream_gene_variant|MODIFIER|PA14_46540|PA14_46540|transcript|ABJ10563.1|protein_coding||c.-4008T>C|||||4008|,C|downstream_gene_variant|MODIFIER|fabF2|PA14_46490|transcript|ABJ10567.1|protein_coding||c.*14T>C|||||14|,C|downstream_gene_variant|MODIFIER|PA14_46510|PA14_46510|transcript|ABJ10566.1|protein_coding||c.*353A>G|||||353|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_46520|PA14_46520|transcript|ABJ10565.1|protein_coding||c.*1708A>G|||||1708|,C|downstream_gene_variant|MODIFIER|PA14_46530|PA14_46530|transcript|ABJ10564.1|protein_coding||c.*3433A>G|||||3433|,C|intergenic_region|MODIFIER|fabF2-PA14_46510|PA14_46490-PA14_46510|intergenic_region|PA14_46490-PA14_46510|||n.4138393T>C|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:12:12,2:10:358:2:4:0,-32.1719 0:21:21,1:20:674:1:2:0,-60.7503 0:24:24,5:19:714:5:10:0,-63.6585 0:29:29,4:25:924:4:8:0,-82.7218 +Chromosome 4144720 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=10;CIGAR=1X;DP=130;DPB=130;DPRA=1.16092;EPP=16.9077;EPPR=8.87328;GTI=0;LEN=1;MEANALT=1;MQM=59.2;MQMR=60;NS=4;NUMALT=1;ODDS=155.667;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=149;QR=4245;RO=120;RPL=8;RPP=10.8276;RPPR=4.16842;RPR=2;RUN=1;SAF=9;SAP=16.9077;SAR=1;SRF=45;SRP=19.2963;SRR=75;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_46550|PA14_46550|transcript|ABJ10562.1|protein_coding|1/1|c.148T>C|p.Ser50Pro|148/729|148/729|50/242||,C|upstream_gene_variant|MODIFIER|PA14_46510|PA14_46510|transcript|ABJ10566.1|protein_coding||c.-4616A>G|||||4616|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_46520|PA14_46520|transcript|ABJ10565.1|protein_coding||c.-3480A>G|||||3480|,C|upstream_gene_variant|MODIFIER|PA14_46530|PA14_46530|transcript|ABJ10564.1|protein_coding||c.-2469A>G|||||2469|,C|upstream_gene_variant|MODIFIER|PA14_46570|PA14_46570|transcript|ABJ10560.1|protein_coding||c.-1417T>C|||||1417|,C|upstream_gene_variant|MODIFIER|PA14_46580|PA14_46580|transcript|ABJ10559.1|protein_coding||c.-2106T>C|||||2106|,C|upstream_gene_variant|MODIFIER|PA14_46590|PA14_46590|transcript|ABJ10558.1|protein_coding||c.-3218T>C|||||3218|,C|downstream_gene_variant|MODIFIER|PA14_46540|PA14_46540|transcript|ABJ10563.1|protein_coding||c.*619T>C|||||619|,C|downstream_gene_variant|MODIFIER|PA14_46560|PA14_46560|transcript|ABJ10561.1|protein_coding||c.*744A>G|||||744|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:24:24,5:19:664:5:63:0,-54.2639 0:38:38,2:36:1328:2:54:0,-114.662 0:29:29,0:29:972:0:0:0,-87.7506 0:39:39,3:36:1281:3:32:0,-112.567 +Chromosome 4149040 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=59;DPB=59;DPRA=0.966667;EPP=11.6962;EPPR=3.04978;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=82.8814;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=63;QR=2084;RO=55;RPL=0;RPP=11.6962;RPPR=3.04978;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=29;SRP=3.36563;SRR=26;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_46590|PA14_46590|transcript|ABJ10558.1|protein_coding|1/1|c.1103T>G|p.Val368Gly|1103/3090|1103/3090|368/1029||,G|upstream_gene_variant|MODIFIER|PA14_46560|PA14_46560|transcript|ABJ10561.1|protein_coding||c.-3175A>C|||||3175|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_46600|PA14_46600|transcript|ABJ10557.1|protein_coding||c.-2018T>G|||||2018|,G|downstream_gene_variant|MODIFIER|PA14_46540|PA14_46540|transcript|ABJ10563.1|protein_coding||c.*4939T>G|||||4939|,G|downstream_gene_variant|MODIFIER|PA14_46550|PA14_46550|transcript|ABJ10562.1|protein_coding||c.*3739T>G|||||3739|,G|downstream_gene_variant|MODIFIER|PA14_46570|PA14_46570|transcript|ABJ10560.1|protein_coding||c.*2286T>G|||||2286|,G|downstream_gene_variant|MODIFIER|PA14_46580|PA14_46580|transcript|ABJ10559.1|protein_coding||c.*1099T>G|||||1099|,G|downstream_gene_variant|MODIFIER|PA14_46610|PA14_46610|transcript|ABJ10556.1|protein_coding||c.*3309A>C|||||3309|,G|downstream_gene_variant|MODIFIER|PA14_46620|PA14_46620|transcript|ABJ10555.1|protein_coding||c.*3804A>C|||||3804| GT:DP:DPR:RO:QR:AO:QA:GL 0:18:18,0:18:687:0:0:0,-62.1515 0:12:12,3:9:353:3:61:0,-26.4377 0:17:17,1:16:581:1:2:0,-52.4059 0:12:12,0:12:463:0:0:0,-42.0187 +Chromosome 4155825 . G T 6.94641E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=9;CIGAR=1X;DP=70;DPB=70;DPRA=0;EPP=14.8328;EPPR=3.33068;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=72.663;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=121;QR=1670;RO=61;RPL=8;RPP=14.8328;RPPR=13.2981;RPR=1;RUN=1;SAF=9;SAP=22.5536;SAR=0;SRF=40;SRP=15.8611;SRR=21;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|PA14_46640|PA14_46640|transcript|ABJ10553.1|protein_coding|1/1|c.2406C>A|p.Gly802Gly|2406/2442|2406/2442|802/813||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|PA14_46610|PA14_46610|transcript|ABJ10556.1|protein_coding||c.-3003C>A|||||3003|,T|upstream_gene_variant|MODIFIER|PA14_46620|PA14_46620|transcript|ABJ10555.1|protein_coding||c.-1701C>A|||||1701|,T|upstream_gene_variant|MODIFIER|norM|PA14_46680|transcript|ABJ10549.1|protein_coding||c.-4844G>T|||||4844|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|PA14_46590|PA14_46590|transcript|ABJ10558.1|protein_coding||c.*4798G>T|||||4798|,T|downstream_gene_variant|MODIFIER|PA14_46600|PA14_46600|transcript|ABJ10557.1|protein_coding||c.*3961G>T|||||3961|,T|downstream_gene_variant|MODIFIER|PA14_46630|PA14_46630|transcript|ABJ10554.1|protein_coding||c.*196G>T|||||196|,T|downstream_gene_variant|MODIFIER|PA14_46650|PA14_46650|transcript|ABJ10552.1|protein_coding||c.*2483C>A|||||2483|,T|downstream_gene_variant|MODIFIER|PA14_46660|PA14_46660|transcript|ABJ10551.1|protein_coding||c.*3322C>A|||||3322|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|PA14_46670|PA14_46670|transcript|ABJ10550.1|protein_coding||c.*4075C>A|||||4075| GT:DP:DPR:RO:QR:AO:QA:GL 0:15:15,3:12:300:3:44:0,-23.1347 0:15:15,1:14:412:1:15:0,-35.8544 0:16:16,2:14:356:2:30:0,-29.4354 0:24:24,3:21:602:3:32:0,-51.4522 +Chromosome 4158370 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=35;DPB=35;DPRA=0.962963;EPP=11.6962;EPPR=14.8483;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=45.1988;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1090;RO=31;RPL=0;RPP=11.6962;RPPR=28.2974;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=5;SRP=33.9012;SRR=26;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_46650|PA14_46650|transcript|ABJ10552.1|protein_coding|1/1|c.781G>C|p.Val261Leu|781/843|781/843|261/280||,G|upstream_gene_variant|MODIFIER|PA14_46620|PA14_46620|transcript|ABJ10555.1|protein_coding||c.-4246G>C|||||4246|,G|upstream_gene_variant|MODIFIER|PA14_46640|PA14_46640|transcript|ABJ10553.1|protein_coding||c.-140G>C|||||140|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|norM|PA14_46680|transcript|ABJ10549.1|protein_coding||c.-2299C>G|||||2299|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_46710|PA14_46710|transcript|ABJ10548.1|protein_coding||c.-4607C>G|||||4607|,G|downstream_gene_variant|MODIFIER|PA14_46630|PA14_46630|transcript|ABJ10554.1|protein_coding||c.*2741C>G|||||2741|,G|downstream_gene_variant|MODIFIER|PA14_46660|PA14_46660|transcript|ABJ10551.1|protein_coding||c.*777G>C|||||777|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_46670|PA14_46670|transcript|ABJ10550.1|protein_coding||c.*1530G>C|||||1530|,G|downstream_gene_variant|MODIFIER|ybiF|PA14_46700|transcript|ABJ10547.1|protein_coding||c.*3715G>C|||||3715| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,0:9:306:0:0:0,-27.8569 0:7:7,1:6:214:1:15:0,-18.1072 0:7:7,2:5:148:2:17:0,-11.9926 0:12:12,1:11:422:1:2:0,-38.1295 +Chromosome 4167242 . T G 2.90452E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=28;DPB=28;DPRA=1.66667;EPP=7.35324;EPPR=11.3621;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=46.185;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=936;RO=26;RPL=0;RPP=7.35324;RPPR=19.3799;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=10;SRP=6.01695;SRR=16;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|ybiF|PA14_46700|transcript|ABJ10547.1|protein_coding||c.-4264A>C|||||4264|,G|upstream_gene_variant|MODIFIER|PA14_46740|PA14_46740|transcript|ABJ10545.1|protein_coding||c.-2687A>C|||||2687|,G|upstream_gene_variant|MODIFIER|PA14_46750|PA14_46750|transcript|ABJ10544.1|protein_coding||c.-1512A>C|||||1512|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_46760|PA14_46760|transcript|ABJ10543.1|protein_coding||c.-1109A>C|||||1109|,G|upstream_gene_variant|MODIFIER|PA14_46800|PA14_46800|transcript|ABJ10540.1|protein_coding||c.-85T>G|||||85|,G|upstream_gene_variant|MODIFIER|PA14_46850|PA14_46850|transcript|ABJ10535.1|protein_coding||c.-4775T>G|||||4775|,G|downstream_gene_variant|MODIFIER|PA14_46710|PA14_46710|transcript|ABJ10548.1|protein_coding||c.*3615T>G|||||3615|,G|downstream_gene_variant|MODIFIER|PA14_46720|PA14_46720|transcript|ABJ10546.1|protein_coding||c.*3179T>G|||||3179|,G|downstream_gene_variant|MODIFIER|PA14_46770|PA14_46770|transcript|ABJ10542.1|protein_coding||c.*537T>G|||||537|,G|downstream_gene_variant|MODIFIER|PA14_46780|PA14_46780|transcript|ABJ10541.1|protein_coding||c.*87T>G|||||87|,G|downstream_gene_variant|MODIFIER|PA14_46810|PA14_46810|transcript|ABJ10539.1|protein_coding||c.*1304A>C|||||1304|,G|downstream_gene_variant|MODIFIER|PA14_46820|PA14_46820|transcript|ABJ10538.1|protein_coding||c.*2545A>C|||||2545|,G|downstream_gene_variant|MODIFIER|PA14_46830|PA14_46830|transcript|ABJ10537.1|protein_coding||c.*3469A>C|||||3469|,G|downstream_gene_variant|MODIFIER|PA14_46840|PA14_46840|transcript|ABJ10536.1|protein_coding||c.*4002A>C|||||4002|WARNING_TRANSCRIPT_NO_START_CODON,G|intergenic_region|MODIFIER|PA14_46780-PA14_46800|PA14_46780-PA14_46800|intergenic_region|PA14_46780-PA14_46800|||n.4167242T>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:160:0:0:0,-14.7109 0:9:9,0:9:337:0:0:0,-30.6788 0:10:10,2:8:294:2:4:0,-26.4296 0:4:4,0:4:145:0:0:0,-13.4052 +Chromosome 4189891 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=36;DPB=36;DPRA=1;EPP=3.73412;EPPR=3.60252;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=58.7576;NS=4;NUMALT=1;ODDS=46.3337;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=43;QR=964;RO=33;RPL=2;RPP=3.73412;RPPR=3.60252;RPR=1;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=16;SRP=3.0761;SRR=17;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_47030|PA14_47030|transcript|ABJ10520.1|protein_coding|1/1|c.524A>C|p.Gln175Pro|524/552|524/552|175/183||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|yegH|PA14_47040|transcript|ABJ10519.1|protein_coding||c.-297A>C|||||297|,C|upstream_gene_variant|MODIFIER|PA14_47080|PA14_47080|transcript|ABJ10516.1|protein_coding||c.-3201A>C|||||3201|,C|downstream_gene_variant|MODIFIER|PA14_46980|PA14_46980|transcript|ABJ10524.1|protein_coding||c.*3792A>C|||||3792|,C|downstream_gene_variant|MODIFIER|PA14_46990|PA14_46990|transcript|ABJ10523.1|protein_coding||c.*2470A>C|||||2470|,C|downstream_gene_variant|MODIFIER|PA14_47000|PA14_47000|transcript|ABJ10522.1|protein_coding||c.*1074A>C|||||1074|,C|downstream_gene_variant|MODIFIER|PA14_47010|PA14_47010|transcript|ABJ10521.1|protein_coding||c.*673A>C|||||673|,C|downstream_gene_variant|MODIFIER|PA14_47060|PA14_47060|transcript|ABJ10518.1|protein_coding||c.*1900T>G|||||1900|,C|downstream_gene_variant|MODIFIER|PA14_47070|PA14_47070|transcript|ABJ10517.1|protein_coding||c.*2685T>G|||||2685|,C|downstream_gene_variant|MODIFIER|PA14_47090|PA14_47090|transcript|ABJ10515.1|protein_coding||c.*4113T>G|||||4113| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:282:0:0:0,-25.7121 0:7:7,0:7:166:0:0:0,-15.06 0:9:9,3:6:189:3:43:0,-13.2968 0:12:12,0:12:327:0:0:0,-29.6831 +Chromosome 4196002 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=51;DPB=51;DPRA=0.731707;EPP=7.35324;EPPR=22.5536;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=59.1724;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1622;RO=49;RPL=0;RPP=7.35324;RPPR=12.9813;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=25;SRP=3.05462;SRR=24;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|PA14_47060|PA14_47060|transcript|ABJ10518.1|protein_coding||c.-3432G>C|||||3432|,G|upstream_gene_variant|MODIFIER|PA14_47070|PA14_47070|transcript|ABJ10517.1|protein_coding||c.-2995G>C|||||2995|,G|upstream_gene_variant|MODIFIER|PA14_47090|PA14_47090|transcript|ABJ10515.1|protein_coding||c.-70G>C|||||70|,G|upstream_gene_variant|MODIFIER|P9|EBG00001225109|transcript|EBT00001793442.1|lincRNA||n.-2013C>G|||||2013|,G|downstream_gene_variant|MODIFIER|yegH|PA14_47040|transcript|ABJ10519.1|protein_coding||c.*4267C>G|||||4267|,G|downstream_gene_variant|MODIFIER|PA14_47080|PA14_47080|transcript|ABJ10516.1|protein_coding||c.*2002C>G|||||2002|,G|downstream_gene_variant|MODIFIER|ilvA2|PA14_47100|transcript|ABJ10514.1|protein_coding||c.*17G>C|||||17|,G|downstream_gene_variant|MODIFIER|yybH|PA14_47110|transcript|ABJ10513.1|protein_coding||c.*1561G>C|||||1561|,G|downstream_gene_variant|MODIFIER|PA14_47120|PA14_47120|transcript|ABJ10512.1|protein_coding||c.*2234G>C|||||2234|,G|downstream_gene_variant|MODIFIER|PA14_47130|PA14_47130|transcript|ABJ10511.1|protein_coding||c.*2806G>C|||||2806|,G|downstream_gene_variant|MODIFIER|pfuA|PA14_47140|transcript|ABJ10510.1|protein_coding||c.*3267G>C|||||3267|,G|intergenic_region|MODIFIER|PA14_47090-ilvA2|PA14_47090-PA14_47100|intergenic_region|PA14_47090-PA14_47100|||n.4196002C>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:192:0:0:0,-17.59 0:13:13,0:13:398:0:0:0,-36.1036 0:10:10,2:8:299:2:4:0,-26.8805 0:22:22,0:22:733:0:0:0,-66.257 +Chromosome 4202451 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=29;DPB=29;DPRA=1.14286;EPP=7.35324;EPPR=5.02092;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=53.4521;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=995;RO=27;RPL=2;RPP=7.35324;RPPR=3.09072;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=18;SRP=9.52472;SRR=9;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|cyoE|PA14_47150|transcript|ABJ10509.1|protein_coding|1/1|c.146T>G|p.Val49Gly|146/891|146/891|49/296||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ilvA2|PA14_47100|transcript|ABJ10514.1|protein_coding||c.-4885T>G|||||4885|,C|upstream_gene_variant|MODIFIER|yybH|PA14_47110|transcript|ABJ10513.1|protein_coding||c.-4481T>G|||||4481|,C|upstream_gene_variant|MODIFIER|PA14_47120|PA14_47120|transcript|ABJ10512.1|protein_coding||c.-3703T>G|||||3703|,C|upstream_gene_variant|MODIFIER|PA14_47130|PA14_47130|transcript|ABJ10511.1|protein_coding||c.-3311T>G|||||3311|,C|upstream_gene_variant|MODIFIER|pfuA|PA14_47140|transcript|ABJ10510.1|protein_coding||c.-984T>G|||||984|,C|downstream_gene_variant|MODIFIER|P9|EBG00001225109|transcript|EBT00001793442.1|lincRNA||n.*4363A>C|||||4363|,C|downstream_gene_variant|MODIFIER|cyoD|PA14_47160|transcript|ABJ10508.1|protein_coding||c.*156T>G|||||156|,C|downstream_gene_variant|MODIFIER|cyoC|PA14_47180|transcript|ABJ10507.1|protein_coding||c.*491T>G|||||491|,C|downstream_gene_variant|MODIFIER|cyoB|PA14_47190|transcript|ABJ10506.1|protein_coding||c.*1124T>G|||||1124|,C|downstream_gene_variant|MODIFIER|cyoA|PA14_47210|transcript|ABJ10505.1|protein_coding||c.*3107T>G|||||3107|,C|downstream_gene_variant|MODIFIER|PA14_47230|PA14_47230|transcript|ABJ10504.1|protein_coding||c.*4729T>G|||||4729| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,2:6:188:2:4:0,-16.8381 0:5:5,0:5:193:0:0:0,-17.7405 0:9:9,0:9:340:0:0:0,-30.9516 0:7:7,0:7:274:0:0:0,-25.0282 +Chromosome 4210481 . G C 1.26803E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=23;DPB=23;DPRA=1.05882;EPP=7.35324;EPPR=5.59539;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=46.8281;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=760;RO=21;RPL=2;RPP=7.35324;RPPR=8.07707;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=10;SRP=3.1137;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_47260|PA14_47260|transcript|ABJ10501.1|protein_coding|1/1|c.779C>G|p.Thr260Arg|779/1359|779/1359|260/452||,C|upstream_gene_variant|MODIFIER|cyoB|PA14_47190|transcript|ABJ10506.1|protein_coding||c.-4930C>G|||||4930|,C|upstream_gene_variant|MODIFIER|cyoA|PA14_47210|transcript|ABJ10505.1|protein_coding||c.-3928C>G|||||3928|,C|upstream_gene_variant|MODIFIER|PA14_47230|PA14_47230|transcript|ABJ10504.1|protein_coding||c.-1760C>G|||||1760|,C|upstream_gene_variant|MODIFIER|PA14_47250|PA14_47250|transcript|ABJ10502.1|protein_coding||c.-594C>G|||||594|,C|upstream_gene_variant|MODIFIER|PA14_47270|PA14_47270|transcript|ABJ10500.1|protein_coding||c.-886G>C|||||886|,C|upstream_gene_variant|MODIFIER|phnR|PA14_47310|transcript|ABJ10497.1|protein_coding||c.-3994G>C|||||3994|,C|downstream_gene_variant|MODIFIER|PA14_47240|PA14_47240|transcript|ABJ10503.1|protein_coding||c.*988G>C|||||988|,C|downstream_gene_variant|MODIFIER|phnX|PA14_47280|transcript|ABJ10499.1|protein_coding||c.*1848C>G|||||1848|,C|downstream_gene_variant|MODIFIER|phnW|PA14_47300|transcript|ABJ10498.1|protein_coding||c.*2711C>G|||||2711|,C|downstream_gene_variant|MODIFIER|PA14_47320|PA14_47320|transcript|ABJ10496.1|protein_coding||c.*4864C>G|||||4864| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:222:0:0:0,-20.3362 0:6:6,0:6:194:0:0:0,-17.7681 0:5:5,0:5:186:0:0:0,-17.0967 0:6:6,2:4:158:2:4:0,-14.2207 +Chromosome 4213211 . A G 1.55973E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=37;DPB=37;DPRA=0.580645;EPP=7.35324;EPPR=6.05036;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=44.9163;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=1289;RO=35;RPL=0;RPP=7.35324;RPPR=10.5174;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=22;SRP=8.03571;SRR=13;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|phnW|PA14_47300|transcript|ABJ10498.1|protein_coding|1/1|c.1097T>C|p.Leu366Pro|1097/1116|1097/1116|366/371||,G|upstream_gene_variant|MODIFIER|PA14_47230|PA14_47230|transcript|ABJ10504.1|protein_coding||c.-4490T>C|||||4490|,G|upstream_gene_variant|MODIFIER|PA14_47250|PA14_47250|transcript|ABJ10502.1|protein_coding||c.-3324T>C|||||3324|,G|upstream_gene_variant|MODIFIER|PA14_47260|PA14_47260|transcript|ABJ10501.1|protein_coding||c.-1952T>C|||||1952|,G|upstream_gene_variant|MODIFIER|phnX|PA14_47280|transcript|ABJ10499.1|protein_coding||c.-55T>C|||||55|,G|upstream_gene_variant|MODIFIER|phnR|PA14_47310|transcript|ABJ10497.1|protein_coding||c.-1264A>G|||||1264|,G|upstream_gene_variant|MODIFIER|PA14_47360|PA14_47360|transcript|ABJ10492.1|protein_coding||c.-4609A>G|||||4609|,G|downstream_gene_variant|MODIFIER|PA14_47240|PA14_47240|transcript|ABJ10503.1|protein_coding||c.*3718A>G|||||3718|,G|downstream_gene_variant|MODIFIER|PA14_47270|PA14_47270|transcript|ABJ10500.1|protein_coding||c.*933A>G|||||933|,G|downstream_gene_variant|MODIFIER|PA14_47320|PA14_47320|transcript|ABJ10496.1|protein_coding||c.*2134T>C|||||2134|,G|downstream_gene_variant|MODIFIER|yafJ|PA14_47330|transcript|ABJ10495.1|protein_coding||c.*2685T>C|||||2685|,G|downstream_gene_variant|MODIFIER|PA14_47340|PA14_47340|transcript|ABJ10494.1|protein_coding||c.*3462T>C|||||3462|,G|downstream_gene_variant|MODIFIER|PA14_47350|PA14_47350|transcript|ABJ10493.1|protein_coding||c.*3987T>C|||||3987| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:219:0:0:0,-20.0617 0:6:6,2:4:149:2:16:0,-12.2522 0:11:11,0:11:417:0:0:0,-37.8789 0:14:14,0:14:504:0:0:0,-45.6862 +Chromosome 4225244 . A G 7.45871E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=7;CIGAR=1X;DP=59;DPB=59;DPRA=0;EPP=18.2106;EPPR=4.51363;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=87.3966;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1792;RO=52;RPL=0;RPP=18.2106;RPPR=5.68288;RPR=7;RUN=1;SAF=0;SAP=18.2106;SAR=7;SRF=27;SRP=3.17734;SRR=25;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|ycgN|PA14_47410|transcript|ABJ10487.1|protein_coding|1/1|c.41T>C|p.Leu14Pro|41/450|41/450|14/149||,G|upstream_gene_variant|MODIFIER|hxuC|PA14_47380|transcript|ABJ10490.1|protein_coding||c.-2195T>C|||||2195|,G|upstream_gene_variant|MODIFIER|PA14_47390|PA14_47390|transcript|ABJ10489.1|protein_coding||c.-1083T>C|||||1083|,G|upstream_gene_variant|MODIFIER|PA14_47400|PA14_47400|transcript|ABJ10488.1|protein_coding||c.-559T>C|||||559|,G|upstream_gene_variant|MODIFIER|czcD|PA14_47430|transcript|ABJ10485.1|protein_coding||c.-460A>G|||||460|,G|upstream_gene_variant|MODIFIER|PA14_47490|PA14_47490|transcript|ABJ10481.1|protein_coding||c.-4164A>G|||||4164|,G|downstream_gene_variant|MODIFIER|PA14_47370|PA14_47370|transcript|ABJ10491.1|protein_coding||c.*4757A>G|||||4757|,G|downstream_gene_variant|MODIFIER|PA14_47420|PA14_47420|transcript|ABJ10486.1|protein_coding||c.*117T>C|||||117|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_47440|PA14_47440|transcript|ABJ10484.1|protein_coding||c.*1422T>C|||||1422|,G|downstream_gene_variant|MODIFIER|ycgL|PA14_47450|transcript|ABJ10483.1|protein_coding||c.*2609T>C|||||2609|,G|downstream_gene_variant|MODIFIER|rnd|PA14_47460|transcript|ABJ10482.1|protein_coding||c.*2899T>C|||||2899|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:14:14,1:13:494:1:13:0,-43.5029 0:12:12,1:11:331:1:2:0,-29.8736 0:14:14,1:13:476:1:15:0,-41.6705 0:19:19,4:15:491:4:46:0,-40.2335 +Chromosome 4239719 . G C 3.24672E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=27;DPB=27;DPRA=2.78571;EPP=9.52472;EPPR=3.37221;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.4583;NS=4;NUMALT=1;ODDS=32.8309;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=624;RO=24;RPL=0;RPP=9.52472;RPPR=6.26751;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=16;SRP=8.80089;SRR=8;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_47600|PA14_47600|transcript|ABJ10472.1|protein_coding|1/1|c.1723G>C|p.Ala575Pro|1723/1821|1723/1821|575/606||,C|upstream_gene_variant|MODIFIER|PA14_47550|PA14_47550|transcript|ABJ10475.1|protein_coding||c.-3740C>G|||||3740|,C|upstream_gene_variant|MODIFIER|PA14_47560|PA14_47560|transcript|ABJ10474.1|protein_coding||c.-2376C>G|||||2376|,C|upstream_gene_variant|MODIFIER|PA14_47580|PA14_47580|transcript|ABJ10473.1|protein_coding||c.-1853C>G|||||1853|,C|upstream_gene_variant|MODIFIER|PA14_47640|PA14_47640|transcript|ABJ10470.1|protein_coding||c.-808G>C|||||808|,C|downstream_gene_variant|MODIFIER|ompP1|PA14_47540|transcript|ABJ10476.1|protein_coding||c.*4349G>C|||||4349|,C|downstream_gene_variant|MODIFIER|PA14_47610|PA14_47610|transcript|ABJ10471.1|protein_coding||c.*129C>G|||||129|,C|downstream_gene_variant|MODIFIER|cobV|PA14_47650|transcript|ABJ10469.1|protein_coding||c.*2276C>G|||||2276|,C|downstream_gene_variant|MODIFIER|cobC|PA14_47660|transcript|ABJ10468.1|protein_coding||c.*3016C>G|||||3016|,C|downstream_gene_variant|MODIFIER|cobU|PA14_47670|transcript|ABJ10467.1|protein_coding||c.*3597C>G|||||3597|,C|downstream_gene_variant|MODIFIER|cobP|PA14_47680|transcript|ABJ10466.1|protein_coding||c.*4649C>G|||||4649| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:196:0:0:0,-18.0152 0:4:4,0:4:120:0:0:0,-11.0896 0:5:5,0:5:94:0:0:0,-8.64388 0:13:13,3:10:214:3:6:0,-18.8999 +Chromosome 4240663 . T C 5.57556E-12 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=30;DPB=30;DPRA=0.461538;EPP=7.35324;EPPR=28.1373;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=27.3817;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=1055;RO=28;RPL=2;RPP=7.35324;RPPR=47.6806;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=40.5458;SRR=25;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_47640|PA14_47640|transcript|ABJ10470.1|protein_coding|1/1|c.137T>C|p.Leu46Pro|137/1506|137/1506|46/501||,C|upstream_gene_variant|MODIFIER|PA14_47550|PA14_47550|transcript|ABJ10475.1|protein_coding||c.-4684A>G|||||4684|,C|upstream_gene_variant|MODIFIER|PA14_47560|PA14_47560|transcript|ABJ10474.1|protein_coding||c.-3320A>G|||||3320|,C|upstream_gene_variant|MODIFIER|PA14_47580|PA14_47580|transcript|ABJ10473.1|protein_coding||c.-2797A>G|||||2797|,C|upstream_gene_variant|MODIFIER|PA14_47610|PA14_47610|transcript|ABJ10471.1|protein_coding||c.-255A>G|||||255|,C|downstream_gene_variant|MODIFIER|PA14_47600|PA14_47600|transcript|ABJ10472.1|protein_coding||c.*846T>C|||||846|,C|downstream_gene_variant|MODIFIER|cobV|PA14_47650|transcript|ABJ10469.1|protein_coding||c.*1332A>G|||||1332|,C|downstream_gene_variant|MODIFIER|cobC|PA14_47660|transcript|ABJ10468.1|protein_coding||c.*2072A>G|||||2072|,C|downstream_gene_variant|MODIFIER|cobU|PA14_47670|transcript|ABJ10467.1|protein_coding||c.*2653A>G|||||2653|,C|downstream_gene_variant|MODIFIER|cobP|PA14_47680|transcript|ABJ10466.1|protein_coding||c.*3705A>G|||||3705|,C|downstream_gene_variant|MODIFIER|cobQ|PA14_47690|transcript|ABJ10465.1|protein_coding||c.*4219A>G|||||4219| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,0:10:383:0:0:0,-34.8217 0:6:6,0:6:233:0:0:0,-21.3389 0:4:4,2:2:77:2:30:0,-4.45886 0:10:10,0:10:362:0:0:0,-32.9111 +Chromosome 4244364 . A G 4.90119E-9 . AB=0;ABP=0;AC=0;AF=0;AN=3;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=1.66667;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=20.616;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=79;QR=279;RO=9;RPL=0;RPP=7.35324;RPPR=9.04217;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=6;SRP=5.18177;SRR=3;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|cobU|PA14_47670|transcript|ABJ10467.1|protein_coding|1/1|c.8T>C|p.Leu3Pro|8/1056|8/1056|3/351||,G|upstream_gene_variant|MODIFIER|PA14_47610|PA14_47610|transcript|ABJ10471.1|protein_coding||c.-3956T>C|||||3956|,G|upstream_gene_variant|MODIFIER|cobV|PA14_47650|transcript|ABJ10469.1|protein_coding||c.-1632T>C|||||1632|,G|upstream_gene_variant|MODIFIER|cobC|PA14_47660|transcript|ABJ10468.1|protein_coding||c.-1045T>C|||||1045|,G|downstream_gene_variant|MODIFIER|PA14_47600|PA14_47600|transcript|ABJ10472.1|protein_coding||c.*4547A>G|||||4547|,G|downstream_gene_variant|MODIFIER|PA14_47640|PA14_47640|transcript|ABJ10470.1|protein_coding||c.*2332A>G|||||2332|,G|downstream_gene_variant|MODIFIER|cobP|PA14_47680|transcript|ABJ10466.1|protein_coding||c.*4T>C|||||4|,G|downstream_gene_variant|MODIFIER|cobQ|PA14_47690|transcript|ABJ10465.1|protein_coding||c.*518T>C|||||518|,G|downstream_gene_variant|MODIFIER|cobC|PA14_47720|transcript|ABJ10464.1|protein_coding||c.*1983T>C|||||1983|,G|downstream_gene_variant|MODIFIER|cobD|PA14_47730|transcript|ABJ10463.1|protein_coding||c.*2971T>C|||||2971|,G|downstream_gene_variant|MODIFIER|PA14_47750|PA14_47750|transcript|ABJ10462.1|protein_coding||c.*3906T>C|||||3906|,G|downstream_gene_variant|MODIFIER|cobB|PA14_47760|transcript|ABJ10461.1|protein_coding||c.*4564T>C|||||4564| GT:DP:DPR:RO:QR:AO:QA:GL . 0:3:3,0:3:76:0:0:0,-7.08885 0:3:3,0:3:87:0:0:0,-8.11544 0:5:5,2:3:116:2:79:0,-3.31936 +Chromosome 4252135 . T G 3.56373E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=6;CIGAR=1X;DP=72;DPB=72;DPRA=0.626667;EPP=16.0391;EPPR=25.2514;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=86.7906;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=2359;RO=66;RPL=0;RPP=16.0391;RPPR=3.1419;RPR=6;RUN=1;SAF=0;SAP=16.0391;SAR=6;SRF=16;SRP=41.044;SRR=50;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|btuB|PA14_47800|transcript|ABJ10459.1|protein_coding|1/1|c.658A>C|p.Asn220His|658/1851|658/1851|220/616||,G|upstream_gene_variant|MODIFIER|cobC|PA14_47720|transcript|ABJ10464.1|protein_coding||c.-4793A>C|||||4793|,G|upstream_gene_variant|MODIFIER|cobD|PA14_47730|transcript|ABJ10463.1|protein_coding||c.-3862A>C|||||3862|,G|upstream_gene_variant|MODIFIER|PA14_47750|PA14_47750|transcript|ABJ10462.1|protein_coding||c.-3209A>C|||||3209|,G|upstream_gene_variant|MODIFIER|cobB|PA14_47760|transcript|ABJ10461.1|protein_coding||c.-1900A>C|||||1900|,G|upstream_gene_variant|MODIFIER|cobO|PA14_47790|transcript|ABJ10460.1|protein_coding||c.-1257A>C|||||1257|,G|upstream_gene_variant|MODIFIER|PA14_47820|PA14_47820|transcript|ABJ10457.1|protein_coding||c.-3293T>G|||||3293|,G|upstream_gene_variant|MODIFIER|PA14_47840|PA14_47840|transcript|ABJ10456.1|protein_coding||c.-4078T>G|||||4078|,G|downstream_gene_variant|MODIFIER|PA14_47810|PA14_47810|transcript|ABJ10458.1|protein_coding||c.*1009A>C|||||1009| GT:DP:DPR:RO:QR:AO:QA:GL 0:11:11,3:8:310:3:6:0,-27.7021 0:22:22,1:21:753:1:2:0,-67.8718 0:14:14,2:12:426:2:4:0,-38.2802 0:25:25,0:25:870:0:0:0,-78.5868 +Chromosome 4256151 . A G 1.36666E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=39;DPB=39;DPRA=1.83333;EPP=11.6962;EPPR=8.03571;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=40.4296;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=725;RO=35;RPL=0;RPP=11.6962;RPPR=10.5174;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=3;SRP=55.1877;SRR=32;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|btuB|PA14_47800|transcript|ABJ10459.1|protein_coding||c.-3359T>C|||||3359|,G|upstream_gene_variant|MODIFIER|PA14_47810|PA14_47810|transcript|ABJ10458.1|protein_coding||c.-968T>C|||||968|,G|upstream_gene_variant|MODIFIER|PA14_47840|PA14_47840|transcript|ABJ10456.1|protein_coding||c.-62A>G|||||62|,G|upstream_gene_variant|MODIFIER|PA14_47850|PA14_47850|transcript|ABJ10455.1|protein_coding||c.-1003A>G|||||1003|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_47860|PA14_47860|transcript|ABJ10454.1|protein_coding||c.-2348A>G|||||2348|,G|upstream_gene_variant|MODIFIER|PA14_47880|PA14_47880|transcript|ABJ10452.1|protein_coding||c.-4600A>G|||||4600|,G|downstream_gene_variant|MODIFIER|PA14_47820|PA14_47820|transcript|ABJ10457.1|protein_coding||c.*55A>G|||||55|,G|downstream_gene_variant|MODIFIER|PA14_47870|PA14_47870|transcript|ABJ10453.1|protein_coding||c.*3598T>C|||||3598|,G|intergenic_region|MODIFIER|PA14_47820-PA14_47840|PA14_47820-PA14_47840|intergenic_region|PA14_47820-PA14_47840|||n.4256151A>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,2:8:159:2:4:0,-14.1212 0:6:6,0:6:149:0:0:0,-13.6527 0:12:12,1:11:248:1:11:0,-21.4351 0:11:11,1:10:169:1:12:0,-14.1784 +Chromosome 4264653 . C T 3.43979E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=19;DPB=19;DPRA=1.75;EPP=7.35324;EPPR=3.13803;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=30.1668;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=29;QR=525;RO=17;RPL=0;RPP=7.35324;RPPR=13.3567;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=5;SRP=9.26925;SRR=12;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|PA14_47910|PA14_47910|transcript|ABJ10449.1|protein_coding|1/1|c.150C>T|p.Leu50Leu|150/675|150/675|50/224||,T|upstream_gene_variant|MODIFIER|PA14_47870|PA14_47870|transcript|ABJ10453.1|protein_coding||c.-4002G>A|||||4002|,T|upstream_gene_variant|MODIFIER|PA14_47890|PA14_47890|transcript|ABJ10451.1|protein_coding||c.-1795G>A|||||1795|,T|upstream_gene_variant|MODIFIER|PA14_47920|PA14_47920|transcript|ABJ10448.1|protein_coding||c.-782C>T|||||782|,T|upstream_gene_variant|MODIFIER|PA14_47930|PA14_47930|transcript|ABJ10447.1|protein_coding||c.-1662C>T|||||1662|,T|upstream_gene_variant|MODIFIER|PA14_47940|PA14_47940|transcript|ABJ10446.1|protein_coding||c.-3404C>T|||||3404|,T|upstream_gene_variant|MODIFIER|PA14_47950|PA14_47950|transcript|ABJ10445.1|protein_coding||c.-4080C>T|||||4080|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|glnQ|PA14_47960|transcript|ABJ10444.1|protein_coding||c.-4721C>T|||||4721|,T|downstream_gene_variant|MODIFIER|PA14_47860|PA14_47860|transcript|ABJ10454.1|protein_coding||c.*4901C>T|||||4901|,T|downstream_gene_variant|MODIFIER|PA14_47880|PA14_47880|transcript|ABJ10452.1|protein_coding||c.*3036C>T|||||3036|,T|downstream_gene_variant|MODIFIER|PA14_47900|PA14_47900|transcript|ABJ10450.1|protein_coding||c.*314C>T|||||314| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:120:0:0:0,-11.1879 0:4:4,0:4:96:0:0:0,-8.8766 0:5:5,0:5:163:0:0:0,-14.987 0:7:7,2:5:146:2:29:0,-10.668 +Chromosome 4265157 . T C 4.70121E-11 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=15;DPB=15;DPRA=1.5;EPP=9.52472;EPPR=5.9056;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=25.9168;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=375;RO=12;RPL=0;RPP=9.52472;RPPR=3.73412;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=5;SRP=3.73412;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|PA14_47910|PA14_47910|transcript|ABJ10449.1|protein_coding|1/1|c.654T>C|p.His218His|654/675|654/675|218/224||,C|upstream_gene_variant|MODIFIER|PA14_47870|PA14_47870|transcript|ABJ10453.1|protein_coding||c.-4506A>G|||||4506|,C|upstream_gene_variant|MODIFIER|PA14_47890|PA14_47890|transcript|ABJ10451.1|protein_coding||c.-2299A>G|||||2299|,C|upstream_gene_variant|MODIFIER|PA14_47920|PA14_47920|transcript|ABJ10448.1|protein_coding||c.-278T>C|||||278|,C|upstream_gene_variant|MODIFIER|PA14_47930|PA14_47930|transcript|ABJ10447.1|protein_coding||c.-1158T>C|||||1158|,C|upstream_gene_variant|MODIFIER|PA14_47940|PA14_47940|transcript|ABJ10446.1|protein_coding||c.-2900T>C|||||2900|,C|upstream_gene_variant|MODIFIER|PA14_47950|PA14_47950|transcript|ABJ10445.1|protein_coding||c.-3576T>C|||||3576|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|glnQ|PA14_47960|transcript|ABJ10444.1|protein_coding||c.-4217T>C|||||4217|,C|upstream_gene_variant|MODIFIER|PA14_47970|PA14_47970|transcript|ABJ10443.1|protein_coding||c.-4965T>C|||||4965|,C|downstream_gene_variant|MODIFIER|PA14_47880|PA14_47880|transcript|ABJ10452.1|protein_coding||c.*3540T>C|||||3540|,C|downstream_gene_variant|MODIFIER|PA14_47900|PA14_47900|transcript|ABJ10450.1|protein_coding||c.*818T>C|||||818| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:65:0:0:0,-6.1722 0:5:5,3:2:74:3:6:0,-6.46543 0:5:5,0:5:161:0:0:0,-14.7969 0:3:3,0:3:75:0:0:0,-6.99617 +Chromosome 4287049 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=6;CIGAR=1X;DP=55;DPB=55;DPRA=1.5;EPP=16.0391;EPPR=45.5977;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=51.5119;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=89;QR=1358;RO=49;RPL=6;RPP=16.0391;RPPR=22.5536;RPR=0;RUN=1;SAF=6;SAP=16.0391;SAR=0;SRF=34;SRP=19.0083;SRR=15;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_48160|PA14_48160|transcript|ABJ10432.1|protein_coding|1/1|c.278T>C|p.Leu93Pro|278/2577|278/2577|93/858||,C|upstream_gene_variant|MODIFIER|aprE|PA14_48100|transcript|ABJ10435.1|protein_coding||c.-4979A>G|||||4979|,C|upstream_gene_variant|MODIFIER|aprD|PA14_48115|transcript|ABJ15657.1|protein_coding||c.-3201A>G|||||3201|,C|upstream_gene_variant|MODIFIER|aprX|PA14_48140|transcript|ABJ10434.1|protein_coding||c.-1870A>G|||||1870|,C|upstream_gene_variant|MODIFIER|C4|EBG00001225163|transcript|EBT00001793387.1|antisense||n.-881A>G|||||881|,C|upstream_gene_variant|MODIFIER|PA14_48200|PA14_48200|transcript|ABJ10429.1|protein_coding||c.-4899T>C|||||4899|,C|downstream_gene_variant|MODIFIER|PA14_48150|PA14_48150|transcript|ABJ10433.1|protein_coding||c.*513T>C|||||513|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_48170|PA14_48170|transcript|ABJ10431.1|protein_coding||c.*2322A>G|||||2322|,C|downstream_gene_variant|MODIFIER|PA14_48190|PA14_48190|transcript|ABJ10430.1|protein_coding||c.*4174A>G|||||4174|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,0:10:291:0:0:0,-26.466 0:18:18,1:17:431:1:13:0,-37.7292 0:16:16,2:14:423:2:26:0,-35.883 0:11:11,3:8:213:3:50:0,-14.7588 +Chromosome 4287073 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=50;DPB=50;DPRA=1.54545;EPP=11.6962;EPPR=18.305;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=57.7627;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1233;RO=46;RPL=4;RPP=11.6962;RPPR=3.76559;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=27;SRP=6.03148;SRR=19;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_48160|PA14_48160|transcript|ABJ10432.1|protein_coding|1/1|c.302G>T|p.Trp101Leu|302/2577|302/2577|101/858||,T|upstream_gene_variant|MODIFIER|aprD|PA14_48115|transcript|ABJ15657.1|protein_coding||c.-3225C>A|||||3225|,T|upstream_gene_variant|MODIFIER|aprX|PA14_48140|transcript|ABJ10434.1|protein_coding||c.-1894C>A|||||1894|,T|upstream_gene_variant|MODIFIER|C4|EBG00001225163|transcript|EBT00001793387.1|antisense||n.-905C>A|||||905|,T|upstream_gene_variant|MODIFIER|PA14_48200|PA14_48200|transcript|ABJ10429.1|protein_coding||c.-4875G>T|||||4875|,T|downstream_gene_variant|MODIFIER|PA14_48150|PA14_48150|transcript|ABJ10433.1|protein_coding||c.*537G>T|||||537|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|PA14_48170|PA14_48170|transcript|ABJ10431.1|protein_coding||c.*2298C>A|||||2298|,T|downstream_gene_variant|MODIFIER|PA14_48190|PA14_48190|transcript|ABJ10430.1|protein_coding||c.*4150C>A|||||4150|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:190:0:0:0,-17.3562 0:17:17,4:13:326:4:8:0,-28.8314 0:13:13,0:13:326:0:0:0,-29.5663 0:13:13,0:13:391:0:0:0,-35.4589 +Chromosome 4318015 . C G 8.10236E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=17;DPB=17;DPRA=2.4;EPP=9.52472;EPPR=8.59409;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=20.1005;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=357;RO=14;RPL=0;RPP=9.52472;RPPR=5.49198;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=9;SRP=5.49198;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_48560|PA14_48560|transcript|ABJ10402.1|protein_coding|1/1|c.68C>G|p.Ala23Gly|68/879|68/879|23/292||,G|upstream_gene_variant|MODIFIER|PA14_48570|PA14_48570|transcript|ABJ10401.1|protein_coding||c.-808C>G|||||808|,G|upstream_gene_variant|MODIFIER|PA14_48590|PA14_48590|transcript|ABJ10400.1|protein_coding||c.-2172C>G|||||2172|,G|upstream_gene_variant|MODIFIER|PA14_48600|PA14_48600|transcript|ABJ10399.1|protein_coding||c.-3120C>G|||||3120|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_48610|PA14_48610|transcript|ABJ10398.1|protein_coding||c.-4406C>G|||||4406|,G|downstream_gene_variant|MODIFIER|mltA|PA14_48520|transcript|ABJ10406.1|protein_coding||c.*4471C>G|||||4471|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_48530|PA14_48530|transcript|ABJ10405.1|protein_coding||c.*1931C>G|||||1931|,G|downstream_gene_variant|MODIFIER|PA14_48540|PA14_48540|transcript|ABJ10404.1|protein_coding||c.*672C>G|||||672|,G|downstream_gene_variant|MODIFIER|PA14_48550|PA14_48550|transcript|ABJ10403.1|protein_coding||c.*64C>G|||||64| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:41:0:0:0,-3.89174 0:7:7,1:6:139:1:2:0,-12.5357 0:3:3,0:3:75:0:0:0,-6.99851 0:5:5,2:3:102:2:4:0,-9.13498 +Chromosome 4322632 . A G 6.97663E-8 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=2.5;EPP=7.35324;EPPR=9.04217;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=17.9545;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=55;QR=304;RO=9;RPL=0;RPP=7.35324;RPPR=9.04217;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=7;SRP=9.04217;SRR=2;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_48610|PA14_48610|transcript|ABJ10398.1|protein_coding|1/1|c.212A>G|p.Glu71Gly|212/1599|212/1599|71/532||,G|upstream_gene_variant|MODIFIER|PA14_48620|PA14_48620|transcript|ABJ10397.1|protein_coding||c.-1384A>G|||||1384|,G|upstream_gene_variant|MODIFIER|PA14_48630|PA14_48630|transcript|ABJ10396.1|protein_coding||c.-2340A>G|||||2340|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_48640|PA14_48640|transcript|ABJ10395.1|protein_coding||c.-3566A>G|||||3566|,G|upstream_gene_variant|MODIFIER|yhhW|PA14_48650|transcript|ABJ10394.1|protein_coding||c.-4319A>G|||||4319|,G|downstream_gene_variant|MODIFIER|PA14_48550|PA14_48550|transcript|ABJ10403.1|protein_coding||c.*4681A>G|||||4681|,G|downstream_gene_variant|MODIFIER|PA14_48560|PA14_48560|transcript|ABJ10402.1|protein_coding||c.*3806A>G|||||3806|,G|downstream_gene_variant|MODIFIER|PA14_48570|PA14_48570|transcript|ABJ10401.1|protein_coding||c.*2442A>G|||||2442|,G|downstream_gene_variant|MODIFIER|PA14_48590|PA14_48590|transcript|ABJ10400.1|protein_coding||c.*1699A>G|||||1699|,G|downstream_gene_variant|MODIFIER|PA14_48600|PA14_48600|transcript|ABJ10399.1|protein_coding||c.*211A>G|||||211|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:74:0:0:0,-7.02543 0:1:1,0:1:39:0:0:0,-3.89656 0:3:3,0:3:80:0:0:0,-7.46487 0:5:5,2:3:111:2:55:0,-5.13054 +Chromosome 4331121 . T C 2.37601E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=20;DPB=20;DPRA=1;EPP=9.52472;EPPR=13.3567;GTI=0;LEN=1;MEANALT=1;MQM=55.6667;MQMR=59.0588;NS=4;NUMALT=1;ODDS=21.3264;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=439;RO=17;RPL=2;RPP=3.73412;RPPR=3.13803;RPR=1;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=10;SRP=4.1599;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|kefB|PA14_48700|transcript|ABJ10391.1|protein_coding|1/1|c.1169A>G|p.Glu390Gly|1169/1842|1169/1842|390/613||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_48680|PA14_48680|transcript|ABJ10392.1|protein_coding||c.-840A>G|||||840|,C|upstream_gene_variant|MODIFIER|PA14_48770|PA14_48770|transcript|ABJ10385.1|protein_coding||c.-4832T>C|||||4832|,C|downstream_gene_variant|MODIFIER|PA14_48630|PA14_48630|transcript|ABJ10396.1|protein_coding||c.*4920T>C|||||4920|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_48640|PA14_48640|transcript|ABJ10395.1|protein_coding||c.*4288T>C|||||4288|,C|downstream_gene_variant|MODIFIER|yhhW|PA14_48650|transcript|ABJ10394.1|protein_coding||c.*3472T>C|||||3472|,C|downstream_gene_variant|MODIFIER|PA14_48660|PA14_48660|transcript|ABJ10393.1|protein_coding||c.*2356T>C|||||2356|,C|downstream_gene_variant|MODIFIER|PA14_48710|PA14_48710|transcript|ABJ10390.1|protein_coding||c.*1171A>G|||||1171|,C|downstream_gene_variant|MODIFIER|PA14_48730|PA14_48730|transcript|ABJ10389.1|protein_coding||c.*1804A>G|||||1804|,C|downstream_gene_variant|MODIFIER|yieF|PA14_48740|transcript|ABJ10388.1|protein_coding||c.*2778A>G|||||2778|,C|downstream_gene_variant|MODIFIER|PA14_48750|PA14_48750|transcript|ABJ10387.1|protein_coding||c.*3364A>G|||||3364|,C|downstream_gene_variant|MODIFIER|ycaC|PA14_48760|transcript|ABJ10386.1|protein_coding||c.*3914A>G|||||3914| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,1:2:42:1:2:0,-3.7859 0:5:5,0:5:129:0:0:0,-11.8607 0:5:5,0:5:99:0:0:0,-9.10588 0:7:7,2:5:169:2:16:0,-14.0192 +Chromosome 4336382 . A T 1.45049E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=49;DPB=49;DPRA=0.814815;EPP=9.52472;EPPR=7.73089;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=64.5694;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=1220;RO=46;RPL=0;RPP=9.52472;RPPR=4.70971;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=18;SRP=7.73089;SRR=28;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_48770|PA14_48770|transcript|ABJ10385.1|protein_coding|1/1|c.430A>T|p.Ile144Phe|430/915|430/915|144/304||,T|upstream_gene_variant|MODIFIER|kefB|PA14_48700|transcript|ABJ10391.1|protein_coding||c.-4093T>A|||||4093|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|PA14_48710|PA14_48710|transcript|ABJ10390.1|protein_coding||c.-3617T>A|||||3617|,T|upstream_gene_variant|MODIFIER|PA14_48730|PA14_48730|transcript|ABJ10389.1|protein_coding||c.-2510T>A|||||2510|,T|upstream_gene_variant|MODIFIER|yieF|PA14_48740|transcript|ABJ10388.1|protein_coding||c.-1926T>A|||||1926|,T|upstream_gene_variant|MODIFIER|PA14_48750|PA14_48750|transcript|ABJ10387.1|protein_coding||c.-1490T>A|||||1490|,T|upstream_gene_variant|MODIFIER|ycaC|PA14_48760|transcript|ABJ10386.1|protein_coding||c.-730T>A|||||730|,T|upstream_gene_variant|MODIFIER|PA14_48840|PA14_48840|transcript|ABJ10379.1|protein_coding||c.-4868A>T|||||4868|,T|downstream_gene_variant|MODIFIER|PA14_48780|PA14_48780|transcript|ABJ10384.1|protein_coding||c.*493T>A|||||493|,T|downstream_gene_variant|MODIFIER|PA14_48790|PA14_48790|transcript|ABJ10383.1|protein_coding||c.*1175T>A|||||1175|,T|downstream_gene_variant|MODIFIER|PA14_48800|PA14_48800|transcript|ABJ10382.1|protein_coding||c.*1791T>A|||||1791|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|PA14_48810|PA14_48810|transcript|ABJ10381.1|protein_coding||c.*2474T>A|||||2474|,T|downstream_gene_variant|MODIFIER|PA14_48830|PA14_48830|transcript|ABJ10380.1|protein_coding||c.*3257T>A|||||3257| GT:DP:DPR:RO:QR:AO:QA:GL 0:11:11,0:11:302:0:0:0,-27.4367 0:9:9,2:7:224:2:4:0,-20.0844 0:13:13,1:12:300:1:2:0,-27.0367 0:16:16,0:16:394:0:0:0,-35.688 +Chromosome 4338959 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=9;CIGAR=1X;DP=68;DPB=68;DPRA=1.08333;EPP=22.5536;EPPR=26.0132;GTI=0;LEN=1;MEANALT=1;MQM=53.2222;MQMR=59.661;NS=4;NUMALT=1;ODDS=83.5496;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=53;QR=1614;RO=59;RPL=3;RPP=5.18177;RPPR=11.2913;RPR=6;RUN=1;SAF=3;SAP=5.18177;SAR=6;SRF=44;SRP=33.963;SRR=15;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_48810|PA14_48810|transcript|ABJ10381.1|protein_coding|1/1|c.668A>G|p.Glu223Gly|668/771|668/771|223/256||,C|upstream_gene_variant|MODIFIER|yieF|PA14_48740|transcript|ABJ10388.1|protein_coding||c.-4503A>G|||||4503|,C|upstream_gene_variant|MODIFIER|PA14_48750|PA14_48750|transcript|ABJ10387.1|protein_coding||c.-4067A>G|||||4067|,C|upstream_gene_variant|MODIFIER|ycaC|PA14_48760|transcript|ABJ10386.1|protein_coding||c.-3307A>G|||||3307|,C|upstream_gene_variant|MODIFIER|PA14_48780|PA14_48780|transcript|ABJ10384.1|protein_coding||c.-1422A>G|||||1422|,C|upstream_gene_variant|MODIFIER|PA14_48790|PA14_48790|transcript|ABJ10383.1|protein_coding||c.-869A>G|||||869|,C|upstream_gene_variant|MODIFIER|PA14_48800|PA14_48800|transcript|ABJ10382.1|protein_coding||c.-169A>G|||||169|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_48840|PA14_48840|transcript|ABJ10379.1|protein_coding||c.-2291T>C|||||2291|,C|upstream_gene_variant|MODIFIER|PA14_48850|PA14_48850|transcript|ABJ10378.1|protein_coding||c.-3160T>C|||||3160|,C|downstream_gene_variant|MODIFIER|PA14_48770|PA14_48770|transcript|ABJ10385.1|protein_coding||c.*2092T>C|||||2092|,C|downstream_gene_variant|MODIFIER|PA14_48830|PA14_48830|transcript|ABJ10380.1|protein_coding||c.*680A>G|||||680|,C|downstream_gene_variant|MODIFIER|PA14_48860|PA14_48860|transcript|ABJ10377.1|protein_coding||c.*4580A>G|||||4580| GT:DP:DPR:RO:QR:AO:QA:GL 0:17:17,1:16:493:1:15:0,-43.1504 0:14:14,1:13:395:1:2:0,-35.6285 0:16:16,0:16:326:0:0:0,-29.5321 0:21:21,7:14:400:7:36:0,-32.9729 +Chromosome 4340336 . A G 8.57018E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=33;DPB=33;DPRA=0.941176;EPP=9.52472;EPPR=13.4334;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=39.4855;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=1047;RO=30;RPL=0;RPP=9.52472;RPPR=3.29983;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=19;SRP=7.64277;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_48830|PA14_48830|transcript|ABJ10380.1|protein_coding|1/1|c.704T>C|p.Leu235Pro|704/1401|704/1401|235/466||,G|upstream_gene_variant|MODIFIER|ycaC|PA14_48760|transcript|ABJ10386.1|protein_coding||c.-4684T>C|||||4684|,G|upstream_gene_variant|MODIFIER|PA14_48780|PA14_48780|transcript|ABJ10384.1|protein_coding||c.-2799T>C|||||2799|,G|upstream_gene_variant|MODIFIER|PA14_48790|PA14_48790|transcript|ABJ10383.1|protein_coding||c.-2246T>C|||||2246|,G|upstream_gene_variant|MODIFIER|PA14_48800|PA14_48800|transcript|ABJ10382.1|protein_coding||c.-1546T>C|||||1546|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_48810|PA14_48810|transcript|ABJ10381.1|protein_coding||c.-710T>C|||||710|,G|upstream_gene_variant|MODIFIER|PA14_48840|PA14_48840|transcript|ABJ10379.1|protein_coding||c.-914A>G|||||914|,G|upstream_gene_variant|MODIFIER|PA14_48850|PA14_48850|transcript|ABJ10378.1|protein_coding||c.-1783A>G|||||1783|,G|downstream_gene_variant|MODIFIER|PA14_48770|PA14_48770|transcript|ABJ10385.1|protein_coding||c.*3469A>G|||||3469|,G|downstream_gene_variant|MODIFIER|PA14_48860|PA14_48860|transcript|ABJ10377.1|protein_coding||c.*3203T>C|||||3203|,G|downstream_gene_variant|MODIFIER|ydaO|PA14_48870|transcript|ABJ10376.1|protein_coding||c.*3921T>C|||||3921|,G|downstream_gene_variant|MODIFIER|intT|PA14_48880|transcript|ABJ10375.1|protein_coding||c.*4851T>C|||||4851| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,2:3:114:2:4:0,-10.2515 0:6:6,0:6:215:0:0:0,-19.6957 0:11:11,0:11:384:0:0:0,-34.8803 0:11:11,1:10:334:1:2:0,-30.1705 +Chromosome 4346955 . A C 8.5909E-16 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=13;CIGAR=1X;DP=91;DPB=91;DPRA=0.88;EPP=31.2394;EPPR=37.5565;GTI=0;LEN=1;MEANALT=1.33333;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=113.427;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=26;QR=2364;RO=77;RPL=13;RPP=31.2394;RPPR=6.42261;RPR=0;RUN=1;SAF=13;SAP=31.2394;SAR=0;SRF=39;SRP=3.0385;SRR=38;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_48890|PA14_48890|transcript|ABJ10374.1|protein_coding|1/1|c.547T>G|p.Cys183Gly|547/1299|547/1299|183/432||,C|upstream_gene_variant|MODIFIER|PA14_48860|PA14_48860|transcript|ABJ10377.1|protein_coding||c.-2745T>G|||||2745|,C|upstream_gene_variant|MODIFIER|ydaO|PA14_48870|transcript|ABJ10376.1|protein_coding||c.-1874T>G|||||1874|,C|upstream_gene_variant|MODIFIER|intT|PA14_48880|transcript|ABJ10375.1|protein_coding||c.-752T>G|||||752|,C|downstream_gene_variant|MODIFIER|PA14_48840|PA14_48840|transcript|ABJ10379.1|protein_coding||c.*4941A>C|||||4941|,C|downstream_gene_variant|MODIFIER|PA14_48850|PA14_48850|transcript|ABJ10378.1|protein_coding||c.*3418A>C|||||3418|,C|downstream_gene_variant|MODIFIER|PA14_48900|PA14_48900|transcript|ABJ10373.1|protein_coding||c.*677T>G|||||677|,C|downstream_gene_variant|MODIFIER|PA14_48910|PA14_48910|transcript|ABJ10372.1|protein_coding||c.*775T>G|||||775|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_48920|PA14_48920|transcript|ABJ10371.1|protein_coding||c.*2062T>G|||||2062|,C|downstream_gene_variant|MODIFIER|PA14_48930|PA14_48930|transcript|ABJ10370.1|protein_coding||c.*2423T>G|||||2423|,C|downstream_gene_variant|MODIFIER|coaB|PA14_48940|transcript|ABJ10369.1|protein_coding||c.*3896T>G|||||3896|,C|downstream_gene_variant|MODIFIER|PA14_48950|PA14_48950|transcript|ABJ10368.1|protein_coding||c.*4157T>G|||||4157|,C|downstream_gene_variant|MODIFIER|PA14_48960|PA14_48960|transcript|ABJ10367.1|protein_coding||c.*4421T>G|||||4421|,C|downstream_gene_variant|MODIFIER|PA14_48970|PA14_48970|transcript|ABJ10366.1|protein_coding||c.*4530T>G|||||4530| GT:DP:DPR:RO:QR:AO:QA:GL 0:21:21,6:15:554:6:12:0,-49.0863 0:19:19,4:14:435:4:8:0,-38.652 0:25:25,0:25:691:0:0:0,-62.4211 0:26:26,3:23:684:3:6:0,-61.2469 +Chromosome 4352220 . A G 1.36814E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=7;CIGAR=1X;DP=81;DPB=81;DPRA=1.59524;EPP=5.80219;EPPR=3.12768;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=82.2831;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=129;QR=2109;RO=74;RPL=2;RPP=5.80219;RPPR=4.88833;RPR=5;RUN=1;SAF=0;SAP=18.2106;SAR=7;SRF=9;SRP=95.0338;SRR=65;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_48980|PA14_48980|transcript|ABJ10365.1|protein_coding|1/1|c.212T>C|p.Leu71Pro|212/378|212/378|71/125||,G|upstream_gene_variant|MODIFIER|PA14_48890|PA14_48890|transcript|ABJ10374.1|protein_coding||c.-4719T>C|||||4719|,G|upstream_gene_variant|MODIFIER|PA14_48900|PA14_48900|transcript|ABJ10373.1|protein_coding||c.-4487T>C|||||4487|,G|upstream_gene_variant|MODIFIER|PA14_48910|PA14_48910|transcript|ABJ10372.1|protein_coding||c.-3207T>C|||||3207|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_48920|PA14_48920|transcript|ABJ10371.1|protein_coding||c.-2847T>C|||||2847|,G|upstream_gene_variant|MODIFIER|PA14_48930|PA14_48930|transcript|ABJ10370.1|protein_coding||c.-1556T>C|||||1556|,G|upstream_gene_variant|MODIFIER|coaB|PA14_48940|transcript|ABJ10369.1|protein_coding||c.-1121T>C|||||1121|,G|upstream_gene_variant|MODIFIER|PA14_48950|PA14_48950|transcript|ABJ10368.1|protein_coding||c.-857T>C|||||857|,G|upstream_gene_variant|MODIFIER|PA14_48960|PA14_48960|transcript|ABJ10367.1|protein_coding||c.-752T>C|||||752|,G|upstream_gene_variant|MODIFIER|PA14_48970|PA14_48970|transcript|ABJ10366.1|protein_coding||c.-301T>C|||||301|,G|upstream_gene_variant|MODIFIER|PA14_49020|PA14_49020|transcript|ABJ10361.1|protein_coding||c.-1067A>G|||||1067|,G|upstream_gene_variant|MODIFIER|PA14_49030|PA14_49030|transcript|ABJ10360.1|protein_coding||c.-1622A>G|||||1622|,G|upstream_gene_variant|MODIFIER|PA14_49040|PA14_49040|transcript|ABJ10359.1|protein_coding||c.-3629A>G|||||3629|,G|upstream_gene_variant|MODIFIER|yohC|PA14_49050|transcript|ABJ10358.1|protein_coding||c.-4381A>G|||||4381|,G|downstream_gene_variant|MODIFIER|PA14_48990|PA14_48990|transcript|ABJ10364.1|protein_coding||c.*215T>C|||||215|,G|downstream_gene_variant|MODIFIER|PA14_49000|PA14_49000|transcript|ABJ10363.1|protein_coding||c.*509T>C|||||509|,G|downstream_gene_variant|MODIFIER|PA14_49010|PA14_49010|transcript|ABJ10362.1|protein_coding||c.*724T>C|||||724| GT:DP:DPR:RO:QR:AO:QA:GL 0:14:14,3:11:353:3:50:0,-27.4115 0:14:14,0:14:363:0:0:0,-32.9178 0:24:24,1:23:633:1:13:0,-55.9233 0:29:29,3:26:760:3:66:0,-62.5115 +Chromosome 4379380 . T G 6.66766E-15 . AB=0;ABP=0;AC=0;AF=0;AN=3;AO=3;CIGAR=1X;DP=40;DPB=40;DPRA=0.666667;EPP=9.52472;EPPR=3.5385;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=66.9559;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=1328;RO=37;RPL=0;RPP=9.52472;RPPR=3.5385;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=35;SRP=66.922;SRR=2;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|PA14_49300|PA14_49300|transcript|ABJ10337.1|protein_coding|1/1|c.1953A>C|p.Ala651Ala|1953/2058|1953/2058|651/685||,G|upstream_gene_variant|MODIFIER|PA14_49280|PA14_49280|transcript|ABJ10339.1|protein_coding||c.-1340A>C|||||1340|,G|upstream_gene_variant|MODIFIER|PA14_49330|PA14_49330|transcript|ABJ10334.1|protein_coding||c.-3697T>G|||||3697|,G|upstream_gene_variant|MODIFIER|pcpS|PA14_49340|transcript|ABJ10333.1|protein_coding||c.-4713T>G|||||4713|,G|downstream_gene_variant|MODIFIER|napA|PA14_49250|transcript|ABJ10342.1|protein_coding||c.*3677T>G|||||3677|,G|downstream_gene_variant|MODIFIER|napB|PA14_49260|transcript|ABJ10341.1|protein_coding||c.*3175T>G|||||3175|,G|downstream_gene_variant|MODIFIER|napc|PA14_49270|transcript|ABJ10340.1|protein_coding||c.*2568T>G|||||2568|,G|downstream_gene_variant|MODIFIER|PA14_49290|PA14_49290|transcript|ABJ10338.1|protein_coding||c.*149T>G|||||149|,G|downstream_gene_variant|MODIFIER|PA14_49310|PA14_49310|transcript|ABJ10336.1|protein_coding||c.*2030A>C|||||2030|,G|downstream_gene_variant|MODIFIER|PA14_49320|PA14_49320|transcript|ABJ10335.1|protein_coding||c.*2850A>C|||||2850| GT:DP:DPR:RO:QR:AO:QA:GL . 0:13:13,0:13:481:0:0:0,-43.6231 0:10:10,3:7:259:3:18:0,-21.9812 0:17:17,0:17:588:0:0:0,-53.219 +Chromosome 4385434 . G A 7.3824E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=32;DPB=32;DPRA=0.692308;EPP=7.35324;EPPR=5.61607;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=31.8462;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=80;QR=1152;RO=30;RPL=0;RPP=7.35324;RPPR=5.61607;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=14;SRP=3.29983;SRR=16;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|PA14_49350|PA14_49350|transcript|ABJ10332.1|protein_coding|1/1|c.201C>T|p.Arg67Arg|201/813|201/813|67/270||,A|upstream_gene_variant|MODIFIER|PA14_49300|PA14_49300|transcript|ABJ10337.1|protein_coding||c.-4102C>T|||||4102|,A|upstream_gene_variant|MODIFIER|PA14_49310|PA14_49310|transcript|ABJ10336.1|protein_coding||c.-3704C>T|||||3704|,A|upstream_gene_variant|MODIFIER|PA14_49320|PA14_49320|transcript|ABJ10335.1|protein_coding||c.-2533C>T|||||2533|,A|upstream_gene_variant|MODIFIER|PA14_49360|PA14_49360|transcript|ABJ10331.1|protein_coding||c.-412G>A|||||412|,A|upstream_gene_variant|MODIFIER|dapE|PA14_49380|transcript|ABJ10330.1|protein_coding||c.-3136G>A|||||3136|,A|upstream_gene_variant|MODIFIER|rrmA|PA14_49390|transcript|ABJ10329.1|protein_coding||c.-4287G>A|||||4287|,A|downstream_gene_variant|MODIFIER|PA14_49330|PA14_49330|transcript|ABJ10334.1|protein_coding||c.*1569G>A|||||1569|,A|downstream_gene_variant|MODIFIER|pcpS|PA14_49340|transcript|ABJ10333.1|protein_coding||c.*613G>A|||||613| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,2:4:158:2:80:0,-7.00886 0:7:7,0:7:251:0:0:0,-22.9351 0:9:9,0:9:353:0:0:0,-32.1318 0:10:10,0:10:390:0:0:0,-35.4549 +Chromosome 4424203 . A T 1.34587E-8 . AB=0;ABP=0;AC=0;AF=0;AN=3;AO=2;CIGAR=1X;DP=8;DPB=8;DPRA=2;EPP=7.35324;EPPR=8.80089;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=19.5937;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=212;RO=6;RPL=2;RPP=7.35324;RPPR=8.80089;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=4;SRP=4.45795;SRR=2;TYPE=snp;technology.ILLUMINA=1;ANN=T|upstream_gene_variant|MODIFIER|PA14_49660|PA14_49660|transcript|ABJ10307.1|protein_coding||c.-4581T>A|||||4581|,T|upstream_gene_variant|MODIFIER|PA14_49680|PA14_49680|transcript|ABJ10306.1|protein_coding||c.-3615T>A|||||3615|,T|upstream_gene_variant|MODIFIER|PA14_49700|PA14_49700|transcript|ABJ10304.1|protein_coding||c.-1745T>A|||||1745|,T|upstream_gene_variant|MODIFIER|PA14_49730|PA14_49730|transcript|ABJ10301.1|protein_coding||c.-38A>T|||||38|,T|upstream_gene_variant|MODIFIER|PA14_49750|PA14_49750|transcript|ABJ10299.1|protein_coding||c.-1400A>T|||||1400|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|rhlC|PA14_49760|transcript|ABJ10298.1|protein_coding||c.-2656A>T|||||2656|,T|downstream_gene_variant|MODIFIER|PA14_49690|PA14_49690|transcript|ABJ10305.1|protein_coding||c.*2483A>T|||||2483|,T|downstream_gene_variant|MODIFIER|yedU|PA14_49710|transcript|ABJ10303.1|protein_coding||c.*698A>T|||||698|,T|downstream_gene_variant|MODIFIER|PA14_49720|PA14_49720|transcript|ABJ10302.1|protein_coding||c.*29A>T|||||29|,T|downstream_gene_variant|MODIFIER|PA14_49740|PA14_49740|transcript|ABJ10300.1|protein_coding||c.*398T>A|||||398|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|PA14_49780|PA14_49780|transcript|ABJ10297.1|protein_coding||c.*3630T>A|||||3630|,T|downstream_gene_variant|MODIFIER|PA14_49790|PA14_49790|transcript|ABJ10296.1|protein_coding||c.*4072T>A|||||4072|,T|intergenic_region|MODIFIER|PA14_49720-PA14_49730|PA14_49720-PA14_49730|intergenic_region|PA14_49720-PA14_49730|||n.4424203A>T|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:95:0:0:0,-8.85941 0:4:4,2:2:78:2:4:0,-7.02347 0:1:1,0:1:39:0:0:0,-3.89656 . +Chromosome 4428240 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=45;DPB=45;DPRA=0.75;EPP=7.35324;EPPR=14.3727;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=72.6109;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1636;RO=43;RPL=0;RPP=7.35324;RPPR=9.12072;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=27;SRP=9.12072;SRR=16;TYPE=snp;technology.ILLUMINA=1;ANN=G|initiator_codon_variant|LOW|PA14_49780|PA14_49780|transcript|ABJ10297.1|protein_coding|1/1|c.1A>C|p.Met1?|1/408|1/408|1/135||,G|upstream_gene_variant|MODIFIER|PA14_49740|PA14_49740|transcript|ABJ10300.1|protein_coding||c.-2950A>C|||||2950|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|gsp69|PA14_49800|transcript|ABJ10295.1|protein_coding||c.-1081T>G|||||1081|,G|upstream_gene_variant|MODIFIER|PA14_49810|PA14_49810|transcript|ABJ10294.1|protein_coding||c.-2165T>G|||||2165|,G|downstream_gene_variant|MODIFIER|yedU|PA14_49710|transcript|ABJ10303.1|protein_coding||c.*4735T>G|||||4735|,G|downstream_gene_variant|MODIFIER|PA14_49720|PA14_49720|transcript|ABJ10302.1|protein_coding||c.*4066T>G|||||4066|,G|downstream_gene_variant|MODIFIER|PA14_49730|PA14_49730|transcript|ABJ10301.1|protein_coding||c.*3649T>G|||||3649|,G|downstream_gene_variant|MODIFIER|PA14_49750|PA14_49750|transcript|ABJ10299.1|protein_coding||c.*1369T>G|||||1369|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|rhlC|PA14_49760|transcript|ABJ10298.1|protein_coding||c.*404T>G|||||404|,G|downstream_gene_variant|MODIFIER|PA14_49790|PA14_49790|transcript|ABJ10296.1|protein_coding||c.*35A>C|||||35|,G|downstream_gene_variant|MODIFIER|cobB|PA14_49820|transcript|ABJ10293.1|protein_coding||c.*2759A>C|||||2759|,G|downstream_gene_variant|MODIFIER|dgt|PA14_49840|transcript|ABJ10292.1|protein_coding||c.*3525A>C|||||3525| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,0:10:379:0:0:0,-34.4619 0:9:9,2:7:270:2:4:0,-24.2835 0:10:10,0:10:358:0:0:0,-32.5559 0:16:16,0:16:629:0:0:0,-56.9471 +Chromosome 4428745 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=29;DPB=29;DPRA=0.954545;EPP=7.35324;EPPR=6.95112;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=50.7493;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1000;RO=27;RPL=0;RPP=7.35324;RPPR=9.52472;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=24;SRP=38.4777;SRR=3;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_49790|PA14_49790|transcript|ABJ10296.1|protein_coding|1/1|c.442A>C|p.Ile148Leu|442/912|442/912|148/303||,G|upstream_gene_variant|MODIFIER|PA14_49740|PA14_49740|transcript|ABJ10300.1|protein_coding||c.-3455A>C|||||3455|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_49780|PA14_49780|transcript|ABJ10297.1|protein_coding||c.-505A>C|||||505|,G|upstream_gene_variant|MODIFIER|gsp69|PA14_49800|transcript|ABJ10295.1|protein_coding||c.-576T>G|||||576|,G|upstream_gene_variant|MODIFIER|PA14_49810|PA14_49810|transcript|ABJ10294.1|protein_coding||c.-1660T>G|||||1660|,G|upstream_gene_variant|MODIFIER|PA14_49850|PA14_49850|transcript|ABJ10291.1|protein_coding||c.-4747T>G|||||4747|,G|downstream_gene_variant|MODIFIER|PA14_49720|PA14_49720|transcript|ABJ10302.1|protein_coding||c.*4571T>G|||||4571|,G|downstream_gene_variant|MODIFIER|PA14_49730|PA14_49730|transcript|ABJ10301.1|protein_coding||c.*4154T>G|||||4154|,G|downstream_gene_variant|MODIFIER|PA14_49750|PA14_49750|transcript|ABJ10299.1|protein_coding||c.*1874T>G|||||1874|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|rhlC|PA14_49760|transcript|ABJ10298.1|protein_coding||c.*909T>G|||||909|,G|downstream_gene_variant|MODIFIER|cobB|PA14_49820|transcript|ABJ10293.1|protein_coding||c.*2254A>C|||||2254|,G|downstream_gene_variant|MODIFIER|dgt|PA14_49840|transcript|ABJ10292.1|protein_coding||c.*3020A>C|||||3020| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:192:0:0:0,-17.5871 0:6:6,0:6:228:0:0:0,-20.8841 0:10:10,0:10:390:0:0:0,-35.4572 0:7:7,2:5:190:2:4:0,-17.0864 +Chromosome 4440891 . T G 1.74408E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=31;DPB=31;DPRA=1.21429;EPP=9.52472;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=50.4165;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=1001;RO=28;RPL=0;RPP=9.52472;RPPR=10.7656;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=8;SRP=14.1779;SRR=20;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_49940|PA14_49940|transcript|ABJ10282.1|protein_coding|1/1|c.1262T>G|p.Val421Gly|1262/2325|1262/2325|421/774||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_49930|PA14_49930|transcript|ABJ10283.1|protein_coding||c.-1516A>C|||||1516|,G|upstream_gene_variant|MODIFIER|PA14_49960|PA14_49960|transcript|ABJ10281.1|protein_coding||c.-1167T>G|||||1167|,G|upstream_gene_variant|MODIFIER|PA14_49990|PA14_49990|transcript|ABJ10279.1|protein_coding||c.-3742T>G|||||3742|,G|upstream_gene_variant|MODIFIER|PA14_50000|PA14_50000|transcript|ABJ10278.1|protein_coding||c.-4034T>G|||||4034|,G|downstream_gene_variant|MODIFIER|PA14_49890|PA14_49890|transcript|ABJ10287.1|protein_coding||c.*4153T>G|||||4153|,G|downstream_gene_variant|MODIFIER|PA14_49900|PA14_49900|transcript|ABJ10286.1|protein_coding||c.*3675T>G|||||3675|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_49910|PA14_49910|transcript|ABJ10285.1|protein_coding||c.*2846T>G|||||2846|,G|downstream_gene_variant|MODIFIER|PA14_49920|PA14_49920|transcript|ABJ10284.1|protein_coding||c.*2365T>G|||||2365|,G|downstream_gene_variant|MODIFIER|PA14_49970|PA14_49970|transcript|ABJ10280.1|protein_coding||c.*1505A>C|||||1505|,G|downstream_gene_variant|MODIFIER|yliI|PA14_50010|transcript|ABJ10277.1|protein_coding||c.*4259A>C|||||4259| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:173:0:0:0,-15.9082 0:9:9,2:7:244:2:4:0,-21.9119 0:8:8,1:7:267:1:2:0,-24.1898 0:9:9,0:9:317:0:0:0,-28.8625 +Chromosome 4444680 . T C 3.36615E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=11;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=26.8965;EPPR=39.7082;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=38.1321;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=1135;RO=40;RPL=11;RPP=26.8965;RPPR=20.5992;RPR=0;RUN=1;SAF=11;SAP=26.8965;SAR=0;SRF=24;SRP=6.48466;SRR=16;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|PA14_49990|PA14_49990|transcript|ABJ10279.1|protein_coding|1/1|c.48T>C|p.Ala16Ala|48/192|48/192|16/63||,C|upstream_gene_variant|MODIFIER|PA14_49970|PA14_49970|transcript|ABJ10280.1|protein_coding||c.-518A>G|||||518|,C|upstream_gene_variant|MODIFIER|PA14_50000|PA14_50000|transcript|ABJ10278.1|protein_coding||c.-245T>C|||||245|,C|upstream_gene_variant|MODIFIER|PA14_50030|PA14_50030|transcript|ABJ10275.1|protein_coding||c.-2447T>C|||||2447|,C|upstream_gene_variant|MODIFIER|PA14_50050|PA14_50050|transcript|ABJ10273.1|protein_coding||c.-4031T>C|||||4031|,C|downstream_gene_variant|MODIFIER|PA14_49940|PA14_49940|transcript|ABJ10282.1|protein_coding||c.*2726T>C|||||2726|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_49960|PA14_49960|transcript|ABJ10281.1|protein_coding||c.*2287T>C|||||2287|,C|downstream_gene_variant|MODIFIER|yliI|PA14_50010|transcript|ABJ10277.1|protein_coding||c.*470A>G|||||470|,C|downstream_gene_variant|MODIFIER|PA14_50020|PA14_50020|transcript|ABJ10276.1|protein_coding||c.*1711A>G|||||1711|,C|downstream_gene_variant|MODIFIER|PA14_50040|PA14_50040|transcript|ABJ10274.1|protein_coding||c.*3162A>G|||||3162|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:11:11,2:9:295:2:15:0,-25.4371 0:16:16,1:15:442:1:13:0,-38.7505 0:15:15,5:10:271:5:21:0,-22.7176 0:9:9,3:6:127:3:17:0,-10.05 +Chromosome 4461103 . G T 5.41681E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=6;CIGAR=1X;DP=38;DPB=38;DPRA=1.25;EPP=16.0391;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=49.7325;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=45;QR=944;RO=32;RPL=6;RPP=16.0391;RPPR=3.28173;RPR=0;RUN=1;SAF=6;SAP=16.0391;SAR=0;SRF=23;SRP=16.3106;SRR=9;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|fleQ|PA14_50220|transcript|ABJ10262.1|protein_coding|1/1|c.1242C>A|p.Ile414Ile|1242/1473|1242/1473|414/490||,T|upstream_gene_variant|MODIFIER|fliF|PA14_50140|transcript|ABJ10266.1|protein_coding||c.-3577C>A|||||3577|,T|upstream_gene_variant|MODIFIER|fliE|PA14_50160|transcript|ABJ10265.1|protein_coding||c.-3225C>A|||||3225|,T|upstream_gene_variant|MODIFIER|fleR|PA14_50180|transcript|ABJ10264.1|protein_coding||c.-1557C>A|||||1557|,T|upstream_gene_variant|MODIFIER|fleS|PA14_50200|transcript|ABJ10263.1|protein_coding||c.-344C>A|||||344|,T|downstream_gene_variant|MODIFIER|PA14_50240|PA14_50240|transcript|ABJ10261.1|protein_coding||c.*1523C>A|||||1523|,T|downstream_gene_variant|MODIFIER|fliS|PA14_50250|transcript|ABJ10260.1|protein_coding||c.*1842C>A|||||1842|,T|downstream_gene_variant|MODIFIER|fliD|PA14_50270|transcript|ABJ10259.1|protein_coding||c.*2344C>A|||||2344|,T|downstream_gene_variant|MODIFIER|flaG|PA14_50280|transcript|ABJ10258.1|protein_coding||c.*3854C>A|||||3854|,T|downstream_gene_variant|MODIFIER|fliC|PA14_50290|transcript|ABJ10257.1|protein_coding||c.*4304C>A|||||4304| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,2:6:186:2:26:0,-14.5702 0:11:11,2:9:260:2:4:0,-23.2972 0:11:11,2:9:278:2:15:0,-23.8892 0:8:8,0:8:220:0:0:0,-20.0652 +Chromosome 4486142 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=54;DPB=54;DPRA=0.6;EPP=7.35324;EPPR=13.7006;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=69.8874;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1735;RO=52;RPL=0;RPP=7.35324;RPPR=9.02361;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=16;SRP=19.7139;SRR=36;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|PA14_50500|PA14_50500|transcript|ABJ10241.1|protein_coding|1/1|c.126G>T|p.Met42Ile|126/363|126/363|42/120||,A|upstream_gene_variant|MODIFIER|flgG|PA14_50430|transcript|ABJ10247.1|protein_coding||c.-4498G>T|||||4498|,A|upstream_gene_variant|MODIFIER|flgF|PA14_50440|transcript|ABJ10246.1|protein_coding||c.-3702G>T|||||3702|,A|upstream_gene_variant|MODIFIER|flgE|PA14_50450|transcript|ABJ10245.1|protein_coding||c.-2097G>T|||||2097|,A|upstream_gene_variant|MODIFIER|flgD|PA14_50460|transcript|ABJ10244.1|protein_coding||c.-1356G>T|||||1356|,A|upstream_gene_variant|MODIFIER|flgC|PA14_50470|transcript|ABJ10243.1|protein_coding||c.-903G>T|||||903|,A|upstream_gene_variant|MODIFIER|flgB|PA14_50480|transcript|ABJ10242.1|protein_coding||c.-490G>T|||||490|,A|upstream_gene_variant|MODIFIER|braC|PA14_50520|transcript|ABJ10239.1|protein_coding||c.-808C>A|||||808|,A|upstream_gene_variant|MODIFIER|braD|PA14_50530|transcript|ABJ10238.1|protein_coding||c.-2190C>A|||||2190|,A|upstream_gene_variant|MODIFIER|braE|PA14_50540|transcript|ABJ10237.1|protein_coding||c.-3110C>A|||||3110|,A|upstream_gene_variant|MODIFIER|braF|PA14_50550|transcript|ABJ10236.1|protein_coding||c.-4360C>A|||||4360|,A|downstream_gene_variant|MODIFIER|PA14_50510|PA14_50510|transcript|ABJ10240.1|protein_coding||c.*192G>T|||||192| GT:DP:DPR:RO:QR:AO:QA:GL 0:11:11,0:11:363:0:0:0,-32.9796 0:12:12,0:12:390:0:0:0,-35.399 0:22:22,0:22:737:0:0:0,-66.6231 0:9:9,2:7:245:2:17:0,-20.7672 +Chromosome 4494254 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=35;DPB=35;DPRA=1.33333;EPP=13.8677;EPPR=3.29983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=54.7107;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1134;RO=30;RPL=0;RPP=13.8677;RPPR=13.4334;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=9;SRP=13.4334;SRR=21;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_50570|PA14_50570|transcript|ABJ10234.1|protein_coding|1/1|c.91G>C|p.Ala31Pro|91/2295|91/2295|31/764||,G|upstream_gene_variant|MODIFIER|PA14_50610|PA14_50610|transcript|ABJ10231.1|protein_coding||c.-3084C>G|||||3084|,G|upstream_gene_variant|MODIFIER|PA14_50630|PA14_50630|transcript|ABJ10229.1|protein_coding||c.-4259C>G|||||4259|,G|downstream_gene_variant|MODIFIER|braD|PA14_50530|transcript|ABJ10238.1|protein_coding||c.*4999C>G|||||4999|,G|downstream_gene_variant|MODIFIER|braE|PA14_50540|transcript|ABJ10237.1|protein_coding||c.*3749C>G|||||3749|,G|downstream_gene_variant|MODIFIER|braF|PA14_50550|transcript|ABJ10236.1|protein_coding||c.*2985C>G|||||2985|,G|downstream_gene_variant|MODIFIER|braG|PA14_50560|transcript|ABJ10235.1|protein_coding||c.*2281C>G|||||2281|,G|downstream_gene_variant|MODIFIER|PA14_50590|PA14_50590|transcript|ABJ10233.1|protein_coding||c.*127G>C|||||127|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_50600|PA14_50600|transcript|ABJ10232.1|protein_coding||c.*2136G>C|||||2136|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_50620|PA14_50620|transcript|ABJ10230.1|protein_coding||c.*3766G>C|||||3766|,G|downstream_gene_variant|MODIFIER|PA14_50640|PA14_50640|transcript|ABJ10228.1|protein_coding||c.*4953G>C|||||4953| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:268:0:0:0,-24.4822 0:13:13,2:11:417:2:30:0,-35.0285 0:7:7,1:6:224:1:15:0,-19.0156 0:8:8,2:6:225:2:30:0,-17.7569 +Chromosome 4499474 . T G 6.11769E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=32;DPB=32;DPRA=0.84;EPP=7.35324;EPPR=4.16842;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=45.1855;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=41;QR=982;RO=30;RPL=0;RPP=7.35324;RPPR=4.16842;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=20;SRP=10.2485;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_50650|PA14_50650|transcript|ABJ10227.1|protein_coding|1/1|c.503A>C|p.Gln168Pro|503/522|503/522|168/173||,G|upstream_gene_variant|MODIFIER|PA14_50590|PA14_50590|transcript|ABJ10233.1|protein_coding||c.-3183A>C|||||3183|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_50600|PA14_50600|transcript|ABJ10232.1|protein_coding||c.-2170A>C|||||2170|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_50620|PA14_50620|transcript|ABJ10230.1|protein_coding||c.-981A>C|||||981|,G|upstream_gene_variant|MODIFIER|PA14_50640|PA14_50640|transcript|ABJ10228.1|protein_coding||c.-16A>C|||||16|,G|downstream_gene_variant|MODIFIER|PA14_50610|PA14_50610|transcript|ABJ10231.1|protein_coding||c.*1465T>G|||||1465|,G|downstream_gene_variant|MODIFIER|PA14_50630|PA14_50630|transcript|ABJ10229.1|protein_coding||c.*296T>G|||||296|,G|downstream_gene_variant|MODIFIER|PA14_50660|PA14_50660|transcript|ABJ10226.1|protein_coding||c.*513A>C|||||513|,G|downstream_gene_variant|MODIFIER|PA14_50670|PA14_50670|transcript|ABJ10225.1|protein_coding||c.*1621A>C|||||1621|,G|downstream_gene_variant|MODIFIER|phaG|PA14_50680|transcript|ABJ10224.1|protein_coding||c.*2640A>C|||||2640|,G|downstream_gene_variant|MODIFIER|phaF|PA14_50690|transcript|ABJ10223.1|protein_coding||c.*2984A>C|||||2984|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|phaE|PA14_50700|transcript|ABJ10222.1|protein_coding||c.*3238A>C|||||3238|,G|downstream_gene_variant|MODIFIER|phaD|PA14_50710|transcript|ABJ10221.1|protein_coding||c.*3759A>C|||||3759| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:211:0:0:0,-19.2799 0:12:12,0:12:396:0:0:0,-35.941 0:7:7,2:5:185:2:41:0,-13.1147 0:6:6,0:6:190:0:0:0,-17.4039 +Chromosome 4500585 . A T 7.00668E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=32;DPB=32;DPRA=1.28571;EPP=9.52472;EPPR=3.08518;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=45.113;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=834;RO=29;RPL=0;RPP=9.52472;RPPR=6.67934;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=22;SRP=19.8579;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_50660|PA14_50660|transcript|ABJ10226.1|protein_coding|1/1|c.500T>A|p.Ile167Asn|500/1098|500/1098|167/365||,T|upstream_gene_variant|MODIFIER|PA14_50590|PA14_50590|transcript|ABJ10233.1|protein_coding||c.-4294T>A|||||4294|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|PA14_50600|PA14_50600|transcript|ABJ10232.1|protein_coding||c.-3281T>A|||||3281|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|PA14_50620|PA14_50620|transcript|ABJ10230.1|protein_coding||c.-2092T>A|||||2092|,T|upstream_gene_variant|MODIFIER|PA14_50640|PA14_50640|transcript|ABJ10228.1|protein_coding||c.-1127T>A|||||1127|,T|upstream_gene_variant|MODIFIER|PA14_50650|PA14_50650|transcript|ABJ10227.1|protein_coding||c.-609T>A|||||609|,T|downstream_gene_variant|MODIFIER|PA14_50610|PA14_50610|transcript|ABJ10231.1|protein_coding||c.*2576A>T|||||2576|,T|downstream_gene_variant|MODIFIER|PA14_50630|PA14_50630|transcript|ABJ10229.1|protein_coding||c.*1407A>T|||||1407|,T|downstream_gene_variant|MODIFIER|PA14_50670|PA14_50670|transcript|ABJ10225.1|protein_coding||c.*510T>A|||||510|,T|downstream_gene_variant|MODIFIER|phaG|PA14_50680|transcript|ABJ10224.1|protein_coding||c.*1529T>A|||||1529|,T|downstream_gene_variant|MODIFIER|phaF|PA14_50690|transcript|ABJ10223.1|protein_coding||c.*1873T>A|||||1873|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|phaE|PA14_50700|transcript|ABJ10222.1|protein_coding||c.*2127T>A|||||2127|,T|downstream_gene_variant|MODIFIER|phaD|PA14_50710|transcript|ABJ10221.1|protein_coding||c.*2648T>A|||||2648|,T|downstream_gene_variant|MODIFIER|phaC|PA14_50720|transcript|ABJ10220.1|protein_coding||c.*4144T>A|||||4144|,T|downstream_gene_variant|MODIFIER|phaA|PA14_50730|transcript|ABJ10219.1|protein_coding||c.*4482T>A|||||4482| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,1:7:168:1:15:0,-13.8507 0:7:7,0:7:173:0:0:0,-15.8083 0:10:10,2:8:261:2:17:0,-22.1876 0:7:7,0:7:232:0:0:0,-21.1936 +Chromosome 4500595 . T C 7.50367E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=7;CIGAR=1X;DP=36;DPB=36;DPRA=1;EPP=18.2106;EPPR=4.88226;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=39.969;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=25;QR=693;RO=29;RPL=0;RPP=18.2106;RPPR=15.6647;RPR=7;RUN=1;SAF=0;SAP=18.2106;SAR=7;SRF=18;SRP=6.67934;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_50660|PA14_50660|transcript|ABJ10226.1|protein_coding|1/1|c.490A>G|p.Asn164Asp|490/1098|490/1098|164/365||,C|upstream_gene_variant|MODIFIER|PA14_50590|PA14_50590|transcript|ABJ10233.1|protein_coding||c.-4304A>G|||||4304|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_50600|PA14_50600|transcript|ABJ10232.1|protein_coding||c.-3291A>G|||||3291|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_50620|PA14_50620|transcript|ABJ10230.1|protein_coding||c.-2102A>G|||||2102|,C|upstream_gene_variant|MODIFIER|PA14_50640|PA14_50640|transcript|ABJ10228.1|protein_coding||c.-1137A>G|||||1137|,C|upstream_gene_variant|MODIFIER|PA14_50650|PA14_50650|transcript|ABJ10227.1|protein_coding||c.-619A>G|||||619|,C|downstream_gene_variant|MODIFIER|PA14_50610|PA14_50610|transcript|ABJ10231.1|protein_coding||c.*2586T>C|||||2586|,C|downstream_gene_variant|MODIFIER|PA14_50630|PA14_50630|transcript|ABJ10229.1|protein_coding||c.*1417T>C|||||1417|,C|downstream_gene_variant|MODIFIER|PA14_50670|PA14_50670|transcript|ABJ10225.1|protein_coding||c.*500A>G|||||500|,C|downstream_gene_variant|MODIFIER|phaG|PA14_50680|transcript|ABJ10224.1|protein_coding||c.*1519A>G|||||1519|,C|downstream_gene_variant|MODIFIER|phaF|PA14_50690|transcript|ABJ10223.1|protein_coding||c.*1863A>G|||||1863|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|phaE|PA14_50700|transcript|ABJ10222.1|protein_coding||c.*2117A>G|||||2117|,C|downstream_gene_variant|MODIFIER|phaD|PA14_50710|transcript|ABJ10221.1|protein_coding||c.*2638A>G|||||2638|,C|downstream_gene_variant|MODIFIER|phaC|PA14_50720|transcript|ABJ10220.1|protein_coding||c.*4134A>G|||||4134|,C|downstream_gene_variant|MODIFIER|phaA|PA14_50730|transcript|ABJ10219.1|protein_coding||c.*4472A>G|||||4472| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,0:9:130:0:0:0,-11.8365 0:8:8,3:5:116:3:6:0,-10.1047 0:13:13,3:10:250:3:17:0,-21.1454 0:6:6,1:5:197:1:2:0,-17.9066 +Chromosome 4507398 . G T 2.03436E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=34;DPB=34;DPRA=1.25;EPP=7.35324;EPPR=3.28173;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=52.8318;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=965;RO=32;RPL=2;RPP=7.35324;RPPR=35.8538;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=20;SRP=7.35324;SRR=12;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|phaA|PA14_50730|transcript|ABJ10219.1|protein_coding|1/1|c.471C>A|p.Arg157Arg|471/2802|471/2802|157/933||,T|upstream_gene_variant|MODIFIER|phaG|PA14_50680|transcript|ABJ10224.1|protein_coding||c.-4937C>A|||||4937|,T|upstream_gene_variant|MODIFIER|phaF|PA14_50690|transcript|ABJ10223.1|protein_coding||c.-4683C>A|||||4683|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|phaE|PA14_50700|transcript|ABJ10222.1|protein_coding||c.-4162C>A|||||4162|,T|upstream_gene_variant|MODIFIER|phaD|PA14_50710|transcript|ABJ10221.1|protein_coding||c.-2666C>A|||||2666|,T|upstream_gene_variant|MODIFIER|phaC|PA14_50720|transcript|ABJ10220.1|protein_coding||c.-2331C>A|||||2331|,T|upstream_gene_variant|MODIFIER|PA14_50750|PA14_50750|transcript|ABJ10217.1|protein_coding||c.-1451G>T|||||1451|,T|downstream_gene_variant|MODIFIER|PA14_50740|PA14_50740|transcript|ABJ10218.1|protein_coding||c.*799C>A|||||799|,T|downstream_gene_variant|MODIFIER|PA14_50760|PA14_50760|transcript|ABJ10216.1|protein_coding||c.*1672C>A|||||1672|,T|downstream_gene_variant|MODIFIER|PA14_50770|PA14_50770|transcript|ABJ10215.1|protein_coding||c.*2859C>A|||||2859|,T|downstream_gene_variant|MODIFIER|yeaG|PA14_50790|transcript|ABJ10214.1|protein_coding||c.*4377C>A|||||4377| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:200:0:0:0,-18.2788 0:11:11,0:11:298:0:0:0,-27.081 0:6:6,0:6:186:0:0:0,-17.0423 0:10:10,2:8:281:2:17:0,-24.012 +Chromosome 4508919 . T C 1.92136E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=6;CIGAR=1X;DP=48;DPB=48;DPRA=0.666667;EPP=16.0391;EPPR=4.33437;GTI=0;LEN=1;MEANALT=1.33333;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=68.9487;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=1409;RO=41;RPL=0;RPP=16.0391;RPPR=7.30028;RPR=6;RUN=1;SAF=0;SAP=16.0391;SAR=6;SRF=17;SRP=5.60547;SRR=24;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_50750|PA14_50750|transcript|ABJ10217.1|protein_coding|1/1|c.71T>C|p.Ile24Thr|71/243|71/243|24/80||,C|upstream_gene_variant|MODIFIER|phaD|PA14_50710|transcript|ABJ10221.1|protein_coding||c.-4187A>G|||||4187|,C|upstream_gene_variant|MODIFIER|phaC|PA14_50720|transcript|ABJ10220.1|protein_coding||c.-3852A>G|||||3852|,C|upstream_gene_variant|MODIFIER|phaA|PA14_50730|transcript|ABJ10219.1|protein_coding||c.-1051A>G|||||1051|,C|upstream_gene_variant|MODIFIER|PA14_50740|PA14_50740|transcript|ABJ10218.1|protein_coding||c.-258A>G|||||258|,C|downstream_gene_variant|MODIFIER|PA14_50760|PA14_50760|transcript|ABJ10216.1|protein_coding||c.*151A>G|||||151|,C|downstream_gene_variant|MODIFIER|PA14_50770|PA14_50770|transcript|ABJ10215.1|protein_coding||c.*1338A>G|||||1338|,C|downstream_gene_variant|MODIFIER|yeaG|PA14_50790|transcript|ABJ10214.1|protein_coding||c.*2856A>G|||||2856|,C|downstream_gene_variant|MODIFIER|pdxH|PA14_50800|transcript|ABJ10213.1|protein_coding||c.*3976A>G|||||3976|,C|downstream_gene_variant|MODIFIER|PA14_50810|PA14_50810|transcript|ABJ10212.1|protein_coding||c.*4722A>G|||||4722| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,2:8:250:2:4:0,-22.4181 0:10:10,2:7:272:2:4:0,-24.3945 0:12:12,2:10:300:2:4:0,-26.8985 0:16:16,0:16:587:0:0:0,-53.1469 +Chromosome 4521011 . G T 0.00639626 . AB=0;ABP=0;AC=1;AF=0.25;AN=4;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=0.666667;EPP=7.35324;EPPR=3.25157;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=6.51986;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=208;RO=9;RPL=2;RPP=7.35324;RPPR=3.25157;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=8;SRP=14.8328;SRR=1;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_50850|PA14_50850|transcript|ABJ10208.1|protein_coding|1/1|c.403G>T|p.Gly135Cys|403/465|403/465|135/154||,T|upstream_gene_variant|MODIFIER|PA14_50830|PA14_50830|transcript|ABJ10210.1|protein_coding||c.-2755C>A|||||2755|,T|upstream_gene_variant|MODIFIER|PA14_50840|PA14_50840|transcript|ABJ10209.1|protein_coding||c.-532C>A|||||532|,T|upstream_gene_variant|MODIFIER|PA14_50890|PA14_50890|transcript|ABJ10204.1|protein_coding||c.-2081G>T|||||2081|,T|upstream_gene_variant|MODIFIER|PA14_50900|PA14_50900|transcript|ABJ10203.1|protein_coding||c.-2581G>T|||||2581|,T|upstream_gene_variant|MODIFIER|PA14_50910|PA14_50910|transcript|ABJ10202.1|protein_coding||c.-3054G>T|||||3054|,T|upstream_gene_variant|MODIFIER|PA14_50920|PA14_50920|transcript|ABJ10201.1|protein_coding||c.-3454G>T|||||3454|,T|downstream_gene_variant|MODIFIER|PA14_50860|PA14_50860|transcript|ABJ10207.1|protein_coding||c.*101C>A|||||101|,T|downstream_gene_variant|MODIFIER|PA14_50870|PA14_50870|transcript|ABJ10206.1|protein_coding||c.*903C>A|||||903|,T|downstream_gene_variant|MODIFIER|PA14_50880|PA14_50880|transcript|ABJ10205.1|protein_coding||c.*1318C>A|||||1318|,T|downstream_gene_variant|MODIFIER|PA14_50930|PA14_50930|transcript|ABJ10200.1|protein_coding||c.*4192C>A|||||4192| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:74:0:0:0,-6.90589 1:2:2,2:0:0:2:32:-3.03997,0 0:2:2,0:2:49:0:0:0,-4.65395 0:4:4,0:4:85:0:0:0,-7.85997 +Chromosome 4527598 . A G 1.04873E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=56;DPB=56;DPRA=1.74074;EPP=13.8677;EPPR=21.7871;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=51.7289;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=43;QR=1405;RO=51;RPL=0;RPP=13.8677;RPPR=21.7871;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=8;SRP=55.1682;SRR=43;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|PA14_50880|PA14_50880|transcript|ABJ10205.1|protein_coding||c.-4637T>C|||||4637|,G|upstream_gene_variant|MODIFIER|PA14_50930|PA14_50930|transcript|ABJ10200.1|protein_coding||c.-1835T>C|||||1835|,G|upstream_gene_variant|MODIFIER|pac|PA14_50980|transcript|ABJ10196.1|protein_coding||c.-113A>G|||||113|,G|upstream_gene_variant|MODIFIER|P8|EBG00001225159|transcript|EBT00001793479.1|sRNA||n.-4722A>G|||||4722|,G|downstream_gene_variant|MODIFIER|PA14_50890|PA14_50890|transcript|ABJ10204.1|protein_coding||c.*4009A>G|||||4009|,G|downstream_gene_variant|MODIFIER|PA14_50900|PA14_50900|transcript|ABJ10203.1|protein_coding||c.*3533A>G|||||3533|,G|downstream_gene_variant|MODIFIER|PA14_50910|PA14_50910|transcript|ABJ10202.1|protein_coding||c.*3216A>G|||||3216|,G|downstream_gene_variant|MODIFIER|PA14_50920|PA14_50920|transcript|ABJ10201.1|protein_coding||c.*2513A>G|||||2513|,G|downstream_gene_variant|MODIFIER|PA14_50940|PA14_50940|transcript|ABJ10199.1|protein_coding||c.*1026A>G|||||1026|,G|downstream_gene_variant|MODIFIER|PA14_50950|PA14_50950|transcript|ABJ10198.1|protein_coding||c.*818A>G|||||818|,G|downstream_gene_variant|MODIFIER|yfcG|PA14_50970|transcript|ABJ10197.1|protein_coding||c.*10A>G|||||10|,G|downstream_gene_variant|MODIFIER|yigN|PA14_51000|transcript|ABJ10195.1|protein_coding||c.*2811T>C|||||2811|,G|downstream_gene_variant|MODIFIER|PA14_51010|PA14_51010|transcript|ABJ10194.1|protein_coding||c.*4942T>C|||||4942|WARNING_TRANSCRIPT_NO_START_CODON,G|intergenic_region|MODIFIER|yfcG-pac|PA14_50970-PA14_50980|intergenic_region|PA14_50970-PA14_50980|||n.4527598A>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,0:9:251:0:0:0,-22.8619 0:10:10,2:8:209:2:26:0,-16.5978 0:18:18,1:17:470:1:2:0,-42.3573 0:19:19,2:17:475:2:15:0,-41.5851 +Chromosome 4562659 . A C 2.97821E-16 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=6;CIGAR=1X;DP=62;DPB=62;DPRA=0.958333;EPP=16.0391;EPPR=6.88793;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.8393;NS=4;NUMALT=1;ODDS=96.1387;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=1953;RO=56;RPL=6;RPP=16.0391;RPPR=3.63072;RPR=0;RUN=1;SAF=6;SAP=16.0391;SAR=0;SRF=19;SRP=15.5738;SRR=37;TYPE=snp;technology.ILLUMINA=1;ANN=C|upstream_gene_variant|MODIFIER|perM|PA14_51300|transcript|ABJ10171.1|protein_coding||c.-3619T>G|||||3619|,C|upstream_gene_variant|MODIFIER|yrkI|PA14_51310|transcript|ABJ10170.1|protein_coding||c.-3334T>G|||||3334|,C|upstream_gene_variant|MODIFIER|nadA|PA14_51330|transcript|ABJ10168.1|protein_coding||c.-571T>G|||||571|,C|upstream_gene_variant|MODIFIER|mvfR|PA14_51340|transcript|ABJ10167.1|protein_coding||c.-178A>C|||||178|,C|downstream_gene_variant|MODIFIER|bcp|PA14_51290|transcript|ABJ10172.1|protein_coding||c.*4753A>C|||||4753|,C|downstream_gene_variant|MODIFIER|PA14_51320|PA14_51320|transcript|ABJ10169.1|protein_coding||c.*1738A>C|||||1738|,C|downstream_gene_variant|MODIFIER|phnB|PA14_51350|transcript|ABJ10166.1|protein_coding||c.*1129T>G|||||1129|,C|downstream_gene_variant|MODIFIER|phnA|PA14_51360|transcript|ABJ10165.1|protein_coding||c.*1709T>G|||||1709|,C|downstream_gene_variant|MODIFIER|pqsE|PA14_51380|transcript|ABJ10164.1|protein_coding||c.*3418T>G|||||3418|,C|downstream_gene_variant|MODIFIER|pqsD|PA14_51390|transcript|ABJ10163.1|protein_coding||c.*4317T>G|||||4317|,C|intergenic_region|MODIFIER|nadA-mvfR|PA14_51330-PA14_51340|intergenic_region|PA14_51330-PA14_51340|||n.4562659A>C|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:18:18,1:17:595:1:2:0,-53.6482 0:16:16,0:16:622:0:0:0,-56.3168 0:15:15,3:12:382:3:6:0,-34.1127 0:13:13,2:11:354:2:4:0,-31.7753 +Chromosome 4567792 . A G 8.49084E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=30;DPB=30;DPRA=1.14286;EPP=9.52472;EPPR=5.02092;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=37.1193;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=866;RO=27;RPL=0;RPP=9.52472;RPPR=3.73412;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=22;SRP=26.2531;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|pqsD|PA14_51390|transcript|ABJ10163.1|protein_coding|1/1|c.198T>C|p.Ala66Ala|198/1014|198/1014|66/337||,G|upstream_gene_variant|MODIFIER|phnB|PA14_51350|transcript|ABJ10166.1|protein_coding||c.-3402T>C|||||3402|,G|upstream_gene_variant|MODIFIER|phnA|PA14_51360|transcript|ABJ10165.1|protein_coding||c.-1832T>C|||||1832|,G|upstream_gene_variant|MODIFIER|pqsE|PA14_51380|transcript|ABJ10164.1|protein_coding||c.-810T>C|||||810|,G|upstream_gene_variant|MODIFIER|ogt|PA14_51440|transcript|ABJ10159.1|protein_coding||c.-4236A>G|||||4236|,G|downstream_gene_variant|MODIFIER|mvfR|PA14_51340|transcript|ABJ10167.1|protein_coding||c.*3957A>G|||||3957|,G|downstream_gene_variant|MODIFIER|pqsC|PA14_51410|transcript|ABJ10162.1|protein_coding||c.*240T>C|||||240|,G|downstream_gene_variant|MODIFIER|pqsB|PA14_51420|transcript|ABJ10161.1|protein_coding||c.*1279T>C|||||1279|,G|downstream_gene_variant|MODIFIER|pqsA|PA14_51430|transcript|ABJ10160.1|protein_coding||c.*2124T>C|||||2124|,G|downstream_gene_variant|MODIFIER|cupC3|PA14_51450|transcript|ABJ10158.1|protein_coding||c.*4837T>C|||||4837|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:139:0:0:0,-12.7363 0:11:11,1:10:307:1:16:0,-26.3197 0:5:5,2:3:105:2:4:0,-9.41444 0:8:8,0:8:315:0:0:0,-28.7161 +Chromosome 4571379 . T G 1.44696E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=59;DPB=59;DPRA=0.612245;EPP=7.35324;EPPR=10.6105;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=69.7447;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=1903;RO=56;RPL=0;RPP=7.35324;RPPR=3.63072;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=35;SRP=10.6105;SRR=21;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|pqsA|PA14_51430|transcript|ABJ10160.1|protein_coding|1/1|c.91A>C|p.Ser31Arg|91/1554|91/1554|31/517||,G|upstream_gene_variant|MODIFIER|pqsE|PA14_51380|transcript|ABJ10164.1|protein_coding||c.-4397A>C|||||4397|,G|upstream_gene_variant|MODIFIER|pqsD|PA14_51390|transcript|ABJ10163.1|protein_coding||c.-3390A>C|||||3390|,G|upstream_gene_variant|MODIFIER|pqsC|PA14_51410|transcript|ABJ10162.1|protein_coding||c.-2301A>C|||||2301|,G|upstream_gene_variant|MODIFIER|pqsB|PA14_51420|transcript|ABJ10161.1|protein_coding||c.-1457A>C|||||1457|,G|upstream_gene_variant|MODIFIER|ogt|PA14_51440|transcript|ABJ10159.1|protein_coding||c.-649T>G|||||649|,G|downstream_gene_variant|MODIFIER|cupC3|PA14_51450|transcript|ABJ10158.1|protein_coding||c.*1250A>C|||||1250|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|cupC2|PA14_51460|transcript|ABJ10157.1|protein_coding||c.*3865A>C|||||3865|,G|downstream_gene_variant|MODIFIER|cupC1|PA14_51470|transcript|ABJ10156.1|protein_coding||c.*4636A>C|||||4636|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:12:12,0:12:413:0:0:0,-37.4951 0:10:10,2:7:259:2:30:0,-20.8109 0:21:21,0:21:669:0:0:0,-60.4867 0:16:16,0:16:562:0:0:0,-50.8905 +Chromosome 4578807 . G C 2.55144E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=24;DPB=24;DPRA=1.5;EPP=7.35324;EPPR=3.40511;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=30.4857;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=761;RO=22;RPL=2;RPP=7.35324;RPPR=4.58955;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=15;SRP=9.32731;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=C|upstream_gene_variant|MODIFIER|cupC3|PA14_51450|transcript|ABJ10158.1|protein_coding||c.-3659C>G|||||3659|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|cupC2|PA14_51460|transcript|ABJ10157.1|protein_coding||c.-2850C>G|||||2850|,C|upstream_gene_variant|MODIFIER|cupC1|PA14_51470|transcript|ABJ10156.1|protein_coding||c.-2175C>G|||||2175|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_51480|PA14_51480|transcript|ABJ10155.1|protein_coding||c.-1353C>G|||||1353|,C|upstream_gene_variant|MODIFIER|PA14_51500|PA14_51500|transcript|ABJ10153.1|protein_coding||c.-262G>C|||||262|,C|upstream_gene_variant|MODIFIER|PA14_51550|PA14_51550|transcript|ABJ10148.1|protein_coding||c.-4954G>C|||||4954|,C|downstream_gene_variant|MODIFIER|PA14_51490|PA14_51490|transcript|ABJ10154.1|protein_coding||c.*116G>C|||||116|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_51510|PA14_51510|transcript|ABJ10152.1|protein_coding||c.*943C>G|||||943|,C|downstream_gene_variant|MODIFIER|spcU|PA14_51520|transcript|ABJ10151.1|protein_coding||c.*1740C>G|||||1740|,C|downstream_gene_variant|MODIFIER|exoU|PA14_51530|transcript|ABJ10150.1|protein_coding||c.*2150C>G|||||2150|,C|downstream_gene_variant|MODIFIER|PA14_51540|PA14_51540|transcript|ABJ10149.1|protein_coding||c.*4350C>G|||||4350|,C|intergenic_region|MODIFIER|PA14_51490-PA14_51500|PA14_51490-PA14_51500|intergenic_region|PA14_51490-PA14_51500|||n.4578807G>C|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:80:0:0:0,-7.46025 0:8:8,0:8:304:0:0:0,-27.7178 0:5:5,0:5:188:0:0:0,-17.2835 0:8:8,2:6:189:2:30:0,-14.4625 +Chromosome 4618036 . G C 8.57394E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=33;DPB=33;DPRA=1.0625;EPP=9.52472;EPPR=4.16842;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=34.1287;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=976;RO=30;RPL=3;RPP=9.52472;RPPR=5.61607;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=23;SRP=21.5402;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|purM|PA14_52040|transcript|ABJ10105.1|protein_coding|1/1|c.304G>C|p.Glu102Gln|304/1062|304/1062|102/353||,C|upstream_gene_variant|MODIFIER|rbn|PA14_51960|transcript|ABJ10111.1|protein_coding||c.-4152C>G|||||4152|,C|upstream_gene_variant|MODIFIER|PA14_52010|PA14_52010|transcript|ABJ10107.1|protein_coding||c.-1756C>G|||||1756|,C|upstream_gene_variant|MODIFIER|PA14_52020|PA14_52020|transcript|ABJ10106.1|protein_coding||c.-517C>G|||||517|,C|upstream_gene_variant|MODIFIER|purN|PA14_52050|transcript|ABJ10104.1|protein_coding||c.-758G>C|||||758|,C|upstream_gene_variant|MODIFIER|PA14_52060|PA14_52060|transcript|ABJ10103.1|protein_coding||c.-1419G>C|||||1419|,C|upstream_gene_variant|MODIFIER|PA14_52080|PA14_52080|transcript|ABJ10101.1|protein_coding||c.-2865G>C|||||2865|,C|upstream_gene_variant|MODIFIER|PA14_52090|PA14_52090|transcript|ABJ10100.1|protein_coding||c.-3110G>C|||||3110|,C|upstream_gene_variant|MODIFIER|PA14_52110|PA14_52110|transcript|ABJ10099.1|protein_coding||c.-3370G>C|||||3370|,C|upstream_gene_variant|MODIFIER|PA14_52120|PA14_52120|transcript|ABJ10098.1|protein_coding||c.-3789G>C|||||3789|,C|downstream_gene_variant|MODIFIER|PA14_51980|PA14_51980|transcript|ABJ10110.1|protein_coding||c.*3674G>C|||||3674|,C|downstream_gene_variant|MODIFIER|wrbA|PA14_51990|transcript|ABJ10109.1|protein_coding||c.*3081G>C|||||3081|,C|downstream_gene_variant|MODIFIER|PA14_52000|PA14_52000|transcript|ABJ10108.1|protein_coding||c.*2660G>C|||||2660|,C|downstream_gene_variant|MODIFIER|PA14_52070|PA14_52070|transcript|ABJ10102.1|protein_coding||c.*2189C>G|||||2189|,C|downstream_gene_variant|MODIFIER|PA14_52130|PA14_52130|transcript|ABJ10097.1|protein_coding||c.*4021C>G|||||4021| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,2:5:98:2:4:0,-8.62804 0:10:10,1:9:330:1:2:0,-29.8454 0:11:11,0:11:382:0:0:0,-34.6959 0:5:5,0:5:166:0:0:0,-15.2604 +Chromosome 4625021 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=55;DPB=55;DPRA=1.07692;EPP=13.8677;EPPR=4.57376;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=67.4951;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=55;QR=1583;RO=50;RPL=0;RPP=13.8677;RPPR=3.70517;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=33;SRP=14.1282;SRR=17;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|lpxO2|PA14_52150|transcript|ABJ10095.1|protein_coding|1/1|c.677A>G|p.Glu226Gly|677/939|677/939|226/312||,G|upstream_gene_variant|MODIFIER|PA14_52070|PA14_52070|transcript|ABJ10102.1|protein_coding||c.-4236T>C|||||4236|,G|upstream_gene_variant|MODIFIER|PA14_52130|PA14_52130|transcript|ABJ10097.1|protein_coding||c.-1636T>C|||||1636|,G|upstream_gene_variant|MODIFIER|yaiL|PA14_52140|transcript|ABJ10096.1|protein_coding||c.-909T>C|||||909|,G|downstream_gene_variant|MODIFIER|PA14_52060|PA14_52060|transcript|ABJ10103.1|protein_coding||c.*4850A>G|||||4850|,G|downstream_gene_variant|MODIFIER|PA14_52080|PA14_52080|transcript|ABJ10101.1|protein_coding||c.*3887A>G|||||3887|,G|downstream_gene_variant|MODIFIER|PA14_52090|PA14_52090|transcript|ABJ10100.1|protein_coding||c.*3621A>G|||||3621|,G|downstream_gene_variant|MODIFIER|PA14_52110|PA14_52110|transcript|ABJ10099.1|protein_coding||c.*3289A>G|||||3289|,G|downstream_gene_variant|MODIFIER|PA14_52120|PA14_52120|transcript|ABJ10098.1|protein_coding||c.*3005A>G|||||3005|,G|downstream_gene_variant|MODIFIER|mazG|PA14_52160|transcript|ABJ10094.1|protein_coding||c.*305T>C|||||305|,G|downstream_gene_variant|MODIFIER|relA|PA14_52180|transcript|ABJ10093.1|protein_coding||c.*1240T>C|||||1240|,G|downstream_gene_variant|MODIFIER|ygcA|PA14_52190|transcript|ABJ10092.1|protein_coding||c.*3568T>C|||||3568|,G|downstream_gene_variant|MODIFIER|cysM|PA14_52210|transcript|ABJ10091.1|protein_coding||c.*4929T>C|||||4929| GT:DP:DPR:RO:QR:AO:QA:GL 0:13:13,0:13:408:0:0:0,-37.01 0:10:10,2:8:255:2:26:0,-20.786 0:13:13,1:12:364:1:2:0,-32.8463 0:19:19,2:17:556:2:27:0,-47.7704 +Chromosome 4635943 . C A 3.45847E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=26;DPB=26;DPRA=1.88889;EPP=9.52472;EPPR=10.6577;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=30.2053;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=62;QR=728;RO=23;RPL=0;RPP=9.52472;RPPR=5.3706;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=4;SRP=24.253;SRR=19;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|lemA|PA14_52260|transcript|ABJ10087.1|protein_coding|1/1|c.139C>A|p.Gln47Lys|139/2778|139/2778|47/925||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|pirA|PA14_52230|transcript|ABJ10090.1|protein_coding||c.-2616G>T|||||2616|,A|upstream_gene_variant|MODIFIER|pirS|PA14_52240|transcript|ABJ10089.1|protein_coding||c.-1043G>T|||||1043|,A|upstream_gene_variant|MODIFIER|pirR|PA14_52250|transcript|ABJ10088.1|protein_coding||c.-324G>T|||||324|,A|upstream_gene_variant|MODIFIER|ldhA|PA14_52270|transcript|ABJ10086.1|protein_coding||c.-2642C>A|||||2642|,A|upstream_gene_variant|MODIFIER|PA14_52280|PA14_52280|transcript|ABJ10085.1|protein_coding||c.-3667C>A|||||3667|,A|upstream_gene_variant|MODIFIER|PA14_52290|PA14_52290|transcript|ABJ10084.1|protein_coding||c.-4160C>A|||||4160|,A|upstream_gene_variant|MODIFIER|PA14_52300|PA14_52300|transcript|ABJ10083.1|protein_coding||c.-4680C>A|||||4680| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:79:0:0:0,-7.36758 0:7:7,2:5:191:2:32:0,-14.5177 0:6:6,0:6:212:0:0:0,-19.4228 0:10:10,1:9:246:1:30:0,-19.4049 +Chromosome 4648286 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=10;CIGAR=1X;DP=49;DPB=49;DPRA=1.48148;EPP=24.725;EPPR=7.52028;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=54.3353;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=130;QR=1388;RO=39;RPL=10;RPP=24.725;RPPR=7.52028;RPR=0;RUN=1;SAF=10;SAP=24.725;SAR=0;SRF=14;SRP=9.74743;SRR=25;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_52370|PA14_52370|transcript|ABJ10078.1|protein_coding|1/1|c.694T>C|p.Ser232Pro|694/1284|694/1284|232/427||,C|upstream_gene_variant|MODIFIER|dinP|PA14_52310|transcript|ABJ10082.1|protein_coding||c.-4679A>G|||||4679|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|tRNA|EBG00001225101|transcript|EBT00001793378.1|protein_coding||c.-4459A>G|||||4459|WARNING_TRANSCRIPT_INCOMPLETE,C|upstream_gene_variant|MODIFIER|PA14_52340|PA14_52340|transcript|ABJ10080.1|protein_coding||c.-3589A>G|||||3589|,C|upstream_gene_variant|MODIFIER|PA14_52380|PA14_52380|transcript|ABJ10077.1|protein_coding||c.-749T>C|||||749|,C|upstream_gene_variant|MODIFIER|yliG|PA14_52420|transcript|ABJ10075.1|protein_coding||c.-3503T>C|||||3503|,C|upstream_gene_variant|MODIFIER|yehS|PA14_52430|transcript|ABJ10074.1|protein_coding||c.-4888T>C|||||4888|,C|downstream_gene_variant|MODIFIER|PA14_52320|PA14_52320|transcript|PA14_52320-1.1|protein_coding||c.*4459T>C|||||4459|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|PA14_52330|PA14_52330|transcript|ABJ10081.1|protein_coding||c.*3963T>C|||||3963|,C|downstream_gene_variant|MODIFIER|PA14_52350|PA14_52350|transcript|ABJ10079.1|protein_coding||c.*695T>C|||||695|,C|downstream_gene_variant|MODIFIER|kup|PA14_52400|transcript|ABJ10076.1|protein_coding||c.*1352A>G|||||1352| GT:DP:DPR:RO:QR:AO:QA:GL 0:12:12,3:9:294:3:77:0,-19.5857 0:9:9,0:9:347:0:0:0,-31.5868 0:18:18,3:15:537:3:6:0,-48.0877 0:10:10,4:6:210:4:47:0,-14.8859 +Chromosome 4648857 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=40;DPB=40;DPRA=1;EPP=7.35324;EPPR=8.7247;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=52.0663;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=1284;RO=38;RPL=0;RPP=7.35324;RPPR=6.66752;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=11;SRP=17.6392;SRR=27;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_52370|PA14_52370|transcript|ABJ10078.1|protein_coding|1/1|c.1265A>G|p.Glu422Gly|1265/1284|1265/1284|422/427||,G|upstream_gene_variant|MODIFIER|PA14_52340|PA14_52340|transcript|ABJ10080.1|protein_coding||c.-4160T>C|||||4160|,G|upstream_gene_variant|MODIFIER|PA14_52380|PA14_52380|transcript|ABJ10077.1|protein_coding||c.-178A>G|||||178|,G|upstream_gene_variant|MODIFIER|yliG|PA14_52420|transcript|ABJ10075.1|protein_coding||c.-2932A>G|||||2932|,G|upstream_gene_variant|MODIFIER|yehS|PA14_52430|transcript|ABJ10074.1|protein_coding||c.-4317A>G|||||4317|,G|upstream_gene_variant|MODIFIER|PA14_52440|PA14_52440|transcript|ABJ10073.1|protein_coding||c.-4771A>G|||||4771|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_52330|PA14_52330|transcript|ABJ10081.1|protein_coding||c.*4534A>G|||||4534|,G|downstream_gene_variant|MODIFIER|PA14_52350|PA14_52350|transcript|ABJ10079.1|protein_coding||c.*1266A>G|||||1266|,G|downstream_gene_variant|MODIFIER|kup|PA14_52400|transcript|ABJ10076.1|protein_coding||c.*781T>C|||||781| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,2:8:211:2:30:0,-16.3932 0:7:7,0:7:239:0:0:0,-21.83 0:11:11,0:11:373:0:0:0,-33.8856 0:12:12,0:12:461:0:0:0,-41.839 +Chromosome 4650449 . A G 5.84647E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=63;DPB=63;DPRA=0.716667;EPP=11.6962;EPPR=28.3192;GTI=0;LEN=1;MEANALT=1.33333;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=55.0289;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=35;QR=1487;RO=58;RPL=0;RPP=11.6962;RPPR=3.0103;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=17;SRP=24.5753;SRR=41;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|kup|PA14_52400|transcript|ABJ10076.1|protein_coding|1/1|c.1094T>C|p.Leu365Pro|1094/1905|1094/1905|365/634||,G|upstream_gene_variant|MODIFIER|yliG|PA14_52420|transcript|ABJ10075.1|protein_coding||c.-1340A>G|||||1340|,G|upstream_gene_variant|MODIFIER|yehS|PA14_52430|transcript|ABJ10074.1|protein_coding||c.-2725A>G|||||2725|,G|upstream_gene_variant|MODIFIER|PA14_52440|PA14_52440|transcript|ABJ10073.1|protein_coding||c.-3179A>G|||||3179|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_52350|PA14_52350|transcript|ABJ10079.1|protein_coding||c.*2858A>G|||||2858|,G|downstream_gene_variant|MODIFIER|PA14_52370|PA14_52370|transcript|ABJ10078.1|protein_coding||c.*1573A>G|||||1573|,G|downstream_gene_variant|MODIFIER|PA14_52380|PA14_52380|transcript|ABJ10077.1|protein_coding||c.*866A>G|||||866|,G|downstream_gene_variant|MODIFIER|mgtE|PA14_52460|transcript|ABJ10072.1|protein_coding||c.*3621T>C|||||3621| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,2:5:156:2:4:0,-13.9652 0:19:19,1:17:394:1:15:0,-34.2299 0:17:17,1:16:373:1:16:0,-32.186 0:20:20,0:20:564:0:0:0,-51.0082 +Chromosome 4683714 . A C 6.86434E-7 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=29;DPB=29;DPRA=1.57895;EPP=7.35324;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.3333;NS=4;NUMALT=1;ODDS=15.6603;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=834;RO=27;RPL=2;RPP=7.35324;RPPR=3.09072;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=14;SRP=3.09072;SRR=13;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|dctQ|PA14_52820|transcript|ABJ10045.1|protein_coding|1/1|c.308T>G|p.Val103Gly|308/639|308/639|103/212||,C|upstream_gene_variant|MODIFIER|aotJ|PA14_52790|transcript|ABJ10048.1|protein_coding||c.-4289T>G|||||4289|,C|upstream_gene_variant|MODIFIER|P6|EBG00001225057|transcript|EBT00001793448.1|sRNA||n.-3768T>G|||||3768|,C|upstream_gene_variant|MODIFIER|acsA|PA14_52800|transcript|ABJ10047.1|protein_coding||c.-1793T>G|||||1793|,C|upstream_gene_variant|MODIFIER|dctM|PA14_52810|transcript|ABJ10046.1|protein_coding||c.-328T>G|||||328|,C|downstream_gene_variant|MODIFIER|dctP|PA14_52840|transcript|ABJ10044.1|protein_coding||c.*356T>G|||||356|,C|downstream_gene_variant|MODIFIER|PA14_52850|PA14_52850|transcript|ABJ10043.1|protein_coding||c.*1465T>G|||||1465|,C|downstream_gene_variant|MODIFIER|PA14_52870|PA14_52870|transcript|ABJ10042.1|protein_coding||c.*2303T>G|||||2303|,C|downstream_gene_variant|MODIFIER|PA14_52880|PA14_52880|transcript|ABJ10041.1|protein_coding||c.*3561T>G|||||3561|,C|downstream_gene_variant|MODIFIER|PA14_52890|PA14_52890|transcript|ABJ10040.1|protein_coding||c.*4952T>G|||||4952| GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:2:0:0:0,-0.2 0:7:7,0:7:232:0:0:0,-21.1937 0:10:10,2:8:265:2:4:0,-23.7838 0:11:11,0:11:335:0:0:0,-30.4316 +Chromosome 4687259 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=6;CIGAR=1X;DP=36;DPB=36;DPRA=1.16667;EPP=16.0391;EPPR=4.16842;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=47.3421;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=25;QR=959;RO=30;RPL=0;RPP=16.0391;RPPR=3.29983;RPR=6;RUN=1;SAF=0;SAP=16.0391;SAR=6;SRF=11;SRP=7.64277;SRR=19;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|dctM|PA14_52810|transcript|ABJ10046.1|protein_coding||c.-3873G>C|||||3873|,G|upstream_gene_variant|MODIFIER|dctQ|PA14_52820|transcript|ABJ10045.1|protein_coding||c.-3238G>C|||||3238|,G|upstream_gene_variant|MODIFIER|dctP|PA14_52840|transcript|ABJ10044.1|protein_coding||c.-2194G>C|||||2194|,G|upstream_gene_variant|MODIFIER|PA14_52850|PA14_52850|transcript|ABJ10043.1|protein_coding||c.-1253G>C|||||1253|,G|upstream_gene_variant|MODIFIER|PA14_52870|PA14_52870|transcript|ABJ10042.1|protein_coding||c.-40G>C|||||40|,G|upstream_gene_variant|MODIFIER|PA14_52920|PA14_52920|transcript|ABJ10037.1|protein_coding||c.-3952C>G|||||3952|,G|downstream_gene_variant|MODIFIER|PA14_52880|PA14_52880|transcript|ABJ10041.1|protein_coding||c.*16G>C|||||16|,G|downstream_gene_variant|MODIFIER|PA14_52890|PA14_52890|transcript|ABJ10040.1|protein_coding||c.*1407G>C|||||1407|,G|downstream_gene_variant|MODIFIER|PA14_52900|PA14_52900|transcript|ABJ10039.1|protein_coding||c.*1802G>C|||||1802|,G|downstream_gene_variant|MODIFIER|PA14_52910|PA14_52910|transcript|ABJ10038.1|protein_coding||c.*3008G>C|||||3008|,G|downstream_gene_variant|MODIFIER|PA14_52930|PA14_52930|transcript|ABJ10036.1|protein_coding||c.*4982G>C|||||4982|,G|intergenic_region|MODIFIER|PA14_52870-PA14_52880|PA14_52870-PA14_52880|intergenic_region|PA14_52870-PA14_52880|||n.4687259C>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,2:5:154:2:4:0,-13.7767 0:10:10,1:9:307:1:15:0,-26.4479 0:8:8,0:8:194:0:0:0,-17.6892 0:11:11,3:8:304:3:6:0,-27.1574 +Chromosome 4697358 . G C 6.30043E-12 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=23;DPB=23;DPRA=0.916667;EPP=9.52472;EPPR=6.91895;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=27.3065;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=564;RO=20;RPL=3;RPP=9.52472;RPPR=18.6449;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=13;SRP=6.91895;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|phhR|PA14_52980|transcript|ABJ10033.1|protein_coding|1/1|c.555C>G|p.Arg185Arg|555/1560|555/1560|185/519||,C|upstream_gene_variant|MODIFIER|PA14_52930|PA14_52930|transcript|ABJ10036.1|protein_coding||c.-4173C>G|||||4173|,C|upstream_gene_variant|MODIFIER|phhA|PA14_52990|transcript|ABJ10032.1|protein_coding||c.-839G>C|||||839|,C|upstream_gene_variant|MODIFIER|phhB|PA14_53000|transcript|ABJ10031.1|protein_coding||c.-1732G>C|||||1732|,C|upstream_gene_variant|MODIFIER|phhC|PA14_53010|transcript|ABJ10030.1|protein_coding||c.-2085G>C|||||2085|,C|upstream_gene_variant|MODIFIER|pbpG|PA14_53020|transcript|ABJ10029.1|protein_coding||c.-3599G>C|||||3599|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_52940|PA14_52940|transcript|ABJ10035.1|protein_coding||c.*1758G>C|||||1758|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_52960|PA14_52960|transcript|ABJ10034.1|protein_coding||c.*1223G>C|||||1223|,C|downstream_gene_variant|MODIFIER|yaeJ|PA14_53030|transcript|ABJ10028.1|protein_coding||c.*4554C>G|||||4554| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,1:2:75:1:2:0,-6.91959 0:7:7,0:7:224:0:0:0,-20.4667 0:8:8,2:6:177:2:4:0,-15.836 0:5:5,0:5:88:0:0:0,-8.09314 +Chromosome 4723244 . CGACA GGACG 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X3M1X;DP=25;DPB=27.8;DPRA=0.75;EPP=7.35324;EPPR=9.32731;GTI=0;LEN=5;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=46.6969;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=140;PRO=4;QA=26;QR=762;RO=22;RPL=0;RPP=7.35324;RPPR=4.58955;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=12;SRP=3.40511;SRR=10;TYPE=complex;technology.ILLUMINA=1;ANN=GGACG|missense_variant|MODERATE|trxB2|PA14_53290|transcript|ABJ10008.1|protein_coding|1/1|c.477_481delTGTCGinsCGTCC|p.AlaValGlu159AlaValGln|481/951|477/951|159/316||,GGACG|upstream_gene_variant|MODIFIER|PA14_53270|PA14_53270|transcript|ABJ10009.1|protein_coding||c.-728_-724delTGTCGinsCGTCC|||||724|,GGACG|upstream_gene_variant|MODIFIER|PA14_53310|PA14_53310|transcript|ABJ10006.1|protein_coding||c.-1309_-1305delCGACAinsGGACG|||||1309|,GGACG|upstream_gene_variant|MODIFIER|PA14_53330|PA14_53330|transcript|ABJ10005.1|protein_coding||c.-3439_-3435delCGACAinsGGACG|||||3439|,GGACG|upstream_gene_variant|MODIFIER|PA14_53340|PA14_53340|transcript|ABJ10004.1|protein_coding||c.-4558_-4554delCGACAinsGGACG|||||4558|,GGACG|downstream_gene_variant|MODIFIER|fumC2|PA14_53220|transcript|ABJ10013.1|protein_coding||c.*4358_*4362delCGACAinsGGACG|||||4358|,GGACG|downstream_gene_variant|MODIFIER|PA14_53230|PA14_53230|transcript|ABJ10012.1|protein_coding||c.*3742_*3746delCGACAinsGGACG|||||3742|,GGACG|downstream_gene_variant|MODIFIER|cpbD|PA14_53250|transcript|ABJ10011.1|protein_coding||c.*2293_*2297delCGACAinsGGACG|||||2293|,GGACG|downstream_gene_variant|MODIFIER|PA14_53260|PA14_53260|transcript|ABJ10010.1|protein_coding||c.*1154_*1158delCGACAinsGGACG|||||1154|,GGACG|downstream_gene_variant|MODIFIER|PA14_53300|PA14_53300|transcript|ABJ10007.1|protein_coding||c.*610_*614delTGTCGinsCGTCC|||||614| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:160:0:0:0,-17.8633 0:6:6,0:6:200:0:0:0,-18.3256 0:9:9,0:8:293:0:0:0,-29.8099 0:5:5,2:3:109:2:26:0,-13.9887 +Chromosome 4738132 . T C 4.53559E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=7;CIGAR=1X;DP=60;DPB=60;DPRA=1;EPP=18.2106;EPPR=3.05127;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=40.7159;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=25;QR=1572;RO=53;RPL=7;RPP=18.2106;RPPR=9.93443;RPR=0;RUN=1;SAF=7;SAP=18.2106;SAR=0;SRF=33;SRP=9.93443;SRR=20;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|slyD|PA14_53430|transcript|ABJ09996.1|protein_coding|1/1|c.386A>G|p.Gln129Arg|386/486|386/486|129/161||,C|upstream_gene_variant|MODIFIER|PA14_53390|PA14_53390|transcript|ABJ10000.1|protein_coding||c.-2873A>G|||||2873|,C|upstream_gene_variant|MODIFIER|PA14_53400|PA14_53400|transcript|ABJ09999.1|protein_coding||c.-1570A>G|||||1570|,C|upstream_gene_variant|MODIFIER|PA14_53410|PA14_53410|transcript|ABJ09998.1|protein_coding||c.-939A>G|||||939|,C|upstream_gene_variant|MODIFIER|btuE|PA14_53420|transcript|ABJ09997.1|protein_coding||c.-306A>G|||||306|,C|upstream_gene_variant|MODIFIER|PA14_53450|PA14_53450|transcript|ABJ09995.1|protein_coding||c.-492T>C|||||492|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|P5|EBG00001225038|transcript|EBT00001793408.1|sRNA||n.-610T>C|||||610|,C|upstream_gene_variant|MODIFIER|ackA|PA14_53470|transcript|ABJ09994.1|protein_coding||c.-692T>C|||||692|,C|upstream_gene_variant|MODIFIER|pta|PA14_53480|transcript|ABJ09993.1|protein_coding||c.-1939T>C|||||1939|,C|upstream_gene_variant|MODIFIER|PA14_53490|PA14_53490|transcript|ABJ09992.1|protein_coding||c.-4180T>C|||||4180|,C|downstream_gene_variant|MODIFIER|PA14_53380|PA14_53380|transcript|ABJ10001.1|protein_coding||c.*3836T>C|||||3836| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,3:7:110:3:17:0,-8.46402 0:15:15,0:15:480:0:0:0,-43.491 0:25:25,3:22:685:3:6:0,-61.361 0:10:10,1:9:297:1:2:0,-26.843 +Chromosome 4748041 . A G 1.13031E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=32;DPB=32;DPRA=0.692308;EPP=7.35324;EPPR=4.16842;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=48.4295;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1072;RO=30;RPL=0;RPP=7.35324;RPPR=4.16842;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=12;SRP=5.61607;SRR=18;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|PA14_53550|PA14_53550|transcript|ABJ09986.1|protein_coding|1/1|c.663T>C|p.Ala221Ala|663/684|663/684|221/227||,G|upstream_gene_variant|MODIFIER|PA14_53500|PA14_53500|transcript|ABJ09991.1|protein_coding||c.-4032T>C|||||4032|,G|upstream_gene_variant|MODIFIER|ycbL|PA14_53510|transcript|ABJ09990.1|protein_coding||c.-3285T>C|||||3285|,G|upstream_gene_variant|MODIFIER|oruR|PA14_53520|transcript|ABJ09989.1|protein_coding||c.-2164T>C|||||2164|,G|upstream_gene_variant|MODIFIER|PA14_53540|PA14_53540|transcript|ABJ09987.1|protein_coding||c.-130T>C|||||130|,G|upstream_gene_variant|MODIFIER|PA14_53560|PA14_53560|transcript|ABJ09985.1|protein_coding||c.-750A>G|||||750|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_53580|PA14_53580|transcript|ABJ09983.1|protein_coding||c.-3640A>G|||||3640|,G|upstream_gene_variant|MODIFIER|PA14_53590|PA14_53590|transcript|ABJ09982.1|protein_coding||c.-4247A>G|||||4247|,G|downstream_gene_variant|MODIFIER|PA14_53490|PA14_53490|transcript|ABJ09992.1|protein_coding||c.*4815A>G|||||4815|,G|downstream_gene_variant|MODIFIER|PA14_53530|PA14_53530|transcript|ABJ09988.1|protein_coding||c.*1206A>G|||||1206|,G|downstream_gene_variant|MODIFIER|tmRNA|EBG00001225133|transcript|EBT00001793466.1|lincRNA||n.*1690T>C|||||1690|,G|downstream_gene_variant|MODIFIER|PA14_53570|PA14_53570|transcript|ABJ09984.1|protein_coding||c.*2505T>C|||||2505| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:185:0:0:0,-17.0069 0:8:8,0:8:270:0:0:0,-24.6218 0:6:6,2:4:153:2:4:0,-13.7607 0:13:13,0:13:464:0:0:0,-42.0879 +Chromosome 4780515 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=35;DPB=35;DPRA=1.03846;EPP=7.35324;EPPR=14.1309;GTI=0;LEN=1;MEANALT=1;MQM=58.5;MQMR=60;NS=4;NUMALT=1;ODDS=54.0598;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=29;QR=1060;RO=33;RPL=2;RPP=7.35324;RPPR=3.60252;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=22;SRP=10.9724;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|PA14_53900|PA14_53900|transcript|ABJ09953.1|protein_coding|1/1|c.1737G>T|p.Val579Val|1737/1992|1737/1992|579/663||,T|upstream_gene_variant|MODIFIER|PA14_53860|PA14_53860|transcript|ABJ09957.1|protein_coding||c.-4614C>A|||||4614|,T|upstream_gene_variant|MODIFIER|PA14_53870|PA14_53870|transcript|ABJ09956.1|protein_coding||c.-4205C>A|||||4205|,T|upstream_gene_variant|MODIFIER|PA14_53880|PA14_53880|transcript|ABJ09955.1|protein_coding||c.-2685C>A|||||2685|,T|upstream_gene_variant|MODIFIER|PA14_53890|PA14_53890|transcript|ABJ09954.1|protein_coding||c.-2155C>A|||||2155|,T|upstream_gene_variant|MODIFIER|PA14_53920|PA14_53920|transcript|ABJ09951.1|protein_coding||c.-1037G>T|||||1037|,T|upstream_gene_variant|MODIFIER|prpB|PA14_53940|transcript|ABJ09950.1|protein_coding||c.-1770G>T|||||1770|,T|upstream_gene_variant|MODIFIER|prpC|PA14_53950|transcript|ABJ09949.1|protein_coding||c.-2759G>T|||||2759|,T|upstream_gene_variant|MODIFIER|PA14_53970|PA14_53970|transcript|ABJ09948.1|protein_coding||c.-4017G>T|||||4017|,T|downstream_gene_variant|MODIFIER|pmtA|PA14_53910|transcript|ABJ09952.1|protein_coding||c.*269C>A|||||269| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:224:0:0:0,-20.4297 0:9:9,0:9:301:0:0:0,-27.4077 0:9:9,0:9:315:0:0:0,-28.6793 0:9:9,2:7:220:2:29:0,-17.3466 +Chromosome 4786181 . C G 1.13991E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=22;DPB=22;DPRA=2.14286;EPP=9.52472;EPPR=4.03889;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=37.2317;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=735;RO=19;RPL=0;RPP=9.52472;RPPR=12.2676;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=9;SRP=3.12459;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|PA14_53970|PA14_53970|transcript|ABJ09948.1|protein_coding|1/1|c.1650C>G|p.Gly550Gly|1650/2607|1650/2607|550/868||,G|upstream_gene_variant|MODIFIER|pmtA|PA14_53910|transcript|ABJ09952.1|protein_coding||c.-4747G>C|||||4747|,G|upstream_gene_variant|MODIFIER|PA14_53980|PA14_53980|transcript|ABJ09947.1|protein_coding||c.-1076C>G|||||1076|,G|upstream_gene_variant|MODIFIER|prpD|PA14_54000|transcript|ABJ09946.1|protein_coding||c.-2398C>G|||||2398|,G|upstream_gene_variant|MODIFIER|PA14_54030|PA14_54030|transcript|ABJ09944.1|protein_coding||c.-4755C>G|||||4755|,G|downstream_gene_variant|MODIFIER|PA14_53920|PA14_53920|transcript|ABJ09951.1|protein_coding||c.*3907C>G|||||3907|,G|downstream_gene_variant|MODIFIER|prpB|PA14_53940|transcript|ABJ09950.1|protein_coding||c.*3000C>G|||||3000|,G|downstream_gene_variant|MODIFIER|prpC|PA14_53950|transcript|ABJ09949.1|protein_coding||c.*1780C>G|||||1780|,G|downstream_gene_variant|MODIFIER|PA14_54010|PA14_54010|transcript|ABJ09945.1|protein_coding||c.*3860G>C|||||3860| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:119:0:0:0,-11.0954 0:8:8,2:6:226:2:17:0,-19.086 0:7:7,1:6:232:1:2:0,-21.0475 0:4:4,0:4:158:0:0:0,-14.6007 +Chromosome 4790911 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=39;DPB=39;DPRA=0.625;EPP=9.52472;EPPR=14.8328;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=49.9193;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=1219;RO=36;RPL=0;RPP=9.52472;RPPR=3.25157;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=20;SRP=3.9754;SRR=16;TYPE=snp;technology.ILLUMINA=1;ANN=C|upstream_gene_variant|MODIFIER|PA14_54010|PA14_54010|transcript|ABJ09945.1|protein_coding||c.-82A>G|||||82|,C|upstream_gene_variant|MODIFIER|PA14_54030|PA14_54030|transcript|ABJ09944.1|protein_coding||c.-25T>C|||||25|,C|upstream_gene_variant|MODIFIER|PA14_54080|PA14_54080|transcript|ABJ09940.1|protein_coding||c.-3738T>C|||||3738|,C|downstream_gene_variant|MODIFIER|PA14_53970|PA14_53970|transcript|ABJ09948.1|protein_coding||c.*3773T>C|||||3773|,C|downstream_gene_variant|MODIFIER|PA14_53980|PA14_53980|transcript|ABJ09947.1|protein_coding||c.*2467T>C|||||2467|,C|downstream_gene_variant|MODIFIER|prpD|PA14_54000|transcript|ABJ09946.1|protein_coding||c.*848T>C|||||848|,C|downstream_gene_variant|MODIFIER|PA14_54040|PA14_54040|transcript|ABJ09943.1|protein_coding||c.*966A>G|||||966|,C|downstream_gene_variant|MODIFIER|PA14_54050|PA14_54050|transcript|ABJ09942.1|protein_coding||c.*2704A>G|||||2704|,C|downstream_gene_variant|MODIFIER|PA14_54070|PA14_54070|transcript|ABJ09941.1|protein_coding||c.*3374A>G|||||3374|,C|intergenic_region|MODIFIER|PA14_54010-PA14_54030|PA14_54010-PA14_54030|intergenic_region|PA14_54010-PA14_54030|||n.4790911T>C|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,2:4:154:2:4:0,-13.8526 0:8:8,0:8:306:0:0:0,-27.8989 0:16:16,0:16:481:0:0:0,-43.5615 0:9:9,1:8:278:1:2:0,-25.1453 +Chromosome 4805668 . A G 5.37537E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=21;DPB=21;DPRA=1.5;EPP=7.35324;EPPR=4.03889;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=34.7153;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=651;RO=19;RPL=0;RPP=7.35324;RPPR=3.12459;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=8;SRP=4.03889;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|putA|PA14_54170|transcript|ABJ09934.1|protein_coding|1/1|c.499T>C|p.Ser167Pro|499/3183|499/3183|167/1060||,G|upstream_gene_variant|MODIFIER|putP|PA14_54150|transcript|ABJ09935.1|protein_coding||c.-2996T>C|||||2996|,G|upstream_gene_variant|MODIFIER|PA14_54180|PA14_54180|transcript|ABJ09933.1|protein_coding||c.-962A>G|||||962|,G|upstream_gene_variant|MODIFIER|PA14_54210|PA14_54210|transcript|ABJ09931.1|protein_coding||c.-4090A>G|||||4090|,G|downstream_gene_variant|MODIFIER|PA14_54130|PA14_54130|transcript|ABJ09936.1|protein_coding||c.*4661A>G|||||4661|,G|downstream_gene_variant|MODIFIER|pruR|PA14_54190|transcript|ABJ09932.1|protein_coding||c.*3147T>C|||||3147| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:112:0:0:0,-10.4457 0:7:7,2:5:141:2:15:0,-11.5411 0:3:3,0:3:103:0:0:0,-9.60777 0:8:8,0:8:295:0:0:0,-26.9014 +Chromosome 4808167 . T C 1.15119E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=30;DPB=30;DPRA=0.913043;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=40.4201;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=818;RO=28;RPL=2;RPP=7.35324;RPPR=3.0103;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=22;SRP=22.8638;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_54180|PA14_54180|transcript|ABJ09933.1|protein_coding|1/1|c.1538T>C|p.Leu513Pro|1538/2064|1538/2064|513/687||,C|upstream_gene_variant|MODIFIER|putA|PA14_54170|transcript|ABJ09934.1|protein_coding||c.-2001A>G|||||2001|,C|upstream_gene_variant|MODIFIER|PA14_54210|PA14_54210|transcript|ABJ09931.1|protein_coding||c.-1591T>C|||||1591|,C|upstream_gene_variant|MODIFIER|icp|PA14_54220|transcript|ABJ09930.1|protein_coding||c.-4101T>C|||||4101|,C|upstream_gene_variant|MODIFIER|PA14_54230|PA14_54230|transcript|ABJ09929.1|protein_coding||c.-4604T>C|||||4604|,C|downstream_gene_variant|MODIFIER|pruR|PA14_54190|transcript|ABJ09932.1|protein_coding||c.*648A>G|||||648| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,2:5:133:2:17:0,-10.6123 0:4:4,0:4:129:0:0:0,-11.9243 0:9:9,0:9:241:0:0:0,-21.9495 0:10:10,0:10:315:0:0:0,-28.6512 +Chromosome 4813503 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=58;DPB=58;DPRA=0.55102;EPP=7.35324;EPPR=15.5738;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=56.6115;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=48;QR=1970;RO=56;RPL=0;RPP=7.35324;RPPR=25.3454;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=47;SRP=59.0033;SRR=9;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|PA14_54230|PA14_54230|transcript|ABJ09929.1|protein_coding|1/1|c.733T>A|p.Tyr245Asn|733/753|733/753|245/250||,A|upstream_gene_variant|MODIFIER|pruR|PA14_54190|transcript|ABJ09932.1|protein_coding||c.-3936A>T|||||3936|,A|upstream_gene_variant|MODIFIER|PA14_54240|PA14_54240|transcript|ABJ09928.1|protein_coding||c.-152T>A|||||152|,A|upstream_gene_variant|MODIFIER|yecO|PA14_54260|transcript|ABJ09927.1|protein_coding||c.-829T>A|||||829|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|yecP|PA14_54270|transcript|ABJ09926.1|protein_coding||c.-1566T>A|||||1566|,A|downstream_gene_variant|MODIFIER|PA14_54180|PA14_54180|transcript|ABJ09933.1|protein_coding||c.*4810T>A|||||4810|,A|downstream_gene_variant|MODIFIER|PA14_54210|PA14_54210|transcript|ABJ09931.1|protein_coding||c.*1346T>A|||||1346|,A|downstream_gene_variant|MODIFIER|icp|PA14_54220|transcript|ABJ09930.1|protein_coding||c.*831T>A|||||831|,A|downstream_gene_variant|MODIFIER|pdxJ|PA14_54290|transcript|ABJ09925.1|protein_coding||c.*2625A>T|||||2625|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|recO|PA14_54300|transcript|ABJ09924.1|protein_coding||c.*3364A>T|||||3364|,A|downstream_gene_variant|MODIFIER|era|PA14_54320|transcript|ABJ09923.1|protein_coding||c.*4126A>T|||||4126| GT:DP:DPR:RO:QR:AO:QA:GL 0:12:12,0:12:410:0:0:0,-37.2146 0:13:13,0:13:481:0:0:0,-43.6311 0:24:24,0:24:845:0:0:0,-76.361 0:9:9,2:7:234:2:48:0,-16.8231 +Chromosome 4823634 . C A 9.86082E-8 . AB=0;ABP=0;AC=1;AF=0.25;AN=4;AO=3;CIGAR=1X;DP=35;DPB=35;DPRA=0.590909;EPP=3.73412;EPPR=4.09604;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=17.6007;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1016;RO=32;RPL=1;RPP=3.73412;RPPR=4.09604;RPR=2;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=16;SRP=3.0103;SRR=16;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|mucD|PA14_54390|transcript|ABJ09918.1|protein_coding|1/1|c.372G>T|p.Val124Val|372/1425|372/1425|124/474||,A|upstream_gene_variant|MODIFIER|rnc|PA14_54330|transcript|ABJ09922.1|protein_coding||c.-4406G>T|||||4406|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|PA14_54340|PA14_54340|transcript|ABJ09921.1|protein_coding||c.-4032G>T|||||4032|,A|upstream_gene_variant|MODIFIER|lepB|PA14_54350|transcript|ABJ09920.1|protein_coding||c.-3008G>T|||||3008|,A|upstream_gene_variant|MODIFIER|lepA|PA14_54370|transcript|ABJ09919.1|protein_coding||c.-1203G>T|||||1203|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|nadB|PA14_54450|transcript|ABJ09913.1|protein_coding||c.-3428C>A|||||3428|,A|downstream_gene_variant|MODIFIER|mucC|PA14_54400|transcript|ABJ09917.1|protein_coding||c.*411G>T|||||411|,A|downstream_gene_variant|MODIFIER|mucB|PA14_54410|transcript|ABJ09916.1|protein_coding||c.*863G>T|||||863|,A|downstream_gene_variant|MODIFIER|mucA|PA14_54420|transcript|ABJ09915.1|protein_coding||c.*1822G>T|||||1822|,A|downstream_gene_variant|MODIFIER|algU|PA14_54430|transcript|ABJ09914.1|protein_coding||c.*2438G>T|||||2438| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,1:9:270:1:16:0,-22.9897 1:3:3,2:1:16:2:18:-0.110001,0 0:9:9,0:9:308:0:0:0,-28.0447 0:13:13,0:13:422:0:0:0,-38.2837 +Chromosome 4836369 . T C 3.19457E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=28;DPB=28;DPRA=1.15385;EPP=3.73412;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1.5;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=41.5642;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=45;QR=827;RO=24;RPL=2;RPP=3.73412;RPPR=12.0581;RPR=1;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=19;SRP=20.744;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_54550|PA14_54550|transcript|ABJ09904.1|protein_coding|1/1|c.269T>C|p.Leu90Pro|269/471|269/471|90/156||,C|upstream_gene_variant|MODIFIER|PA14_54500|PA14_54500|transcript|ABJ09908.1|protein_coding||c.-3488A>G|||||3488|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_54510|PA14_54510|transcript|ABJ09907.1|protein_coding||c.-2824A>G|||||2824|,C|upstream_gene_variant|MODIFIER|PA14_54570|PA14_54570|transcript|ABJ09903.1|protein_coding||c.-213T>C|||||213|,C|upstream_gene_variant|MODIFIER|PA14_54580|PA14_54580|transcript|ABJ09902.1|protein_coding||c.-1723T>C|||||1723|,C|downstream_gene_variant|MODIFIER|PA14_54490|PA14_54490|transcript|ABJ09909.1|protein_coding||c.*4878T>C|||||4878|,C|downstream_gene_variant|MODIFIER|opdH|PA14_54520|transcript|ABJ09906.1|protein_coding||c.*1330T>C|||||1330|,C|downstream_gene_variant|MODIFIER|PA14_54540|PA14_54540|transcript|ABJ09905.1|protein_coding||c.*317T>C|||||317|,C|downstream_gene_variant|MODIFIER|ung|PA14_54590|transcript|ABJ09901.1|protein_coding||c.*2886A>G|||||2886|,C|downstream_gene_variant|MODIFIER|PA14_54600|PA14_54600|transcript|ABJ09900.1|protein_coding||c.*3681A>G|||||3681|,C|downstream_gene_variant|MODIFIER|PA14_54610|PA14_54610|transcript|ABJ09899.1|protein_coding||c.*4559A>G|||||4559| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:273:0:0:0,-24.8929 0:5:5,0:5:163:0:0:0,-14.9859 0:5:5,1:4:157:1:16:0,-12.909 0:10:10,2:7:234:2:29:0,-18.6013 +Chromosome 4838412 . G T 0.0185884 . AB=0;ABP=0;AC=1;AF=0.333333;AN=3;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=2;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=5.45168;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=107;RO=4;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=1;SRP=5.18177;SRR=3;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_54580|PA14_54580|transcript|ABJ09902.1|protein_coding|1/1|c.321G>T|p.Met107Ile|321/1038|321/1038|107/345||,T|upstream_gene_variant|MODIFIER|PA14_54510|PA14_54510|transcript|ABJ09907.1|protein_coding||c.-4867C>A|||||4867|,T|upstream_gene_variant|MODIFIER|PA14_54620|PA14_54620|transcript|ABJ09898.1|protein_coding||c.-3530G>T|||||3530|,T|downstream_gene_variant|MODIFIER|opdH|PA14_54520|transcript|ABJ09906.1|protein_coding||c.*3373G>T|||||3373|,T|downstream_gene_variant|MODIFIER|PA14_54540|PA14_54540|transcript|ABJ09905.1|protein_coding||c.*2360G>T|||||2360|,T|downstream_gene_variant|MODIFIER|PA14_54550|PA14_54550|transcript|ABJ09904.1|protein_coding||c.*1841G>T|||||1841|,T|downstream_gene_variant|MODIFIER|PA14_54570|PA14_54570|transcript|ABJ09903.1|protein_coding||c.*313G>T|||||313|,T|downstream_gene_variant|MODIFIER|ung|PA14_54590|transcript|ABJ09901.1|protein_coding||c.*843C>A|||||843|,T|downstream_gene_variant|MODIFIER|PA14_54600|PA14_54600|transcript|ABJ09900.1|protein_coding||c.*1638C>A|||||1638|,T|downstream_gene_variant|MODIFIER|PA14_54610|PA14_54610|transcript|ABJ09899.1|protein_coding||c.*2516C>A|||||2516| GT:DP:DPR:RO:QR:AO:QA:GL . 0:2:2,0:2:74:0:0:0,-7.02543 1:3:3,2:1:2:2:31:-2.74497,0 0:1:1,0:1:31:0:0:0,-3.09945 +Chromosome 4844234 . A T 1.12304E-8 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=14;DPB=14;DPRA=5.4;EPP=7.35324;EPPR=5.9056;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=19.7753;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=426;RO=12;RPL=0;RPP=7.35324;RPPR=3.73412;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=7;SRP=3.73412;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_54630|PA14_54630|transcript|ABJ09897.1|protein_coding|1/1|c.773A>T|p.Gln258Leu|773/1164|773/1164|258/387||,T|upstream_gene_variant|MODIFIER|ung|PA14_54590|transcript|ABJ09901.1|protein_coding||c.-4284T>A|||||4284|,T|upstream_gene_variant|MODIFIER|PA14_54600|PA14_54600|transcript|ABJ09900.1|protein_coding||c.-3363T>A|||||3363|,T|upstream_gene_variant|MODIFIER|PA14_54610|PA14_54610|transcript|ABJ09899.1|protein_coding||c.-2395T>A|||||2395|,T|upstream_gene_variant|MODIFIER|PA14_54640|PA14_54640|transcript|ABJ09896.1|protein_coding||c.-457A>T|||||457|,T|upstream_gene_variant|MODIFIER|PA14_54660|PA14_54660|transcript|ABJ09895.1|protein_coding||c.-1334A>T|||||1334|,T|upstream_gene_variant|MODIFIER|PA14_54670|PA14_54670|transcript|ABJ09894.1|protein_coding||c.-2549A>T|||||2549|,T|upstream_gene_variant|MODIFIER|PA14_54680|PA14_54680|transcript|ABJ09893.1|protein_coding||c.-3838A>T|||||3838|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ywnB|PA14_54690|transcript|ABJ09892.1|protein_coding||c.-4262A>T|||||4262|,T|downstream_gene_variant|MODIFIER|PA14_54620|PA14_54620|transcript|ABJ09898.1|protein_coding||c.*784A>T|||||784|,T|downstream_gene_variant|MODIFIER|yjcS|PA14_54700|transcript|ABJ09891.1|protein_coding||c.*4938T>A|||||4938| GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:40:0:0:0,-3.99568 0:2:2,0:2:80:0:0:0,-7.59179 0:2:2,0:2:71:0:0:0,-6.74038 0:9:9,2:7:235:2:31:0,-18.5214 +Chromosome 4856807 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=37;DPB=37;DPRA=0.827586;EPP=7.35324;EPPR=12.2071;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=58.4474;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1255;RO=34;RPL=2;RPP=7.35324;RPPR=33.9218;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=17;SRP=3.0103;SRR=17;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|PA14_54810|PA14_54810|transcript|ABJ09881.1|protein_coding|1/1|c.10T>A|p.Ser4Thr|10/1044|10/1044|4/347||,A|upstream_gene_variant|MODIFIER|PA14_54720|PA14_54720|transcript|ABJ09889.1|protein_coding||c.-4381A>T|||||4381|,A|upstream_gene_variant|MODIFIER|PA14_54730|PA14_54730|transcript|ABJ09888.1|protein_coding||c.-4082A>T|||||4082|,A|upstream_gene_variant|MODIFIER|PA14_54740|PA14_54740|transcript|ABJ09887.1|protein_coding||c.-3516A>T|||||3516|,A|upstream_gene_variant|MODIFIER|PA14_54750|PA14_54750|transcript|ABJ09886.1|protein_coding||c.-3257A>T|||||3257|,A|upstream_gene_variant|MODIFIER|PA14_54820|PA14_54820|transcript|ABJ09880.1|protein_coding||c.-1114T>A|||||1114|,A|upstream_gene_variant|MODIFIER|PA14_54830|PA14_54830|transcript|ABJ09879.1|protein_coding||c.-2303T>A|||||2303|,A|upstream_gene_variant|MODIFIER|PA14_54840|PA14_54840|transcript|PA14_54840-1.1|protein_coding||c.-3336T>A|||||3336|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,A|upstream_gene_variant|MODIFIER|PA14_54850|PA14_54850|transcript|ABJ09878.1|protein_coding||c.-3606T>A|||||3606|,A|downstream_gene_variant|MODIFIER|PA14_54710|PA14_54710|transcript|ABJ09890.1|protein_coding||c.*4642T>A|||||4642|,A|downstream_gene_variant|MODIFIER|PA14_54760|PA14_54760|transcript|ABJ09885.1|protein_coding||c.*1942T>A|||||1942|,A|downstream_gene_variant|MODIFIER|PA14_54770|PA14_54770|transcript|ABJ09884.1|protein_coding||c.*1130T>A|||||1130|,A|downstream_gene_variant|MODIFIER|PA14_54790|PA14_54790|transcript|ABJ09883.1|protein_coding||c.*837T>A|||||837|,A|downstream_gene_variant|MODIFIER|rsuA|PA14_54800|transcript|ABJ09882.1|protein_coding||c.*145T>A|||||145|,A|downstream_gene_variant|MODIFIER|tRNA|EBG00001225168|transcript|EBT00001793511.1|protein_coding||c.*3336A>T|||||3336|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|PA14_54860|PA14_54860|transcript|ABJ09877.1|protein_coding||c.*4030A>T|||||4030|,A|downstream_gene_variant|MODIFIER|PA14_54870|PA14_54870|transcript|ABJ09876.1|protein_coding||c.*4801A>T|||||4801| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,2:6:227:2:17:0,-19.1733 0:10:10,0:10:366:0:0:0,-33.277 0:7:7,0:7:235:0:0:0,-21.4704 0:12:12,0:11:427:0:0:0,-38.3938 +Chromosome 4857934 . T C 1.14971E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=44;DPB=44;DPRA=1;EPP=11.6962;EPPR=3.22745;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=35.4172;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=73;QR=1145;RO=40;RPL=3;RPP=5.18177;RPPR=13.6505;RPR=1;RUN=1;SAF=3;SAP=5.18177;SAR=1;SRF=20;SRP=3.0103;SRR=20;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_54820|PA14_54820|transcript|ABJ09880.1|protein_coding|1/1|c.14T>C|p.Leu5Pro|14/738|14/738|5/245||,C|upstream_gene_variant|MODIFIER|PA14_54740|PA14_54740|transcript|ABJ09887.1|protein_coding||c.-4643A>G|||||4643|,C|upstream_gene_variant|MODIFIER|PA14_54750|PA14_54750|transcript|ABJ09886.1|protein_coding||c.-4384A>G|||||4384|,C|upstream_gene_variant|MODIFIER|PA14_54830|PA14_54830|transcript|ABJ09879.1|protein_coding||c.-1176T>C|||||1176|,C|upstream_gene_variant|MODIFIER|PA14_54840|PA14_54840|transcript|PA14_54840-1.1|protein_coding||c.-2209T>C|||||2209|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|upstream_gene_variant|MODIFIER|PA14_54850|PA14_54850|transcript|ABJ09878.1|protein_coding||c.-2479T>C|||||2479|,C|downstream_gene_variant|MODIFIER|PA14_54760|PA14_54760|transcript|ABJ09885.1|protein_coding||c.*3069T>C|||||3069|,C|downstream_gene_variant|MODIFIER|PA14_54770|PA14_54770|transcript|ABJ09884.1|protein_coding||c.*2257T>C|||||2257|,C|downstream_gene_variant|MODIFIER|PA14_54790|PA14_54790|transcript|ABJ09883.1|protein_coding||c.*1964T>C|||||1964|,C|downstream_gene_variant|MODIFIER|rsuA|PA14_54800|transcript|ABJ09882.1|protein_coding||c.*1272T>C|||||1272|,C|downstream_gene_variant|MODIFIER|PA14_54810|PA14_54810|transcript|ABJ09881.1|protein_coding||c.*93T>C|||||93|,C|downstream_gene_variant|MODIFIER|tRNA|EBG00001225168|transcript|EBT00001793511.1|protein_coding||c.*2209A>G|||||2209|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|PA14_54860|PA14_54860|transcript|ABJ09877.1|protein_coding||c.*2903A>G|||||2903|,C|downstream_gene_variant|MODIFIER|PA14_54870|PA14_54870|transcript|ABJ09876.1|protein_coding||c.*3674A>G|||||3674|,C|downstream_gene_variant|MODIFIER|PA14_54880|PA14_54880|transcript|ABJ09875.1|protein_coding||c.*4701A>G|||||4701| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,3:6:165:3:71:0,-8.49171 0:10:10,0:10:348:0:0:0,-31.6514 0:12:12,0:12:353:0:0:0,-32.0497 0:13:13,1:12:279:1:2:0,-25.1316 +Chromosome 4871159 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=10;CIGAR=1X;DP=107;DPB=107;DPRA=0;EPP=16.9077;EPPR=44.4026;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=154.929;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=125;QR=3158;RO=97;RPL=9;RPP=16.9077;RPPR=4.10723;RPR=1;RUN=1;SAF=10;SAP=24.725;SAR=0;SRF=49;SRP=3.03269;SRR=48;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_54920|PA14_54920|transcript|ABJ09871.1|protein_coding|1/1|c.809C>A|p.Ala270Glu|809/4464|809/4464|270/1487||,T|upstream_gene_variant|MODIFIER|PA14_54900|PA14_54900|transcript|ABJ09873.1|protein_coding||c.-4690C>A|||||4690|,T|upstream_gene_variant|MODIFIER|PA14_54910|PA14_54910|transcript|ABJ09872.1|protein_coding||c.-3652C>A|||||3652|,T|downstream_gene_variant|MODIFIER|PA14_54930|PA14_54930|transcript|ABJ09870.1|protein_coding||c.*937C>A|||||937|,T|downstream_gene_variant|MODIFIER|PA14_54940|PA14_54940|transcript|ABJ09869.1|protein_coding||c.*4392C>A|||||4392| GT:DP:DPR:RO:QR:AO:QA:GL 0:27:27,6:21:703:6:78:0,-56.4141 0:28:28,1:27:847:1:15:0,-74.9952 0:28:28,2:26:904:2:17:0,-80.0415 0:24:24,1:23:704:1:15:0,-62.1286 +Chromosome 4901124 . C A 1.38926E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=9;CIGAR=1X;DP=92;DPB=92;DPRA=0.846154;EPP=22.5536;EPPR=3.24576;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=127.189;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=135;QR=2827;RO=83;RPL=0;RPP=22.5536;RPPR=3.24576;RPR=9;RUN=1;SAF=0;SAP=22.5536;SAR=9;SRF=40;SRP=3.24576;SRR=43;TYPE=snp;technology.ILLUMINA=1;ANN=A|upstream_gene_variant|MODIFIER|PA14_55110|PA14_55110|transcript|ABJ09854.1|protein_coding||c.-4899G>T|||||4899|,A|upstream_gene_variant|MODIFIER|gloA2|PA14_55130|transcript|ABJ09853.1|protein_coding||c.-3297G>T|||||3297|,A|upstream_gene_variant|MODIFIER|PA14_55140|PA14_55140|transcript|ABJ09852.1|protein_coding||c.-2956G>T|||||2956|,A|upstream_gene_variant|MODIFIER|migA|PA14_55180|transcript|ABJ09848.1|protein_coding||c.-65C>A|||||65|,A|upstream_gene_variant|MODIFIER|PA14_55200|PA14_55200|transcript|ABJ09847.1|protein_coding||c.-1092C>A|||||1092|,A|upstream_gene_variant|MODIFIER|PA14_55220|PA14_55220|transcript|ABJ09846.1|protein_coding||c.-2557C>A|||||2557|,A|upstream_gene_variant|MODIFIER|PA14_55230|PA14_55230|transcript|ABJ09845.1|protein_coding||c.-3952C>A|||||3952|,A|downstream_gene_variant|MODIFIER|PA14_55117|PA14_55117|transcript|ABJ15702.1|protein_coding||c.*3736C>A|||||3736|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_55150|PA14_55150|transcript|ABJ09851.1|protein_coding||c.*1986C>A|||||1986|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|toxR|PA14_55160|transcript|ABJ09850.1|protein_coding||c.*921C>A|||||921|,A|downstream_gene_variant|MODIFIER|cat|PA14_55170|transcript|ABJ09849.1|protein_coding||c.*295C>A|||||295|,A|downstream_gene_variant|MODIFIER|PA14_55240|PA14_55240|transcript|ABJ09844.1|protein_coding||c.*4840G>T|||||4840|,A|intergenic_region|MODIFIER|cat-migA|PA14_55170-PA14_55180|intergenic_region|PA14_55170-PA14_55180|||n.4901124C>A|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:20:20,3:17:607:3:45:0,-50.7508 0:24:24,1:23:801:1:15:0,-70.8868 0:22:22,5:17:554:5:75:0,-43.2564 0:26:26,0:26:865:0:0:0,-78.1333 +Chromosome 4911197 . C A 6.0294E-16 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=43;DPB=43;DPRA=0.969697;EPP=5.18177;EPPR=12.42;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=62.0785;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=49;QR=1340;RO=39;RPL=1;RPP=5.18177;RPPR=3.51141;RPR=3;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=21;SRP=3.51141;SRR=18;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|PA14_55320|PA14_55320|transcript|ABJ09838.1|protein_coding|1/1|c.786G>T|p.Leu262Leu|786/1707|786/1707|262/568||,A|upstream_gene_variant|MODIFIER|PA14_55240|PA14_55240|transcript|ABJ09844.1|protein_coding||c.-4568G>T|||||4568|,A|upstream_gene_variant|MODIFIER|PA14_55250|PA14_55250|transcript|ABJ09843.1|protein_coding||c.-3510G>T|||||3510|,A|upstream_gene_variant|MODIFIER|PA14_55260|PA14_55260|transcript|ABJ09842.1|protein_coding||c.-3075G>T|||||3075|,A|upstream_gene_variant|MODIFIER|PA14_55280|PA14_55280|transcript|ABJ09841.1|protein_coding||c.-2131G>T|||||2131|,A|upstream_gene_variant|MODIFIER|PA14_55290|PA14_55290|transcript|ABJ09840.1|protein_coding||c.-1647G>T|||||1647|,A|upstream_gene_variant|MODIFIER|PA14_55300|PA14_55300|transcript|ABJ09839.1|protein_coding||c.-956G>T|||||956|,A|downstream_gene_variant|MODIFIER|PA14_55330|PA14_55330|transcript|ABJ09837.1|protein_coding||c.*853G>T|||||853|,A|downstream_gene_variant|MODIFIER|exbD2|PA14_55340|transcript|ABJ09836.1|protein_coding||c.*1608G>T|||||1608|,A|downstream_gene_variant|MODIFIER|exbB2|PA14_55360|transcript|ABJ09835.1|protein_coding||c.*2038G>T|||||2038|,A|downstream_gene_variant|MODIFIER|PA14_55380|PA14_55380|transcript|ABJ09834.1|protein_coding||c.*3909G>T|||||3909|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,2:8:280:2:31:0,-22.5862 0:14:14,1:13:454:1:16:0,-39.576 0:11:11,0:11:390:0:0:0,-35.4275 0:8:8,1:7:216:1:2:0,-19.5377 +Chromosome 4928541 . A G 4.57321E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=21;DPB=21;DPRA=1.5;EPP=7.35324;EPPR=5.8675;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=29.8926;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=677;RO=19;RPL=2;RPP=7.35324;RPPR=3.12459;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=12.2676;SRR=14;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_55400|PA14_55400|transcript|ABJ09832.1|protein_coding|1/1|c.1892T>C|p.Ile631Thr|1892/12534|1892/12534|631/4177||,G|downstream_gene_variant|MODIFIER|PA14_55410|PA14_55410|transcript|ABJ09831.1|protein_coding||c.*2091T>C|||||2091|,G|downstream_gene_variant|MODIFIER|P4|EBG00001225172|transcript|EBT00001793447.1|sRNA||n.*3270T>C|||||3270|,G|downstream_gene_variant|MODIFIER|hxcS|PA14_55430|transcript|ABJ09830.1|protein_coding||c.*3783T>C|||||3783|,G|downstream_gene_variant|MODIFIER|hxcR|PA14_55440|transcript|ABJ09829.1|protein_coding||c.*4997T>C|||||4997| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:157:0:0:0,-14.509 0:2:2,0:2:77:0:0:0,-7.30883 0:7:7,2:5:159:2:4:0,-14.2345 0:8:8,0:8:284:0:0:0,-25.8968 +Chromosome 4934081 . G T 8.14828E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=29;DPB=29;DPRA=1.6;EPP=11.6962;EPPR=3.79203;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=38.2934;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=903;RO=25;RPL=4;RPP=11.6962;RPPR=7.26639;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=9;SRP=7.26639;SRR=16;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|hxcR|PA14_55440|transcript|ABJ09829.1|protein_coding|1/1|c.867C>A|p.Val289Val|867/1410|867/1410|289/469||,T|upstream_gene_variant|MODIFIER|PA14_55400|PA14_55400|transcript|ABJ09832.1|protein_coding||c.-3649C>A|||||3649|,T|upstream_gene_variant|MODIFIER|PA14_55410|PA14_55410|transcript|ABJ09831.1|protein_coding||c.-2271C>A|||||2271|,T|upstream_gene_variant|MODIFIER|P4|EBG00001225172|transcript|EBT00001793447.1|sRNA||n.-2056C>A|||||2056|,T|upstream_gene_variant|MODIFIER|hxcS|PA14_55430|transcript|ABJ09830.1|protein_coding||c.-543C>A|||||543|,T|downstream_gene_variant|MODIFIER|hxcQ|PA14_55450|transcript|ABJ09828.1|protein_coding||c.*863C>A|||||863|,T|downstream_gene_variant|MODIFIER|hxcZ|PA14_55460|transcript|ABJ09827.1|protein_coding||c.*3271C>A|||||3271|,T|downstream_gene_variant|MODIFIER|hxcY|PA14_55470|transcript|ABJ09826.1|protein_coding||c.*3851C>A|||||3851| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,2:4:140:2:29:0,-10.1868 0:11:11,1:10:376:1:2:0,-33.9886 0:5:5,0:5:186:0:0:0,-17.0985 0:7:7,1:6:201:1:2:0,-18.212 +Chromosome 4951143 . G C 4.06459E-7 . AB=0;ABP=0;AC=0;AF=0;AN=3;AO=2;CIGAR=1X;DP=8;DPB=8;DPRA=2;EPP=7.35324;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=16.186;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=180;RO=6;RPL=2;RPP=7.35324;RPPR=4.45795;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=6;SRP=16.0391;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_55610|PA14_55610|transcript|ABJ09812.1|protein_coding|1/1|c.2566G>C|p.Ala856Pro|2566/3096|2566/3096|856/1031||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|nemO|PA14_55580|transcript|ABJ09815.1|protein_coding||c.-4821C>G|||||4821|,C|upstream_gene_variant|MODIFIER|5S_rRNA|EBG00001225156|transcript|EBT00001793486.1|rRNA||n.-885G>C|||||885|,C|upstream_gene_variant|MODIFIER|LSU_rRNA_bacteria|EBG00001225118|transcript|EBT00001793513.1|rRNA||n.-1145G>C|||||1145|,C|upstream_gene_variant|MODIFIER|PK-G12rRNA|EBG00001225123|transcript|EBT00001793337.1|rRNA||n.-1659G>C|||||1659|,C|upstream_gene_variant|MODIFIER|5_8S_rRNA|EBG00001225054|transcript|EBT00001793409.1|rRNA||n.-3865G>C|||||3865|,C|upstream_gene_variant|MODIFIER|tRNA|EBG00001225119|transcript|EBT00001793463.1|protein_coding||c.-4258G>C|||||4258|WARNING_TRANSCRIPT_INCOMPLETE,C|upstream_gene_variant|MODIFIER|tRNA|EBG00001225127|transcript|EBT00001793358.1|protein_coding||c.-4362G>C|||||4362|WARNING_TRANSCRIPT_INCOMPLETE,C|upstream_gene_variant|MODIFIER|SSU_rRNA_archaea|EBG00001225151|transcript|EBT00001793468.1|rRNA||n.-4502G>C|||||4502|,C|downstream_gene_variant|MODIFIER|PA14_55590|PA14_55590|transcript|ABJ09814.1|protein_coding||c.*3964G>C|||||3964|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_55600|PA14_55600|transcript|ABJ09813.1|protein_coding||c.*2541G>C|||||2541|,C|downstream_gene_variant|MODIFIER|PA14_55620|PA14_55620|transcript|PA14_55620-1.1|rRNA||n.*877C>G|||||877|,C|downstream_gene_variant|MODIFIER|PA14_55631|PA14_55631|transcript|PA14_55631-1.1|rRNA||n.*1145C>G|||||1145|,C|downstream_gene_variant|MODIFIER|PA14_55634|PA14_55634|transcript|PA14_55634-1.1|protein_coding||c.*4258C>G|||||4258|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|PA14_55635|PA14_55635|transcript|PA14_55635-1.1|protein_coding||c.*4362C>G|||||4362|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|downstream_gene_variant|MODIFIER|PA14_55637|PA14_55637|transcript|PA14_55637-1.1|rRNA||n.*4501C>G|||||4501| GT:DP:DPR:RO:QR:AO:QA:GL . 0:1:1,0:1:34:0:0:0,-3.39891 0:3:3,0:3:68:0:0:0,-6.34326 0:4:4,2:2:78:2:4:0,-7.02347 +Chromosome 4966522 . A C 3.285E-11 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=14;DPB=14;DPRA=1.33333;EPP=9.52472;EPPR=3.20771;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=25.8191;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=28;QR=423;RO=11;RPL=3;RPP=9.52472;RPPR=12.6832;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=8;SRP=7.94546;SRR=3;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|recB|PA14_55670|transcript|ABJ13554.1|protein_coding|1/1|c.2123T>G|p.Leu708Arg|2123/3738|2123/3738|708/1245||,C|upstream_gene_variant|MODIFIER|recD|PA14_55660|transcript|ABJ13553.1|protein_coding||c.-1612T>G|||||1612|,C|downstream_gene_variant|MODIFIER|sbcC|PA14_55650|transcript|ABJ13552.1|protein_coding||c.*3799A>C|||||3799|,C|downstream_gene_variant|MODIFIER|recC|PA14_55690|transcript|ABJ13555.1|protein_coding||c.*2119T>G|||||2119| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:78:0:0:0,-7.40347 0:4:4,0:4:152:0:0:0,-14.0486 0:3:3,1:2:74:1:13:0,-5.72487 0:5:5,2:3:119:2:15:0,-9.6704 +Chromosome 4969672 . A C 2.53434E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=16;DPB=16;DPRA=2.2;EPP=9.52472;EPPR=11.1951;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=21.2638;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=500;RO=13;RPL=3;RPP=9.52472;RPPR=4.51363;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=7;SRP=3.17734;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|recC|PA14_55690|transcript|ABJ13555.1|protein_coding|1/1|c.2485T>G|p.Trp829Gly|2485/3516|2485/3516|829/1171||,C|upstream_gene_variant|MODIFIER|recD|PA14_55660|transcript|ABJ13553.1|protein_coding||c.-4762T>G|||||4762|,C|upstream_gene_variant|MODIFIER|recB|PA14_55670|transcript|ABJ13554.1|protein_coding||c.-1028T>G|||||1028|,C|upstream_gene_variant|MODIFIER|PA14_55730|PA14_55730|transcript|ABJ13558.1|protein_coding||c.-4311A>C|||||4311|,C|downstream_gene_variant|MODIFIER|PA14_55710|PA14_55710|transcript|ABJ13556.1|protein_coding||c.*2525T>G|||||2525|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_55720|PA14_55720|transcript|ABJ13557.1|protein_coding||c.*3321T>G|||||3321| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:74:0:0:0,-7.02486 0:3:3,2:1:39:2:4:0,-3.51656 0:3:3,0:3:115:0:0:0,-10.724 0:8:8,1:7:272:1:2:0,-24.6464 +Chromosome 4977719 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=52;DPB=52;DPRA=1;EPP=9.52472;EPPR=22.5536;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=68.6072;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=1729;RO=49;RPL=0;RPP=9.52472;RPPR=3.40914;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=28;SRP=5.18177;SRR=21;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_55760|PA14_55760|transcript|ABJ13560.1|protein_coding|1/1|c.62C>G|p.Ala21Gly|62/687|62/687|21/228||,G|upstream_gene_variant|MODIFIER|PA14_55710|PA14_55710|transcript|ABJ13556.1|protein_coding||c.-4839G>C|||||4839|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_55720|PA14_55720|transcript|ABJ13557.1|protein_coding||c.-3836G>C|||||3836|,G|upstream_gene_variant|MODIFIER|PA14_55750|PA14_55750|transcript|ABJ13561.1|protein_coding||c.-60G>C|||||60|,G|upstream_gene_variant|MODIFIER|pitA|PA14_55770|transcript|ABJ13562.1|protein_coding||c.-770C>G|||||770|,G|downstream_gene_variant|MODIFIER|PA14_55730|PA14_55730|transcript|ABJ13558.1|protein_coding||c.*2933C>G|||||2933|,G|downstream_gene_variant|MODIFIER|chrA|PA14_55740|transcript|ABJ13559.1|protein_coding||c.*1673C>G|||||1673|,G|downstream_gene_variant|MODIFIER|PA14_55780|PA14_55780|transcript|ABJ13563.1|protein_coding||c.*2307G>C|||||2307| GT:DP:DPR:RO:QR:AO:QA:GL 0:14:14,0:14:501:0:0:0,-45.4121 0:17:17,1:16:573:1:2:0,-51.6855 0:12:12,0:12:418:0:0:0,-37.9411 0:9:9,2:7:237:2:4:0,-21.271 +Chromosome 4978468 . GCT GT 2586.17 . AB=0;ABP=0;AC=4;AF=1;AN=4;AO=78;CIGAR=1M1D1M;DP=78;DPB=57.3333;DPRA=0;EPP=7.01917;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=4;NUMALT=1;ODDS=166.011;PAIRED=0;PAIREDR=0;PAO=8;PQA=187;PQR=20;PRO=3;QA=2746;QR=0;RO=0;RPL=31;RPP=10.1372;RPPR=0;RPR=47;RUN=1;SAF=32;SAP=8.46682;SAR=46;SRF=0;SRP=0;SRR=0;TYPE=del;technology.ILLUMINA=1;ANN=GT|upstream_gene_variant|MODIFIER|PA14_55720|PA14_55720|transcript|ABJ13557.1|protein_coding||c.-4586delG|||||4586|,GT|upstream_gene_variant|MODIFIER|PA14_55750|PA14_55750|transcript|ABJ13561.1|protein_coding||c.-810delG|||||810|,GT|upstream_gene_variant|MODIFIER|pitA|PA14_55770|transcript|ABJ13562.1|protein_coding||c.-20delC|||||20|,GT|upstream_gene_variant|MODIFIER|PA14_55800|PA14_55800|transcript|ABJ13565.1|protein_coding||c.-4905delC|||||4905|,GT|downstream_gene_variant|MODIFIER|PA14_55730|PA14_55730|transcript|ABJ13558.1|protein_coding||c.*3683delC|||||3683|,GT|downstream_gene_variant|MODIFIER|chrA|PA14_55740|transcript|ABJ13559.1|protein_coding||c.*2423delC|||||2423|,GT|downstream_gene_variant|MODIFIER|PA14_55760|PA14_55760|transcript|ABJ13560.1|protein_coding||c.*125delC|||||125|,GT|downstream_gene_variant|MODIFIER|PA14_55780|PA14_55780|transcript|ABJ13563.1|protein_coding||c.*1557delG|||||1557|,GT|downstream_gene_variant|MODIFIER|PA14_55790|PA14_55790|transcript|ABJ13564.1|protein_coding||c.*4335delG|||||4335|,GT|intergenic_region|MODIFIER|PA14_55760-pitA|PA14_55760-PA14_55770|intergenic_region|PA14_55760-PA14_55770|||n.4978469delC|||||| GT:DP:DPR:RO:QR:AO:QA:GL 1:20:20,20:0:0:20:741:-67.0129,0 1:18:18,18:0:0:18:694:-69.084,0 1:23:23,23:0:0:23:730:-65.9756,0 1:17:17,17:0:0:17:581:-61.3284,0 +Chromosome 4980019 . A C 5.0981E-11 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=18;DPB=18;DPRA=1.5;EPP=13.8677;EPPR=4.51363;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=25.298;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=433;RO=13;RPL=0;RPP=13.8677;RPPR=4.51363;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=6;SRP=3.17734;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=C|upstream_gene_variant|MODIFIER|PA14_55750|PA14_55750|transcript|ABJ13561.1|protein_coding||c.-2360T>G|||||2360|,C|upstream_gene_variant|MODIFIER|PA14_55800|PA14_55800|transcript|ABJ13565.1|protein_coding||c.-3355A>C|||||3355|,C|upstream_gene_variant|MODIFIER|PA14_55810|PA14_55810|transcript|ABJ13566.1|protein_coding||c.-3958A>C|||||3958|,C|downstream_gene_variant|MODIFIER|chrA|PA14_55740|transcript|ABJ13559.1|protein_coding||c.*3973A>C|||||3973|,C|downstream_gene_variant|MODIFIER|PA14_55760|PA14_55760|transcript|ABJ13560.1|protein_coding||c.*1675A>C|||||1675|,C|downstream_gene_variant|MODIFIER|pitA|PA14_55770|transcript|ABJ13562.1|protein_coding||c.*61A>C|||||61|,C|downstream_gene_variant|MODIFIER|PA14_55780|PA14_55780|transcript|ABJ13563.1|protein_coding||c.*7T>G|||||7|,C|downstream_gene_variant|MODIFIER|PA14_55790|PA14_55790|transcript|ABJ13564.1|protein_coding||c.*2785T>G|||||2785|,C|downstream_gene_variant|MODIFIER|PA14_55820|PA14_55820|transcript|ABJ13567.1|protein_coding||c.*4811T>G|||||4811|,C|intergenic_region|MODIFIER|pitA-PA14_55780|PA14_55770-PA14_55780|intergenic_region|PA14_55770-PA14_55780|||n.4980019A>C|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:62:0:0:0,-5.88849 0:5:5,0:5:162:0:0:0,-14.8962 0:5:5,0:5:169:0:0:0,-15.5407 0:6:6,5:1:40:5:10:0,-3.07568 +Chromosome 4982858 . G C 5.28897E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=44;DPB=44;DPRA=0.882353;EPP=7.35324;EPPR=32.7905;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=57.7267;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1411;RO=42;RPL=2;RPP=7.35324;RPPR=3.21711;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=19;SRP=3.83753;SRR=23;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|PA14_55790|PA14_55790|transcript|ABJ13564.1|protein_coding|1/1|c.453C>G|p.Gly151Gly|453/507|453/507|151/168||,C|upstream_gene_variant|MODIFIER|PA14_55780|PA14_55780|transcript|ABJ13563.1|protein_coding||c.-64C>G|||||64|,C|upstream_gene_variant|MODIFIER|PA14_55800|PA14_55800|transcript|ABJ13565.1|protein_coding||c.-516G>C|||||516|,C|upstream_gene_variant|MODIFIER|PA14_55810|PA14_55810|transcript|ABJ13566.1|protein_coding||c.-1119G>C|||||1119|,C|downstream_gene_variant|MODIFIER|PA14_55760|PA14_55760|transcript|ABJ13560.1|protein_coding||c.*4514G>C|||||4514|,C|downstream_gene_variant|MODIFIER|pitA|PA14_55770|transcript|ABJ13562.1|protein_coding||c.*2900G>C|||||2900|,C|downstream_gene_variant|MODIFIER|PA14_55820|PA14_55820|transcript|ABJ13567.1|protein_coding||c.*1972C>G|||||1972|,C|downstream_gene_variant|MODIFIER|PA14_55840|PA14_55840|transcript|ABJ13568.1|protein_coding||c.*3667C>G|||||3667|,C|downstream_gene_variant|MODIFIER|PA14_55850|PA14_55850|transcript|ABJ13569.1|protein_coding||c.*3974C>G|||||3974|,C|downstream_gene_variant|MODIFIER|PA14_55860|PA14_55860|transcript|ABJ13570.1|protein_coding||c.*4708C>G|||||4708| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:186:0:0:0,-17.035 0:13:13,0:13:479:0:0:0,-43.4437 0:10:10,2:8:243:2:17:0,-20.5453 0:15:15,0:15:503:0:0:0,-45.5765 +Chromosome 4999686 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=47;DPB=47;DPRA=1.13636;EPP=9.52472;EPPR=31.4368;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=57.3308;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=1406;RO=44;RPL=0;RPP=9.52472;RPPR=3.20771;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=15;SRP=12.6832;SRR=29;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|pctA|PA14_56000|transcript|ABJ13579.1|protein_coding|1/1|c.985A>G|p.Ser329Gly|985/1890|985/1890|329/629||,G|upstream_gene_variant|MODIFIER|yjgR|PA14_55980|transcript|ABJ13578.1|protein_coding||c.-1384T>C|||||1384|,G|upstream_gene_variant|MODIFIER|pctB|PA14_56010|transcript|ABJ13580.1|protein_coding||c.-1140A>G|||||1140|,G|upstream_gene_variant|MODIFIER|PA14_56030|PA14_56030|transcript|ABJ13581.1|protein_coding||c.-3347A>G|||||3347|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_56040|PA14_56040|transcript|ABJ13582.1|protein_coding||c.-4455A>G|||||4455|,G|downstream_gene_variant|MODIFIER|pctC|PA14_55960|transcript|ABJ13577.1|protein_coding||c.*2978A>G|||||2978| GT:DP:DPR:RO:QR:AO:QA:GL 0:12:12,0:12:366:0:0:0,-33.2245 0:10:10,0:10:315:0:0:0,-28.6528 0:9:9,2:7:204:2:4:0,-18.2608 0:16:16,1:15:521:1:2:0,-47.0012 +Chromosome 5010471 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=50;DPB=50;DPRA=1.17391;EPP=9.52472;EPPR=5.27418;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=67.0818;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=84;QR=1764;RO=47;RPL=3;RPP=9.52472;RPPR=16.3625;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=20;SRP=5.27418;SRR=27;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_56100|PA14_56100|transcript|ABJ13588.1|protein_coding|1/1|c.323T>C|p.Leu108Pro|323/798|323/798|108/265||,C|upstream_gene_variant|MODIFIER|purU1|PA14_56060|transcript|ABJ13584.1|protein_coding||c.-3483A>G|||||3483|,C|upstream_gene_variant|MODIFIER|sbcB|PA14_56080|transcript|ABJ13586.1|protein_coding||c.-1322A>G|||||1322|,C|upstream_gene_variant|MODIFIER|PA14_56110|PA14_56110|transcript|ABJ13589.1|protein_coding||c.-472T>C|||||472|,C|upstream_gene_variant|MODIFIER|PA14_56130|PA14_56130|transcript|ABJ13590.1|protein_coding||c.-1439T>C|||||1439|,C|upstream_gene_variant|MODIFIER|PA14_56140|PA14_56140|transcript|ABJ13591.1|protein_coding||c.-3007T>C|||||3007|,C|upstream_gene_variant|MODIFIER|moxR|PA14_56160|transcript|ABJ13592.1|protein_coding||c.-4281T>C|||||4281|,C|downstream_gene_variant|MODIFIER|PA14_56050|PA14_56050|transcript|ABJ13583.1|protein_coding||c.*4571T>C|||||4571|,C|downstream_gene_variant|MODIFIER|mvaT|PA14_56070|transcript|ABJ13585.1|protein_coding||c.*2849T>C|||||2849|,C|downstream_gene_variant|MODIFIER|PA14_56090|PA14_56090|transcript|ABJ13587.1|protein_coding||c.*360T>C|||||360| GT:DP:DPR:RO:QR:AO:QA:GL 0:11:11,0:11:417:0:0:0,-37.8795 0:10:10,2:8:303:2:69:0,-21.0744 0:12:12,0:12:450:0:0:0,-40.8423 0:17:17,1:16:594:1:15:0,-52.2913 +Chromosome 5025755 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=7;CIGAR=1X;DP=68;DPB=68;DPRA=0.925926;EPP=10.7656;EPPR=15.8611;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=88.9938;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=108;QR=1734;RO=61;RPL=6;RPP=10.7656;RPPR=3.33068;RPR=1;RUN=1;SAF=7;SAP=18.2106;SAR=0;SRF=40;SRP=15.8611;SRR=21;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|fumA|PA14_56300|transcript|ABJ13603.1|protein_coding|1/1|c.554G>T|p.Cys185Phe|554/1524|554/1524|185/507||,T|upstream_gene_variant|MODIFIER|PA14_56250|PA14_56250|transcript|ABJ13600.1|protein_coding||c.-2941C>A|||||2941|,T|upstream_gene_variant|MODIFIER|PA14_56260|PA14_56260|transcript|ABJ13601.1|protein_coding||c.-1949C>A|||||1949|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|PA14_56280|PA14_56280|transcript|ABJ13602.1|protein_coding||c.-829C>A|||||829|,T|downstream_gene_variant|MODIFIER|pykA|PA14_56240|transcript|ABJ13599.1|protein_coding||c.*3904G>T|||||3904|,T|downstream_gene_variant|MODIFIER|mntH1|PA14_56340|transcript|ABJ13604.1|protein_coding||c.*1067C>A|||||1067|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|PA14_56360|PA14_56360|transcript|ABJ13605.1|protein_coding||c.*2460C>A|||||2460|,T|downstream_gene_variant|MODIFIER|PA14_56370|PA14_56370|transcript|ABJ13606.1|protein_coding||c.*2789C>A|||||2789|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|PA14_56380|PA14_56380|transcript|ABJ13607.1|protein_coding||c.*3477C>A|||||3477|,T|downstream_gene_variant|MODIFIER|PA14_56390|PA14_56390|transcript|ABJ13608.1|protein_coding||c.*4182C>A|||||4182|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:18:18,0:18:521:0:0:0,-47.1566 0:18:18,4:14:436:4:61:0,-33.8886 0:16:16,2:14:374:2:32:0,-30.8739 0:16:16,1:15:403:1:15:0,-35.0137 +Chromosome 5034431 . T G 5.33251E-10 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=25;DPB=25;DPRA=1.16667;EPP=7.35324;EPPR=7.63648;GTI=0;LEN=1;MEANALT=1;MQM=48;MQMR=60;NS=4;NUMALT=1;ODDS=22.8206;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=734;RO=23;RPL=0;RPP=7.35324;RPPR=7.63648;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=11;SRP=3.10471;SRR=12;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|PA14_56450|PA14_56450|transcript|ABJ13612.1|protein_coding|1/1|c.1032A>C|p.Ala344Ala|1032/1485|1032/1485|344/494||,G|upstream_gene_variant|MODIFIER|PA14_56380|PA14_56380|transcript|ABJ13607.1|protein_coding||c.-4588A>C|||||4588|,G|upstream_gene_variant|MODIFIER|PA14_56390|PA14_56390|transcript|ABJ13608.1|protein_coding||c.-3214A>C|||||3214|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_56410|PA14_56410|transcript|ABJ13609.1|protein_coding||c.-2035A>C|||||2035|,G|upstream_gene_variant|MODIFIER|PA14_56420|PA14_56420|transcript|ABJ13610.1|protein_coding||c.-1388A>C|||||1388|,G|upstream_gene_variant|MODIFIER|PA14_56430|PA14_56430|transcript|ABJ13611.1|protein_coding||c.-553A>C|||||553|,G|downstream_gene_variant|MODIFIER|PA14_56470|PA14_56470|transcript|ABJ13613.1|protein_coding||c.*1032A>C|||||1032|,G|downstream_gene_variant|MODIFIER|PA14_56480|PA14_56480|transcript|ABJ13614.1|protein_coding||c.*2389A>C|||||2389|,G|downstream_gene_variant|MODIFIER|PA14_56510|PA14_56510|transcript|ABJ13615.1|protein_coding||c.*3774A>C|||||3774|,G|downstream_gene_variant|MODIFIER|PA14_56520|PA14_56520|transcript|ABJ13616.1|protein_coding||c.*4425A>C|||||4425|,G|downstream_gene_variant|MODIFIER|PA14_56530|PA14_56530|transcript|ABJ13617.1|protein_coding||c.*4757A>C|||||4757| GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:39:0:0:0,-3.89656 0:7:7,2:5:134:2:15:0,-10.8928 0:10:10,0:10:286:0:0:0,-26.0081 0:7:7,0:7:275:0:0:0,-25.1189 +Chromosome 5047958 . G C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=32;DPB=32;DPRA=0.777778;EPP=9.52472;EPPR=6.67934;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=53.7618;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=1076;RO=29;RPL=3;RPP=9.52472;RPPR=3.08518;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=8;SRP=15.6647;SRR=21;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_56660|PA14_56660|transcript|ABJ13626.1|protein_coding|1/1|c.802G>C|p.Asp268His|802/1053|802/1053|268/350||,C|upstream_gene_variant|MODIFIER|PA14_56590|PA14_56590|transcript|ABJ13622.1|protein_coding||c.-3230C>G|||||3230|,C|upstream_gene_variant|MODIFIER|PA14_56600|PA14_56600|transcript|ABJ13623.1|protein_coding||c.-2508C>G|||||2508|,C|downstream_gene_variant|MODIFIER|PA14_56560|PA14_56560|transcript|ABJ13620.1|protein_coding||c.*4863G>C|||||4863|,C|downstream_gene_variant|MODIFIER|PA14_56570|PA14_56570|transcript|ABJ13621.1|protein_coding||c.*4087G>C|||||4087|,C|downstream_gene_variant|MODIFIER|PA14_56620|PA14_56620|transcript|ABJ13624.1|protein_coding||c.*2053G>C|||||2053|,C|downstream_gene_variant|MODIFIER|PA14_56640|PA14_56640|transcript|ABJ13625.1|protein_coding||c.*838G>C|||||838|,C|downstream_gene_variant|MODIFIER|PA14_56670|PA14_56670|transcript|ABJ13627.1|protein_coding||c.*311C>G|||||311|,C|downstream_gene_variant|MODIFIER|PA14_56680|PA14_56680|transcript|ABJ13628.1|protein_coding||c.*553C>G|||||553|,C|downstream_gene_variant|MODIFIER|feoA|PA14_56690|transcript|ABJ13629.1|protein_coding||c.*2871C>G|||||2871|,C|downstream_gene_variant|MODIFIER|PA14_56700|PA14_56700|transcript|ABJ13630.1|protein_coding||c.*3315C>G|||||3315|,C|downstream_gene_variant|MODIFIER|PA14_56720|PA14_56720|transcript|ABJ13631.1|protein_coding||c.*4706C>G|||||4706| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,0:9:345:0:0:0,-31.4079 0:8:8,2:6:195:2:4:0,-17.4795 0:6:6,1:5:192:1:2:0,-17.4487 0:9:9,0:9:344:0:0:0,-31.3161 +Chromosome 5060060 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=39;DPB=39;DPRA=0.857143;EPP=13.8677;EPPR=15.5282;GTI=0;LEN=1;MEANALT=1;MQM=57.6;MQMR=57.6471;NS=4;NUMALT=1;ODDS=51.5879;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1066;RO=34;RPL=0;RPP=13.8677;RPPR=28.557;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=3;SRP=53.0819;SRR=31;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_56790|PA14_56790|transcript|ABJ13637.1|protein_coding|1/1|c.2050A>G|p.Ser684Gly|2050/2064|2050/2064|684/687||,G|upstream_gene_variant|MODIFIER|iciA|PA14_56740|transcript|ABJ13633.1|protein_coding||c.-4261T>C|||||4261|,G|upstream_gene_variant|MODIFIER|icmP|PA14_56830|transcript|ABJ13640.1|protein_coding||c.-1685A>G|||||1685|,G|upstream_gene_variant|MODIFIER|PA14_56840|PA14_56840|transcript|ABJ13641.1|protein_coding||c.-3188A>G|||||3188|,G|upstream_gene_variant|MODIFIER|PA14_56850|PA14_56850|transcript|ABJ13642.1|protein_coding||c.-4619A>G|||||4619|,G|downstream_gene_variant|MODIFIER|PA14_56750|PA14_56750|transcript|ABJ13634.1|protein_coding||c.*3762A>G|||||3762|,G|downstream_gene_variant|MODIFIER|PA14_56770|PA14_56770|transcript|ABJ13635.1|protein_coding||c.*3158A>G|||||3158|,G|downstream_gene_variant|MODIFIER|sodB|PA14_56780|transcript|ABJ13636.1|protein_coding||c.*2230A>G|||||2230|,G|downstream_gene_variant|MODIFIER|PA14_56800|PA14_56800|transcript|ABJ13638.1|protein_coding||c.*15T>C|||||15|,G|downstream_gene_variant|MODIFIER|PA14_56810|PA14_56810|transcript|ABJ13639.1|protein_coding||c.*919T>C|||||919| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,2:5:199:2:4:0,-17.9089 0:11:11,0:11:393:0:0:0,-35.7002 0:11:11,3:8:204:3:6:0,-18.0337 0:10:10,0:10:270:0:0:0,-24.55 +Chromosome 5081548 . C A 8.26645E-7 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=16;DPB=16;DPRA=1.28571;EPP=11.6962;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=15.4746;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=62;QR=374;RO=12;RPL=0;RPP=11.6962;RPPR=3.73412;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=6;SRP=3.0103;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|PA14_57030|PA14_57030|transcript|ABJ13658.1|protein_coding|1/1|c.138G>T|p.Leu46Phe|138/468|138/468|46/155||,A|upstream_gene_variant|MODIFIER|PA14_56970|PA14_56970|transcript|ABJ13653.1|protein_coding||c.-3889G>T|||||3889|,A|upstream_gene_variant|MODIFIER|crcB|PA14_56980|transcript|ABJ13654.1|protein_coding||c.-3486G>T|||||3486|,A|upstream_gene_variant|MODIFIER|groEL|PA14_57010|transcript|ABJ13656.1|protein_coding||c.-870G>T|||||870|,A|upstream_gene_variant|MODIFIER|groES|PA14_57020|transcript|ABJ13657.1|protein_coding||c.-526G>T|||||526|,A|upstream_gene_variant|MODIFIER|PA14_57050|PA14_57050|transcript|ABJ13660.1|protein_coding||c.-1049C>A|||||1049|,A|upstream_gene_variant|MODIFIER|PA14_57080|PA14_57080|transcript|ABJ13662.1|protein_coding||c.-3988C>A|||||3988|,A|upstream_gene_variant|MODIFIER|ampG|PA14_57100|transcript|ABJ13664.1|protein_coding||c.-4414C>A|||||4414|,A|downstream_gene_variant|MODIFIER|PA14_56960|PA14_56960|transcript|ABJ13652.1|protein_coding||c.*4161C>A|||||4161|,A|downstream_gene_variant|MODIFIER|PA14_56990|PA14_56990|transcript|ABJ13655.1|protein_coding||c.*2570C>A|||||2570|,A|downstream_gene_variant|MODIFIER|PA14_57040|PA14_57040|transcript|ABJ13659.1|protein_coding||c.*206G>T|||||206|,A|downstream_gene_variant|MODIFIER|PA14_57060|PA14_57060|transcript|ABJ13661.1|protein_coding||c.*1866G>T|||||1866|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_57070|PA14_57070|transcript|ABJ13663.1|protein_coding||c.*2988G>T|||||2988| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:63:0:0:0,-5.98315 0:5:5,0:5:168:0:0:0,-15.4493 0:3:3,1:2:32:1:15:0,-1.53998 0:6:6,3:3:111:3:47:0,-5.96645 +Chromosome 5088467 . C G 3.65294E-10 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=2.5;EPP=7.35324;EPPR=3.25157;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=23.4967;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=281;RO=9;RPL=0;RPP=7.35324;RPPR=9.04217;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=5.18177;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_57110|PA14_57110|transcript|ABJ13665.1|protein_coding|1/1|c.173G>C|p.Arg58Pro|173/837|173/837|58/278||,G|upstream_gene_variant|MODIFIER|PA14_57060|PA14_57060|transcript|ABJ13661.1|protein_coding||c.-4046G>C|||||4046|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_57070|PA14_57070|transcript|ABJ13663.1|protein_coding||c.-2930G>C|||||2930|,G|upstream_gene_variant|MODIFIER|PA14_57140|PA14_57140|transcript|ABJ13667.1|protein_coding||c.-988C>G|||||988|,G|upstream_gene_variant|MODIFIER|apbA|PA14_57160|transcript|ABJ13668.1|protein_coding||c.-2125C>G|||||2125|,G|upstream_gene_variant|MODIFIER|PA14_57170|PA14_57170|transcript|ABJ13669.1|protein_coding||c.-3087C>G|||||3087|,G|downstream_gene_variant|MODIFIER|PA14_57080|PA14_57080|transcript|ABJ13662.1|protein_coding||c.*2548C>G|||||2548|,G|downstream_gene_variant|MODIFIER|ampG|PA14_57100|transcript|ABJ13664.1|protein_coding||c.*721C>G|||||721|,G|downstream_gene_variant|MODIFIER|PA14_57130|PA14_57130|transcript|ABJ13666.1|protein_coding||c.*405G>C|||||405| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:66:0:0:0,-6.26653 0:2:2,0:2:74:0:0:0,-7.02543 0:2:2,0:2:74:0:0:0,-7.02543 0:5:5,2:3:67:2:4:0,-5.87011 +Chromosome 5096746 . T G 6.80326E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=41;DPB=41;DPRA=1.73333;EPP=9.52472;EPPR=30.668;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=64.1317;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=1175;RO=38;RPL=0;RPP=9.52472;RPPR=5.06748;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=10;SRP=21.525;SRR=28;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|argJ|PA14_57210|transcript|ABJ13673.1|protein_coding|1/1|c.532A>C|p.Lys178Gln|532/1218|532/1218|178/405||,G|upstream_gene_variant|MODIFIER|mutT|PA14_57190|transcript|ABJ13671.1|protein_coding||c.-1496A>C|||||1496|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_57200|PA14_57200|transcript|ABJ13672.1|protein_coding||c.-807A>C|||||807|,G|upstream_gene_variant|MODIFIER|PA14_57250|PA14_57250|transcript|ABJ13676.1|protein_coding||c.-4632T>G|||||4632|,G|downstream_gene_variant|MODIFIER|PA14_57170|PA14_57170|transcript|ABJ13669.1|protein_coding||c.*3096T>G|||||3096|,G|downstream_gene_variant|MODIFIER|PA14_57180|PA14_57180|transcript|ABJ13670.1|protein_coding||c.*2513T>G|||||2513|,G|downstream_gene_variant|MODIFIER|secA|PA14_57220|transcript|ABJ13674.1|protein_coding||c.*678A>C|||||678|,G|downstream_gene_variant|MODIFIER|PA14_57240|PA14_57240|transcript|ABJ13675.1|protein_coding||c.*3562A>C|||||3562| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:255:0:0:0,-23.254 0:10:10,2:8:314:2:17:0,-27.01 0:16:16,1:15:374:1:2:0,-33.6862 0:7:7,0:7:232:0:0:0,-21.1969 +Chromosome 5105550 . G T 4.46001E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=50;DPB=50;DPRA=0.658537;EPP=7.35324;EPPR=11.8771;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=68.784;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=1670;RO=48;RPL=2;RPP=7.35324;RPPR=17.6677;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=30;SRP=9.52472;SRR=18;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|ftsQ|PA14_57300|transcript|ABJ13679.1|protein_coding|1/1|c.682C>A|p.Gln228Lys|682/864|682/864|228/287||,T|upstream_gene_variant|MODIFIER|PA14_57240|PA14_57240|transcript|ABJ13675.1|protein_coding||c.-4319C>A|||||4319|,T|upstream_gene_variant|MODIFIER|lpxC|PA14_57260|transcript|ABJ13677.1|protein_coding||c.-2805C>A|||||2805|,T|upstream_gene_variant|MODIFIER|ftsZ|PA14_57275|transcript|ABJ15653.1|protein_coding||c.-1508C>A|||||1508|,T|upstream_gene_variant|MODIFIER|ftsA|PA14_57290|transcript|ABJ13678.1|protein_coding||c.-204C>A|||||204|,T|downstream_gene_variant|MODIFIER|PA14_57250|PA14_57250|transcript|ABJ13676.1|protein_coding||c.*3777G>T|||||3777|,T|downstream_gene_variant|MODIFIER|ddlB|PA14_57320|transcript|ABJ13680.1|protein_coding||c.*685C>A|||||685|,T|downstream_gene_variant|MODIFIER|murC|PA14_57330|transcript|ABJ13681.1|protein_coding||c.*1641C>A|||||1641|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|murG|PA14_57340|transcript|ABJ13682.1|protein_coding||c.*3076C>A|||||3076|,T|downstream_gene_variant|MODIFIER|ftsW|PA14_57360|transcript|ABJ13683.1|protein_coding||c.*4139C>A|||||4139| GT:DP:DPR:RO:QR:AO:QA:GL 0:15:15,0:15:521:0:0:0,-47.2065 0:9:9,2:7:246:2:18:0,-20.7682 0:12:12,0:12:385:0:0:0,-34.9514 0:14:14,0:14:518:0:0:0,-46.9584 +Chromosome 5107137 . G C 2.15425E-10 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=27;DPB=27;DPRA=1.45455;EPP=9.52472;EPPR=3.86001;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=23.727;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=858;RO=23;RPL=3;RPP=9.52472;RPPR=3.86001;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=6;SRP=14.4341;SRR=17;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|ddlB|PA14_57320|transcript|ABJ13680.1|protein_coding|1/1|c.58C>G|p.Arg20Gly|58/960|58/960|20/319||,C|upstream_gene_variant|MODIFIER|lpxC|PA14_57260|transcript|ABJ13677.1|protein_coding||c.-4392C>G|||||4392|,C|upstream_gene_variant|MODIFIER|ftsZ|PA14_57275|transcript|ABJ15653.1|protein_coding||c.-3095C>G|||||3095|,C|upstream_gene_variant|MODIFIER|ftsA|PA14_57290|transcript|ABJ13678.1|protein_coding||c.-1791C>G|||||1791|,C|upstream_gene_variant|MODIFIER|ftsQ|PA14_57300|transcript|ABJ13679.1|protein_coding||c.-906C>G|||||906|,C|downstream_gene_variant|MODIFIER|murC|PA14_57330|transcript|ABJ13681.1|protein_coding||c.*54C>G|||||54|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|murG|PA14_57340|transcript|ABJ13682.1|protein_coding||c.*1489C>G|||||1489|,C|downstream_gene_variant|MODIFIER|ftsW|PA14_57360|transcript|ABJ13683.1|protein_coding||c.*2552C>G|||||2552|,C|downstream_gene_variant|MODIFIER|murD|PA14_57370|transcript|ABJ13684.1|protein_coding||c.*3751C>G|||||3751| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:231:0:0:0,-21.1566 0:4:4,2:2:55:2:17:0,-3.6059 0:5:5,0:4:151:0:0:0,-13.7614 0:12:12,1:11:421:1:2:0,-38.0406 +Chromosome 5110632 . C A 1.28079E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=45;DPB=45;DPRA=0.820513;EPP=13.8677;EPPR=6.48466;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=41.0663;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=1274;RO=40;RPL=0;RPP=13.8677;RPPR=16.9077;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=12;SRP=16.9077;SRR=28;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|ftsW|PA14_57360|transcript|ABJ13683.1|protein_coding|1/1|c.257G>T|p.Trp86Leu|257/1200|257/1200|86/399||,A|upstream_gene_variant|MODIFIER|ftsQ|PA14_57300|transcript|ABJ13679.1|protein_coding||c.-4401G>T|||||4401|,A|upstream_gene_variant|MODIFIER|ddlB|PA14_57320|transcript|ABJ13680.1|protein_coding||c.-3438G>T|||||3438|,A|upstream_gene_variant|MODIFIER|murC|PA14_57330|transcript|ABJ13681.1|protein_coding||c.-1999G>T|||||1999|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|murG|PA14_57340|transcript|ABJ13682.1|protein_coding||c.-933G>T|||||933|,A|downstream_gene_variant|MODIFIER|murD|PA14_57370|transcript|ABJ13684.1|protein_coding||c.*256G>T|||||256|,A|downstream_gene_variant|MODIFIER|mraY|PA14_57380|transcript|ABJ13685.1|protein_coding||c.*1616G>T|||||1616|,A|downstream_gene_variant|MODIFIER|murF|PA14_57390|transcript|ABJ13686.1|protein_coding||c.*2698G>T|||||2698|,A|downstream_gene_variant|MODIFIER|murE|PA14_57410|transcript|ABJ13687.1|protein_coding||c.*4067G>T|||||4067| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,2:4:123:2:15:0,-9.9459 0:15:15,2:13:402:2:4:0,-36.0913 0:13:13,0:13:401:0:0:0,-36.3819 0:11:11,1:10:348:1:2:0,-31.4509 +Chromosome 5134711 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=40;DPB=40;DPRA=0.870968;EPP=7.35324;EPPR=3.5385;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=56.6649;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=1267;RO=37;RPL=0;RPP=7.35324;RPPR=7.76406;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=15;SRP=5.88603;SRR=22;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_57650|PA14_57650|transcript|ABJ13706.1|protein_coding|1/1|c.772G>C|p.Asp258His|772/1095|772/1095|258/364||,G|upstream_gene_variant|MODIFIER|PA14_57690|PA14_57690|transcript|ABJ13709.1|protein_coding||c.-3054C>G|||||3054|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_57600|PA14_57600|transcript|ABJ13703.1|protein_coding||c.*3926C>G|||||3926|,G|downstream_gene_variant|MODIFIER|PA14_57630|PA14_57630|transcript|ABJ13704.1|protein_coding||c.*1509C>G|||||1509|,G|downstream_gene_variant|MODIFIER|PA14_57640|PA14_57640|transcript|ABJ13705.1|protein_coding||c.*388C>G|||||388|,G|downstream_gene_variant|MODIFIER|trpS|PA14_57670|transcript|ABJ13707.1|protein_coding||c.*866G>C|||||866|,G|downstream_gene_variant|MODIFIER|PA14_57680|PA14_57680|transcript|ABJ13708.1|protein_coding||c.*2280G>C|||||2280|,G|downstream_gene_variant|MODIFIER|cysN|PA14_57710|transcript|ABJ13710.1|protein_coding||c.*3574G>C|||||3574| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,2:7:248:2:30:0,-19.8099 0:6:6,0:6:191:0:0:0,-17.4971 0:13:13,0:12:357:0:0:0,-32.0131 0:12:12,0:12:471:0:0:0,-42.7411 +Chromosome 5146376 . C T 6.93887E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=28;DPB=28;DPRA=0.75;EPP=9.52472;EPPR=10.0459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=36.5722;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=804;RO=25;RPL=0;RPP=9.52472;RPPR=10.0459;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=12;SRP=3.09716;SRR=13;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|hisD|PA14_57780|transcript|ABJ13716.1|protein_coding|1/1|c.642G>A|p.Lys214Lys|642/1323|642/1323|214/440||,T|upstream_gene_variant|MODIFIER|PA14_57740|PA14_57740|transcript|ABJ13713.1|protein_coding||c.-3068G>A|||||3068|,T|upstream_gene_variant|MODIFIER|hisC1|PA14_57770|transcript|ABJ13715.1|protein_coding||c.-684G>A|||||684|,T|upstream_gene_variant|MODIFIER|P35|EBG00001225116|transcript|EBT00001793425.1|sRNA||n.-2997C>T|||||2997|,T|downstream_gene_variant|MODIFIER|mltB1|PA14_57730|transcript|ABJ13712.1|protein_coding||c.*3813C>T|||||3813|,T|downstream_gene_variant|MODIFIER|algW|PA14_57760|transcript|ABJ13714.1|protein_coding||c.*1782C>T|||||1782|,T|downstream_gene_variant|MODIFIER|hisG|PA14_57800|transcript|ABJ13717.1|protein_coding||c.*767G>A|||||767|,T|downstream_gene_variant|MODIFIER|murA|PA14_57810|transcript|ABJ13718.1|protein_coding||c.*1420G>A|||||1420|,T|downstream_gene_variant|MODIFIER|PA14_57820|PA14_57820|transcript|ABJ13719.1|protein_coding||c.*2706G>A|||||2706|,T|downstream_gene_variant|MODIFIER|PA14_57830|PA14_57830|transcript|ABJ13720.1|protein_coding||c.*3062G>A|||||3062|,T|downstream_gene_variant|MODIFIER|ttg2D|PA14_57840|transcript|ABJ13721.1|protein_coding||c.*3367G>A|||||3367|,T|downstream_gene_variant|MODIFIER|PA14_57850|PA14_57850|transcript|ABJ13722.1|protein_coding||c.*4026G>A|||||4026|,T|downstream_gene_variant|MODIFIER|PA14_57870|PA14_57870|transcript|ABJ13723.1|protein_coding||c.*4500G>A|||||4500| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,2:5:120:2:4:0,-10.6505 0:5:5,1:4:138:1:2:0,-12.5585 0:13:13,0:13:437:0:0:0,-39.6453 0:3:3,0:3:109:0:0:0,-10.1676 +Chromosome 5156272 . C G 1.0552E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=13;CIGAR=1X;DP=109;DPB=109;DPRA=0;EPP=31.2394;EPPR=55.1256;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=140.294;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=52;QR=2909;RO=96;RPL=0;RPP=31.2394;RPPR=26.1727;RPR=13;RUN=1;SAF=0;SAP=31.2394;SAR=13;SRF=40;SRP=8.80089;SRR=56;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|PA14_57870|PA14_57870|transcript|ABJ13723.1|protein_coding||c.-4599G>C|||||4599|,G|upstream_gene_variant|MODIFIER|PA14_57880|PA14_57880|transcript|ABJ13724.1|protein_coding||c.-3790G>C|||||3790|,G|upstream_gene_variant|MODIFIER|rpoN|PA14_57940|transcript|ABJ13730.1|protein_coding||c.-189C>G|||||189|,G|upstream_gene_variant|MODIFIER|PA14_57950|PA14_57950|transcript|ABJ13731.1|protein_coding||c.-1760C>G|||||1760|,G|upstream_gene_variant|MODIFIER|ptsN|PA14_57960|transcript|ABJ13732.1|protein_coding||c.-2082C>G|||||2082|,G|upstream_gene_variant|MODIFIER|PA14_57970|PA14_57970|transcript|ABJ13733.1|protein_coding||c.-2548C>G|||||2548|,G|upstream_gene_variant|MODIFIER|PA14_57980|PA14_57980|transcript|ABJ13734.1|protein_coding||c.-3438C>G|||||3438|,G|downstream_gene_variant|MODIFIER|yrbH|PA14_57890|transcript|ABJ13725.1|protein_coding||c.*2396C>G|||||2396|,G|downstream_gene_variant|MODIFIER|PA14_57900|PA14_57900|transcript|ABJ13726.1|protein_coding||c.*1857C>G|||||1857|,G|downstream_gene_variant|MODIFIER|PA14_57910|PA14_57910|transcript|ABJ13727.1|protein_coding||c.*1276C>G|||||1276|,G|downstream_gene_variant|MODIFIER|PA14_57920|PA14_57920|transcript|ABJ13728.1|protein_coding||c.*762C>G|||||762|,G|downstream_gene_variant|MODIFIER|PA14_57930|PA14_57930|transcript|ABJ13729.1|protein_coding||c.*37C>G|||||37|,G|downstream_gene_variant|MODIFIER|PA14_57990|PA14_57990|transcript|ABJ13735.1|protein_coding||c.*3807G>C|||||3807|,G|downstream_gene_variant|MODIFIER|sodM|PA14_58000|transcript|ABJ13736.1|protein_coding||c.*4758G>C|||||4758|,G|intergenic_region|MODIFIER|PA14_57930-rpoN|PA14_57930-PA14_57940|intergenic_region|PA14_57930-PA14_57940|||n.5156272C>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:23:23,5:18:567:5:23:0,-49.1928 0:29:29,5:24:741:5:23:0,-64.8368 0:33:33,1:32:970:1:2:0,-87.3426 0:24:24,2:22:631:2:4:0,-56.6566 +Chromosome 5159618 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=18;CIGAR=1X;DP=102;DPB=102;DPRA=0;EPP=33.8935;EPPR=3.24576;GTI=0;LEN=1;MEANALT=1.25;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=101.56;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=220;QR=2499;RO=83;RPL=17;RPP=33.8935;RPPR=31.5011;RPR=1;RUN=1;SAF=18;SAP=42.0968;SAR=0;SRF=35;SRP=7.43173;SRR=48;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_57970|PA14_57970|transcript|ABJ13733.1|protein_coding|1/1|c.799G>T|p.Gly267Cys|799/861|799/861|267/286||,T|upstream_gene_variant|MODIFIER|PA14_57980|PA14_57980|transcript|ABJ13734.1|protein_coding||c.-92G>T|||||92|,T|downstream_gene_variant|MODIFIER|PA14_57910|PA14_57910|transcript|ABJ13727.1|protein_coding||c.*4622G>T|||||4622|,T|downstream_gene_variant|MODIFIER|PA14_57920|PA14_57920|transcript|ABJ13728.1|protein_coding||c.*4108G>T|||||4108|,T|downstream_gene_variant|MODIFIER|PA14_57930|PA14_57930|transcript|ABJ13729.1|protein_coding||c.*3383G>T|||||3383|,T|downstream_gene_variant|MODIFIER|rpoN|PA14_57940|transcript|ABJ13730.1|protein_coding||c.*1664G>T|||||1664|,T|downstream_gene_variant|MODIFIER|PA14_57950|PA14_57950|transcript|ABJ13731.1|protein_coding||c.*1278G>T|||||1278|,T|downstream_gene_variant|MODIFIER|ptsN|PA14_57960|transcript|ABJ13732.1|protein_coding||c.*800G>T|||||800|,T|downstream_gene_variant|MODIFIER|PA14_57990|PA14_57990|transcript|ABJ13735.1|protein_coding||c.*461C>A|||||461|,T|downstream_gene_variant|MODIFIER|sodM|PA14_58000|transcript|ABJ13736.1|protein_coding||c.*1412C>A|||||1412|,T|downstream_gene_variant|MODIFIER|PA14_58010|PA14_58010|transcript|ABJ13737.1|protein_coding||c.*2036C>A|||||2036|,T|downstream_gene_variant|MODIFIER|fumC1|PA14_58030|transcript|ABJ13738.1|protein_coding||c.*2513C>A|||||2513|,T|downstream_gene_variant|MODIFIER|PA14_58040|PA14_58040|transcript|ABJ13739.1|protein_coding||c.*3882C>A|||||3882|,T|downstream_gene_variant|MODIFIER|pmbA|PA14_58050|transcript|ABJ13740.1|protein_coding||c.*4425C>A|||||4425| GT:DP:DPR:RO:QR:AO:QA:GL 0:25:25,2:23:671:2:4:0,-60.261 0:20:20,3:17:413:3:48:0,-32.9105 0:30:30,5:25:797:5:80:0,-64.6296 0:27:27,8:18:618:8:88:0,-47.8836 +Chromosome 5166552 . C T 1.67251E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=34;DPB=34;DPRA=1.63636;EPP=9.52472;EPPR=6.44263;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=52.3963;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=1004;RO=31;RPL=0;RPP=9.52472;RPPR=8.68415;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=10;SRP=11.486;SRR=21;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_58070|PA14_58070|transcript|ABJ13742.1|protein_coding|1/1|c.937G>A|p.Gly313Ser|937/1443|937/1443|313/480||,T|upstream_gene_variant|MODIFIER|sodM|PA14_58000|transcript|ABJ13736.1|protein_coding||c.-4911G>A|||||4911|,T|upstream_gene_variant|MODIFIER|PA14_58010|PA14_58010|transcript|ABJ13737.1|protein_coding||c.-4449G>A|||||4449|,T|upstream_gene_variant|MODIFIER|fumC1|PA14_58030|transcript|ABJ13738.1|protein_coding||c.-3045G>A|||||3045|,T|upstream_gene_variant|MODIFIER|PA14_58040|PA14_58040|transcript|ABJ13739.1|protein_coding||c.-2657G>A|||||2657|,T|upstream_gene_variant|MODIFIER|pmbA|PA14_58050|transcript|ABJ13740.1|protein_coding||c.-1160G>A|||||1160|,T|downstream_gene_variant|MODIFIER|PA14_58060|PA14_58060|transcript|ABJ13741.1|protein_coding||c.*537C>T|||||537|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|PA14_58080|PA14_58080|transcript|ABJ13743.1|protein_coding||c.*939G>A|||||939|,T|downstream_gene_variant|MODIFIER|PA14_58090|PA14_58090|transcript|ABJ13744.1|protein_coding||c.*1836G>A|||||1836| GT:DP:DPR:RO:QR:AO:QA:GL 0:12:12,3:9:299:3:19:0,-25.4492 0:11:11,0:11:344:0:0:0,-31.249 0:6:6,0:6:180:0:0:0,-16.4903 0:5:5,0:5:181:0:0:0,-16.6402 +Chromosome 5183822 . C A 2.49743E-8 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=15;DPB=15;DPRA=2.75;EPP=9.52472;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=19.036;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=48;QR=345;RO=12;RPL=0;RPP=9.52472;RPPR=5.9056;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=5;SRP=3.73412;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|PA14_58240|PA14_58240|transcript|ABJ13756.1|protein_coding|1/1|c.165G>T|p.Leu55Phe|165/1650|165/1650|55/549||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|PA14_58230|PA14_58230|transcript|ABJ13755.1|protein_coding||c.-1490G>T|||||1490|,A|downstream_gene_variant|MODIFIER|gatA|PA14_58180|transcript|ABJ13751.1|protein_coding||c.*4803C>A|||||4803|,A|downstream_gene_variant|MODIFIER|gatB|PA14_58190|transcript|ABJ13752.1|protein_coding||c.*3251C>A|||||3251|,A|downstream_gene_variant|MODIFIER|PA14_58210|PA14_58210|transcript|ABJ13753.1|protein_coding||c.*2814C>A|||||2814|,A|downstream_gene_variant|MODIFIER|PA14_58220|PA14_58220|transcript|ABJ13754.1|protein_coding||c.*2396C>A|||||2396|,A|downstream_gene_variant|MODIFIER|PA14_58250|PA14_58250|transcript|ABJ13757.1|protein_coding||c.*161G>T|||||161|,A|downstream_gene_variant|MODIFIER|PA14_58260|PA14_58260|transcript|ABJ13758.1|protein_coding||c.*4738G>T|||||4738|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:54:0:0:0,-5.12672 0:5:5,2:3:90:2:32:0,-5.35497 0:6:6,1:5:160:1:16:0,-13.1119 0:2:2,0:2:41:0:0:0,-3.89174 +Chromosome 5208331 . A G 3.64613E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=35;DPB=35;DPRA=0.75;EPP=7.35324;EPPR=26.7649;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=50.8783;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1025;RO=33;RPL=0;RPP=7.35324;RPPR=10.9724;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=6;SRP=32.0291;SRR=27;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|dppD|PA14_58470|transcript|ABJ13772.1|protein_coding|1/1|c.690A>G|p.Glu230Glu|690/975|690/975|230/324||,G|upstream_gene_variant|MODIFIER|dppF|PA14_58490|transcript|ABJ13773.1|protein_coding||c.-285A>G|||||285|,G|upstream_gene_variant|MODIFIER|PA14_58510|PA14_58510|transcript|ABJ13775.1|protein_coding||c.-2063A>G|||||2063|,G|downstream_gene_variant|MODIFIER|PA14_58410|PA14_58410|transcript|ABJ13768.1|protein_coding||c.*4394A>G|||||4394|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_58420|PA14_58420|transcript|ABJ13769.1|protein_coding||c.*2743A>G|||||2743|,G|downstream_gene_variant|MODIFIER|PA14_58440|PA14_58440|transcript|ABJ13770.1|protein_coding||c.*1665A>G|||||1665|,G|downstream_gene_variant|MODIFIER|dppC|PA14_58450|transcript|ABJ13771.1|protein_coding||c.*742A>G|||||742|,G|downstream_gene_variant|MODIFIER|PA14_58500|PA14_58500|transcript|ABJ13774.1|protein_coding||c.*1289T>C|||||1289|,G|downstream_gene_variant|MODIFIER|PA14_58515|PA14_58515|transcript|ABJ15673.1|protein_coding||c.*2541T>C|||||2541|,G|downstream_gene_variant|MODIFIER|PA14_58530|PA14_58530|transcript|ABJ13776.1|protein_coding||c.*3467T>C|||||3467|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_58540|PA14_58540|transcript|ABJ13777.1|protein_coding||c.*4141T>C|||||4141| GT:DP:DPR:RO:QR:AO:QA:GL 0:11:11,0:11:334:0:0:0,-30.3437 0:7:7,2:5:175:2:4:0,-15.7104 0:8:8,0:8:241:0:0:0,-21.9783 0:9:9,0:9:275:0:0:0,-25.0433 +Chromosome 5208725 . T G 6.30373E-11 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=29;DPB=29;DPRA=4.5;EPP=13.8677;EPPR=6.26751;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=24.9559;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=23;QR=838;RO=24;RPL=0;RPP=13.8677;RPPR=12.0581;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=12;SRP=3.0103;SRR=12;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|dppF|PA14_58490|transcript|ABJ13773.1|protein_coding|1/1|c.110T>G|p.Leu37Arg|110/972|110/972|37/323||,G|upstream_gene_variant|MODIFIER|PA14_58510|PA14_58510|transcript|ABJ13775.1|protein_coding||c.-1669T>G|||||1669|,G|upstream_gene_variant|MODIFIER|lpxO1|PA14_58550|transcript|ABJ13778.1|protein_coding||c.-4632T>G|||||4632|,G|downstream_gene_variant|MODIFIER|PA14_58410|PA14_58410|transcript|ABJ13768.1|protein_coding||c.*4788T>G|||||4788|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_58420|PA14_58420|transcript|ABJ13769.1|protein_coding||c.*3137T>G|||||3137|,G|downstream_gene_variant|MODIFIER|PA14_58440|PA14_58440|transcript|ABJ13770.1|protein_coding||c.*2059T>G|||||2059|,G|downstream_gene_variant|MODIFIER|dppC|PA14_58450|transcript|ABJ13771.1|protein_coding||c.*1136T>G|||||1136|,G|downstream_gene_variant|MODIFIER|dppD|PA14_58470|transcript|ABJ13772.1|protein_coding||c.*109T>G|||||109|,G|downstream_gene_variant|MODIFIER|PA14_58500|PA14_58500|transcript|ABJ13774.1|protein_coding||c.*895A>C|||||895|,G|downstream_gene_variant|MODIFIER|PA14_58515|PA14_58515|transcript|ABJ15673.1|protein_coding||c.*2147A>C|||||2147|,G|downstream_gene_variant|MODIFIER|PA14_58530|PA14_58530|transcript|ABJ13776.1|protein_coding||c.*3073A>C|||||3073|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_58540|PA14_58540|transcript|ABJ13777.1|protein_coding||c.*3747A>C|||||3747| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:50:0:0:0,-4.74895 0:12:12,1:11:424:1:15:0,-37.0129 0:7:7,1:6:167:1:2:0,-15.0968 0:8:8,3:5:197:3:6:0,-17.5466 +Chromosome 5215188 . T G 1.15081E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=26;DPB=26;DPRA=0.714286;EPP=7.35324;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=39.2766;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=859;RO=24;RPL=0;RPP=7.35324;RPPR=12.0581;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=7;SRP=12.0581;SRR=17;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|piuB|PA14_58560|transcript|ABJ13779.1|protein_coding|1/1|c.1919A>C|p.His640Pro|1919/2553|1919/2553|640/850||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_58500|PA14_58500|transcript|ABJ13774.1|protein_coding||c.-4936A>C|||||4936|,G|upstream_gene_variant|MODIFIER|PA14_58515|PA14_58515|transcript|ABJ15673.1|protein_coding||c.-3387A>C|||||3387|,G|upstream_gene_variant|MODIFIER|PA14_58530|PA14_58530|transcript|ABJ13776.1|protein_coding||c.-2713A>C|||||2713|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_58540|PA14_58540|transcript|ABJ13777.1|protein_coding||c.-1961A>C|||||1961|,G|upstream_gene_variant|MODIFIER|piuC|PA14_58580|transcript|ABJ13781.1|protein_coding||c.-4613T>G|||||4613|,G|downstream_gene_variant|MODIFIER|PA14_58510|PA14_58510|transcript|ABJ13775.1|protein_coding||c.*4321T>G|||||4321|,G|downstream_gene_variant|MODIFIER|lpxO1|PA14_58550|transcript|ABJ13778.1|protein_coding||c.*932T>G|||||932|,G|downstream_gene_variant|MODIFIER|piuA|PA14_58570|transcript|ABJ13780.1|protein_coding||c.*2134A>C|||||2134| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,2:3:117:2:4:0,-10.5302 0:7:7,0:7:246:0:0:0,-22.4744 0:5:5,0:5:169:0:0:0,-15.5391 0:9:9,0:9:327:0:0:0,-29.7672 +Chromosome 5220560 . A G 1.4601E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=36;DPB=36;DPRA=0.724138;EPP=7.35324;EPPR=7.09778;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=40.5626;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=43;QR=1174;RO=34;RPL=2;RPP=7.35324;RPPR=4.03217;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=60.4905;SRR=32;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_58600|PA14_58600|transcript|ABJ13782.1|protein_coding|1/1|c.77A>G|p.Glu26Gly|77/816|77/816|26/271||,G|upstream_gene_variant|MODIFIER|piuB|PA14_58560|transcript|ABJ13779.1|protein_coding||c.-3454T>C|||||3454|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|piuA|PA14_58570|transcript|ABJ13780.1|protein_coding||c.-977T>C|||||977|,G|upstream_gene_variant|MODIFIER|PA14_58610|PA14_58610|transcript|ABJ13783.1|protein_coding||c.-862A>G|||||862|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|piuC|PA14_58580|transcript|ABJ13781.1|protein_coding||c.*79A>G|||||79|,G|downstream_gene_variant|MODIFIER|PA14_58620|PA14_58620|transcript|ABJ13784.1|protein_coding||c.*2720T>C|||||2720|,G|downstream_gene_variant|MODIFIER|speC|PA14_58630|transcript|ABJ13785.1|protein_coding||c.*3261T>C|||||3261|,G|downstream_gene_variant|MODIFIER|PA14_58650|PA14_58650|transcript|ABJ13786.1|protein_coding||c.*4876T>C|||||4876|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,0:9:302:0:0:0,-27.5 0:9:9,0:9:326:0:0:0,-29.6766 0:7:7,2:5:174:2:43:0,-11.9166 0:11:11,0:11:372:0:0:0,-33.8002 +Chromosome 5222810 . C G 6.7882E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=8;CIGAR=1X;DP=69;DPB=69;DPRA=0;EPP=20.3821;EPPR=17.4868;GTI=0;LEN=1;MEANALT=1.25;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=106.272;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=1959;RO=60;RPL=0;RPP=20.3821;RPPR=3.15506;RPR=8;RUN=1;SAF=0;SAP=20.3821;SAR=8;SRF=37;SRP=10.1038;SRR=23;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|PA14_58610|PA14_58610|transcript|ABJ13783.1|protein_coding|1/1|c.1389C>G|p.Gly463Gly|1389/1803|1389/1803|463/600||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|piuA|PA14_58570|transcript|ABJ13780.1|protein_coding||c.-3227G>C|||||3227|,G|downstream_gene_variant|MODIFIER|piuC|PA14_58580|transcript|ABJ13781.1|protein_coding||c.*2329C>G|||||2329|,G|downstream_gene_variant|MODIFIER|PA14_58600|PA14_58600|transcript|ABJ13782.1|protein_coding||c.*1511C>G|||||1511|,G|downstream_gene_variant|MODIFIER|PA14_58620|PA14_58620|transcript|ABJ13784.1|protein_coding||c.*470G>C|||||470|,G|downstream_gene_variant|MODIFIER|speC|PA14_58630|transcript|ABJ13785.1|protein_coding||c.*1011G>C|||||1011|,G|downstream_gene_variant|MODIFIER|PA14_58650|PA14_58650|transcript|ABJ13786.1|protein_coding||c.*2626G>C|||||2626|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ampE|PA14_58660|transcript|ABJ13787.1|protein_coding||c.*4837G>C|||||4837| GT:DP:DPR:RO:QR:AO:QA:GL 0:15:15,2:13:416:2:4:0,-37.3498 0:21:21,1:19:633:1:2:0,-56.9789 0:14:14,1:13:425:1:2:0,-38.345 0:19:19,4:15:485:4:8:0,-43.204 +Chromosome 5230048 . G T 1.43378E-16 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=7;CIGAR=1X;DP=52;DPB=52;DPRA=0.822222;EPP=10.7656;EPPR=11.1654;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=71.8126;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=26;QR=1491;RO=45;RPL=6;RPP=10.7656;RPPR=4.21667;RPR=1;RUN=1;SAF=7;SAP=18.2106;SAR=0;SRF=26;SRP=5.37479;SRR=19;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_58690|PA14_58690|transcript|ABJ13789.1|protein_coding|1/1|c.1405C>A|p.Gln469Lys|1405/2256|1405/2256|469/751||,T|upstream_gene_variant|MODIFIER|PA14_58650|PA14_58650|transcript|ABJ13786.1|protein_coding||c.-2591C>A|||||2591|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ampE|PA14_58660|transcript|ABJ13787.1|protein_coding||c.-1565C>A|||||1565|,T|upstream_gene_variant|MODIFIER|ampD|PA14_58670|transcript|ABJ13788.1|protein_coding||c.-1002C>A|||||1002|,T|upstream_gene_variant|MODIFIER|nadC|PA14_58700|transcript|ABJ13790.1|protein_coding||c.-1690G>T|||||1690|,T|upstream_gene_variant|MODIFIER|tRNA|EBG00001225178|transcript|EBT00001793401.1|protein_coding||c.-2592G>T|||||2592|WARNING_TRANSCRIPT_INCOMPLETE,T|upstream_gene_variant|MODIFIER|pilB|PA14_58750|transcript|ABJ13794.1|protein_coding||c.-4231G>T|||||4231|,T|downstream_gene_variant|MODIFIER|PA14_58710|PA14_58710|transcript|PA14_58710-1.1|protein_coding||c.*2592C>A|||||2592|WARNING_TRANSCRIPT_INCOMPLETE,T|downstream_gene_variant|MODIFIER|PA14_58720|PA14_58720|transcript|ABJ13791.1|protein_coding||c.*2701C>A|||||2701|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|pilA|PA14_58730|transcript|ABJ13792.1|protein_coding||c.*3463C>A|||||3463|,T|downstream_gene_variant|MODIFIER|PA14_58740|PA14_58740|transcript|ABJ13793.1|protein_coding||c.*4095C>A|||||4095| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,2:7:255:2:4:0,-22.9168 0:15:15,0:15:442:0:0:0,-40.0567 0:16:16,3:13:428:3:18:0,-37.1504 0:12:12,2:10:366:2:4:0,-32.902 +Chromosome 5248885 . C A 2.20034E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=52;DPB=52;DPRA=0.75;EPP=6.91895;EPPR=16.3625;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=64.0357;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=63;QR=1635;RO=47;RPL=1;RPP=6.91895;RPPR=3.42611;RPR=4;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=20;SRP=5.27418;SRR=27;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|PA14_58900|PA14_58900|transcript|ABJ13809.1|protein_coding|1/1|c.1932C>A|p.Arg644Arg|1932/4254|1932/4254|644/1417||,A|upstream_gene_variant|MODIFIER|PA14_58880|PA14_58880|transcript|ABJ13807.1|protein_coding||c.-4166G>T|||||4166|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|PA14_58910|PA14_58910|transcript|ABJ13810.1|protein_coding||c.-2695C>A|||||2695|,A|upstream_gene_variant|MODIFIER|PA14_58920|PA14_58920|transcript|ABJ13811.1|protein_coding||c.-3620C>A|||||3620|,A|upstream_gene_variant|MODIFIER|PA14_58930|PA14_58930|transcript|ABJ13812.1|protein_coding||c.-4297C>A|||||4297|,A|upstream_gene_variant|MODIFIER|PA14_58940|PA14_58940|transcript|ABJ13813.1|protein_coding||c.-4791C>A|||||4791|,A|upstream_gene_variant|MODIFIER|PA14_58950|PA14_58950|transcript|ABJ13814.1|protein_coding||c.-4937C>A|||||4937|,A|downstream_gene_variant|MODIFIER|PA14_58890|PA14_58890|transcript|ABJ13808.1|protein_coding||c.*1980C>A|||||1980| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,2:7:242:2:18:0,-20.4004 0:14:14,1:13:404:1:15:0,-35.1456 0:13:13,2:11:411:2:30:0,-34.4846 0:16:16,0:16:578:0:0:0,-52.338 +Chromosome 5250986 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=9;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=22.5536;EPPR=7.30028;GTI=0;LEN=1;MEANALT=1;MQM=57.2222;MQMR=60;NS=4;NUMALT=1;ODDS=50.3345;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=40;QR=1214;RO=41;RPL=8;RPP=14.8328;RPPR=26.3669;RPR=1;RUN=1;SAF=8;SAP=14.8328;SAR=1;SRF=33;SRP=36.112;SRR=8;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_58900|PA14_58900|transcript|ABJ13809.1|protein_coding|1/1|c.4033T>C|p.Ser1345Pro|4033/4254|4033/4254|1345/1417||,C|upstream_gene_variant|MODIFIER|PA14_58910|PA14_58910|transcript|ABJ13810.1|protein_coding||c.-594T>C|||||594|,C|upstream_gene_variant|MODIFIER|PA14_58920|PA14_58920|transcript|ABJ13811.1|protein_coding||c.-1519T>C|||||1519|,C|upstream_gene_variant|MODIFIER|PA14_58930|PA14_58930|transcript|ABJ13812.1|protein_coding||c.-2196T>C|||||2196|,C|upstream_gene_variant|MODIFIER|PA14_58940|PA14_58940|transcript|ABJ13813.1|protein_coding||c.-2690T>C|||||2690|,C|upstream_gene_variant|MODIFIER|PA14_58950|PA14_58950|transcript|ABJ13814.1|protein_coding||c.-2836T>C|||||2836|,C|upstream_gene_variant|MODIFIER|PA14_58960|PA14_58960|transcript|ABJ13815.1|protein_coding||c.-3522T>C|||||3522|,C|upstream_gene_variant|MODIFIER|PA14_58970|PA14_58970|transcript|ABJ13816.1|protein_coding||c.-4220T>C|||||4220|,C|upstream_gene_variant|MODIFIER|PA14_58980|PA14_58980|transcript|ABJ13817.1|protein_coding||c.-4911T>C|||||4911|,C|downstream_gene_variant|MODIFIER|PA14_58890|PA14_58890|transcript|ABJ13808.1|protein_coding||c.*4081T>C|||||4081| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,2:6:170:2:15:0,-14.1463 0:10:10,2:8:263:2:15:0,-22.5546 0:17:17,4:13:372:4:8:0,-33.0038 0:15:15,1:14:409:1:2:0,-36.8758 +Chromosome 5262171 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=8;CIGAR=1X;DP=116;DPB=116;DPRA=0;EPP=20.3821;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=169.492;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=3737;RO=108;RPL=0;RPP=20.3821;RPPR=6.95112;RPR=8;RUN=1;SAF=0;SAP=20.3821;SAR=8;SRF=54;SRP=3.0103;SRR=54;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_59090|PA14_59090|transcript|ABJ13826.1|protein_coding|1/1|c.11C>G|p.Ser4Trp|11/768|11/768|4/255||,G|upstream_gene_variant|MODIFIER|PA14_59100|PA14_59100|transcript|ABJ13827.1|protein_coding||c.-754C>G|||||754|,G|upstream_gene_variant|MODIFIER|PA14_59110|PA14_59110|transcript|ABJ13828.1|protein_coding||c.-2076C>G|||||2076|,G|upstream_gene_variant|MODIFIER|PA14_59120|PA14_59120|transcript|ABJ13829.1|protein_coding||c.-2342C>G|||||2342|,G|upstream_gene_variant|MODIFIER|PA14_59130|PA14_59130|transcript|ABJ13830.1|protein_coding||c.-2851C>G|||||2851|,G|upstream_gene_variant|MODIFIER|PA14_59140|PA14_59140|transcript|ABJ13831.1|protein_coding||c.-3585C>G|||||3585|,G|upstream_gene_variant|MODIFIER|PA14_59150|PA14_59150|transcript|ABJ13832.1|protein_coding||c.-4132C>G|||||4132|,G|downstream_gene_variant|MODIFIER|PA14_58990|PA14_58990|transcript|ABJ13818.1|protein_coding||c.*4707C>G|||||4707|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_59000|PA14_59000|transcript|ABJ13819.1|protein_coding||c.*4008C>G|||||4008|,G|downstream_gene_variant|MODIFIER|PA14_59010|PA14_59010|transcript|ABJ13820.1|protein_coding||c.*3754C>G|||||3754|,G|downstream_gene_variant|MODIFIER|PA14_59020|PA14_59020|transcript|ABJ13821.1|protein_coding||c.*3267C>G|||||3267|,G|downstream_gene_variant|MODIFIER|PA14_59030|PA14_59030|transcript|ABJ13822.1|protein_coding||c.*3041C>G|||||3041|,G|downstream_gene_variant|MODIFIER|PA14_59050|PA14_59050|transcript|ABJ13823.1|protein_coding||c.*2025C>G|||||2025|,G|downstream_gene_variant|MODIFIER|PA14_59060|PA14_59060|transcript|ABJ13824.1|protein_coding||c.*1774C>G|||||1774|,G|downstream_gene_variant|MODIFIER|PA14_59070|PA14_59070|transcript|ABJ13825.1|protein_coding||c.*38C>G|||||38| GT:DP:DPR:RO:QR:AO:QA:GL 0:23:23,5:18:661:5:10:0,-58.8925 0:24:24,1:23:811:1:2:0,-73.0856 0:30:30,1:29:938:1:2:0,-84.481 0:39:39,1:38:1327:1:2:0,-119.489 +Chromosome 5317754 . C G 3.29981E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=6;CIGAR=1X;DP=68;DPB=68;DPRA=0.619048;EPP=16.0391;EPPR=11.9764;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=70.1176;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=64;QR=1980;RO=62;RPL=0;RPP=16.0391;RPPR=3.0103;RPR=6;RUN=1;SAF=0;SAP=16.0391;SAR=6;SRF=36;SRP=6.51267;SRR=26;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|cupD4|PA14_59750|transcript|ABJ13884.1|protein_coding|1/1|c.251C>G|p.Ser84Trp|251/1347|251/1347|84/448||,G|upstream_gene_variant|MODIFIER|cupD5|PA14_59760|transcript|ABJ13885.1|protein_coding||c.-1086C>G|||||1086|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_59700|PA14_59700|transcript|ABJ13881.1|protein_coding||c.*4665C>G|||||4665|,G|downstream_gene_variant|MODIFIER|cupD1|PA14_59710|transcript|ABJ13882.1|protein_coding||c.*3679C>G|||||3679|,G|downstream_gene_variant|MODIFIER|cupD2|PA14_59720|transcript|ABJ13883.1|protein_coding||c.*2844C>G|||||2844|,G|downstream_gene_variant|MODIFIER|rcsB|PA14_59770|transcript|ABJ13886.1|protein_coding||c.*1846G>C|||||1846|,G|downstream_gene_variant|MODIFIER|rcsC|PA14_59780|transcript|ABJ13887.1|protein_coding||c.*2541G>C|||||2541|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:14:14,4:10:345:4:34:0,-28.2325 0:26:26,0:26:865:0:0:0,-78.1302 0:16:16,0:16:516:0:0:0,-46.7347 0:12:12,2:10:254:2:30:0,-20.2489 +Chromosome 5348514 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=60;DPB=60;DPRA=0.673469;EPP=9.52472;EPPR=6.09608;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7193;NS=4;NUMALT=1;ODDS=64.7636;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=28;QR=1793;RO=57;RPL=0;RPP=9.52472;RPPR=3.9627;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=26;SRP=3.9627;SRR=31;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_60070|PA14_60070|transcript|ABJ13915.1|protein_coding|1/1|c.503C>G|p.Ala168Gly|503/2424|503/2424|168/807||,G|upstream_gene_variant|MODIFIER|PA14_60030|PA14_60030|transcript|ABJ13911.1|protein_coding||c.-2169G>C|||||2169|,G|upstream_gene_variant|MODIFIER|PA14_60080|PA14_60080|transcript|ABJ13916.1|protein_coding||c.-1918C>G|||||1918|,G|upstream_gene_variant|MODIFIER|PA14_60090|PA14_60090|transcript|ABJ13917.1|protein_coding||c.-4276C>G|||||4276|,G|downstream_gene_variant|MODIFIER|PA14_60000|PA14_60000|transcript|ABJ13908.1|protein_coding||c.*4388C>G|||||4388|,G|downstream_gene_variant|MODIFIER|PA14_60010|PA14_60010|transcript|ABJ13909.1|protein_coding||c.*4047C>G|||||4047|,G|downstream_gene_variant|MODIFIER|PA14_60020|PA14_60020|transcript|ABJ13910.1|protein_coding||c.*2539C>G|||||2539|,G|downstream_gene_variant|MODIFIER|PA14_60040|PA14_60040|transcript|ABJ13912.1|protein_coding||c.*1778C>G|||||1778|,G|downstream_gene_variant|MODIFIER|PA14_60050|PA14_60050|transcript|ABJ13913.1|protein_coding||c.*1424C>G|||||1424|,G|downstream_gene_variant|MODIFIER|PA14_60060|PA14_60060|transcript|ABJ13914.1|protein_coding||c.*680C>G|||||680|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|dtD|PA14_60100|transcript|ABJ13918.1|protein_coding||c.*4996G>C|||||4996| GT:DP:DPR:RO:QR:AO:QA:GL 0:11:11,3:8:289:3:28:0,-23.7401 0:8:8,0:8:206:0:0:0,-18.7906 0:22:22,0:22:667:0:0:0,-60.2943 0:19:19,0:19:631:0:0:0,-57.0722 +Chromosome 5366340 . G C 2.08686E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=35;DPB=35;DPRA=1.1875;EPP=11.6962;EPPR=28.2974;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=55.7957;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1023;RO=31;RPL=4;RPP=11.6962;RPPR=4.76149;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=20;SRP=8.68415;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|pilS|PA14_60250|transcript|ABJ13928.1|protein_coding|1/1|c.496G>C|p.Ala166Pro|496/1593|496/1593|166/530||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|clpB|PA14_60190|transcript|ABJ13923.1|protein_coding||c.-3901C>G|||||3901|,C|upstream_gene_variant|MODIFIER|PA14_60200|PA14_60200|transcript|ABJ13924.1|protein_coding||c.-3017C>G|||||3017|,C|upstream_gene_variant|MODIFIER|rluD|PA14_60210|transcript|ABJ13925.1|protein_coding||c.-2058C>G|||||2058|,C|upstream_gene_variant|MODIFIER|pilR|PA14_60260|transcript|ABJ13929.1|protein_coding||c.-1112G>C|||||1112|,C|upstream_gene_variant|MODIFIER|fimU|PA14_60280|transcript|ABJ13931.1|protein_coding||c.-4352G>C|||||4352|,C|downstream_gene_variant|MODIFIER|comL|PA14_60230|transcript|ABJ13926.1|protein_coding||c.*887G>C|||||887|,C|downstream_gene_variant|MODIFIER|PA14_60240|PA14_60240|transcript|ABJ13927.1|protein_coding||c.*485G>C|||||485|,C|downstream_gene_variant|MODIFIER|PA14_60270|PA14_60270|transcript|ABJ13930.1|protein_coding||c.*2495C>G|||||2495|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:269:0:0:0,-24.5736 0:11:11,1:10:227:1:2:0,-20.4416 0:8:8,3:5:191:3:6:0,-16.9979 0:9:9,0:9:336:0:0:0,-30.5895 +Chromosome 5369314 . T C 2.04169E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=37;DPB=37;DPRA=3.77778;EPP=11.6962;EPPR=4.65535;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=40.1094;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=57;QR=1029;RO=33;RPL=4;RPP=11.6962;RPPR=8.34028;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=16;SRP=3.0761;SRR=17;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_60270|PA14_60270|transcript|ABJ13930.1|protein_coding|1/1|c.616A>G|p.Ser206Gly|616/1095|616/1095|206/364||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|fimU|PA14_60280|transcript|ABJ13931.1|protein_coding||c.-1378T>C|||||1378|,C|upstream_gene_variant|MODIFIER|pilW|PA14_60290|transcript|ABJ13932.1|protein_coding||c.-2397T>C|||||2397|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|pilX|PA14_60300|transcript|ABJ13933.1|protein_coding||c.-3227T>C|||||3227|,C|upstream_gene_variant|MODIFIER|pilY1|PA14_60310|transcript|ABJ13934.1|protein_coding||c.-3840T>C|||||3840|,C|downstream_gene_variant|MODIFIER|comL|PA14_60230|transcript|ABJ13926.1|protein_coding||c.*3861T>C|||||3861|,C|downstream_gene_variant|MODIFIER|PA14_60240|PA14_60240|transcript|ABJ13927.1|protein_coding||c.*3459T>C|||||3459|,C|downstream_gene_variant|MODIFIER|pilS|PA14_60250|transcript|ABJ13928.1|protein_coding||c.*1877T>C|||||1877|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|pilR|PA14_60260|transcript|ABJ13929.1|protein_coding||c.*525T>C|||||525| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:111:0:0:0,-10.3514 0:7:7,1:6:185:1:13:0,-15.6464 0:10:10,2:8:250:2:42:0,-18.8115 0:17:17,1:16:483:1:2:0,-43.5449 +Chromosome 5379661 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=46;DPB=46;DPRA=1.3;EPP=3.73412;EPPR=3.0608;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=51.5814;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=48;QR=1524;RO=43;RPL=1;RPP=3.73412;RPPR=14.3727;RPR=2;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=16;SRP=9.12072;SRR=27;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|ileS|PA14_60370|transcript|ABJ13939.1|protein_coding|1/1|c.2586C>A|p.Gly862Gly|2586/2832|2586/2832|862/943||,T|upstream_gene_variant|MODIFIER|lytB|PA14_60330|transcript|ABJ13936.1|protein_coding||c.-1267C>A|||||1267|,T|upstream_gene_variant|MODIFIER|PA14_60350|PA14_60350|transcript|ABJ13937.1|protein_coding||c.-741C>A|||||741|,T|upstream_gene_variant|MODIFIER|lspA|PA14_60360|transcript|ABJ13938.1|protein_coding||c.-239C>A|||||239|,T|downstream_gene_variant|MODIFIER|pilY1|PA14_60310|transcript|ABJ13934.1|protein_coding||c.*3031G>T|||||3031|,T|downstream_gene_variant|MODIFIER|pilE|PA14_60320|transcript|ABJ13935.1|protein_coding||c.*2280G>T|||||2280|,T|downstream_gene_variant|MODIFIER|ribF|PA14_60380|transcript|ABJ13940.1|protein_coding||c.*2609C>A|||||2609|,T|downstream_gene_variant|MODIFIER|mviN|PA14_60390|transcript|ABJ13941.1|protein_coding||c.*3644C>A|||||3644| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,2:6:199:2:32:0,-15.191 0:11:11,0:11:413:0:0:0,-37.5166 0:18:18,1:17:586:1:16:0,-51.4545 0:9:9,0:9:326:0:0:0,-29.675 +Chromosome 5381591 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=51;DPB=51;DPRA=0.642857;EPP=7.35324;EPPR=8.37251;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=71.5209;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=1596;RO=49;RPL=2;RPP=7.35324;RPPR=3.40914;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=40;SRP=45.5977;SRR=9;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|ileS|PA14_60370|transcript|ABJ13939.1|protein_coding|1/1|c.656T>G|p.Leu219Arg|656/2832|656/2832|219/943||,C|upstream_gene_variant|MODIFIER|lytB|PA14_60330|transcript|ABJ13936.1|protein_coding||c.-3197T>G|||||3197|,C|upstream_gene_variant|MODIFIER|PA14_60350|PA14_60350|transcript|ABJ13937.1|protein_coding||c.-2671T>G|||||2671|,C|upstream_gene_variant|MODIFIER|lspA|PA14_60360|transcript|ABJ13938.1|protein_coding||c.-2169T>G|||||2169|,C|upstream_gene_variant|MODIFIER|rpsT|PA14_60400|transcript|ABJ13942.1|protein_coding||c.-3536A>C|||||3536|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|pilY1|PA14_60310|transcript|ABJ13934.1|protein_coding||c.*4961A>C|||||4961|,C|downstream_gene_variant|MODIFIER|pilE|PA14_60320|transcript|ABJ13935.1|protein_coding||c.*4210A>C|||||4210|,C|downstream_gene_variant|MODIFIER|ribF|PA14_60380|transcript|ABJ13940.1|protein_coding||c.*679T>G|||||679|,C|downstream_gene_variant|MODIFIER|mviN|PA14_60390|transcript|ABJ13941.1|protein_coding||c.*1714T>G|||||1714|,C|downstream_gene_variant|MODIFIER|PA14_60410|PA14_60410|transcript|ABJ13943.1|protein_coding||c.*3878T>G|||||3878|,C|downstream_gene_variant|MODIFIER|proB|PA14_60420|transcript|ABJ13944.1|protein_coding||c.*4354T>G|||||4354| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:251:0:0:0,-22.9339 0:9:9,2:7:268:2:15:0,-23.0561 0:17:17,0:17:486:0:0:0,-43.9993 0:18:18,0:18:591:0:0:0,-53.49 +Chromosome 5391852 . T C 4.44518E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=60;DPB=60;DPRA=0.719298;EPP=11.6962;EPPR=8.59409;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=82.7775;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1945;RO=56;RPL=0;RPP=11.6962;RPPR=8.59409;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=16;SRP=25.3454;SRR=40;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_60490|PA14_60490|transcript|ABJ13949.1|protein_coding|1/1|c.850T>C|p.Ser284Pro|850/2028|850/2028|284/675||,C|upstream_gene_variant|MODIFIER|proB|PA14_60420|transcript|ABJ13944.1|protein_coding||c.-4789A>G|||||4789|,C|upstream_gene_variant|MODIFIER|obg|PA14_60445|transcript|ABJ15631.1|protein_coding||c.-3498A>G|||||3498|,C|upstream_gene_variant|MODIFIER|rpmA|PA14_60450|transcript|ABJ13945.1|protein_coding||c.-3098A>G|||||3098|,C|upstream_gene_variant|MODIFIER|rplU|PA14_60460|transcript|ABJ13946.1|protein_coding||c.-2763A>G|||||2763|,C|downstream_gene_variant|MODIFIER|ispB|PA14_60470|transcript|ABJ13947.1|protein_coding||c.*1554T>C|||||1554|,C|downstream_gene_variant|MODIFIER|PA14_60480|PA14_60480|transcript|ABJ13948.1|protein_coding||c.*1192T>C|||||1192|,C|downstream_gene_variant|MODIFIER|fklB|PA14_60500|transcript|ABJ13950.1|protein_coding||c.*1248A>G|||||1248|,C|downstream_gene_variant|MODIFIER|PA14_60520|PA14_60520|transcript|ABJ13951.1|protein_coding||c.*1950A>G|||||1950|,C|downstream_gene_variant|MODIFIER|PA14_60530|PA14_60530|transcript|ABJ13952.1|protein_coding||c.*2512A>G|||||2512|,C|downstream_gene_variant|MODIFIER|PA14_60540|PA14_60540|transcript|ABJ13953.1|protein_coding||c.*3174A>G|||||3174|,C|downstream_gene_variant|MODIFIER|PA14_60550|PA14_60550|transcript|ABJ13954.1|protein_coding||c.*3668A>G|||||3668| GT:DP:DPR:RO:QR:AO:QA:GL 0:11:11,1:10:382:1:2:0,-34.5343 0:10:10,2:8:302:2:4:0,-27.1565 0:19:19,0:19:612:0:0:0,-55.364 0:20:20,1:19:649:1:2:0,-58.5154 +Chromosome 5417813 . A G 2.76768E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=18;DPB=18;DPRA=3.5;EPP=9.52472;EPPR=3.15506;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=21.1742;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=407;RO=15;RPL=0;RPP=9.52472;RPPR=3.15506;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=7;SRP=3.15506;SRR=8;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_60780|PA14_60780|transcript|ABJ13971.1|protein_coding|1/1|c.377T>C|p.Leu126Pro|377/1194|377/1194|126/397||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_60730|PA14_60730|transcript|ABJ13967.1|protein_coding||c.-4904T>C|||||4904|,G|upstream_gene_variant|MODIFIER|pra|PA14_60750|transcript|ABJ13968.1|protein_coding||c.-4156T>C|||||4156|,G|upstream_gene_variant|MODIFIER|PA14_60760|PA14_60760|transcript|ABJ13969.1|protein_coding||c.-2281T>C|||||2281|,G|upstream_gene_variant|MODIFIER|PA14_60770|PA14_60770|transcript|ABJ13970.1|protein_coding||c.-810T>C|||||810|,G|upstream_gene_variant|MODIFIER|nfxB|PA14_60810|transcript|ABJ13974.1|protein_coding||c.-3720A>G|||||3720|,G|downstream_gene_variant|MODIFIER|PA14_60790|PA14_60790|transcript|ABJ13972.1|protein_coding||c.*373T>C|||||373|,G|downstream_gene_variant|MODIFIER|PA14_60800|PA14_60800|transcript|ABJ13973.1|protein_coding||c.*1563T>C|||||1563|,G|downstream_gene_variant|MODIFIER|oprJ|PA14_60820|transcript|ABJ13975.1|protein_coding||c.*4289T>C|||||4289| GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:40:0:0:0,-3.99568 0:7:7,1:6:168:1:27:0,-12.6934 0:7:7,2:5:117:2:4:0,-10.3764 0:3:3,0:3:82:0:0:0,-7.65103 +Chromosome 5422395 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=6;CIGAR=1X;DP=48;DPB=48;DPRA=1.95238;EPP=16.0391;EPPR=16.2459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=62.57;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=25;QR=1361;RO=42;RPL=0;RPP=16.0391;RPPR=3.21711;RPR=6;RUN=1;SAF=0;SAP=16.0391;SAR=6;SRF=17;SRP=6.31921;SRR=25;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|oprJ|PA14_60820|transcript|ABJ13975.1|protein_coding|1/1|c.1147G>C|p.Glu383Gln|1147/1440|1147/1440|383/479||,G|upstream_gene_variant|MODIFIER|PA14_60780|PA14_60780|transcript|ABJ13971.1|protein_coding||c.-4206G>C|||||4206|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_60790|PA14_60790|transcript|ABJ13972.1|protein_coding||c.-3523G>C|||||3523|,G|upstream_gene_variant|MODIFIER|PA14_60800|PA14_60800|transcript|ABJ13973.1|protein_coding||c.-1355G>C|||||1355|,G|downstream_gene_variant|MODIFIER|nfxB|PA14_60810|transcript|ABJ13974.1|protein_coding||c.*344C>G|||||344|,G|downstream_gene_variant|MODIFIER|mexD|PA14_60830|transcript|ABJ13976.1|protein_coding||c.*1152G>C|||||1152|,G|downstream_gene_variant|MODIFIER|mexC|PA14_60850|transcript|ABJ13977.1|protein_coding||c.*4311G>C|||||4311| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:214:0:0:0,-19.5541 0:15:15,4:11:348:4:8:0,-30.8687 0:9:9,1:8:292:1:15:0,-25.1259 0:17:17,1:16:507:1:2:0,-45.7183 +Chromosome 5431912 . T C 6.44918E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=44;DPB=44;DPRA=1.4;EPP=3.73412;EPPR=5.60547;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=43.6231;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=44;QR=1396;RO=41;RPL=0;RPP=9.52472;RPPR=3.48696;RPR=3;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=20;SRP=3.06326;SRR=21;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|morA|PA14_60870|transcript|ABJ13979.1|protein_coding|1/1|c.3076T>C|p.Ser1026Pro|3076/4248|3076/4248|1026/1415||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|mexC|PA14_60850|transcript|ABJ13977.1|protein_coding||c.-4043A>G|||||4043|,C|upstream_gene_variant|MODIFIER|glyA|PA14_60890|transcript|ABJ13980.1|protein_coding||c.-1295T>C|||||1295|,C|downstream_gene_variant|MODIFIER|nfxB|PA14_60860|transcript|ABJ13978.1|protein_coding||c.*3319T>C|||||3319|,C|downstream_gene_variant|MODIFIER|PA14_60900|PA14_60900|transcript|ABJ13981.1|protein_coding||c.*2626A>G|||||2626|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_60920|PA14_60920|transcript|ABJ13982.1|protein_coding||c.*3017A>G|||||3017|,C|downstream_gene_variant|MODIFIER|PA14_60930|PA14_60930|transcript|ABJ13983.1|protein_coding||c.*4081A>G|||||4081|,C|downstream_gene_variant|MODIFIER|cstA|PA14_60950|transcript|ABJ13984.1|protein_coding||c.*4333A>G|||||4333| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:120:0:0:0,-11.0305 0:9:9,0:9:306:0:0:0,-27.8548 0:14:14,3:11:367:3:44:0,-29.2394 0:16:16,0:16:603:0:0:0,-54.6035 +Chromosome 5434981 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=9;CIGAR=1X;DP=74;DPB=74;DPRA=0;EPP=22.5536;EPPR=3.14602;GTI=0;LEN=1;MEANALT=1.25;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=107.934;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=43;QR=2046;RO=64;RPL=9;RPP=22.5536;RPPR=6.40323;RPR=0;RUN=1;SAF=9;SAP=22.5536;SAR=0;SRF=42;SRP=16.582;SRR=22;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_60920|PA14_60920|transcript|ABJ13982.1|protein_coding|1/1|c.953T>G|p.Leu318Arg|953/1005|953/1005|318/334||,C|upstream_gene_variant|MODIFIER|PA14_60900|PA14_60900|transcript|ABJ13981.1|protein_coding||c.-63T>G|||||63|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_60970|PA14_60970|transcript|ABJ13986.1|protein_coding||c.-4377A>C|||||4377|,C|downstream_gene_variant|MODIFIER|morA|PA14_60870|transcript|ABJ13979.1|protein_coding||c.*1897A>C|||||1897|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|glyA|PA14_60890|transcript|ABJ13980.1|protein_coding||c.*521A>C|||||521|,C|downstream_gene_variant|MODIFIER|PA14_60930|PA14_60930|transcript|ABJ13983.1|protein_coding||c.*1012T>G|||||1012|,C|downstream_gene_variant|MODIFIER|cstA|PA14_60950|transcript|ABJ13984.1|protein_coding||c.*1264T>G|||||1264|,C|downstream_gene_variant|MODIFIER|PA14_60960|PA14_60960|transcript|ABJ13985.1|protein_coding||c.*3668T>G|||||3668|,C|downstream_gene_variant|MODIFIER|radA|PA14_60990|transcript|ABJ13987.1|protein_coding||c.*4761T>G|||||4761| GT:DP:DPR:RO:QR:AO:QA:GL 0:17:17,1:16:583:1:2:0,-52.6 0:23:23,3:19:503:3:6:0,-44.912 0:19:19,4:15:518:4:8:0,-46.1882 0:15:15,1:14:442:1:27:0,-37.3647 +Chromosome 5445498 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=21;CIGAR=1X;DP=90;DPB=90;DPRA=0;EPP=48.6112;EPPR=50.8771;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=90.5631;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=263;QR=2097;RO=69;RPL=0;RPP=48.6112;RPPR=16.8888;RPR=21;RUN=1;SAF=0;SAP=48.6112;SAR=21;SRF=33;SRP=3.29354;SRR=36;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|fnr-2|PA14_61060|transcript|ABJ13993.1|protein_coding|1/1|c.509T>C|p.Leu170Pro|509/777|509/777|170/258||,G|upstream_gene_variant|MODIFIER|radA|PA14_60990|transcript|ABJ13987.1|protein_coding||c.-4395T>C|||||4395|,G|upstream_gene_variant|MODIFIER|PA14_61010|PA14_61010|transcript|ABJ13989.1|protein_coding||c.-3535T>C|||||3535|,G|upstream_gene_variant|MODIFIER|ankB|PA14_61020|transcript|ABJ13990.1|protein_coding||c.-2909T>C|||||2909|,G|upstream_gene_variant|MODIFIER|katB|PA14_61040|transcript|ABJ13991.1|protein_coding||c.-1314T>C|||||1314|,G|upstream_gene_variant|MODIFIER|PA14_61090|PA14_61090|transcript|ABJ13995.1|protein_coding||c.-1941A>G|||||1941|,G|downstream_gene_variant|MODIFIER|PA14_61000|PA14_61000|transcript|ABJ13988.1|protein_coding||c.*3851A>G|||||3851|,G|downstream_gene_variant|MODIFIER|mscL|PA14_61050|transcript|ABJ13992.1|protein_coding||c.*373A>G|||||373|,G|downstream_gene_variant|MODIFIER|dctP|PA14_61080|transcript|ABJ13994.1|protein_coding||c.*615T>C|||||615|,G|downstream_gene_variant|MODIFIER|PA14_61110|PA14_61110|transcript|ABJ13996.1|protein_coding||c.*3066T>C|||||3066|,G|downstream_gene_variant|MODIFIER|PA14_61120|PA14_61120|transcript|ABJ13997.1|protein_coding||c.*3641T>C|||||3641|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_61130|PA14_61130|transcript|ABJ13998.1|protein_coding||c.*4616T>C|||||4616| GT:DP:DPR:RO:QR:AO:QA:GL 0:16:16,5:11:365:5:49:0,-28.6526 0:22:22,2:20:525:2:17:0,-45.8655 0:26:26,7:19:621:7:115:0,-45.6654 0:26:26,7:19:586:7:82:0,-45.5114 +Chromosome 5460322 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=50;DPB=50;DPRA=0.947368;EPP=9.52472;EPPR=15.095;GTI=0;LEN=1;MEANALT=1;MQM=45.6667;MQMR=19.1087;NS=4;NUMALT=1;ODDS=41.767;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=1338;RO=46;RPL=0;RPP=9.52472;RPPR=40.0197;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=18;SRP=7.73089;SRR=28;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|PA14_61200|PA14_61200|transcript|ABJ14004.1|protein_coding|1/1|c.4533G>T|p.Val1511Val|4533/5985|4533/5985|1511/1994||,A|upstream_gene_variant|MODIFIER|PA14_61180|PA14_61180|transcript|ABJ14002.1|protein_coding||c.-3524G>T|||||3524|,A|upstream_gene_variant|MODIFIER|PA14_61190|PA14_61190|transcript|ABJ14003.1|protein_coding||c.-1515G>T|||||1515|,A|upstream_gene_variant|MODIFIER|hprA|PA14_61210|transcript|ABJ14005.1|protein_coding||c.-4853C>A|||||4853|,A|downstream_gene_variant|MODIFIER|PA14_61170|PA14_61170|transcript|ABJ14001.1|protein_coding||c.*4073C>A|||||4073| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:284:0:0:0,-9.79688 0:12:12,3:9:238:3:6:0,-10.1883 0:18:18,0:18:482:0:0:0,-19.1181 0:12:12,0:11:334:0:0:0,-19.7134 +Chromosome 5517891 . C G 1.76781E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=36;DPB=36;DPRA=0.857143;EPP=7.35324;EPPR=28.557;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=30.8618;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1047;RO=34;RPL=0;RPP=7.35324;RPPR=7.09778;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=12;SRP=9.39698;SRR=22;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|yadF|PA14_61860|transcript|ABJ14057.1|protein_coding|1/1|c.175G>C|p.Asp59His|175/648|175/648|59/215||,G|upstream_gene_variant|MODIFIER|tRNA|EBG00001225052|transcript|EBT00001793423.1|protein_coding||c.-3849G>C|||||3849|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,G|upstream_gene_variant|MODIFIER|vapI|PA14_61840|transcript|ABJ14055.1|protein_coding||c.-3390G>C|||||3390|,G|downstream_gene_variant|MODIFIER|ychF|PA14_61820|transcript|ABJ14054.1|protein_coding||c.*4101C>G|||||4101|,G|downstream_gene_variant|MODIFIER|PA14_61830|PA14_61830|transcript|PA14_61830-1.1|protein_coding||c.*3849C>G|||||3849|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,G|downstream_gene_variant|MODIFIER|iutA|PA14_61850|transcript|ABJ14056.1|protein_coding||c.*543C>G|||||543|,G|downstream_gene_variant|MODIFIER|PA14_61870|PA14_61870|transcript|ABJ14058.1|protein_coding||c.*236G>C|||||236|,G|downstream_gene_variant|MODIFIER|rimI|PA14_61880|transcript|ABJ14059.1|protein_coding||c.*1673G>C|||||1673|,G|downstream_gene_variant|MODIFIER|PA14_61890|PA14_61890|transcript|ABJ14060.1|protein_coding||c.*2122G>C|||||2122|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_61910|PA14_61910|transcript|ABJ14061.1|protein_coding||c.*3083G>C|||||3083|,G|downstream_gene_variant|MODIFIER|PA14_61920|PA14_61920|transcript|ABJ14062.1|protein_coding||c.*3650G>C|||||3650|,G|downstream_gene_variant|MODIFIER|PA14_61940|PA14_61940|transcript|ABJ14063.1|protein_coding||c.*4671G>C|||||4671| GT:DP:DPR:RO:QR:AO:QA:GL 0:11:11,0:11:344:0:0:0,-31.2539 0:13:13,0:13:402:0:0:0,-36.4673 0:8:8,2:6:218:2:4:0,-19.5915 0:4:4,0:4:83:0:0:0,-7.67688 +Chromosome 5521066 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=49;DPB=49;DPRA=0.769231;EPP=3.0103;EPPR=6.75262;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=74.3115;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=42;QR=1686;RO=47;RPL=1;RPP=3.0103;RPPR=3.0565;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=21;SRP=4.16534;SRR=26;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_61910|PA14_61910|transcript|ABJ14061.1|protein_coding|1/1|c.445G>C|p.Gly149Arg|445/537|445/537|149/178||,G|upstream_gene_variant|MODIFIER|yadF|PA14_61860|transcript|ABJ14057.1|protein_coding||c.-3001G>C|||||3001|,G|upstream_gene_variant|MODIFIER|PA14_61870|PA14_61870|transcript|ABJ14058.1|protein_coding||c.-1701G>C|||||1701|,G|upstream_gene_variant|MODIFIER|rimI|PA14_61880|transcript|ABJ14059.1|protein_coding||c.-1050G>C|||||1050|,G|upstream_gene_variant|MODIFIER|PA14_61890|PA14_61890|transcript|ABJ14060.1|protein_coding||c.-352G>C|||||352|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_61960|PA14_61960|transcript|ABJ14065.1|protein_coding||c.-3625C>G|||||3625|,G|upstream_gene_variant|MODIFIER|PA14_61980|PA14_61980|transcript|ABJ14066.1|protein_coding||c.-4913C>G|||||4913|,G|downstream_gene_variant|MODIFIER|iutA|PA14_61850|transcript|ABJ14056.1|protein_coding||c.*3718C>G|||||3718|,G|downstream_gene_variant|MODIFIER|PA14_61920|PA14_61920|transcript|ABJ14062.1|protein_coding||c.*475G>C|||||475|,G|downstream_gene_variant|MODIFIER|PA14_61940|PA14_61940|transcript|ABJ14063.1|protein_coding||c.*1496G>C|||||1496|,G|downstream_gene_variant|MODIFIER|PA14_61950|PA14_61950|transcript|ABJ14064.1|protein_coding||c.*2738G>C|||||2738| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:282:0:0:0,-25.713 0:11:11,0:11:424:0:0:0,-38.5084 0:20:20,0:20:670:0:0:0,-60.5875 0:10:10,2:8:310:2:42:0,-24.2758 +Chromosome 5554402 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=30;DPB=30;DPRA=0.913043;EPP=7.35324;EPPR=4.25114;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=42.768;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=28;QR=841;RO=28;RPL=0;RPP=7.35324;RPPR=5.80219;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=15;SRP=3.32051;SRR=13;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|PA14_62240|PA14_62240|transcript|ABJ14084.1|protein_coding|1/1|c.312C>T|p.Asn104Asn|312/348|312/348|104/115||,T|upstream_gene_variant|MODIFIER|PA14_62190|PA14_62190|transcript|ABJ14081.1|protein_coding||c.-4519G>A|||||4519|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|mrcB|PA14_62200|transcript|ABJ14082.1|protein_coding||c.-2178G>A|||||2178|,T|upstream_gene_variant|MODIFIER|PA14_62250|PA14_62250|transcript|ABJ14085.1|protein_coding||c.-262C>T|||||262|,T|upstream_gene_variant|MODIFIER|PA14_62260|PA14_62260|transcript|ABJ14086.1|protein_coding||c.-639C>T|||||639|,T|downstream_gene_variant|MODIFIER|PA14_62230|PA14_62230|transcript|ABJ14083.1|protein_coding||c.*403C>T|||||403|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|PrrF|EBG00001225069|transcript|EBT00001793506.1|sRNA||n.*1490G>A|||||1490|,T|downstream_gene_variant|MODIFIER|PrrF|EBG00001225022|transcript|EBT00001793477.1|sRNA||n.*1702G>A|||||1702|,T|downstream_gene_variant|MODIFIER|phuW|PA14_62270|transcript|ABJ14087.1|protein_coding||c.*1900G>A|||||1900|,T|downstream_gene_variant|MODIFIER|phuV|PA14_62280|transcript|ABJ14088.1|protein_coding||c.*2798G>A|||||2798|,T|downstream_gene_variant|MODIFIER|phuU|PA14_62290|transcript|ABJ14089.1|protein_coding||c.*3565G>A|||||3565|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|phuT|PA14_62300|transcript|ABJ14090.1|protein_coding||c.*4599G>A|||||4599| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:139:0:0:0,-12.734 0:7:7,2:5:177:2:28:0,-13.6115 0:10:10,0:10:287:0:0:0,-26.1016 0:7:7,0:7:238:0:0:0,-21.7425 +Chromosome 5575437 . C T 6.31636E-8 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=17;DPB=17;DPRA=0.923077;EPP=7.35324;EPPR=3.15506;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=18.0461;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=56;QR=561;RO=15;RPL=2;RPP=7.35324;RPPR=3.15506;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=20.5268;SRR=13;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|yadB|PA14_62510|transcript|ABJ14106.1|protein_coding|1/1|c.607C>T|p.Leu203Phe|607/882|607/882|203/293||,T|upstream_gene_variant|MODIFIER|sfsA|PA14_62470|transcript|ABJ14103.1|protein_coding||c.-2485G>A|||||2485|,T|upstream_gene_variant|MODIFIER|aspC|PA14_62480|transcript|ABJ14104.1|protein_coding||c.-1313G>A|||||1313|,T|upstream_gene_variant|MODIFIER|PA14_62520|PA14_62520|transcript|ABJ14107.1|protein_coding||c.-345C>T|||||345|,T|upstream_gene_variant|MODIFIER|cbrA|PA14_62530|transcript|ABJ14108.1|protein_coding||c.-505C>T|||||505|,T|upstream_gene_variant|MODIFIER|cbrB|PA14_62540|transcript|ABJ14109.1|protein_coding||c.-3483C>T|||||3483|,T|downstream_gene_variant|MODIFIER|yieG|PA14_62440|transcript|ABJ14101.1|protein_coding||c.*4314C>T|||||4314|,T|downstream_gene_variant|MODIFIER|trmA|PA14_62450|transcript|ABJ14102.1|protein_coding||c.*3226C>T|||||3226|,T|downstream_gene_variant|MODIFIER|dksA|PA14_62490|transcript|ABJ14105.1|protein_coding||c.*674C>T|||||674|,T|downstream_gene_variant|MODIFIER|P36|EBG00001225135|transcript|EBT00001793473.1|sRNA||n.*4927G>A|||||4927| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:215:0:0:0,-19.6967 0:4:4,2:2:80:2:56:0,-2.27591 0:5:5,0:5:190:0:0:0,-17.4659 0:2:2,0:2:76:0:0:0,-7.21426 +Chromosome 5588852 . C A 5.20059E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=28;DPB=28;DPRA=1;EPP=13.8677;EPPR=3.86001;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=29.7651;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=63;QR=821;RO=23;RPL=0;RPP=13.8677;RPPR=5.3706;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=14;SRP=5.3706;SRR=9;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|acsB|PA14_62630|transcript|ABJ14116.1|protein_coding|1/1|c.1389C>A|p.Ile463Ile|1389/1938|1389/1938|463/645||,A|upstream_gene_variant|MODIFIER|PA14_62640|PA14_62640|transcript|ABJ14117.1|protein_coding||c.-646C>A|||||646|,A|upstream_gene_variant|MODIFIER|PA14_62650|PA14_62650|transcript|ABJ14118.1|protein_coding||c.-1652C>A|||||1652|,A|upstream_gene_variant|MODIFIER|PA14_62660|PA14_62660|transcript|ABJ14119.1|protein_coding||c.-4923C>A|||||4923|,A|downstream_gene_variant|MODIFIER|panB|PA14_62580|transcript|ABJ14112.1|protein_coding||c.*4658C>A|||||4658|,A|downstream_gene_variant|MODIFIER|panC|PA14_62590|transcript|ABJ14113.1|protein_coding||c.*3810C>A|||||3810|,A|downstream_gene_variant|MODIFIER|panD|PA14_62600|transcript|ABJ14114.1|protein_coding||c.*3336C>A|||||3336|,A|downstream_gene_variant|MODIFIER|pgi|PA14_62620|transcript|ABJ14115.1|protein_coding||c.*1582C>A|||||1582| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,1:3:90:1:15:0,-6.89495 0:7:7,0:7:273:0:0:0,-24.9367 0:6:6,1:5:179:1:15:0,-14.9588 0:11:11,3:8:279:3:33:0,-22.3594 +Chromosome 5589178 . T C 9.72619E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=43;DPB=43;DPRA=0.794118;EPP=3.73412;EPPR=3.87889;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=31.8188;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=120;QR=1384;RO=40;RPL=2;RPP=3.73412;RPPR=8.43898;RPR=1;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=29;SRP=20.5992;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|acsB|PA14_62630|transcript|ABJ14116.1|protein_coding|1/1|c.1715T>C|p.Leu572Pro|1715/1938|1715/1938|572/645||,C|upstream_gene_variant|MODIFIER|PA14_62640|PA14_62640|transcript|ABJ14117.1|protein_coding||c.-320T>C|||||320|,C|upstream_gene_variant|MODIFIER|PA14_62650|PA14_62650|transcript|ABJ14118.1|protein_coding||c.-1326T>C|||||1326|,C|upstream_gene_variant|MODIFIER|PA14_62660|PA14_62660|transcript|ABJ14119.1|protein_coding||c.-4597T>C|||||4597|,C|upstream_gene_variant|MODIFIER|PA14_62670|PA14_62670|transcript|ABJ14120.1|protein_coding||c.-4983T>C|||||4983|,C|downstream_gene_variant|MODIFIER|panB|PA14_62580|transcript|ABJ14112.1|protein_coding||c.*4984T>C|||||4984|,C|downstream_gene_variant|MODIFIER|panC|PA14_62590|transcript|ABJ14113.1|protein_coding||c.*4136T>C|||||4136|,C|downstream_gene_variant|MODIFIER|panD|PA14_62600|transcript|ABJ14114.1|protein_coding||c.*3662T>C|||||3662|,C|downstream_gene_variant|MODIFIER|pgi|PA14_62620|transcript|ABJ14115.1|protein_coding||c.*1908T>C|||||1908| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:206:0:0:0,-18.8254 0:10:10,0:10:377:0:0:0,-34.28 0:9:9,3:6:198:3:120:0,-6.9504 0:17:17,0:17:603:0:0:0,-54.5849 +Chromosome 5606347 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=11;CIGAR=1X;DP=58;DPB=58;DPRA=2.42857;EPP=26.8965;EPPR=4.16534;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=67.714;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=139;QR=1580;RO=47;RPL=11;RPP=26.8965;RPPR=31.8863;RPR=0;RUN=1;SAF=11;SAP=26.8965;SAR=0;SRF=27;SRP=5.27418;SRR=20;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|glmM|PA14_62840|transcript|ABJ14132.1|protein_coding|1/1|c.487A>G|p.Ser163Gly|487/1338|487/1338|163/445||,C|upstream_gene_variant|MODIFIER|infB|PA14_62760|transcript|ABJ14127.1|protein_coding||c.-4469A>G|||||4469|,C|upstream_gene_variant|MODIFIER|nusA|PA14_62770|transcript|ABJ14128.1|protein_coding||c.-2960A>G|||||2960|,C|upstream_gene_variant|MODIFIER|yhbC|PA14_62780|transcript|ABJ14129.1|protein_coding||c.-2457A>G|||||2457|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_62790|PA14_62790|transcript|PA14_62790-1.1|protein_coding||c.-2254A>G|||||2254|WARNING_TRANSCRIPT_INCOMPLETE,C|upstream_gene_variant|MODIFIER|PA14_62800|PA14_62800|transcript|PA14_62800-1.1|protein_coding||c.-2078A>G|||||2078|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|upstream_gene_variant|MODIFIER|secG|PA14_62810|transcript|ABJ14130.1|protein_coding||c.-1675A>G|||||1675|,C|upstream_gene_variant|MODIFIER|tpiA|PA14_62830|transcript|ABJ14131.1|protein_coding||c.-917A>G|||||917|,C|upstream_gene_variant|MODIFIER|yhbY|PA14_62880|transcript|ABJ14136.1|protein_coding||c.-4200T>C|||||4200|,C|downstream_gene_variant|MODIFIER|tRNA|EBG00001225112|transcript|EBT00001793488.1|protein_coding||c.*2254T>C|||||2254|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|tRNA|EBG00001225152|transcript|EBT00001793502.1|protein_coding||c.*2078T>C|||||2078|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|folP|PA14_62850|transcript|ABJ14133.1|protein_coding||c.*503A>G|||||503|,C|downstream_gene_variant|MODIFIER|ftsH|PA14_62860|transcript|ABJ14134.1|protein_coding||c.*1364A>G|||||1364|,C|downstream_gene_variant|MODIFIER|rrmJ|PA14_62870|transcript|ABJ14135.1|protein_coding||c.*3482A>G|||||3482|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_62890|PA14_62890|transcript|ABJ14137.1|protein_coding||c.*4555A>G|||||4555|,C|downstream_gene_variant|MODIFIER|greA|PA14_62900|transcript|ABJ14138.1|protein_coding||c.*4973A>G|||||4973| GT:DP:DPR:RO:QR:AO:QA:GL 0:17:17,3:14:498:3:45:0,-40.9443 0:7:7,0:7:231:0:0:0,-21.1088 0:20:20,4:16:494:4:60:0,-39.1942 0:14:14,4:10:357:4:34:0,-29.3177 +Chromosome 5613248 . G C 5.14559E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=42;DPB=42;DPRA=0.666667;EPP=6.91895;EPPR=4.47751;GTI=0;LEN=1;MEANALT=1;MQM=51.8;MQMR=60;NS=4;NUMALT=1;ODDS=50.2219;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=65;QR=1052;RO=37;RPL=4;RPP=6.91895;RPPR=10.1116;RPR=1;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=26;SRP=16.2152;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|carB|PA14_62910|transcript|ABJ14139.1|protein_coding|1/1|c.1767C>G|p.Arg589Arg|1767/3222|1767/3222|589/1073||,C|upstream_gene_variant|MODIFIER|ftsH|PA14_62860|transcript|ABJ14134.1|protein_coding||c.-3618C>G|||||3618|,C|upstream_gene_variant|MODIFIER|rrmJ|PA14_62870|transcript|ABJ14135.1|protein_coding||c.-2796C>G|||||2796|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_62890|PA14_62890|transcript|ABJ14137.1|protein_coding||c.-1939C>G|||||1939|,C|upstream_gene_variant|MODIFIER|greA|PA14_62900|transcript|ABJ14138.1|protein_coding||c.-1452C>G|||||1452|,C|downstream_gene_variant|MODIFIER|yhbY|PA14_62880|transcript|ABJ14136.1|protein_coding||c.*2387G>C|||||2387|,C|downstream_gene_variant|MODIFIER|yeaS|PA14_62920|transcript|ABJ14140.1|protein_coding||c.*1786C>G|||||1786|,C|downstream_gene_variant|MODIFIER|carA|PA14_62930|transcript|ABJ14141.1|protein_coding||c.*2448C>G|||||2448|,C|downstream_gene_variant|MODIFIER|P31|EBG00001225141|transcript|EBT00001793518.1|sRNA||n.*3584C>G|||||3584|,C|downstream_gene_variant|MODIFIER|dapB|PA14_62940|transcript|ABJ14142.1|protein_coding||c.*3767C>G|||||3767|,C|downstream_gene_variant|MODIFIER|dnaJ|PA14_62960|transcript|ABJ14143.1|protein_coding||c.*4630C>G|||||4630| GT:DP:DPR:RO:QR:AO:QA:GL 0:14:14,0:14:436:0:0:0,-39.5281 0:9:9,3:6:179:3:33:0,-13.3186 0:10:10,1:9:207:1:16:0,-17.2511 0:9:9,1:8:230:1:16:0,-19.547 +Chromosome 5622311 . T C 5.82787E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=6;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=16.0391;EPPR=5.59539;GTI=0;LEN=1;MEANALT=1.25;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=37.9495;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=672;RO=21;RPL=6;RPP=16.0391;RPPR=3.1137;RPR=0;RUN=1;SAF=6;SAP=16.0391;SAR=0;SRF=10;SRP=3.1137;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|recN|PA14_63010|transcript|ABJ14146.1|protein_coding|1/1|c.454T>C|p.Cys152Arg|454/1677|454/1677|152/558||,C|upstream_gene_variant|MODIFIER|dapB|PA14_62940|transcript|ABJ14142.1|protein_coding||c.-4490A>G|||||4490|,C|upstream_gene_variant|MODIFIER|dnaJ|PA14_62960|transcript|ABJ14143.1|protein_coding||c.-3300A>G|||||3300|,C|upstream_gene_variant|MODIFIER|dnaK|PA14_62970|transcript|ABJ14144.1|protein_coding||c.-1271A>G|||||1271|,C|upstream_gene_variant|MODIFIER|grpE|PA14_62990|transcript|ABJ14145.1|protein_coding||c.-621A>G|||||621|,C|upstream_gene_variant|MODIFIER|omlA|PA14_63030|transcript|ABJ14148.1|protein_coding||c.-1795T>C|||||1795|,C|upstream_gene_variant|MODIFIER|smpB|PA14_63060|transcript|ABJ14151.1|protein_coding||c.-3400T>C|||||3400|,C|downstream_gene_variant|MODIFIER|fur|PA14_63020|transcript|ABJ14147.1|protein_coding||c.*1293A>G|||||1293|,C|downstream_gene_variant|MODIFIER|yfjF|PA14_63040|transcript|ABJ14149.1|protein_coding||c.*2393A>G|||||2393|,C|downstream_gene_variant|MODIFIER|yfjG|PA14_63050|transcript|ABJ14150.1|protein_coding||c.*2691A>G|||||2691|,C|downstream_gene_variant|MODIFIER|pdhR|PA14_63070|transcript|ABJ14152.1|protein_coding||c.*3902A>G|||||3902| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,1:4:119:1:2:0,-10.8028 0:8:8,1:6:215:1:2:0,-19.404 0:8:8,3:5:187:3:6:0,-16.6301 0:7:7,1:6:151:1:2:0,-13.6326 +Chromosome 5633687 . A G 1.4254E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=15;CIGAR=1X;DP=66;DPB=66;DPRA=0;EPP=35.5824;EPPR=12.5903;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=73.1683;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=1616;RO=51;RPL=0;RPP=35.5824;RPPR=12.5903;RPR=15;RUN=1;SAF=0;SAP=35.5824;SAR=15;SRF=10;SRP=43.9277;SRR=41;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_63110|PA14_63110|transcript|ABJ14156.1|protein_coding|1/1|c.178A>G|p.Ser60Gly|178/483|178/483|60/160||,G|upstream_gene_variant|MODIFIER|PA14_63120|PA14_63120|transcript|ABJ14157.1|protein_coding||c.-383A>G|||||383|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_63130|PA14_63130|transcript|ABJ14158.1|protein_coding||c.-1435A>G|||||1435|,G|upstream_gene_variant|MODIFIER|pmrA|PA14_63150|transcript|ABJ14159.1|protein_coding||c.-2308A>G|||||2308|,G|upstream_gene_variant|MODIFIER|pmrB|PA14_63160|transcript|ABJ14160.1|protein_coding||c.-2997A>G|||||2997|,G|upstream_gene_variant|MODIFIER|cueR|PA14_63170|transcript|ABJ14161.1|protein_coding||c.-4494A>G|||||4494|,G|downstream_gene_variant|MODIFIER|lldP|PA14_63080|transcript|ABJ14153.1|protein_coding||c.*4690A>G|||||4690|,G|downstream_gene_variant|MODIFIER|lldD|PA14_63090|transcript|ABJ14154.1|protein_coding||c.*3389A>G|||||3389|,G|downstream_gene_variant|MODIFIER|PA14_63100|PA14_63100|transcript|ABJ14155.1|protein_coding||c.*506A>G|||||506| GT:DP:DPR:RO:QR:AO:QA:GL 0:16:16,2:14:424:2:4:0,-38.0534 0:13:13,4:9:280:4:19:0,-23.7408 0:18:18,6:12:366:6:12:0,-32.1177 0:19:19,3:16:546:3:31:0,-46.5563 +Chromosome 5637807 . A G 9.45917E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=31;DPB=31;DPRA=1.81818;EPP=9.52472;EPPR=5.80219;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=37.0988;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=822;RO=28;RPL=0;RPP=9.52472;RPPR=4.25114;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=5;SRP=28.1373;SRR=23;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|pmrB|PA14_63160|transcript|ABJ14160.1|protein_coding|1/1|c.1124A>G|p.Glu375Gly|1124/1434|1124/1434|375/477||,G|upstream_gene_variant|MODIFIER|cueR|PA14_63170|transcript|ABJ14161.1|protein_coding||c.-374A>G|||||374|,G|downstream_gene_variant|MODIFIER|PA14_63100|PA14_63100|transcript|ABJ14155.1|protein_coding||c.*4626A>G|||||4626|,G|downstream_gene_variant|MODIFIER|PA14_63110|PA14_63110|transcript|ABJ14156.1|protein_coding||c.*3815A>G|||||3815|,G|downstream_gene_variant|MODIFIER|PA14_63120|PA14_63120|transcript|ABJ14157.1|protein_coding||c.*2688A>G|||||2688|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_63130|PA14_63130|transcript|ABJ14158.1|protein_coding||c.*1825A>G|||||1825|,G|downstream_gene_variant|MODIFIER|pmrA|PA14_63150|transcript|ABJ14159.1|protein_coding||c.*1147A>G|||||1147|,G|downstream_gene_variant|MODIFIER|PA14_63190|PA14_63190|transcript|ABJ14162.1|protein_coding||c.*1304T>C|||||1304|,G|downstream_gene_variant|MODIFIER|PA14_63200|PA14_63200|transcript|ABJ14163.1|protein_coding||c.*2287T>C|||||2287|,G|downstream_gene_variant|MODIFIER|PA14_63210|PA14_63210|transcript|ABJ14164.1|protein_coding||c.*3304T>C|||||3304|,G|downstream_gene_variant|MODIFIER|PA14_63220|PA14_63220|transcript|ABJ14165.1|protein_coding||c.*4593T>C|||||4593|,G|downstream_gene_variant|MODIFIER|yedA|PA14_63230|transcript|ABJ14166.1|protein_coding||c.*4872T>C|||||4872| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:109:0:0:0,-10.167 0:8:8,0:8:185:0:0:0,-16.8734 0:8:8,2:6:215:2:4:0,-19.3177 0:12:12,1:11:313:1:2:0,-28.2422 +Chromosome 5653330 . T C 7.94864E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=34;DPB=34;DPRA=1.25;EPP=7.35324;EPPR=5.45321;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=41.3556;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1212;RO=32;RPL=2;RPP=7.35324;RPPR=5.45321;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=6;SRP=30.1537;SRR=26;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_63350|PA14_63350|transcript|ABJ14177.1|protein_coding|1/1|c.452T>C|p.Leu151Pro|452/483|452/483|151/160||,C|upstream_gene_variant|MODIFIER|PA14_63330|PA14_63330|transcript|ABJ14175.1|protein_coding||c.-1148A>G|||||1148|,C|upstream_gene_variant|MODIFIER|PA14_63360|PA14_63360|transcript|ABJ14178.1|protein_coding||c.-21T>C|||||21|,C|upstream_gene_variant|MODIFIER|PA14_63370|PA14_63370|transcript|ABJ14179.1|protein_coding||c.-395T>C|||||395|,C|upstream_gene_variant|MODIFIER|PA14_63380|PA14_63380|transcript|ABJ14180.1|protein_coding||c.-979T>C|||||979|,C|upstream_gene_variant|MODIFIER|PA14_63440|PA14_63440|transcript|ABJ14185.1|protein_coding||c.-3990T>C|||||3990|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_63450|PA14_63450|transcript|ABJ14186.1|protein_coding||c.-4645T>C|||||4645|,C|downstream_gene_variant|MODIFIER|phaJ3|PA14_63290|transcript|ABJ14171.1|protein_coding||c.*3887T>C|||||3887|,C|downstream_gene_variant|MODIFIER|PA14_63300|PA14_63300|transcript|ABJ14172.1|protein_coding||c.*3500T>C|||||3500|,C|downstream_gene_variant|MODIFIER|smtA|PA14_63310|transcript|ABJ14173.1|protein_coding||c.*2754T>C|||||2754|,C|downstream_gene_variant|MODIFIER|PA14_63320|PA14_63320|transcript|ABJ14174.1|protein_coding||c.*2068T>C|||||2068|,C|downstream_gene_variant|MODIFIER|PA14_63340|PA14_63340|transcript|ABJ14176.1|protein_coding||c.*453T>C|||||453|,C|downstream_gene_variant|MODIFIER|PA14_63390|PA14_63390|transcript|ABJ14181.1|protein_coding||c.*1730A>G|||||1730|,C|downstream_gene_variant|MODIFIER|PA14_63410|PA14_63410|transcript|ABJ14182.1|protein_coding||c.*2305A>G|||||2305|,C|downstream_gene_variant|MODIFIER|PA14_63420|PA14_63420|transcript|ABJ14183.1|protein_coding||c.*3164A>G|||||3164|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_63430|PA14_63430|transcript|ABJ14184.1|protein_coding||c.*3401A>G|||||3401| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:112:0:0:0,-10.446 0:12:12,0:12:470:0:0:0,-42.6518 0:9:9,0:9:330:0:0:0,-30.0428 0:10:10,2:8:300:2:4:0,-26.9724 +Chromosome 5663326 . C G 4.43848E-6 . AB=0;ABP=0;AC=0;AF=0;AN=3;AO=3;CIGAR=1X;DP=10;DPB=10;DPRA=2;EPP=9.52472;EPPR=10.7656;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=13.8042;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=45;QR=236;RO=7;RPL=0;RPP=9.52472;RPPR=5.80219;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=6;SRP=10.7656;SRR=1;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|selB|PA14_63530|transcript|ABJ14191.1|protein_coding|1/1|c.1763G>C|p.Arg588Pro|1763/1926|1763/1926|588/641||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_63460|PA14_63460|transcript|PA14_63460-1.1|protein_coding||c.-4828G>C|||||4828|WARNING_TRANSCRIPT_INCOMPLETE,G|upstream_gene_variant|MODIFIER|PA14_63470|PA14_63470|transcript|ABJ14187.1|protein_coding||c.-4079G>C|||||4079|,G|upstream_gene_variant|MODIFIER|PA14_63480|PA14_63480|transcript|ABJ14188.1|protein_coding||c.-2587G>C|||||2587|,G|upstream_gene_variant|MODIFIER|PA14_63500|PA14_63500|transcript|ABJ14189.1|protein_coding||c.-1132G>C|||||1132|,G|downstream_gene_variant|MODIFIER|tRNA|EBG00001225111|transcript|EBT00001793453.1|protein_coding||c.*4829C>G|||||4829|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|tRNA-Sec|EBG00001225106|transcript|EBT00001793375.1|protein_coding||c.*4828C>G|||||4828|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|PA14_63520|PA14_63520|transcript|ABJ14190.1|protein_coding||c.*167C>G|||||167|,G|downstream_gene_variant|MODIFIER|selA|PA14_63540|transcript|ABJ14192.1|protein_coding||c.*1759G>C|||||1759|,G|downstream_gene_variant|MODIFIER|fdhE|PA14_63550|transcript|ABJ14193.1|protein_coding||c.*3244G>C|||||3244|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|fdnI|PA14_63570|transcript|ABJ14194.1|protein_coding||c.*4306G>C|||||4306| GT:DP:DPR:RO:QR:AO:QA:GL . 0:2:2,0:2:42:0:0:0,-3.98589 0:3:3,2:1:38:2:30:0,-0.947294 0:5:5,1:4:156:1:15:0,-12.9168 +Chromosome 5678104 . G C 55.5936 . AB=0;ABP=0;AC=2;AF=0.666667;AN=3;AO=5;CIGAR=1X;DP=9;DPB=9;DPRA=1.75;EPP=13.8677;EPPR=11.6962;GTI=0;LEN=1;MEANALT=1;MQM=59.6;MQMR=60;NS=3;NUMALT=1;ODDS=4.40922;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=97;QR=43;RO=4;RPL=4;RPP=6.91895;RPPR=11.6962;RPR=1;RUN=1;SAF=4;SAP=6.91895;SAR=1;SRF=0;SRP=11.6962;SRR=4;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_63680|PA14_63680|transcript|ABJ14200.1|protein_coding|1/1|c.89G>C|p.Arg30Pro|89/495|89/495|30/164||,C|upstream_gene_variant|MODIFIER|lipC|PA14_63620|transcript|ABJ14196.1|protein_coding||c.-4519C>G|||||4519|,C|upstream_gene_variant|MODIFIER|PA14_63730|PA14_63730|transcript|ABJ14204.1|protein_coding||c.-3412G>C|||||3412|,C|downstream_gene_variant|MODIFIER|fadH2|PA14_63640|transcript|ABJ14197.1|protein_coding||c.*2114G>C|||||2114|,C|downstream_gene_variant|MODIFIER|PA14_63650|PA14_63650|transcript|ABJ14198.1|protein_coding||c.*1456G>C|||||1456|,C|downstream_gene_variant|MODIFIER|PA14_63660|PA14_63660|transcript|ABJ14199.1|protein_coding||c.*64G>C|||||64|,C|downstream_gene_variant|MODIFIER|PA14_63700|PA14_63700|transcript|ABJ14201.1|protein_coding||c.*409C>G|||||409|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|gtrB|PA14_63710|transcript|ABJ14202.1|protein_coding||c.*1842C>G|||||1842|,C|downstream_gene_variant|MODIFIER|PA14_63720|PA14_63720|transcript|ABJ14203.1|protein_coding||c.*2813C>G|||||2813|,C|downstream_gene_variant|MODIFIER|PA14_63740|PA14_63740|transcript|ABJ14205.1|protein_coding||c.*4749C>G|||||4749| GT:DP:DPR:RO:QR:AO:QA:GL . 0:2:2,0:2:39:0:0:0,-3.70479 1:3:3,2:1:2:2:68:-6.2574,0 1:4:4,3:1:2:3:29:-2.50665,0 +Chromosome 5690320 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=40;DPB=40;DPRA=0.870968;EPP=7.35324;EPPR=3.23888;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=64.863;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=1282;RO=38;RPL=2;RPP=7.35324;RPPR=11.239;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=15;SRP=6.66752;SRR=23;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_63830|PA14_63830|transcript|ABJ14211.1|protein_coding|1/1|c.59A>C|p.Asp20Ala|59/840|59/840|20/279||,G|upstream_gene_variant|MODIFIER|PA14_63780|PA14_63780|transcript|ABJ14208.1|protein_coding||c.-4365A>C|||||4365|,G|upstream_gene_variant|MODIFIER|mgtA|PA14_63800|transcript|ABJ14209.1|protein_coding||c.-1556A>C|||||1556|,G|upstream_gene_variant|MODIFIER|PA14_63820|PA14_63820|transcript|ABJ14210.1|protein_coding||c.-1111A>C|||||1111|,G|upstream_gene_variant|MODIFIER|PA14_63840|PA14_63840|transcript|ABJ14212.1|protein_coding||c.-183T>G|||||183|,G|upstream_gene_variant|MODIFIER|PA14_63860|PA14_63860|transcript|ABJ14214.1|protein_coding||c.-2219T>G|||||2219|,G|upstream_gene_variant|MODIFIER|PA14_63880|PA14_63880|transcript|ABJ14215.1|protein_coding||c.-2826T>G|||||2826|,G|upstream_gene_variant|MODIFIER|PA14_63900|PA14_63900|transcript|ABJ14217.1|protein_coding||c.-4419T>G|||||4419|,G|downstream_gene_variant|MODIFIER|lpd3|PA14_63850|transcript|ABJ14213.1|protein_coding||c.*643A>C|||||643|,G|downstream_gene_variant|MODIFIER|PA14_63890|PA14_63890|transcript|ABJ14216.1|protein_coding||c.*3391A>C|||||3391| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,2:7:236:2:4:0,-21.1813 0:11:11,0:11:361:0:0:0,-32.7969 0:11:11,0:11:340:0:0:0,-30.8872 0:9:9,0:9:345:0:0:0,-31.4073 +Chromosome 5711343 . G C 1.8519E-11 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=17;DPB=17;DPRA=2.66667;EPP=7.35324;EPPR=3.15506;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=26.4341;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=469;RO=15;RPL=2;RPP=7.35324;RPPR=4.31318;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=4;SRP=10.1038;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|dipZ|PA14_64080|transcript|ABJ14229.1|protein_coding|1/1|c.774G>C|p.Ala258Ala|774/1776|774/1776|258/591||,C|upstream_gene_variant|MODIFIER|PA14_64030|PA14_64030|transcript|ABJ14226.1|protein_coding||c.-4965C>G|||||4965|,C|upstream_gene_variant|MODIFIER|aroQ1|PA14_64090|transcript|ABJ14230.1|protein_coding||c.-1146G>C|||||1146|,C|upstream_gene_variant|MODIFIER|accB|PA14_64100|transcript|ABJ14231.1|protein_coding||c.-1613G>C|||||1613|,C|upstream_gene_variant|MODIFIER|accC|PA14_64110|transcript|ABJ14232.1|protein_coding||c.-2101G>C|||||2101|,C|upstream_gene_variant|MODIFIER|PA14_64120|PA14_64120|transcript|ABJ14233.1|protein_coding||c.-3561G>C|||||3561|,C|upstream_gene_variant|MODIFIER|prmA|PA14_64140|transcript|ABJ14234.1|protein_coding||c.-4509G>C|||||4509|,C|downstream_gene_variant|MODIFIER|PA14_64050|PA14_64050|transcript|ABJ14227.1|protein_coding||c.*2984G>C|||||2984|,C|downstream_gene_variant|MODIFIER|ctpL|PA14_64060|transcript|ABJ14228.1|protein_coding||c.*933G>C|||||933| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:71:0:0:0,-6.74038 0:8:8,2:6:190:2:4:0,-17.022 0:5:5,0:5:134:0:0:0,-12.3169 0:2:2,0:2:74:0:0:0,-7.02543 +Chromosome 5719777 . G C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=7;CIGAR=1X;DP=45;DPB=45;DPRA=1.80952;EPP=18.2106;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=55.7256;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=1203;RO=38;RPL=7;RPP=18.2106;RPPR=5.06748;RPR=0;RUN=1;SAF=7;SAP=18.2106;SAR=0;SRF=29;SRP=25.8679;SRR=9;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|purH|PA14_64200|transcript|ABJ14238.1|protein_coding|1/1|c.67G>C|p.Val23Leu|67/1608|67/1608|23/535||,C|upstream_gene_variant|MODIFIER|purD|PA14_64220|transcript|ABJ14239.1|protein_coding||c.-1645G>C|||||1645|,C|upstream_gene_variant|MODIFIER|retS|PA14_64230|transcript|ABJ14240.1|protein_coding||c.-3038G>C|||||3038|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|accC|PA14_64110|transcript|ABJ14232.1|protein_coding||c.*4984G>C|||||4984|,C|downstream_gene_variant|MODIFIER|PA14_64120|PA14_64120|transcript|ABJ14233.1|protein_coding||c.*4007G>C|||||4007|,C|downstream_gene_variant|MODIFIER|prmA|PA14_64140|transcript|ABJ14234.1|protein_coding||c.*3041G>C|||||3041|,C|downstream_gene_variant|MODIFIER|PA14_64170|PA14_64170|transcript|ABJ14235.1|protein_coding||c.*1668G>C|||||1668|,C|downstream_gene_variant|MODIFIER|yhdG|PA14_64180|transcript|ABJ14236.1|protein_coding||c.*466G>C|||||466|,C|downstream_gene_variant|MODIFIER|fis|PA14_64190|transcript|ABJ14237.1|protein_coding||c.*146G>C|||||146| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:197:0:0:0,-17.997 0:11:11,1:10:382:1:2:0,-34.5343 0:14:14,1:13:428:1:2:0,-38.622 0:13:13,5:8:196:5:10:0,-16.955 +Chromosome 5730311 . T C 1.76218E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=45;DPB=45;DPRA=0.875;EPP=9.52472;EPPR=10.4553;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=39.9334;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=1267;RO=42;RPL=3;RPP=9.52472;RPPR=8.18047;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=31;SRP=23.691;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|PA14_64290|PA14_64290|transcript|ABJ14245.1|protein_coding|1/1|c.198T>C|p.Ala66Ala|198/1080|198/1080|66/359||,C|upstream_gene_variant|MODIFIER|PA14_64300|PA14_64300|transcript|ABJ14246.1|protein_coding||c.-879T>C|||||879|,C|upstream_gene_variant|MODIFIER|PA14_64310|PA14_64310|transcript|ABJ14247.1|protein_coding||c.-1873T>C|||||1873|,C|upstream_gene_variant|MODIFIER|PA14_64320|PA14_64320|transcript|ABJ14248.1|protein_coding||c.-2655T>C|||||2655|,C|upstream_gene_variant|MODIFIER|ureD|PA14_64335|transcript|ABJ15649.1|protein_coding||c.-3116T>C|||||3116|,C|upstream_gene_variant|MODIFIER|ureA|PA14_64350|transcript|ABJ14249.1|protein_coding||c.-3960T>C|||||3960|,C|upstream_gene_variant|MODIFIER|yncA|PA14_64360|transcript|ABJ14250.1|protein_coding||c.-4271T>C|||||4271|,C|upstream_gene_variant|MODIFIER|ureB|PA14_64370|transcript|ABJ14251.1|protein_coding||c.-4806T>C|||||4806|,C|downstream_gene_variant|MODIFIER|retS|PA14_64230|transcript|ABJ14240.1|protein_coding||c.*4668T>C|||||4668|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_64240|PA14_64240|transcript|ABJ14241.1|protein_coding||c.*3620T>C|||||3620|,C|downstream_gene_variant|MODIFIER|PA14_64260|PA14_64260|transcript|ABJ14242.1|protein_coding||c.*3237T>C|||||3237|,C|downstream_gene_variant|MODIFIER|PA14_64270|PA14_64270|transcript|ABJ14243.1|protein_coding||c.*1930T>C|||||1930|,C|downstream_gene_variant|MODIFIER|PA14_64280|PA14_64280|transcript|ABJ14244.1|protein_coding||c.*194T>C|||||194| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,2:4:128:2:26:0,-9.36281 0:11:11,0:11:315:0:0:0,-28.6218 0:13:13,0:13:449:0:0:0,-40.7296 0:15:15,1:14:375:1:13:0,-32.704 +Chromosome 5734941 . G T 8.00079E-6 . AB=0;ABP=0;AC=1;AF=0.25;AN=4;AO=4;CIGAR=1X;DP=16;DPB=16;DPRA=1.28571;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=13.7369;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=64;QR=268;RO=12;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=3;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=10;SRP=14.5915;SRR=2;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|yncA|PA14_64360|transcript|ABJ14250.1|protein_coding|1/1|c.360G>T|p.Val120Val|360/519|360/519|120/172||,T|upstream_gene_variant|MODIFIER|ureB|PA14_64370|transcript|ABJ14251.1|protein_coding||c.-176G>T|||||176|,T|upstream_gene_variant|MODIFIER|ureC|PA14_64390|transcript|ABJ14252.1|protein_coding||c.-544G>T|||||544|,T|upstream_gene_variant|MODIFIER|5_ureB_sRNA|EBG00001225143|transcript|EBT00001793474.1|sRNA||n.-690G>T|||||690|,T|upstream_gene_variant|MODIFIER|PA14_64400|PA14_64400|transcript|ABJ14253.1|protein_coding||c.-2513G>T|||||2513|,T|upstream_gene_variant|MODIFIER|PA14_64420|PA14_64420|transcript|ABJ14255.1|protein_coding||c.-4132G>T|||||4132|,T|upstream_gene_variant|MODIFIER|PA14_64430|PA14_64430|transcript|ABJ14256.1|protein_coding||c.-4898G>T|||||4898|,T|downstream_gene_variant|MODIFIER|PA14_64280|PA14_64280|transcript|ABJ14244.1|protein_coding||c.*4824G>T|||||4824|,T|downstream_gene_variant|MODIFIER|PA14_64290|PA14_64290|transcript|ABJ14245.1|protein_coding||c.*3748G>T|||||3748|,T|downstream_gene_variant|MODIFIER|PA14_64300|PA14_64300|transcript|ABJ14246.1|protein_coding||c.*2894G>T|||||2894|,T|downstream_gene_variant|MODIFIER|PA14_64310|PA14_64310|transcript|ABJ14247.1|protein_coding||c.*2059G>T|||||2059|,T|downstream_gene_variant|MODIFIER|PA14_64320|PA14_64320|transcript|ABJ14248.1|protein_coding||c.*1523G>T|||||1523|,T|downstream_gene_variant|MODIFIER|ureD|PA14_64335|transcript|ABJ15649.1|protein_coding||c.*672G>T|||||672|,T|downstream_gene_variant|MODIFIER|ureA|PA14_64350|transcript|ABJ14249.1|protein_coding||c.*368G>T|||||368|,T|downstream_gene_variant|MODIFIER|ybiI|PA14_64410|transcript|ABJ14254.1|protein_coding||c.*3740C>A|||||3740| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:102:0:0:0,-9.43129 0:3:3,1:2:32:1:16:0,-1.43998 1:6:6,3:3:47:3:48:-0.09333,0 0:3:3,0:3:87:0:0:0,-8.11544 +Chromosome 5737268 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=34;DPB=34;DPRA=1.26667;EPP=11.6962;EPPR=5.61607;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=50.1483;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=52;QR=939;RO=30;RPL=0;RPP=11.6962;RPPR=13.4334;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=21;SRP=13.4334;SRR=9;TYPE=snp;technology.ILLUMINA=1;ANN=A|upstream_gene_variant|MODIFIER|PA14_64400|PA14_64400|transcript|ABJ14253.1|protein_coding||c.-186C>A|||||186|,A|upstream_gene_variant|MODIFIER|PA14_64420|PA14_64420|transcript|ABJ14255.1|protein_coding||c.-1805C>A|||||1805|,A|upstream_gene_variant|MODIFIER|PA14_64430|PA14_64430|transcript|ABJ14256.1|protein_coding||c.-2571C>A|||||2571|,A|upstream_gene_variant|MODIFIER|yegD|PA14_64450|transcript|ABJ14258.1|protein_coding||c.-4344C>A|||||4344|,A|downstream_gene_variant|MODIFIER|PA14_64310|PA14_64310|transcript|ABJ14247.1|protein_coding||c.*4386C>A|||||4386|,A|downstream_gene_variant|MODIFIER|PA14_64320|PA14_64320|transcript|ABJ14248.1|protein_coding||c.*3850C>A|||||3850|,A|downstream_gene_variant|MODIFIER|ureD|PA14_64335|transcript|ABJ15649.1|protein_coding||c.*2999C>A|||||2999|,A|downstream_gene_variant|MODIFIER|ureA|PA14_64350|transcript|ABJ14249.1|protein_coding||c.*2695C>A|||||2695|,A|downstream_gene_variant|MODIFIER|yncA|PA14_64360|transcript|ABJ14250.1|protein_coding||c.*2168C>A|||||2168|,A|downstream_gene_variant|MODIFIER|ureB|PA14_64370|transcript|ABJ14251.1|protein_coding||c.*1846C>A|||||1846|,A|downstream_gene_variant|MODIFIER|ureC|PA14_64390|transcript|ABJ14252.1|protein_coding||c.*83C>A|||||83|,A|downstream_gene_variant|MODIFIER|5_ureB_sRNA|EBG00001225143|transcript|EBT00001793474.1|sRNA||n.*1351C>A|||||1351|,A|downstream_gene_variant|MODIFIER|ybiI|PA14_64410|transcript|ABJ14254.1|protein_coding||c.*1413G>T|||||1413|,A|downstream_gene_variant|MODIFIER|bcpA|PA14_64440|transcript|ABJ14257.1|protein_coding||c.*3273G>T|||||3273|,A|intergenic_region|MODIFIER|ureC-PA14_64400|PA14_64390-PA14_64400|intergenic_region|PA14_64390-PA14_64400|||n.5737268C>A|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:249:0:0:0,-22.704 0:7:7,0:7:202:0:0:0,-18.4608 0:12:12,3:9:302:3:39:0,-23.8526 0:7:7,1:6:186:1:13:0,-15.7376 +Chromosome 5744636 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=32;DPB=32;DPRA=0.84;EPP=7.35324;EPPR=5.61607;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=49.1054;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=1079;RO=30;RPL=2;RPP=7.35324;RPPR=7.64277;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=19;SRP=7.64277;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_64490|PA14_64490|transcript|ABJ14262.1|protein_coding|1/1|c.392C>A|p.Ala131Glu|392/408|392/408|131/135||,T|upstream_gene_variant|MODIFIER|bcpA|PA14_64440|transcript|ABJ14257.1|protein_coding||c.-3232C>A|||||3232|,T|upstream_gene_variant|MODIFIER|psiF|PA14_64460|transcript|ABJ14259.1|protein_coding||c.-1187C>A|||||1187|,T|upstream_gene_variant|MODIFIER|PA14_64500|PA14_64500|transcript|ABJ14263.1|protein_coding||c.-538G>T|||||538|,T|upstream_gene_variant|MODIFIER|PA14_64520|PA14_64520|transcript|ABJ14265.1|protein_coding||c.-3717G>T|||||3717|,T|upstream_gene_variant|MODIFIER|PA14_64530|PA14_64530|transcript|ABJ14266.1|protein_coding||c.-4524G>T|||||4524|,T|downstream_gene_variant|MODIFIER|PA14_64420|PA14_64420|transcript|ABJ14255.1|protein_coding||c.*4949G>T|||||4949|,T|downstream_gene_variant|MODIFIER|PA14_64430|PA14_64430|transcript|ABJ14256.1|protein_coding||c.*4102G>T|||||4102|,T|downstream_gene_variant|MODIFIER|yegD|PA14_64450|transcript|ABJ14258.1|protein_coding||c.*1759G>T|||||1759|,T|downstream_gene_variant|MODIFIER|PA14_64470|PA14_64470|transcript|ABJ14260.1|protein_coding||c.*493G>T|||||493|,T|downstream_gene_variant|MODIFIER|osmE|PA14_64480|transcript|ABJ14261.1|protein_coding||c.*60G>T|||||60|,T|downstream_gene_variant|MODIFIER|yhjG|PA14_64510|transcript|ABJ14264.1|protein_coding||c.*1352C>A|||||1352|,T|downstream_gene_variant|MODIFIER|PA14_64540|PA14_64540|transcript|ABJ14267.1|protein_coding||c.*4979C>A|||||4979| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,2:5:180:2:18:0,-14.838 0:6:6,0:6:206:0:0:0,-18.8693 0:8:8,0:8:308:0:0:0,-28.0805 0:11:11,0:11:385:0:0:0,-34.9771 +Chromosome 5752465 . GAGGA GGGGG 1.46561E-5 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1M1X2M1X;DP=13;DPB=15;DPRA=2.25;EPP=9.52472;EPPR=4.09604;GTI=0;LEN=5;MEANALT=1.5;MQM=56.3333;MQMR=59.625;NS=4;NUMALT=1;ODDS=12.5992;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=102;PRO=3;QA=6;QR=219;RO=8;RPL=0;RPP=9.52472;RPPR=4.09604;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=2;SRP=7.35324;SRR=6;TYPE=complex;technology.ILLUMINA=1;ANN=GGGGG|missense_variant|MODERATE|irlR|PA14_64570|transcript|ABJ14270.1|protein_coding|1/1|c.659_662delAGGAinsGGGG|p.GluGlu220GlyGly|659/690|659/690|220/229||,GGGGG|upstream_gene_variant|MODIFIER|yhjG|PA14_64510|transcript|ABJ14264.1|protein_coding||c.-4412_-4409delTCCTinsCCCC|||||4409|,GGGGG|upstream_gene_variant|MODIFIER|PA14_64540|PA14_64540|transcript|ABJ14267.1|protein_coding||c.-2087_-2084delTCCTinsCCCC|||||2084|,GGGGG|upstream_gene_variant|MODIFIER|PA14_64550|PA14_64550|transcript|ABJ14268.1|protein_coding||c.-1476_-1473delTCCTinsCCCC|||||1473|,GGGGG|upstream_gene_variant|MODIFIER|PA14_64560|PA14_64560|transcript|ABJ14269.1|protein_coding||c.-799_-796delTCCTinsCCCC|||||796|,GGGGG|upstream_gene_variant|MODIFIER|PA14_64580|PA14_64580|transcript|ABJ14271.1|protein_coding||c.-10_-7delAGGAinsGGGG|||||10|WARNING_TRANSCRIPT_NO_START_CODON,GGGGG|downstream_gene_variant|MODIFIER|PA14_64520|PA14_64520|transcript|ABJ14265.1|protein_coding||c.*3580_*3583delAGGAinsGGGG|||||3580|,GGGGG|downstream_gene_variant|MODIFIER|PA14_64530|PA14_64530|transcript|ABJ14266.1|protein_coding||c.*2965_*2968delAGGAinsGGGG|||||2965|,GGGGG|downstream_gene_variant|MODIFIER|PA14_64590|PA14_64590|transcript|ABJ14272.1|protein_coding||c.*1389_*1392delTCCTinsCCCC|||||1392|,GGGGG|downstream_gene_variant|MODIFIER|PA14_64610|PA14_64610|transcript|ABJ14273.1|protein_coding||c.*2925_*2928delTCCTinsCCCC|||||2928|WARNING_TRANSCRIPT_NO_START_CODON,GGGGG|downstream_gene_variant|MODIFIER|PA14_64620|PA14_64620|transcript|ABJ14274.1|protein_coding||c.*4034_*4037delTCCTinsCCCC|||||4037| GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:37:0:0:0,-12.8524 0:3:3,0:2:76:0:0:0,-6.99436 0:6:6,2:3:102:2:4:0,-9.05355 0:3:3,1:2:4:1:2:0,-0.18 +Chromosome 5752572 . T C 2.16978E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=23;DPB=23;DPRA=1.92857;EPP=3.0103;EPPR=20.4855;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=35.7649;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=41;QR=796;RO=21;RPL=2;RPP=7.35324;RPPR=32.8939;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=19;SRP=32.8939;SRR=2;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_64580|PA14_64580|transcript|ABJ14271.1|protein_coding|1/1|c.97T>C|p.Ser33Pro|97/1392|97/1392|33/463||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|yhjG|PA14_64510|transcript|ABJ14264.1|protein_coding||c.-4515A>G|||||4515|,C|upstream_gene_variant|MODIFIER|PA14_64540|PA14_64540|transcript|ABJ14267.1|protein_coding||c.-2190A>G|||||2190|,C|upstream_gene_variant|MODIFIER|PA14_64550|PA14_64550|transcript|ABJ14268.1|protein_coding||c.-1579A>G|||||1579|,C|upstream_gene_variant|MODIFIER|PA14_64560|PA14_64560|transcript|ABJ14269.1|protein_coding||c.-902A>G|||||902|,C|downstream_gene_variant|MODIFIER|PA14_64520|PA14_64520|transcript|ABJ14265.1|protein_coding||c.*3686T>C|||||3686|,C|downstream_gene_variant|MODIFIER|PA14_64530|PA14_64530|transcript|ABJ14266.1|protein_coding||c.*3071T>C|||||3071|,C|downstream_gene_variant|MODIFIER|irlR|PA14_64570|transcript|ABJ14270.1|protein_coding||c.*75T>C|||||75|,C|downstream_gene_variant|MODIFIER|PA14_64590|PA14_64590|transcript|ABJ14272.1|protein_coding||c.*1286A>G|||||1286|,C|downstream_gene_variant|MODIFIER|PA14_64610|PA14_64610|transcript|ABJ14273.1|protein_coding||c.*2822A>G|||||2822|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_64620|PA14_64620|transcript|ABJ14274.1|protein_coding||c.*3931A>G|||||3931| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:112:0:0:0,-10.4459 0:4:4,0:4:153:0:0:0,-14.1403 0:7:7,0:7:261:0:0:0,-23.846 0:9:9,2:7:270:2:41:0,-20.7731 +Chromosome 5757837 . A G 1.16151E-11 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=14;DPB=14;DPRA=1.2;EPP=7.35324;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=26.6586;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=450;RO=12;RPL=0;RPP=7.35324;RPPR=14.5915;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=9.52472;SRR=9;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_64640|PA14_64640|transcript|ABJ14275.1|protein_coding|1/1|c.76A>G|p.Ser26Gly|76/630|76/630|26/209||,G|upstream_gene_variant|MODIFIER|PA14_64590|PA14_64590|transcript|ABJ14272.1|protein_coding||c.-2663T>C|||||2663|,G|upstream_gene_variant|MODIFIER|PA14_64610|PA14_64610|transcript|ABJ14273.1|protein_coding||c.-1331T>C|||||1331|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_64620|PA14_64620|transcript|ABJ14274.1|protein_coding||c.-234T>C|||||234|,G|upstream_gene_variant|MODIFIER|ureE|PA14_64650|transcript|ABJ14276.1|protein_coding||c.-784A>G|||||784|,G|upstream_gene_variant|MODIFIER|ureF|PA14_64660|transcript|ABJ14277.1|protein_coding||c.-1284A>G|||||1284|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ureG|PA14_64670|transcript|ABJ14278.1|protein_coding||c.-1966A>G|||||1966|,G|upstream_gene_variant|MODIFIER|ureJ|PA14_64680|transcript|ABJ14279.1|protein_coding||c.-2610A>G|||||2610|,G|upstream_gene_variant|MODIFIER|PA14_64710|PA14_64710|transcript|ABJ14282.1|protein_coding||c.-4915A>G|||||4915|,G|downstream_gene_variant|MODIFIER|PA14_64580|PA14_64580|transcript|ABJ14271.1|protein_coding||c.*3970A>G|||||3970|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_64690|PA14_64690|transcript|ABJ14280.1|protein_coding||c.*3198T>C|||||3198|,G|downstream_gene_variant|MODIFIER|PA14_64700|PA14_64700|transcript|ABJ14281.1|protein_coding||c.*4213T>C|||||4213| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:115:0:0:0,-10.7245 0:3:3,0:3:118:0:0:0,-11.0029 0:4:4,2:2:75:2:15:0,-5.6946 0:4:4,0:4:142:0:0:0,-13.1272 +Chromosome 5763577 . T C 9.01067E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=35;DPB=35;DPRA=1.69231;EPP=3.73412;EPPR=9.79615;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=51.7411;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=41;QR=974;RO=32;RPL=2;RPP=3.73412;RPPR=9.79615;RPR=1;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=30;SRP=56.2114;SRR=2;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_64710|PA14_64710|transcript|ABJ14282.1|protein_coding|1/1|c.826T>C|p.Ser276Pro|826/2970|826/2970|276/989||,C|upstream_gene_variant|MODIFIER|PA14_64690|PA14_64690|transcript|ABJ14280.1|protein_coding||c.-1520A>G|||||1520|,C|upstream_gene_variant|MODIFIER|PA14_64700|PA14_64700|transcript|ABJ14281.1|protein_coding||c.-991A>G|||||991|,C|downstream_gene_variant|MODIFIER|ureE|PA14_64650|transcript|ABJ14276.1|protein_coding||c.*4453T>C|||||4453|,C|downstream_gene_variant|MODIFIER|ureF|PA14_64660|transcript|ABJ14277.1|protein_coding||c.*3785T>C|||||3785|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ureG|PA14_64670|transcript|ABJ14278.1|protein_coding||c.*3160T>C|||||3160|,C|downstream_gene_variant|MODIFIER|ureJ|PA14_64680|transcript|ABJ14279.1|protein_coding||c.*2558T>C|||||2558|,C|downstream_gene_variant|MODIFIER|opdK|PA14_64720|transcript|ABJ14283.1|protein_coding||c.*2289A>G|||||2289|,C|downstream_gene_variant|MODIFIER|pchA|PA14_64740|transcript|ABJ14284.1|protein_coding||c.*3650A>G|||||3650| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:198:0:0:0,-18.1436 0:7:7,0:7:225:0:0:0,-20.5659 0:12:12,1:11:341:1:14:0,-29.5862 0:10:10,2:8:210:2:27:0,-16.5907 +Chromosome 5779337 . T C 5.40739E-15 . AB=0;ABP=0;AC=0;AF=0;AN=3;AO=2;CIGAR=1X;DP=19;DPB=19;DPRA=1.16667;EPP=7.35324;EPPR=4.1599;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=35.4267;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=485;RO=17;RPL=2;RPP=7.35324;RPPR=6.20364;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=8;SRP=3.13803;SRR=9;TYPE=snp;technology.ILLUMINA=1;ANN=C|stop_lost&splice_region_variant|HIGH|livF|PA14_64860|transcript|ABJ14294.1|protein_coding|1/1|c.717A>G|p.Ter239Trpext*?|717/717|717/717|239/238||,C|upstream_gene_variant|MODIFIER|vanR|PA14_64820|transcript|ABJ14291.1|protein_coding||c.-2147A>G|||||2147|,C|upstream_gene_variant|MODIFIER|PA14_64840|PA14_64840|transcript|ABJ14292.1|protein_coding||c.-1322A>G|||||1322|,C|upstream_gene_variant|MODIFIER|PA14_64850|PA14_64850|transcript|ABJ14293.1|protein_coding||c.-71A>G|||||71|,C|downstream_gene_variant|MODIFIER|vanA|PA14_64800|transcript|ABJ14289.1|protein_coding||c.*3825T>C|||||3825|,C|downstream_gene_variant|MODIFIER|vanB|PA14_64810|transcript|ABJ14290.1|protein_coding||c.*2857T>C|||||2857|,C|downstream_gene_variant|MODIFIER|braF|PA14_64870|transcript|ABJ14295.1|protein_coding||c.*713A>G|||||713|,C|downstream_gene_variant|MODIFIER|braE|PA14_64880|transcript|ABJ14296.1|protein_coding||c.*1582A>G|||||1582|,C|downstream_gene_variant|MODIFIER|braD|PA14_64890|transcript|ABJ14297.1|protein_coding||c.*2870A>G|||||2870|,C|downstream_gene_variant|MODIFIER|PA14_64900|PA14_64900|transcript|ABJ14298.1|protein_coding||c.*4019A>G|||||4019| GT:DP:DPR:RO:QR:AO:QA:GL . 0:7:7,0:7:236:0:0:0,-21.5612 0:5:5,0:5:114:0:0:0,-10.4828 0:7:7,2:5:135:2:4:0,-12.035 +Chromosome 5779361 . G T 6.2985E-15 . AB=0;ABP=0;AC=0;AF=0;AN=3;AO=2;CIGAR=1X;DP=17;DPB=17;DPRA=1.77778;EPP=7.35324;EPPR=4.31318;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=34.5643;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=425;RO=15;RPL=2;RPP=7.35324;RPPR=3.15506;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=7;SRP=3.15506;SRR=8;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|livF|PA14_64860|transcript|ABJ14294.1|protein_coding|1/1|c.693C>A|p.Arg231Arg|693/717|693/717|231/238||,T|upstream_gene_variant|MODIFIER|vanR|PA14_64820|transcript|ABJ14291.1|protein_coding||c.-2171C>A|||||2171|,T|upstream_gene_variant|MODIFIER|PA14_64840|PA14_64840|transcript|ABJ14292.1|protein_coding||c.-1346C>A|||||1346|,T|upstream_gene_variant|MODIFIER|PA14_64850|PA14_64850|transcript|ABJ14293.1|protein_coding||c.-95C>A|||||95|,T|downstream_gene_variant|MODIFIER|vanA|PA14_64800|transcript|ABJ14289.1|protein_coding||c.*3849G>T|||||3849|,T|downstream_gene_variant|MODIFIER|vanB|PA14_64810|transcript|ABJ14290.1|protein_coding||c.*2881G>T|||||2881|,T|downstream_gene_variant|MODIFIER|braF|PA14_64870|transcript|ABJ14295.1|protein_coding||c.*689C>A|||||689|,T|downstream_gene_variant|MODIFIER|braE|PA14_64880|transcript|ABJ14296.1|protein_coding||c.*1558C>A|||||1558|,T|downstream_gene_variant|MODIFIER|braD|PA14_64890|transcript|ABJ14297.1|protein_coding||c.*2846C>A|||||2846|,T|downstream_gene_variant|MODIFIER|PA14_64900|PA14_64900|transcript|ABJ14298.1|protein_coding||c.*3995C>A|||||3995| GT:DP:DPR:RO:QR:AO:QA:GL . 0:8:8,2:6:193:2:4:0,-17.2973 0:3:3,0:3:119:0:0:0,-11.0954 0:6:6,0:6:113:0:0:0,-10.3523 +Chromosome 5783740 . G T 8.28954E-16 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=11;CIGAR=1X;DP=84;DPB=84;DPRA=0;EPP=26.8965;EPPR=3.27802;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=117.377;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=138;QR=2326;RO=73;RPL=11;RPP=26.8965;RPPR=16.1284;RPR=0;RUN=1;SAF=11;SAP=26.8965;SAR=0;SRF=39;SRP=3.75395;SRR=34;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|PA14_64900|PA14_64900|transcript|ABJ14298.1|protein_coding|1/1|c.741C>A|p.Ala247Ala|741/1125|741/1125|247/374||,T|upstream_gene_variant|MODIFIER|PA14_64850|PA14_64850|transcript|ABJ14293.1|protein_coding||c.-4474C>A|||||4474|,T|upstream_gene_variant|MODIFIER|livF|PA14_64860|transcript|ABJ14294.1|protein_coding||c.-3687C>A|||||3687|,T|upstream_gene_variant|MODIFIER|braF|PA14_64870|transcript|ABJ14295.1|protein_coding||c.-2818C>A|||||2818|,T|upstream_gene_variant|MODIFIER|braE|PA14_64880|transcript|ABJ14296.1|protein_coding||c.-1544C>A|||||1544|,T|upstream_gene_variant|MODIFIER|braD|PA14_64890|transcript|ABJ14297.1|protein_coding||c.-619C>A|||||619|,T|upstream_gene_variant|MODIFIER|PA14_64910|PA14_64910|transcript|ABJ14299.1|protein_coding||c.-1360G>T|||||1360|,T|upstream_gene_variant|MODIFIER|PA14_64920|PA14_64920|transcript|ABJ14300.1|protein_coding||c.-2355G>T|||||2355|,T|downstream_gene_variant|MODIFIER|PA14_64930|PA14_64930|transcript|ABJ14301.1|protein_coding||c.*4027C>A|||||4027|,T|downstream_gene_variant|MODIFIER|PA14_64940|PA14_64940|transcript|ABJ14302.1|protein_coding||c.*4737C>A|||||4737| GT:DP:DPR:RO:QR:AO:QA:GL 0:19:19,3:16:496:3:19:0,-43.1426 0:20:20,4:16:507:4:60:0,-40.3608 0:22:22,1:21:675:1:2:0,-60.8314 0:23:23,3:20:648:3:57:0,-53.2793 +Chromosome 5800466 . G T 1.5522E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=69;DPB=69;DPRA=1.22581;EPP=6.91895;EPPR=3.14602;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=90.0812;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=44;QR=1849;RO=64;RPL=4;RPP=6.91895;RPPR=11.6962;RPR=1;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=49;SRP=42.2325;SRR=15;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|ygiR|PA14_65080|transcript|ABJ14313.1|protein_coding|1/1|c.1812C>A|p.Ala604Ala|1812/2244|1812/2244|604/747||,T|upstream_gene_variant|MODIFIER|PA14_65040|PA14_65040|transcript|ABJ14310.1|protein_coding||c.-4378C>A|||||4378|,T|upstream_gene_variant|MODIFIER|PA14_65050|PA14_65050|transcript|ABJ14311.1|protein_coding||c.-3192C>A|||||3192|,T|upstream_gene_variant|MODIFIER|PA14_65060|PA14_65060|transcript|ABJ14312.1|protein_coding||c.-694C>A|||||694|,T|upstream_gene_variant|MODIFIER|PA14_65090|PA14_65090|transcript|ABJ14314.1|protein_coding||c.-1904G>T|||||1904|,T|downstream_gene_variant|MODIFIER|alr|PA14_65110|transcript|ABJ14315.1|protein_coding||c.*3927C>A|||||3927| GT:DP:DPR:RO:QR:AO:QA:GL 0:13:13,0:13:332:0:0:0,-30.1231 0:18:18,0:18:486:0:0:0,-43.9848 0:22:22,1:21:628:1:14:0,-55.3864 0:16:16,4:12:403:4:30:0,-33.8098 +Chromosome 5805188 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=44;DPB=44;DPRA=2.38462;EPP=6.91895;EPPR=12.42;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=49.4745;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=87;QR=1205;RO=39;RPL=1;RPP=6.91895;RPPR=4.40227;RPR=4;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=24;SRP=7.52028;SRR=15;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|alr|PA14_65110|transcript|ABJ14315.1|protein_coding|1/1|c.282G>T|p.Leu94Phe|282/1077|282/1077|94/358||,A|upstream_gene_variant|MODIFIER|ygiR|PA14_65080|transcript|ABJ14313.1|protein_coding||c.-2911G>T|||||2911|,A|downstream_gene_variant|MODIFIER|PA14_65090|PA14_65090|transcript|ABJ14314.1|protein_coding||c.*797C>A|||||797|,A|downstream_gene_variant|MODIFIER|dnaB|PA14_65130|transcript|ABJ14316.1|protein_coding||c.*350G>T|||||350|,A|downstream_gene_variant|MODIFIER|rplI|PA14_65150|transcript|ABJ14317.1|protein_coding||c.*1873G>T|||||1873|,A|downstream_gene_variant|MODIFIER|PA14_65160|PA14_65160|transcript|ABJ14318.1|protein_coding||c.*2341G>T|||||2341|,A|downstream_gene_variant|MODIFIER|rpsR|PA14_65170|transcript|ABJ14319.1|protein_coding||c.*3247G>T|||||3247|,A|downstream_gene_variant|MODIFIER|rpsF|PA14_65180|transcript|ABJ14320.1|protein_coding||c.*3507G>T|||||3507|,A|downstream_gene_variant|MODIFIER|yjfH|PA14_65190|transcript|ABJ14321.1|protein_coding||c.*4145G>T|||||4145|,A|downstream_gene_variant|MODIFIER|rnr|PA14_65200|transcript|ABJ14322.1|protein_coding||c.*4888G>T|||||4888| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:151:0:0:0,-13.8809 0:8:8,0:8:199:0:0:0,-18.1541 0:14:14,4:10:250:4:63:0,-16.9097 0:17:17,1:16:605:1:24:0,-52.3786 +Chromosome 5809294 . GGGCG GG 718.189 . AB=0;ABP=0;AC=4;AF=1;AN=4;AO=30;CIGAR=1M3D1M;DP=30;DPB=13.4;DPRA=0;EPP=51.9408;EPPR=0;GTI=0;LEN=3;MEANALT=1;MQM=40.6;MQMR=0;NS=4;NUMALT=1;ODDS=49.2497;PAIRED=0;PAIREDR=0;PAO=2;PQA=71.5;PQR=71.5;PRO=2;QA=981;QR=0;RO=0;RPL=8;RPP=17.1973;RPPR=0;RPR=22;RUN=1;SAF=8;SAP=17.1973;SAR=22;SRF=0;SRP=0;SRR=0;TYPE=del;technology.ILLUMINA=1;ANN=GG|upstream_gene_variant|MODIFIER|alr|PA14_65110|transcript|ABJ14315.1|protein_coding||c.-3829_-3827delCGC|||||3827|,GG|upstream_gene_variant|MODIFIER|dnaB|PA14_65130|transcript|ABJ14316.1|protein_coding||c.-2366_-2364delCGC|||||2364|,GG|upstream_gene_variant|MODIFIER|rplI|PA14_65150|transcript|ABJ14317.1|protein_coding||c.-1791_-1789delCGC|||||1789|,GG|upstream_gene_variant|MODIFIER|PA14_65160|PA14_65160|transcript|ABJ14318.1|protein_coding||c.-900_-898delCGC|||||898|,GG|upstream_gene_variant|MODIFIER|rpsR|PA14_65170|transcript|ABJ14319.1|protein_coding||c.-633_-631delCGC|||||631|,GG|upstream_gene_variant|MODIFIER|rpsF|PA14_65180|transcript|ABJ14320.1|protein_coding||c.-184_-182delCGC|||||182|,GG|upstream_gene_variant|MODIFIER|PA14_65210|PA14_65210|transcript|PA14_65210-1.1|protein_coding||c.-3708_-3706delGCG|||||3708|WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|PA14_65220|PA14_65220|transcript|PA14_65220-1.1|protein_coding||c.-3924_-3922delGCG|||||3924|WARNING_TRANSCRIPT_NO_START_CODON,GG|downstream_gene_variant|MODIFIER|PA14_65090|PA14_65090|transcript|ABJ14314.1|protein_coding||c.*4905_*4907delGCG|||||4905|,GG|downstream_gene_variant|MODIFIER|yjfH|PA14_65190|transcript|ABJ14321.1|protein_coding||c.*35_*37delCGC|||||37|,GG|downstream_gene_variant|MODIFIER|rnr|PA14_65200|transcript|ABJ14322.1|protein_coding||c.*778_*780delCGC|||||780|,GG|downstream_gene_variant|MODIFIER|tRNA|EBG00001225099|transcript|EBT00001793514.1|protein_coding||c.*3706_*3708delCGC|||||3708|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,GG|downstream_gene_variant|MODIFIER|tRNA|EBG00001225145|transcript|EBT00001793399.1|protein_coding||c.*3922_*3924delCGC|||||3924|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,GG|downstream_gene_variant|MODIFIER|purA|PA14_65230|transcript|ABJ14323.1|protein_coding||c.*4165_*4167delCGC|||||4167|,GG|intergenic_region|MODIFIER|rpsF-yjfH|PA14_65180-PA14_65190|intergenic_region|PA14_65180-PA14_65190|||n.5809296_5809298delGCG|||||| GT:DP:DPR:RO:QR:AO:QA:GL 1:7:7,7:0:0:7:247:-20.7107,0 1:7:7,7:0:0:7:240:-20.9006,0 1:8:8,8:0:0:8:229:-19.0419,0 1:8:8,8:0:0:8:265:-22.0852,0 +Chromosome 5818779 . G C 4.14595E-16 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=33;DPB=33;DPRA=1.125;EPP=7.35324;EPPR=11.486;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=49.2174;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=1027;RO=31;RPL=2;RPP=7.35324;RPPR=4.76149;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=19;SRP=6.44263;SRR=12;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|hflX|PA14_65300|transcript|ABJ14328.1|protein_coding|1/1|c.996C>G|p.Arg332Arg|996/1302|996/1302|332/433||,C|upstream_gene_variant|MODIFIER|purA|PA14_65230|transcript|ABJ14323.1|protein_coding||c.-4024C>G|||||4024|,C|upstream_gene_variant|MODIFIER|hisX|PA14_65250|transcript|ABJ14324.1|protein_coding||c.-2788C>G|||||2788|,C|upstream_gene_variant|MODIFIER|PA14_65260|PA14_65260|transcript|ABJ14325.1|protein_coding||c.-2568C>G|||||2568|,C|upstream_gene_variant|MODIFIER|hflC|PA14_65270|transcript|ABJ14326.1|protein_coding||c.-1603C>G|||||1603|,C|upstream_gene_variant|MODIFIER|hflK|PA14_65280|transcript|ABJ14327.1|protein_coding||c.-401C>G|||||401|,C|downstream_gene_variant|MODIFIER|hfq|PA14_65310|transcript|ABJ14329.1|protein_coding||c.*1008C>G|||||1008|,C|downstream_gene_variant|MODIFIER|miaA|PA14_65320|transcript|ABJ14330.1|protein_coding||c.*1362C>G|||||1362|,C|downstream_gene_variant|MODIFIER|mutL|PA14_65350|transcript|ABJ14331.1|protein_coding||c.*2391C>G|||||2391|,C|downstream_gene_variant|MODIFIER|amiB|PA14_65370|transcript|ABJ14332.1|protein_coding||c.*4292C>G|||||4292| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:158:0:0:0,-14.6007 0:9:9,2:7:199:2:30:0,-15.3334 0:7:7,0:7:227:0:0:0,-20.7403 0:13:13,0:13:443:0:0:0,-40.1827 +Chromosome 5822686 . G A 5.15738E-10 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=18;DPB=18;DPRA=1.15385;EPP=7.35324;EPPR=3.55317;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=22.854;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=62;QR=603;RO=16;RPL=1;RPP=3.0103;RPPR=7.89611;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=6;SRP=5.18177;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|mutL|PA14_65350|transcript|ABJ14331.1|protein_coding|1/1|c.386C>T|p.Thr129Ile|386/1902|386/1902|129/633||,A|upstream_gene_variant|MODIFIER|hflK|PA14_65280|transcript|ABJ14327.1|protein_coding||c.-4308C>T|||||4308|,A|upstream_gene_variant|MODIFIER|hflX|PA14_65300|transcript|ABJ14328.1|protein_coding||c.-2912C>T|||||2912|,A|upstream_gene_variant|MODIFIER|hfq|PA14_65310|transcript|ABJ14329.1|protein_coding||c.-2651C>T|||||2651|,A|upstream_gene_variant|MODIFIER|miaA|PA14_65320|transcript|ABJ14330.1|protein_coding||c.-1574C>T|||||1574|,A|upstream_gene_variant|MODIFIER|yjeS|PA14_65400|transcript|ABJ14335.1|protein_coding||c.-3866G>A|||||3866|,A|downstream_gene_variant|MODIFIER|amiB|PA14_65370|transcript|ABJ14332.1|protein_coding||c.*385C>T|||||385|,A|downstream_gene_variant|MODIFIER|PA14_65380|PA14_65380|transcript|ABJ14333.1|protein_coding||c.*1821C>T|||||1821|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|yjeF|PA14_65390|transcript|ABJ14334.1|protein_coding||c.*2276C>T|||||2276|,A|downstream_gene_variant|MODIFIER|orn|PA14_65410|transcript|ABJ14336.1|protein_coding||c.*4985C>T|||||4985| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:110:0:0:0,-10.2601 0:5:5,2:3:114:2:62:0,-4.74243 0:3:3,0:3:112:0:0:0,-10.4463 0:7:7,0:7:267:0:0:0,-24.3921 +Chromosome 5834451 . G T 1.06154E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=28;DPB=28;DPRA=1.42105;EPP=7.35324;EPPR=3.34437;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=38.723;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=945;RO=26;RPL=2;RPP=7.35324;RPPR=8.35546;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=11;SRP=4.34659;SRR=15;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|psd|PA14_65500|transcript|ABJ14342.1|protein_coding|1/1|c.644G>T|p.Trp215Leu|644/870|644/870|215/289||,T|upstream_gene_variant|MODIFIER|motB|PA14_65430|transcript|ABJ14338.1|protein_coding||c.-4060C>A|||||4060|,T|upstream_gene_variant|MODIFIER|motA|PA14_65450|transcript|ABJ14339.1|protein_coding||c.-3189C>A|||||3189|,T|upstream_gene_variant|MODIFIER|PA14_65520|PA14_65520|transcript|ABJ14343.1|protein_coding||c.-904G>T|||||904|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|fimX|PA14_65540|transcript|ABJ14344.1|protein_coding||c.-2432G>T|||||2432|,T|downstream_gene_variant|MODIFIER|PA14_65470|PA14_65470|transcript|ABJ14340.1|protein_coding||c.*1537G>T|||||1537|,T|downstream_gene_variant|MODIFIER|rhdA|PA14_65480|transcript|ABJ14341.1|protein_coding||c.*647G>T|||||647|,T|downstream_gene_variant|MODIFIER|serB|PA14_65560|transcript|ABJ14345.1|protein_coding||c.*4594C>A|||||4594| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:288:0:0:0,-26.2628 0:3:3,0:3:117:0:0:0,-10.9099 0:9:9,2:7:260:2:4:0,-23.3723 0:8:8,0:8:280:0:0:0,-25.524 +Chromosome 5839026 . C A 1.2702E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=9;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=14.8328;EPPR=3.64073;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=31.3479;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=131;QR=670;RO=31;RPL=1;RPP=14.8328;RPPR=3.64073;RPR=8;RUN=1;SAF=0;SAP=22.5536;SAR=9;SRF=4;SRP=40.0654;SRR=27;TYPE=snp;technology.ILLUMINA=1;ANN=A|upstream_gene_variant|MODIFIER|PA14_65570|PA14_65570|transcript|ABJ14346.1|protein_coding||c.-1454C>A|||||1454|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ybcI|PA14_65580|transcript|ABJ14347.1|protein_coding||c.-2989C>A|||||2989|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|psd|PA14_65500|transcript|ABJ14342.1|protein_coding||c.*4349C>A|||||4349|,A|downstream_gene_variant|MODIFIER|PA14_65520|PA14_65520|transcript|ABJ14343.1|protein_coding||c.*2208C>A|||||2208|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|fimX|PA14_65540|transcript|ABJ14344.1|protein_coding||c.*68C>A|||||68|,A|downstream_gene_variant|MODIFIER|serB|PA14_65560|transcript|ABJ14345.1|protein_coding||c.*19G>T|||||19|,A|downstream_gene_variant|MODIFIER|PA14_65590|PA14_65590|transcript|ABJ14348.1|protein_coding||c.*3583G>T|||||3583|,A|downstream_gene_variant|MODIFIER|parC|PA14_65605|transcript|ABJ15660.1|protein_coding||c.*4586G>T|||||4586|,A|intergenic_region|MODIFIER|fimX-serB|PA14_65540-PA14_65560|intergenic_region|PA14_65540-PA14_65560|||n.5839026C>A|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:11:11,1:10:221:1:16:0,-18.5026 0:9:9,3:6:136:3:46:0,-8.17223 0:10:10,4:6:131:4:55:0,-6.91738 0:10:10,1:9:182:1:14:0,-15.1805 +Chromosome 5840369 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=16;CIGAR=1X;DP=111;DPB=111;DPRA=0;EPP=37.7539;EPPR=34.3024;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=162.592;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=2918;RO=95;RPL=0;RPP=37.7539;RPPR=4.86177;RPR=16;RUN=1;SAF=0;SAP=37.7539;SAR=16;SRF=44;SRP=4.13032;SRR=51;TYPE=snp;technology.ILLUMINA=1;ANN=C|upstream_gene_variant|MODIFIER|serB|PA14_65560|transcript|ABJ14345.1|protein_coding||c.-35T>G|||||35|,C|upstream_gene_variant|MODIFIER|PA14_65570|PA14_65570|transcript|ABJ14346.1|protein_coding||c.-111A>C|||||111|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ybcI|PA14_65580|transcript|ABJ14347.1|protein_coding||c.-1646A>C|||||1646|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_65520|PA14_65520|transcript|ABJ14343.1|protein_coding||c.*3551A>C|||||3551|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|fimX|PA14_65540|transcript|ABJ14344.1|protein_coding||c.*1411A>C|||||1411|,C|downstream_gene_variant|MODIFIER|PA14_65590|PA14_65590|transcript|ABJ14348.1|protein_coding||c.*2240T>G|||||2240|,C|downstream_gene_variant|MODIFIER|parC|PA14_65605|transcript|ABJ15660.1|protein_coding||c.*3243T>G|||||3243|,C|intergenic_region|MODIFIER|serB-PA14_65570|PA14_65560-PA14_65570|intergenic_region|PA14_65560-PA14_65570|||n.5840369A>C|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:23:23,3:20:668:3:6:0,-59.8489 0:28:28,3:25:785:3:6:0,-70.3377 0:24:24,2:22:684:2:4:0,-61.4387 0:36:36,8:28:781:8:16:0,-69.0562 +Chromosome 5867833 . C A 3.26214E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=32;DPB=32;DPRA=1;EPP=11.6962;EPPR=22.8638;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=45.0829;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=884;RO=28;RPL=0;RPP=11.6962;RPPR=3.0103;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=14;SRP=3.0103;SRR=14;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|PA14_65860|PA14_65860|transcript|ABJ14365.1|protein_coding|1/1|c.1156G>T|p.Asp386Tyr|1156/2313|1156/2313|386/770||,A|upstream_gene_variant|MODIFIER|PA14_65820|PA14_65820|transcript|ABJ14362.1|protein_coding||c.-3824G>T|||||3824|,A|upstream_gene_variant|MODIFIER|PA14_65840|PA14_65840|transcript|ABJ14363.1|protein_coding||c.-3012G>T|||||3012|,A|upstream_gene_variant|MODIFIER|rocE|PA14_65850|transcript|ABJ14364.1|protein_coding||c.-1341G>T|||||1341|,A|upstream_gene_variant|MODIFIER|PA14_65940|PA14_65940|transcript|ABJ14370.1|protein_coding||c.-4713C>A|||||4713|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_65870|PA14_65870|transcript|ABJ14366.1|protein_coding||c.*1092G>T|||||1092|,A|downstream_gene_variant|MODIFIER|dmsR|PA14_65880|transcript|ABJ14367.1|protein_coding||c.*1872G>T|||||1872|,A|downstream_gene_variant|MODIFIER|PA14_65900|PA14_65900|transcript|ABJ14368.1|protein_coding||c.*2724G>T|||||2724|,A|downstream_gene_variant|MODIFIER|PA14_65920|PA14_65920|transcript|ABJ14369.1|protein_coding||c.*3448G>T|||||3448| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,1:8:268:1:2:0,-24.2355 0:8:8,2:6:165:2:17:0,-13.4996 0:8:8,0:8:261:0:0:0,-23.799 0:7:7,1:6:190:1:2:0,-17.2028 +Chromosome 5877539 . G C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=11;CIGAR=1X;DP=66;DPB=66;DPRA=0;EPP=26.8965;EPPR=7.78754;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=99.6357;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=22;QR=1944;RO=55;RPL=11;RPP=26.8965;RPPR=11.8936;RPR=0;RUN=1;SAF=11;SAP=26.8965;SAR=0;SRF=26;SRP=3.36563;SRR=29;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|qacH|PA14_65990|transcript|ABJ14374.1|protein_coding|1/1|c.40G>C|p.Glu14Gln|40/333|40/333|14/110||,C|upstream_gene_variant|MODIFIER|waaA|PA14_65960|transcript|ABJ14372.1|protein_coding||c.-1044C>G|||||1044|,C|upstream_gene_variant|MODIFIER|PA14_65970|PA14_65970|transcript|ABJ14373.1|protein_coding||c.-124C>G|||||124|,C|upstream_gene_variant|MODIFIER|PA14_66000|PA14_66000|transcript|ABJ14375.1|protein_coding||c.-354G>C|||||354|,C|upstream_gene_variant|MODIFIER|PA14_66010|PA14_66010|transcript|ABJ14376.1|protein_coding||c.-1526G>C|||||1526|,C|upstream_gene_variant|MODIFIER|PA14_66020|PA14_66020|transcript|ABJ14377.1|protein_coding||c.-2507G>C|||||2507|,C|downstream_gene_variant|MODIFIER|PA14_65940|PA14_65940|transcript|ABJ14370.1|protein_coding||c.*3047G>C|||||3047|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_65950|PA14_65950|transcript|ABJ14371.1|protein_coding||c.*2370G>C|||||2370|,C|downstream_gene_variant|MODIFIER|PA14_66040|PA14_66040|transcript|ABJ14378.1|protein_coding||c.*3452C>G|||||3452|,C|downstream_gene_variant|MODIFIER|PA14_66050|PA14_66050|transcript|ABJ14379.1|protein_coding||c.*4709C>G|||||4709| GT:DP:DPR:RO:QR:AO:QA:GL 0:13:13,2:11:388:2:4:0,-34.8644 0:18:18,3:15:564:3:6:0,-50.5317 0:16:16,4:12:399:4:8:0,-35.4785 0:19:19,2:17:593:2:4:0,-53.2986 +Chromosome 5881832 . T C 1.11121E-6 . AB=0;ABP=0;AC=0;AF=0;AN=3;AO=2;CIGAR=1X;DP=8;DPB=8;DPRA=2;EPP=3.0103;EPPR=16.0391;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=15.4117;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=42;QR=237;RO=6;RPL=2;RPP=7.35324;RPPR=16.0391;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=16.0391;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_66040|PA14_66040|transcript|ABJ14378.1|protein_coding|1/1|c.368A>G|p.Gln123Arg|368/1209|368/1209|123/402||,C|upstream_gene_variant|MODIFIER|PA14_65970|PA14_65970|transcript|ABJ14373.1|protein_coding||c.-4417A>G|||||4417|,C|downstream_gene_variant|MODIFIER|qacH|PA14_65990|transcript|ABJ14374.1|protein_coding||c.*4000T>C|||||4000|,C|downstream_gene_variant|MODIFIER|PA14_66000|PA14_66000|transcript|ABJ14375.1|protein_coding||c.*2764T>C|||||2764|,C|downstream_gene_variant|MODIFIER|PA14_66010|PA14_66010|transcript|ABJ14376.1|protein_coding||c.*1955T>C|||||1955|,C|downstream_gene_variant|MODIFIER|PA14_66020|PA14_66020|transcript|ABJ14377.1|protein_coding||c.*866T>C|||||866|,C|downstream_gene_variant|MODIFIER|PA14_66050|PA14_66050|transcript|ABJ14379.1|protein_coding||c.*416A>G|||||416|,C|downstream_gene_variant|MODIFIER|rfaE|PA14_66060|transcript|ABJ14380.1|protein_coding||c.*1833A>G|||||1833|,C|downstream_gene_variant|MODIFIER|msbA|PA14_66080|transcript|ABJ14381.1|protein_coding||c.*3298A>G|||||3298| GT:DP:DPR:RO:QR:AO:QA:GL . 0:3:3,0:3:118:0:0:0,-11.0029 0:1:1,0:1:40:0:0:0,-3.99568 0:4:4,2:2:79:2:42:0,-3.51174 +Chromosome 5881990 . G T 6.28365E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=9;CIGAR=1X;DP=35;DPB=35;DPRA=1.33333;EPP=22.5536;EPPR=4.34659;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=29.6307;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=135;QR=794;RO=26;RPL=9;RPP=22.5536;RPPR=4.34659;RPR=0;RUN=1;SAF=9;SAP=22.5536;SAR=0;SRF=22;SRP=30.0702;SRR=4;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|PA14_66040|PA14_66040|transcript|ABJ14378.1|protein_coding|1/1|c.210C>A|p.Gly70Gly|210/1209|210/1209|70/402||,T|upstream_gene_variant|MODIFIER|PA14_65970|PA14_65970|transcript|ABJ14373.1|protein_coding||c.-4575C>A|||||4575|,T|downstream_gene_variant|MODIFIER|qacH|PA14_65990|transcript|ABJ14374.1|protein_coding||c.*4158G>T|||||4158|,T|downstream_gene_variant|MODIFIER|PA14_66000|PA14_66000|transcript|ABJ14375.1|protein_coding||c.*2922G>T|||||2922|,T|downstream_gene_variant|MODIFIER|PA14_66010|PA14_66010|transcript|ABJ14376.1|protein_coding||c.*2113G>T|||||2113|,T|downstream_gene_variant|MODIFIER|PA14_66020|PA14_66020|transcript|ABJ14377.1|protein_coding||c.*1024G>T|||||1024|,T|downstream_gene_variant|MODIFIER|PA14_66050|PA14_66050|transcript|ABJ14379.1|protein_coding||c.*258C>A|||||258|,T|downstream_gene_variant|MODIFIER|rfaE|PA14_66060|transcript|ABJ14380.1|protein_coding||c.*1675C>A|||||1675|,T|downstream_gene_variant|MODIFIER|msbA|PA14_66080|transcript|ABJ14381.1|protein_coding||c.*3140C>A|||||3140| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,2:4:102:2:30:0,-6.58172 0:7:7,0:7:248:0:0:0,-22.6609 0:12:12,4:8:230:4:60:0,-15.4272 0:10:10,3:7:214:3:45:0,-15.3492 +Chromosome 5882040 . T C 1.34027E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=29;DPB=29;DPRA=1.23077;EPP=9.52472;EPPR=11.3621;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=31.1508;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=867;RO=26;RPL=3;RPP=9.52472;RPPR=15.0369;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=11;SRP=4.34659;SRR=15;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_66040|PA14_66040|transcript|ABJ14378.1|protein_coding|1/1|c.160A>G|p.Ser54Gly|160/1209|160/1209|54/402||,C|upstream_gene_variant|MODIFIER|PA14_65970|PA14_65970|transcript|ABJ14373.1|protein_coding||c.-4625A>G|||||4625|,C|downstream_gene_variant|MODIFIER|qacH|PA14_65990|transcript|ABJ14374.1|protein_coding||c.*4208T>C|||||4208|,C|downstream_gene_variant|MODIFIER|PA14_66000|PA14_66000|transcript|ABJ14375.1|protein_coding||c.*2972T>C|||||2972|,C|downstream_gene_variant|MODIFIER|PA14_66010|PA14_66010|transcript|ABJ14376.1|protein_coding||c.*2163T>C|||||2163|,C|downstream_gene_variant|MODIFIER|PA14_66020|PA14_66020|transcript|ABJ14377.1|protein_coding||c.*1074T>C|||||1074|,C|downstream_gene_variant|MODIFIER|PA14_66050|PA14_66050|transcript|ABJ14379.1|protein_coding||c.*208A>G|||||208|,C|downstream_gene_variant|MODIFIER|rfaE|PA14_66060|transcript|ABJ14380.1|protein_coding||c.*1625A>G|||||1625|,C|downstream_gene_variant|MODIFIER|msbA|PA14_66080|transcript|ABJ14381.1|protein_coding||c.*3090A>G|||||3090| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:74:0:0:0,-7.02486 0:7:7,1:6:200:1:13:0,-17.0217 0:9:9,2:7:260:2:4:0,-23.3748 0:11:11,0:11:333:0:0:0,-30.2536 +Chromosome 5882270 . A C 2.44113E-11 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=24;DPB=24;DPRA=0.789474;EPP=3.0103;EPPR=6.56362;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=25.9048;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=56;QR=824;RO=22;RPL=0;RPP=7.35324;RPPR=4.58955;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=7;SRP=9.32731;SRR=15;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_66050|PA14_66050|transcript|ABJ14379.1|protein_coding|1/1|c.1268T>G|p.Met423Arg|1268/1290|1268/1290|423/429||,C|upstream_gene_variant|MODIFIER|PA14_65970|PA14_65970|transcript|ABJ14373.1|protein_coding||c.-4855T>G|||||4855|,C|upstream_gene_variant|MODIFIER|PA14_66040|PA14_66040|transcript|ABJ14378.1|protein_coding||c.-71T>G|||||71|,C|upstream_gene_variant|MODIFIER|PA14_66090|PA14_66090|transcript|ABJ14382.1|protein_coding||c.-4779A>C|||||4779|,C|downstream_gene_variant|MODIFIER|qacH|PA14_65990|transcript|ABJ14374.1|protein_coding||c.*4438A>C|||||4438|,C|downstream_gene_variant|MODIFIER|PA14_66000|PA14_66000|transcript|ABJ14375.1|protein_coding||c.*3202A>C|||||3202|,C|downstream_gene_variant|MODIFIER|PA14_66010|PA14_66010|transcript|ABJ14376.1|protein_coding||c.*2393A>C|||||2393|,C|downstream_gene_variant|MODIFIER|PA14_66020|PA14_66020|transcript|ABJ14377.1|protein_coding||c.*1304A>C|||||1304|,C|downstream_gene_variant|MODIFIER|rfaE|PA14_66060|transcript|ABJ14380.1|protein_coding||c.*1395T>G|||||1395|,C|downstream_gene_variant|MODIFIER|msbA|PA14_66080|transcript|ABJ14381.1|protein_coding||c.*2860T>G|||||2860| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:192:0:0:0,-17.6491 0:5:5,2:3:119:2:56:0,-5.77952 0:7:7,0:7:237:0:0:0,-21.6527 0:7:7,0:7:276:0:0:0,-25.2099 +Chromosome 5883247 . G C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=72;DPB=72;DPRA=1.15385;EPP=11.6962;EPPR=76.5849;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=99.9116;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1901;RO=68;RPL=4;RPP=11.6962;RPPR=54.1038;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=50;SRP=35.7101;SRR=18;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_66050|PA14_66050|transcript|ABJ14379.1|protein_coding|1/1|c.291C>G|p.Asp97Glu|291/1290|291/1290|97/429||,C|upstream_gene_variant|MODIFIER|PA14_66040|PA14_66040|transcript|ABJ14378.1|protein_coding||c.-1048C>G|||||1048|,C|upstream_gene_variant|MODIFIER|PA14_66090|PA14_66090|transcript|ABJ14382.1|protein_coding||c.-3802G>C|||||3802|,C|upstream_gene_variant|MODIFIER|PA14_66100|PA14_66100|transcript|ABJ14383.1|protein_coding||c.-4460G>C|||||4460|,C|downstream_gene_variant|MODIFIER|PA14_66000|PA14_66000|transcript|ABJ14375.1|protein_coding||c.*4179G>C|||||4179|,C|downstream_gene_variant|MODIFIER|PA14_66010|PA14_66010|transcript|ABJ14376.1|protein_coding||c.*3370G>C|||||3370|,C|downstream_gene_variant|MODIFIER|PA14_66020|PA14_66020|transcript|ABJ14377.1|protein_coding||c.*2281G>C|||||2281|,C|downstream_gene_variant|MODIFIER|rfaE|PA14_66060|transcript|ABJ14380.1|protein_coding||c.*418C>G|||||418|,C|downstream_gene_variant|MODIFIER|msbA|PA14_66080|transcript|ABJ14381.1|protein_coding||c.*1883C>G|||||1883| GT:DP:DPR:RO:QR:AO:QA:GL 0:18:18,0:18:535:0:0:0,-48.4153 0:19:19,0:19:452:0:0:0,-40.8979 0:15:15,0:15:416:0:0:0,-37.691 0:20:20,4:16:498:4:8:0,-44.3617 +Chromosome 5897114 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=33;DPB=33;DPRA=1.30435;EPP=9.52472;EPPR=5.61607;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=54.6798;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=28;QR=1067;RO=30;RPL=3;RPP=9.52472;RPPR=5.61607;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=20;SRP=10.2485;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_66190|PA14_66190|transcript|ABJ14390.1|protein_coding|1/1|c.663T>G|p.His221Gln|663/1479|663/1479|221/492||,C|upstream_gene_variant|MODIFIER|PA14_66140|PA14_66140|transcript|ABJ14386.1|protein_coding||c.-4691T>G|||||4691|,C|upstream_gene_variant|MODIFIER|PA14_66150|PA14_66150|transcript|ABJ14387.1|protein_coding||c.-3791T>G|||||3791|,C|upstream_gene_variant|MODIFIER|PA14_66160|PA14_66160|transcript|ABJ14388.1|protein_coding||c.-2661T>G|||||2661|,C|upstream_gene_variant|MODIFIER|PA14_66170|PA14_66170|transcript|ABJ14389.1|protein_coding||c.-920T>G|||||920|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|wapQ|PA14_66200|transcript|ABJ14391.1|protein_coding||c.*659T>G|||||659|,C|downstream_gene_variant|MODIFIER|waaX|PA14_66210|transcript|ABJ14392.1|protein_coding||c.*1414T>G|||||1414|,C|downstream_gene_variant|MODIFIER|waaP|PA14_66220|transcript|ABJ14393.1|protein_coding||c.*2148T>G|||||2148|,C|downstream_gene_variant|MODIFIER|waaG|PA14_66230|transcript|ABJ14394.1|protein_coding||c.*2951T>G|||||2951|,C|downstream_gene_variant|MODIFIER|waaC|PA14_66240|transcript|ABJ14395.1|protein_coding||c.*4072T>G|||||4072| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:192:0:0:0,-17.6493 0:10:10,3:7:255:3:28:0,-20.6841 0:6:6,0:6:231:0:0:0,-21.1563 0:12:12,0:12:389:0:0:0,-35.3037 +Chromosome 5902451 . C A 2.71994E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=31;DPB=31;DPRA=0.875;EPP=3.0103;EPPR=6.67934;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=46.9957;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=28;QR=990;RO=29;RPL=1;RPP=3.0103;RPPR=3.08518;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=18;SRP=6.67934;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|waaF|PA14_66250|transcript|ABJ14396.1|protein_coding|1/1|c.834G>T|p.Val278Val|834/1038|834/1038|278/345||,A|upstream_gene_variant|MODIFIER|PA14_66190|PA14_66190|transcript|ABJ14390.1|protein_coding||c.-4675G>T|||||4675|,A|upstream_gene_variant|MODIFIER|wapQ|PA14_66200|transcript|ABJ14391.1|protein_coding||c.-3920G>T|||||3920|,A|upstream_gene_variant|MODIFIER|waaX|PA14_66210|transcript|ABJ14392.1|protein_coding||c.-3189G>T|||||3189|,A|upstream_gene_variant|MODIFIER|waaP|PA14_66220|transcript|ABJ14393.1|protein_coding||c.-2383G>T|||||2383|,A|upstream_gene_variant|MODIFIER|waaG|PA14_66230|transcript|ABJ14394.1|protein_coding||c.-1265G>T|||||1265|,A|upstream_gene_variant|MODIFIER|waaC|PA14_66240|transcript|ABJ14395.1|protein_coding||c.-201G>T|||||201|,A|downstream_gene_variant|MODIFIER|ilvE|PA14_66260|transcript|ABJ14397.1|protein_coding||c.*893G>T|||||893|,A|downstream_gene_variant|MODIFIER|glnE|PA14_66270|transcript|ABJ14398.1|protein_coding||c.*1872G>T|||||1872| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,2:5:187:2:28:0,-14.5315 0:8:8,0:8:250:0:0:0,-22.798 0:6:6,0:6:231:0:0:0,-21.1568 0:10:10,0:10:322:0:0:0,-29.2856 +Chromosome 5914664 . T C 1.73301E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=52;DPB=52;DPRA=0.714286;EPP=7.35324;EPPR=4.57376;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=75.4202;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1794;RO=50;RPL=2;RPP=7.35324;RPPR=3.70517;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=35;SRP=20.3821;SRR=15;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_66320|PA14_66320|transcript|ABJ14401.1|protein_coding|1/1|c.2258T>C|p.Leu753Pro|2258/2700|2258/2700|753/899||,C|upstream_gene_variant|MODIFIER|msrA|PA14_66330|transcript|ABJ14402.1|protein_coding||c.-537T>C|||||537|,C|upstream_gene_variant|MODIFIER|PA14_66350|PA14_66350|transcript|ABJ14404.1|protein_coding||c.-2326T>C|||||2326|,C|upstream_gene_variant|MODIFIER|ycgO|PA14_66380|transcript|ABJ14405.1|protein_coding||c.-4547T>C|||||4547|,C|downstream_gene_variant|MODIFIER|aceA|PA14_66290|transcript|ABJ14399.1|protein_coding||c.*4463T>C|||||4463|,C|downstream_gene_variant|MODIFIER|aceF|PA14_66310|transcript|ABJ14400.1|protein_coding||c.*2675T>C|||||2675|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_66340|PA14_66340|transcript|ABJ14403.1|protein_coding||c.*1188A>G|||||1188| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,2:8:283:2:17:0,-24.1893 0:14:14,0:14:492:0:0:0,-44.6037 0:17:17,0:17:603:0:0:0,-54.5885 0:11:11,0:11:416:0:0:0,-37.7887 +Chromosome 5946067 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=41;DPB=41;DPRA=0.863636;EPP=9.52472;EPPR=3.9246;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=68.4681;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1304;RO=38;RPL=3;RPP=9.52472;RPPR=3.9246;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=32;SRP=41.6397;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|aroB|PA14_66600|transcript|ABJ14422.1|protein_coding|1/1|c.470A>G|p.Gln157Arg|470/1107|470/1107|157/368||,C|upstream_gene_variant|MODIFIER|gltB|PA14_66570|transcript|ABJ14420.1|protein_coding||c.-2524A>G|||||2524|,C|upstream_gene_variant|MODIFIER|PA14_66580|PA14_66580|transcript|ABJ14421.1|protein_coding||c.-644A>G|||||644|,C|downstream_gene_variant|MODIFIER|P37|EBG00001225115|transcript|EBT00001793386.1|sRNA||n.*2302T>C|||||2302|,C|downstream_gene_variant|MODIFIER|aroK|PA14_66610|transcript|ABJ14423.1|protein_coding||c.*519A>G|||||519|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|pilQ|PA14_66620|transcript|ABJ14424.1|protein_coding||c.*1049A>G|||||1049|,C|downstream_gene_variant|MODIFIER|pilP|PA14_66630|transcript|ABJ14425.1|protein_coding||c.*3235A>G|||||3235|,C|downstream_gene_variant|MODIFIER|pilO|PA14_66640|transcript|ABJ14426.1|protein_coding||c.*3756A>G|||||3756|,C|downstream_gene_variant|MODIFIER|pilN|PA14_66650|transcript|ABJ14427.1|protein_coding||c.*4376A>G|||||4376|,C|downstream_gene_variant|MODIFIER|pilM|PA14_66660|transcript|ABJ14428.1|protein_coding||c.*4972A>G|||||4972|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,1:9:308:1:13:0,-26.7382 0:10:10,0:10:341:0:0:0,-31.0076 0:9:9,2:7:258:2:4:0,-23.1915 0:12:12,0:12:397:0:0:0,-36.0323 +Chromosome 5969352 . G C 3.05421E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=37;DPB=37;DPRA=0.7;EPP=7.35324;EPPR=4.56135;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=30.2837;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=879;RO=35;RPL=2;RPP=7.35324;RPPR=3.56868;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=25;SRP=16.9698;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|phaD|PA14_66830|transcript|ABJ14441.1|protein_coding|1/1|c.771G>C|p.Ser257Ser|771/858|771/858|257/285||,C|upstream_gene_variant|MODIFIER|phaC2|PA14_66840|transcript|ABJ14442.1|protein_coding||c.-391G>C|||||391|,C|upstream_gene_variant|MODIFIER|phaD|PA14_66850|transcript|ABJ14443.1|protein_coding||c.-2129G>C|||||2129|,C|upstream_gene_variant|MODIFIER|ubiE|PA14_66900|transcript|ABJ14446.1|protein_coding||c.-4701G>C|||||4701|,C|downstream_gene_variant|MODIFIER|hslV|PA14_66770|transcript|ABJ14437.1|protein_coding||c.*4859G>C|||||4859|,C|downstream_gene_variant|MODIFIER|hslU|PA14_66790|transcript|ABJ14438.1|protein_coding||c.*3487G>C|||||3487|,C|downstream_gene_variant|MODIFIER|PA14_66800|PA14_66800|transcript|ABJ14439.1|protein_coding||c.*3021G>C|||||3021|,C|downstream_gene_variant|MODIFIER|phaC1|PA14_66820|transcript|ABJ14440.1|protein_coding||c.*923G>C|||||923|,C|downstream_gene_variant|MODIFIER|phaF|PA14_66875|transcript|ABJ15691.1|protein_coding||c.*2790C>G|||||2790|,C|downstream_gene_variant|MODIFIER|phaI|PA14_66880|transcript|ABJ14444.1|protein_coding||c.*3730C>G|||||3730|,C|downstream_gene_variant|MODIFIER|PA14_66890|PA14_66890|transcript|ABJ14445.1|protein_coding||c.*4290C>G|||||4290| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,2:5:81:2:17:0,-5.8361 0:6:6,0:6:179:0:0:0,-16.4001 0:12:12,0:12:314:0:0:0,-28.5124 0:12:12,0:12:305:0:0:0,-27.6909 +Chromosome 5969889 . T G 1.62886E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=36;DPB=36;DPRA=0.636364;EPP=3.73412;EPPR=32.0291;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=35.0148;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=46;QR=1263;RO=33;RPL=0;RPP=9.52472;RPPR=32.0291;RPR=3;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=29;SRP=44.1367;SRR=4;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|phaC2|PA14_66840|transcript|ABJ14442.1|protein_coding|1/1|c.147T>G|p.Ser49Arg|147/1683|147/1683|49/560||,G|upstream_gene_variant|MODIFIER|phaD|PA14_66850|transcript|ABJ14443.1|protein_coding||c.-1592T>G|||||1592|,G|upstream_gene_variant|MODIFIER|ubiE|PA14_66900|transcript|ABJ14446.1|protein_coding||c.-4164T>G|||||4164|,G|upstream_gene_variant|MODIFIER|PA14_66910|PA14_66910|transcript|ABJ14447.1|protein_coding||c.-4949T>G|||||4949|,G|downstream_gene_variant|MODIFIER|hslU|PA14_66790|transcript|ABJ14438.1|protein_coding||c.*4024T>G|||||4024|,G|downstream_gene_variant|MODIFIER|PA14_66800|PA14_66800|transcript|ABJ14439.1|protein_coding||c.*3558T>G|||||3558|,G|downstream_gene_variant|MODIFIER|phaC1|PA14_66820|transcript|ABJ14440.1|protein_coding||c.*1460T>G|||||1460|,G|downstream_gene_variant|MODIFIER|phaD|PA14_66830|transcript|ABJ14441.1|protein_coding||c.*450T>G|||||450|,G|downstream_gene_variant|MODIFIER|phaF|PA14_66875|transcript|ABJ15691.1|protein_coding||c.*2253A>C|||||2253|,G|downstream_gene_variant|MODIFIER|phaI|PA14_66880|transcript|ABJ14444.1|protein_coding||c.*3193A>C|||||3193|,G|downstream_gene_variant|MODIFIER|PA14_66890|PA14_66890|transcript|ABJ14445.1|protein_coding||c.*3753A>C|||||3753| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,1:7:268:1:13:0,-23.1822 0:6:6,2:4:153:2:33:0,-11.0064 0:10:10,0:10:382:0:0:0,-34.7326 0:12:12,0:12:460:0:0:0,-41.7476 +Chromosome 5983257 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=37;DPB=37;DPRA=0.947368;EPP=11.6962;EPPR=3.0761;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=44.3475;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=48;QR=1007;RO=33;RPL=4;RPP=11.6962;RPPR=4.65535;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=28;SRP=37.8197;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|PA14_67030|PA14_67030|transcript|ABJ14457.1|protein_coding|1/1|c.339C>A|p.Gly113Gly|339/735|339/735|113/244||WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|tatB|PA14_66970|transcript|ABJ14452.1|protein_coding||c.*4634G>T|||||4634|,T|downstream_gene_variant|MODIFIER|tatC|PA14_66980|transcript|ABJ14453.1|protein_coding||c.*3834G>T|||||3834|,T|downstream_gene_variant|MODIFIER|PA14_66990|PA14_66990|transcript|ABJ14454.1|protein_coding||c.*3130G>T|||||3130|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|PA14_67010|PA14_67010|transcript|ABJ14455.1|protein_coding||c.*975G>T|||||975|,T|downstream_gene_variant|MODIFIER|PA14_67020|PA14_67020|transcript|ABJ14456.1|protein_coding||c.*404G>T|||||404|,T|downstream_gene_variant|MODIFIER|PA14_67040|PA14_67040|transcript|ABJ14458.1|protein_coding||c.*331C>A|||||331|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|PA14_67050|PA14_67050|transcript|ABJ14459.1|protein_coding||c.*1359C>A|||||1359|,T|downstream_gene_variant|MODIFIER|mdoH|PA14_67065|transcript|ABJ15655.1|protein_coding||c.*2397C>A|||||2397|,T|downstream_gene_variant|MODIFIER|mdoG|PA14_67090|transcript|ABJ14460.1|protein_coding||c.*4975C>A|||||4975|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:157:0:0:0,-14.4375 0:6:6,1:5:145:1:16:0,-11.7321 0:14:14,0:14:444:0:0:0,-40.2625 0:12:12,3:9:261:3:32:0,-20.7822 +Chromosome 5985843 . G T 6.22865E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=32;DPB=32;DPRA=1.8;EPP=9.52472;EPPR=9.07545;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=29.6041;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=28;QR=840;RO=29;RPL=3;RPP=9.52472;RPPR=15.6647;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=23;SRP=24.6501;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|mdoH|PA14_67065|transcript|ABJ15655.1|protein_coding|1/1|c.2397C>A|p.Ala799Ala|2397/2586|2397/2586|799/861||,T|upstream_gene_variant|MODIFIER|PA14_67030|PA14_67030|transcript|ABJ14457.1|protein_coding||c.-2248C>A|||||2248|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|PA14_67040|PA14_67040|transcript|ABJ14458.1|protein_coding||c.-1293C>A|||||1293|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|PA14_67050|PA14_67050|transcript|ABJ14459.1|protein_coding||c.-427C>A|||||427|,T|downstream_gene_variant|MODIFIER|PA14_67010|PA14_67010|transcript|ABJ14455.1|protein_coding||c.*3561G>T|||||3561|,T|downstream_gene_variant|MODIFIER|PA14_67020|PA14_67020|transcript|ABJ14456.1|protein_coding||c.*2990G>T|||||2990|,T|downstream_gene_variant|MODIFIER|mdoG|PA14_67090|transcript|ABJ14460.1|protein_coding||c.*2389C>A|||||2389|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|dtD|PA14_67100|transcript|ABJ14461.1|protein_coding||c.*4423C>A|||||4423|,T|downstream_gene_variant|MODIFIER|pap|PA14_67110|transcript|ABJ14462.1|protein_coding||c.*4857C>A|||||4857| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:63:0:0:0,-5.98315 0:4:4,0:4:109:0:0:0,-10.0787 0:14:14,0:14:371:0:0:0,-33.6373 0:12:12,3:9:297:3:28:0,-24.4363 +Chromosome 6009344 . A G 5.46729E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=25;DPB=25;DPRA=1.41176;EPP=3.0103;EPPR=4.58955;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=29.9403;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=73;QR=797;RO=22;RPL=2;RPP=7.35324;RPPR=12.8806;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=15;SRP=9.32731;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|proW|PA14_67280|transcript|ABJ14478.1|protein_coding|1/1|c.236T>C|p.Leu79Pro|236/852|236/852|79/283||,G|upstream_gene_variant|MODIFIER|hutG|PA14_67240|transcript|ABJ14474.1|protein_coding||c.-4170T>C|||||4170|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|hutI|PA14_67250|transcript|ABJ14475.1|protein_coding||c.-2969T>C|||||2969|,G|upstream_gene_variant|MODIFIER|PA14_67260|PA14_67260|transcript|ABJ14476.1|protein_coding||c.-1440T>C|||||1440|,G|upstream_gene_variant|MODIFIER|proV|PA14_67270|transcript|ABJ14477.1|protein_coding||c.-613T>C|||||613|,G|downstream_gene_variant|MODIFIER|proX|PA14_67300|transcript|ABJ14479.1|protein_coding||c.*260T>C|||||260|,G|downstream_gene_variant|MODIFIER|hutT|PA14_67310|transcript|ABJ14480.1|protein_coding||c.*1346T>C|||||1346|,G|downstream_gene_variant|MODIFIER|hutH|PA14_67320|transcript|ABJ14481.1|protein_coding||c.*2812T>C|||||2812|,G|downstream_gene_variant|MODIFIER|codB|PA14_67340|transcript|ABJ14482.1|protein_coding||c.*4438T>C|||||4438| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:77:0:0:0,-7.30883 0:8:8,0:8:280:0:0:0,-25.5318 0:7:7,0:7:272:0:0:0,-24.846 0:8:8,2:5:168:2:73:0,-8.57651 +Chromosome 6010469 . A C 1.64261E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=43;DPB=43;DPRA=2.53333;EPP=13.8677;EPPR=5.06748;GTI=0;LEN=1;MEANALT=1;MQM=58.2;MQMR=60;NS=4;NUMALT=1;ODDS=58.3243;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1311;RO=38;RPL=0;RPP=13.8677;RPPR=3.23888;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=28;SRP=21.525;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|proX|PA14_67300|transcript|ABJ14479.1|protein_coding|1/1|c.104T>G|p.Val35Gly|104/969|104/969|35/322||,C|upstream_gene_variant|MODIFIER|hutI|PA14_67250|transcript|ABJ14475.1|protein_coding||c.-4094T>G|||||4094|,C|upstream_gene_variant|MODIFIER|PA14_67260|PA14_67260|transcript|ABJ14476.1|protein_coding||c.-2565T>G|||||2565|,C|upstream_gene_variant|MODIFIER|proV|PA14_67270|transcript|ABJ14477.1|protein_coding||c.-1738T>G|||||1738|,C|upstream_gene_variant|MODIFIER|proW|PA14_67280|transcript|ABJ14478.1|protein_coding||c.-890T>G|||||890|,C|downstream_gene_variant|MODIFIER|hutT|PA14_67310|transcript|ABJ14480.1|protein_coding||c.*221T>G|||||221|,C|downstream_gene_variant|MODIFIER|hutH|PA14_67320|transcript|ABJ14481.1|protein_coding||c.*1687T>G|||||1687|,C|downstream_gene_variant|MODIFIER|codB|PA14_67340|transcript|ABJ14482.1|protein_coding||c.*3313T>G|||||3313|,C|downstream_gene_variant|MODIFIER|hutU|PA14_67350|transcript|ABJ14483.1|protein_coding||c.*4863T>G|||||4863|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:195:0:0:0,-17.9228 0:9:9,1:8:315:1:2:0,-28.5162 0:14:14,3:11:362:3:6:0,-32.3214 0:15:15,1:14:439:1:2:0,-39.5926 +Chromosome 6041911 . C G 3.48987E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=21;DPB=21;DPRA=0.909091;EPP=9.52472;EPPR=4.1599;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=20.942;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=636;RO=17;RPL=0;RPP=9.52472;RPPR=6.20364;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=10;SRP=4.1599;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_67630|PA14_67630|transcript|ABJ14504.1|protein_coding|1/1|c.992G>C|p.Arg331Pro|992/2208|992/2208|331/735||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|thiI|PA14_67580|transcript|ABJ14501.1|protein_coding||c.-3511G>C|||||3511|,G|upstream_gene_variant|MODIFIER|PA14_67640|PA14_67640|transcript|ABJ14505.1|protein_coding||c.-1279C>G|||||1279|,G|upstream_gene_variant|MODIFIER|PA14_67650|PA14_67650|transcript|ABJ14506.1|protein_coding||c.-1797C>G|||||1797|,G|upstream_gene_variant|MODIFIER|ntrB|PA14_67670|transcript|ABJ14507.1|protein_coding||c.-2640C>G|||||2640|,G|upstream_gene_variant|MODIFIER|ntrC|PA14_67680|transcript|ABJ14508.1|protein_coding||c.-3719C>G|||||3719|,G|downstream_gene_variant|MODIFIER|glnA|PA14_67600|transcript|ABJ14502.1|protein_coding||c.*1765C>G|||||1765|,G|downstream_gene_variant|MODIFIER|PA14_67620|PA14_67620|transcript|ABJ14503.1|protein_coding||c.*1213C>G|||||1213| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:153:0:0:0,-14.1414 0:7:7,0:6:207:0:0:0,-18.8923 0:2:2,1:1:38:1:2:0,-3.59727 0:8:8,2:6:238:2:4:0,-21.4145 +Chromosome 6050827 . C A 2.61041E-11 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=26;DPB=26;DPRA=1.36364;EPP=9.52472;EPPR=7.63648;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=25.8378;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=46;QR=686;RO=23;RPL=0;RPP=9.52472;RPPR=5.3706;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=8;SRP=7.63648;SRR=15;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|pgm|PA14_67770|transcript|ABJ14514.1|protein_coding|1/1|c.531C>A|p.Gly177Gly|531/1548|531/1548|177/515||,A|upstream_gene_variant|MODIFIER|P33|EBG00001225105|transcript|EBT00001793496.1|sRNA||n.-3558G>T|||||3558|,A|upstream_gene_variant|MODIFIER|P33|EBG00001225024|transcript|EBT00001793435.1|sRNA||n.-3354G>T|||||3354|,A|upstream_gene_variant|MODIFIER|PA14_67700|PA14_67700|transcript|ABJ14510.1|protein_coding||c.-2577G>T|||||2577|,A|upstream_gene_variant|MODIFIER|secB|PA14_67720|transcript|ABJ14511.1|protein_coding||c.-1567G>T|||||1567|,A|upstream_gene_variant|MODIFIER|grx|PA14_67740|transcript|ABJ14512.1|protein_coding||c.-1276G>T|||||1276|,A|upstream_gene_variant|MODIFIER|yigN|PA14_67750|transcript|ABJ14513.1|protein_coding||c.-855G>T|||||855|,A|upstream_gene_variant|MODIFIER|PA14_67780|PA14_67780|transcript|ABJ14515.1|protein_coding||c.-1331C>A|||||1331|,A|upstream_gene_variant|MODIFIER|PA14_67790|PA14_67790|transcript|ABJ14516.1|protein_coding||c.-2299C>A|||||2299|,A|upstream_gene_variant|MODIFIER|ctpA|PA14_67810|transcript|ABJ14517.1|protein_coding||c.-3614C>A|||||3614|,A|upstream_gene_variant|MODIFIER|PA14_67820|PA14_67820|transcript|ABJ14518.1|protein_coding||c.-4924C>A|||||4924|,A|downstream_gene_variant|MODIFIER|ntrC|PA14_67680|transcript|ABJ14508.1|protein_coding||c.*3767C>A|||||3767|,A|downstream_gene_variant|MODIFIER|trmH|PA14_67710|transcript|ABJ14509.1|protein_coding||c.*2117C>A|||||2117| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:56:0:0:0,-5.31588 0:8:8,1:7:235:1:15:0,-19.9757 0:9:9,0:9:226:0:0:0,-20.5816 0:7:7,2:5:169:2:31:0,-12.5942 +Chromosome 6065625 . C A 9.13442E-8 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=13;DPB=13;DPRA=3.33333;EPP=3.73412;EPPR=10.8276;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=17.7059;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=327;RO=10;RPL=1;RPP=3.73412;RPPR=10.8276;RPR=2;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=24.725;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|PA14_67970|PA14_67970|transcript|ABJ14530.1|protein_coding|1/1|c.954C>A|p.Pro318Pro|954/1107|954/1107|318/368||,A|upstream_gene_variant|MODIFIER|hisF1|PA14_67880|transcript|ABJ14523.1|protein_coding||c.-4074G>T|||||4074|,A|upstream_gene_variant|MODIFIER|hisA|PA14_67890|transcript|ABJ14524.1|protein_coding||c.-3326G>T|||||3326|,A|upstream_gene_variant|MODIFIER|PA14_67900|PA14_67900|transcript|ABJ14525.1|protein_coding||c.-3017G>T|||||3017|,A|upstream_gene_variant|MODIFIER|hisH1|PA14_67920|transcript|ABJ14526.1|protein_coding||c.-2372G>T|||||2372|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|hisB|PA14_67930|transcript|ABJ14527.1|protein_coding||c.-1782G>T|||||1782|,A|upstream_gene_variant|MODIFIER|PA14_67975|PA14_67975|transcript|ABJ15696.1|protein_coding||c.-247C>A|||||247|,A|upstream_gene_variant|MODIFIER|mutY|PA14_67990|transcript|ABJ14531.1|protein_coding||c.-2496C>A|||||2496|,A|upstream_gene_variant|MODIFIER|PA14_68000|PA14_68000|transcript|ABJ14532.1|protein_coding||c.-3607C>A|||||3607|,A|downstream_gene_variant|MODIFIER|PA14_67940|PA14_67940|transcript|ABJ14528.1|protein_coding||c.*1223C>A|||||1223|,A|downstream_gene_variant|MODIFIER|PA14_67960|PA14_67960|transcript|ABJ14529.1|protein_coding||c.*950C>A|||||950| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:72:0:0:0,-6.83637 0:1:1,0:1:38:0:0:0,-3.79727 0:6:6,1:5:161:1:15:0,-13.3015 0:4:4,2:2:56:2:16:0,-3.79589 +Chromosome 6070078 . T C 238.807 . AB=0;ABP=0;AC=3;AF=1;AN=3;AO=9;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=3.25157;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=39.4444;MQMR=0;NS=3;NUMALT=1;ODDS=24.5175;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=342;QR=0;RO=0;RPL=3;RPP=5.18177;RPPR=0;RPR=6;RUN=1;SAF=1;SAP=14.8328;SAR=8;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=C|upstream_gene_variant|MODIFIER|PA14_68030|PA14_68030|transcript|PA14_68030-1.1|protein_coding||c.-653T>C|||||653|WARNING_TRANSCRIPT_INCOMPLETE,C|upstream_gene_variant|MODIFIER|PA14_68050|PA14_68050|transcript|ABJ14534.1|protein_coding||c.-1681T>C|||||1681|,C|upstream_gene_variant|MODIFIER|PA14_68060|PA14_68060|transcript|ABJ14535.1|protein_coding||c.-2619T>C|||||2619|,C|upstream_gene_variant|MODIFIER|PA14_68070|PA14_68070|transcript|ABJ14536.1|protein_coding||c.-3407T>C|||||3407|,C|upstream_gene_variant|MODIFIER|PA14_68080|PA14_68080|transcript|ABJ14537.1|protein_coding||c.-4221T>C|||||4221|,C|upstream_gene_variant|MODIFIER|PA14_68090|PA14_68090|transcript|ABJ14538.1|protein_coding||c.-4913T>C|||||4913|,C|downstream_gene_variant|MODIFIER|PA14_67970|PA14_67970|transcript|ABJ14530.1|protein_coding||c.*4300T>C|||||4300|,C|downstream_gene_variant|MODIFIER|PA14_67975|PA14_67975|transcript|ABJ15696.1|protein_coding||c.*1954T>C|||||1954|,C|downstream_gene_variant|MODIFIER|mutY|PA14_67990|transcript|ABJ14531.1|protein_coding||c.*890T>C|||||890|,C|downstream_gene_variant|MODIFIER|PA14_68000|PA14_68000|transcript|ABJ14532.1|protein_coding||c.*574T>C|||||574|,C|downstream_gene_variant|MODIFIER|tRNA|EBG00001225092|transcript|EBT00001793489.1|protein_coding||c.*653A>G|||||653|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|fixR|PA14_68040|transcript|ABJ14533.1|protein_coding||c.*785A>G|||||785|,C|intergenic_region|MODIFIER|PA14_68000-tRNA|PA14_68000-EBG00001225092|intergenic_region|PA14_68000-EBG00001225092|||n.6070078T>C|||||| GT:DP:DPR:RO:QR:AO:QA:GL 1:2:2,2:0:0:2:79:-6.65281,0 . 1:3:3,3:0:0:3:113:-9.21893,0 1:4:4,4:0:0:4:150:-11.1579,0 +Chromosome 6070266 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=29;DPB=29;DPRA=1.57895;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=46.2314;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=942;RO=27;RPL=1;RPP=3.0103;RPPR=5.02092;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=5;SRP=26.2531;SRR=22;TYPE=snp;technology.ILLUMINA=1;ANN=T|upstream_gene_variant|MODIFIER|PA14_68030|PA14_68030|transcript|PA14_68030-1.1|protein_coding||c.-465C>T|||||465|WARNING_TRANSCRIPT_INCOMPLETE,T|upstream_gene_variant|MODIFIER|PA14_68050|PA14_68050|transcript|ABJ14534.1|protein_coding||c.-1493C>T|||||1493|,T|upstream_gene_variant|MODIFIER|PA14_68060|PA14_68060|transcript|ABJ14535.1|protein_coding||c.-2431C>T|||||2431|,T|upstream_gene_variant|MODIFIER|PA14_68070|PA14_68070|transcript|ABJ14536.1|protein_coding||c.-3219C>T|||||3219|,T|upstream_gene_variant|MODIFIER|PA14_68080|PA14_68080|transcript|ABJ14537.1|protein_coding||c.-4033C>T|||||4033|,T|upstream_gene_variant|MODIFIER|PA14_68090|PA14_68090|transcript|ABJ14538.1|protein_coding||c.-4725C>T|||||4725|,T|downstream_gene_variant|MODIFIER|PA14_67970|PA14_67970|transcript|ABJ14530.1|protein_coding||c.*4488C>T|||||4488|,T|downstream_gene_variant|MODIFIER|PA14_67975|PA14_67975|transcript|ABJ15696.1|protein_coding||c.*2142C>T|||||2142|,T|downstream_gene_variant|MODIFIER|mutY|PA14_67990|transcript|ABJ14531.1|protein_coding||c.*1078C>T|||||1078|,T|downstream_gene_variant|MODIFIER|PA14_68000|PA14_68000|transcript|ABJ14532.1|protein_coding||c.*762C>T|||||762|,T|downstream_gene_variant|MODIFIER|tRNA|EBG00001225092|transcript|EBT00001793489.1|protein_coding||c.*465G>A|||||465|WARNING_TRANSCRIPT_INCOMPLETE,T|downstream_gene_variant|MODIFIER|fixR|PA14_68040|transcript|ABJ14533.1|protein_coding||c.*597G>A|||||597|,T|intergenic_region|MODIFIER|PA14_68000-tRNA|PA14_68000-EBG00001225092|intergenic_region|PA14_68000-EBG00001225092|||n.6070266C>T|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,0:9:282:0:0:0,-25.6792 0:6:6,0:6:226:0:0:0,-20.6995 0:4:4,0:4:153:0:0:0,-14.1414 0:10:10,2:8:281:2:31:0,-22.6772 +Chromosome 6080493 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=7;CIGAR=1X;DP=52;DPB=52;DPRA=0;EPP=18.2106;EPPR=11.1654;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=77.3057;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=1504;RO=45;RPL=7;RPP=18.2106;RPPR=33.1696;RPR=0;RUN=1;SAF=7;SAP=18.2106;SAR=0;SRF=22;SRP=3.05855;SRR=23;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|emrA|PA14_68130|transcript|ABJ14542.1|protein_coding|1/1|c.1151T>C|p.Leu384Pro|1151/1185|1151/1185|384/394||,C|upstream_gene_variant|MODIFIER|emrB|PA14_68140|transcript|ABJ14543.1|protein_coding||c.-45T>C|||||45|,C|upstream_gene_variant|MODIFIER|PA14_68150|PA14_68150|transcript|PA14_68150-1.1|protein_coding||c.-1648T>C|||||1648|WARNING_TRANSCRIPT_INCOMPLETE,C|upstream_gene_variant|MODIFIER|rmlB|PA14_68170|transcript|ABJ14544.1|protein_coding||c.-1959T>C|||||1959|,C|upstream_gene_variant|MODIFIER|rmlD|PA14_68190|transcript|ABJ14545.1|protein_coding||c.-3014T>C|||||3014|,C|upstream_gene_variant|MODIFIER|rmlA|PA14_68200|transcript|ABJ14546.1|protein_coding||c.-3919T>C|||||3919|,C|upstream_gene_variant|MODIFIER|rmlC|PA14_68210|transcript|ABJ14547.1|protein_coding||c.-4800T>C|||||4800|,C|downstream_gene_variant|MODIFIER|PA14_68090|PA14_68090|transcript|ABJ14538.1|protein_coding||c.*4810T>C|||||4810|,C|downstream_gene_variant|MODIFIER|PA14_68100|PA14_68100|transcript|ABJ14539.1|protein_coding||c.*3521T>C|||||3521|,C|downstream_gene_variant|MODIFIER|PA14_68110|PA14_68110|transcript|ABJ14540.1|protein_coding||c.*2647T>C|||||2647|,C|downstream_gene_variant|MODIFIER|opmG|PA14_68120|transcript|ABJ14541.1|protein_coding||c.*1165T>C|||||1165|,C|downstream_gene_variant|MODIFIER|tRNA|EBG00001225048|transcript|EBT00001793470.1|protein_coding||c.*1648A>G|||||1648|WARNING_TRANSCRIPT_INCOMPLETE GT:DP:DPR:RO:QR:AO:QA:GL 0:11:11,2:9:318:2:17:0,-27.3373 0:11:11,1:10:345:1:2:0,-31.1682 0:15:15,1:14:469:1:2:0,-42.3194 0:15:15,3:12:372:3:6:0,-33.2041 +Chromosome 6112800 . C G 6.22293E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=58;DPB=58;DPRA=0.633333;EPP=13.8677;EPPR=3.05127;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=70.6833;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=62;QR=1903;RO=53;RPL=0;RPP=13.8677;RPPR=9.93443;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=27;SRP=3.05127;SRR=26;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|PA14_68510|PA14_68510|transcript|ABJ14571.1|protein_coding|1/1|c.309G>C|p.Pro103Pro|309/1791|309/1791|103/596||,G|upstream_gene_variant|MODIFIER|PA14_68470|PA14_68470|transcript|ABJ14567.1|protein_coding||c.-3901G>C|||||3901|,G|upstream_gene_variant|MODIFIER|PA14_68490|PA14_68490|transcript|ABJ14569.1|protein_coding||c.-2695G>C|||||2695|,G|upstream_gene_variant|MODIFIER|attL|PA14_68500|transcript|ABJ14570.1|protein_coding||c.-1509G>C|||||1509|,G|upstream_gene_variant|MODIFIER|PA14_68550|PA14_68550|transcript|ABJ14573.1|protein_coding||c.-1688C>G|||||1688|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_68570|PA14_68570|transcript|ABJ14575.1|protein_coding||c.-3465C>G|||||3465|,G|downstream_gene_variant|MODIFIER|PA14_68450|PA14_68450|transcript|ABJ14565.1|protein_coding||c.*4690C>G|||||4690|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_68460|PA14_68460|transcript|ABJ14566.1|protein_coding||c.*4185C>G|||||4185|,G|downstream_gene_variant|MODIFIER|PA14_68480|PA14_68480|transcript|ABJ14568.1|protein_coding||c.*3120C>G|||||3120|,G|downstream_gene_variant|MODIFIER|PA14_68530|PA14_68530|transcript|ABJ14572.1|protein_coding||c.*310G>C|||||310|,G|downstream_gene_variant|MODIFIER|drgA|PA14_68560|transcript|ABJ14574.1|protein_coding||c.*2611G>C|||||2611|,G|downstream_gene_variant|MODIFIER|pckA|PA14_68580|transcript|ABJ14576.1|protein_coding||c.*3878G>C|||||3878| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,1:8:259:1:15:0,-22.1234 0:15:15,1:14:500:1:15:0,-43.8222 0:20:20,0:20:753:0:0:0,-68.0914 0:14:14,3:11:391:3:32:0,-32.5308 +Chromosome 6123341 . C G 4.27967E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=46;DPB=46;DPRA=0.761905;EPP=13.8677;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=67.1194;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=1490;RO=41;RPL=0;RPP=13.8677;RPPR=4.33437;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=19;SRP=3.48696;SRR=22;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_68670|PA14_68670|transcript|ABJ14582.1|protein_coding|1/1|c.893C>G|p.Ala298Gly|893/924|893/924|298/307||,G|upstream_gene_variant|MODIFIER|hslO|PA14_68610|transcript|ABJ14577.1|protein_coding||c.-4113G>C|||||4113|,G|upstream_gene_variant|MODIFIER|hslR|PA14_68630|transcript|ABJ14579.1|protein_coding||c.-2764G>C|||||2764|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|tex|PA14_68710|transcript|ABJ14585.1|protein_coding||c.-2454C>G|||||2454|,G|upstream_gene_variant|MODIFIER|PA14_68720|PA14_68720|transcript|ABJ14586.1|protein_coding||c.-4805C>G|||||4805|,G|downstream_gene_variant|MODIFIER|PA14_68620|PA14_68620|transcript|ABJ14578.1|protein_coding||c.*3197C>G|||||3197|,G|downstream_gene_variant|MODIFIER|PA14_68640|PA14_68640|transcript|ABJ14580.1|protein_coding||c.*2120C>G|||||2120|,G|downstream_gene_variant|MODIFIER|rimK|PA14_68660|transcript|ABJ14581.1|protein_coding||c.*1083C>G|||||1083|,G|downstream_gene_variant|MODIFIER|envZ|PA14_68680|transcript|ABJ14583.1|protein_coding||c.*108G>C|||||108|,G|downstream_gene_variant|MODIFIER|ompR|PA14_68700|transcript|ABJ14584.1|protein_coding||c.*1522G>C|||||1522| GT:DP:DPR:RO:QR:AO:QA:GL 0:14:14,0:14:547:0:0:0,-49.5731 0:9:9,2:7:259:2:26:0,-21.1913 0:11:11,1:10:338:1:15:0,-29.2337 0:12:12,2:10:346:2:17:0,-29.8474 +Chromosome 6142798 . T C 6.5254E-12 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=20;DPB=20;DPRA=3;EPP=9.52472;EPPR=3.13803;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=27.255;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=45;QR=627;RO=17;RPL=3;RPP=9.52472;RPPR=3.13803;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=15;SRP=24.5973;SRR=2;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|gcvP1|PA14_68850|transcript|ABJ14597.1|protein_coding|1/1|c.473A>G|p.Glu158Gly|473/2877|473/2877|158/958||,C|downstream_gene_variant|MODIFIER|gspE|PA14_68820|transcript|ABJ14594.1|protein_coding||c.*3574T>C|||||3574|,C|downstream_gene_variant|MODIFIER|PA14_68830|PA14_68830|transcript|ABJ14595.1|protein_coding||c.*2900T>C|||||2900|,C|downstream_gene_variant|MODIFIER|PA14_68840|PA14_68840|transcript|ABJ14596.1|protein_coding||c.*2439T>C|||||2439|,C|downstream_gene_variant|MODIFIER|gcvH1|PA14_68860|transcript|ABJ14598.1|protein_coding||c.*646A>G|||||646|,C|downstream_gene_variant|MODIFIER|gcvT1|PA14_68870|transcript|ABJ14599.1|protein_coding||c.*1082A>G|||||1082|,C|downstream_gene_variant|MODIFIER|PA14_68890|PA14_68890|transcript|ABJ14600.1|protein_coding||c.*2315A>G|||||2315|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|fbpA|PA14_68900|transcript|ABJ14601.1|protein_coding||c.*4002A>G|||||4002| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:74:0:0:0,-7.02486 0:2:2,0:2:80:0:0:0,-7.59179 0:6:6,0:6:234:0:0:0,-21.4308 0:10:10,3:7:239:3:45:0,-17.6382 +Chromosome 6144696 . G T 4.80657E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=6;CIGAR=1X;DP=67;DPB=67;DPRA=0.681818;EPP=8.80089;EPPR=8.22183;GTI=0;LEN=1;MEANALT=1.33333;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=52.3133;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=53;QR=1893;RO=60;RPL=5;RPP=8.80089;RPPR=3.58936;RPR=1;RUN=1;SAF=6;SAP=16.0391;SAR=0;SRF=32;SRP=3.58936;SRR=28;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|gcvT1|PA14_68870|transcript|ABJ14599.1|protein_coding|1/1|c.267C>A|p.Leu89Leu|267/1083|267/1083|89/360||,T|upstream_gene_variant|MODIFIER|gcvP1|PA14_68850|transcript|ABJ14597.1|protein_coding||c.-1426C>A|||||1426|,T|upstream_gene_variant|MODIFIER|gcvH1|PA14_68860|transcript|ABJ14598.1|protein_coding||c.-863C>A|||||863|,T|upstream_gene_variant|MODIFIER|PA14_68930|PA14_68930|transcript|ABJ14603.1|protein_coding||c.-4181G>T|||||4181|,T|downstream_gene_variant|MODIFIER|PA14_68830|PA14_68830|transcript|ABJ14595.1|protein_coding||c.*4798G>T|||||4798|,T|downstream_gene_variant|MODIFIER|PA14_68840|PA14_68840|transcript|ABJ14596.1|protein_coding||c.*4337G>T|||||4337|,T|downstream_gene_variant|MODIFIER|PA14_68890|PA14_68890|transcript|ABJ14600.1|protein_coding||c.*417C>A|||||417|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|fbpA|PA14_68900|transcript|ABJ14601.1|protein_coding||c.*2104C>A|||||2104|,T|downstream_gene_variant|MODIFIER|PA14_68920|PA14_68920|transcript|ABJ14602.1|protein_coding||c.*3170C>A|||||3170| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,2:5:142:2:4:0,-12.6763 0:22:22,0:22:684:0:0:0,-61.8369 0:19:19,1:17:573:1:2:0,-51.6022 0:19:19,3:16:494:3:47:0,-40.361 +Chromosome 6154103 . A G 5.62241E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=7;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=18.2106;EPPR=13.3567;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=20.5795;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=87;QR=372;RO=17;RPL=0;RPP=18.2106;RPPR=3.13803;RPR=7;RUN=1;SAF=0;SAP=18.2106;SAR=7;SRF=7;SRP=4.1599;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|pepP|PA14_69000|transcript|ABJ14607.1|protein_coding|1/1|c.1124T>C|p.Leu375Pro|1124/1335|1124/1335|375/444||,G|upstream_gene_variant|MODIFIER|PA14_68955|PA14_68955|transcript|ABJ15675.1|protein_coding||c.-1919T>C|||||1919|,G|upstream_gene_variant|MODIFIER|PA14_68970|PA14_68970|transcript|ABJ14605.1|protein_coding||c.-1408T>C|||||1408|,G|upstream_gene_variant|MODIFIER|ubiH|PA14_68980|transcript|ABJ14606.1|protein_coding||c.-219T>C|||||219|,G|upstream_gene_variant|MODIFIER|PA14_69020|PA14_69020|transcript|ABJ14609.1|protein_coding||c.-1774A>G|||||1774|,G|upstream_gene_variant|MODIFIER|PA14_69030|PA14_69030|transcript|ABJ14610.1|protein_coding||c.-2082A>G|||||2082|,G|upstream_gene_variant|MODIFIER|PA14_69040|PA14_69040|transcript|ABJ14611.1|protein_coding||c.-2618A>G|||||2618|,G|upstream_gene_variant|MODIFIER|PA14_69050|PA14_69050|transcript|ABJ14612.1|protein_coding||c.-3596A>G|||||3596|,G|downstream_gene_variant|MODIFIER|PA14_68930|PA14_68930|transcript|ABJ14603.1|protein_coding||c.*4033A>G|||||4033|,G|downstream_gene_variant|MODIFIER|PA14_68940|PA14_68940|transcript|ABJ14604.1|protein_coding||c.*3173A>G|||||3173|,G|downstream_gene_variant|MODIFIER|PA14_69010|PA14_69010|transcript|ABJ14608.1|protein_coding||c.*1133T>C|||||1133|,G|downstream_gene_variant|MODIFIER|6S|EBG00001225146|transcript|EBT00001793497.1|lincRNA||n.*2430T>C|||||2430|,G|downstream_gene_variant|MODIFIER|yhhJ|PA14_69060|transcript|ABJ14613.1|protein_coding||c.*4064T>C|||||4064| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,4:2:55:4:46:0,-0.965917 0:4:4,1:3:81:1:12:0,-6.35277 0:9:9,1:8:164:1:14:0,-13.5569 0:5:5,1:4:72:1:15:0,-5.15958 +Chromosome 6171879 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=41;DPB=41;DPRA=1.1;EPP=9.52472;EPPR=11.239;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.9737;NS=4;NUMALT=1;ODDS=60.2497;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=29;QR=1330;RO=38;RPL=3;RPP=9.52472;RPPR=8.7247;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=21;SRP=3.9246;SRR=17;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|rho|PA14_69190|transcript|ABJ14622.1|protein_coding|1/1|c.459C>A|p.Ser153Ser|459/1260|459/1260|153/419||,T|upstream_gene_variant|MODIFIER|ubiB|PA14_69140|transcript|ABJ14619.1|protein_coding||c.-4405C>A|||||4405|,T|upstream_gene_variant|MODIFIER|ubiD|PA14_69150|transcript|ABJ14620.1|protein_coding||c.-2939C>A|||||2939|,T|upstream_gene_variant|MODIFIER|PA14_69170|PA14_69170|transcript|ABJ14621.1|protein_coding||c.-872C>A|||||872|,T|upstream_gene_variant|MODIFIER|ppx|PA14_69220|transcript|ABJ14624.1|protein_coding||c.-1213G>T|||||1213|,T|downstream_gene_variant|MODIFIER|trxA|PA14_69200|transcript|ABJ14623.1|protein_coding||c.*703C>A|||||703|,T|downstream_gene_variant|MODIFIER|ppk|PA14_69230|transcript|ABJ14625.1|protein_coding||c.*2720C>A|||||2720|,T|downstream_gene_variant|MODIFIER|hemB|PA14_69240|transcript|ABJ14626.1|protein_coding||c.*4948C>A|||||4948|WARNING_TRANSCRIPT_NO_START_CODON GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:209:0:0:0,-19.1484 0:7:7,0:7:267:0:0:0,-24.3916 0:11:11,3:8:311:3:29:0,-25.6468 0:17:17,0:17:543:0:0:0,-49.1571 +Chromosome 6175784 . G T 5.51475E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=7;CIGAR=1X;DP=84;DPB=84;DPRA=1.31373;EPP=10.7656;EPPR=11.1604;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7532;NS=4;NUMALT=1;ODDS=146.112;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=83;QR=2801;RO=77;RPL=6;RPP=10.7656;RPPR=20.6359;RPR=1;RUN=1;SAF=7;SAP=18.2106;SAR=0;SRF=12;SRP=82.2267;SRR=65;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|ppk|PA14_69230|transcript|ABJ14625.1|protein_coding|1/1|c.1026C>A|p.Val342Val|1026/2211|1026/2211|342/736||,T|upstream_gene_variant|MODIFIER|PA14_69170|PA14_69170|transcript|ABJ14621.1|protein_coding||c.-4777C>A|||||4777|,T|upstream_gene_variant|MODIFIER|rho|PA14_69190|transcript|ABJ14622.1|protein_coding||c.-3447C>A|||||3447|,T|upstream_gene_variant|MODIFIER|trxA|PA14_69200|transcript|ABJ14623.1|protein_coding||c.-2876C>A|||||2876|,T|upstream_gene_variant|MODIFIER|PA14_69250|PA14_69250|transcript|ABJ14627.1|protein_coding||c.-2300G>T|||||2300|,T|upstream_gene_variant|MODIFIER|elbB|PA14_69260|transcript|ABJ14628.1|protein_coding||c.-3055G>T|||||3055|,T|upstream_gene_variant|MODIFIER|PA14_69270|PA14_69270|transcript|ABJ14629.1|protein_coding||c.-3819G>T|||||3819|,T|downstream_gene_variant|MODIFIER|ppx|PA14_69220|transcript|ABJ14624.1|protein_coding||c.*1172G>T|||||1172|,T|downstream_gene_variant|MODIFIER|hemB|PA14_69240|transcript|ABJ14626.1|protein_coding||c.*1043C>A|||||1043|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|PA14_69280|PA14_69280|transcript|ABJ14630.1|protein_coding||c.*4277C>A|||||4277|,T|downstream_gene_variant|MODIFIER|PA14_69300|PA14_69300|transcript|ABJ14631.1|protein_coding||c.*4826C>A|||||4826| GT:DP:DPR:RO:QR:AO:QA:GL 0:17:17,0:17:619:0:0:0,-56.0212 0:21:21,1:20:714:1:15:0,-63.0577 0:23:23,1:22:801:1:16:0,-70.787 0:23:23,5:18:667:5:52:0,-55.5575 +Chromosome 6182952 . C A 2.86365E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=45;DPB=45;DPRA=1.0303;EPP=13.8677;EPPR=3.87889;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=33.1508;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=64;QR=1123;RO=40;RPL=0;RPP=13.8677;RPPR=8.43898;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=19;SRP=3.22745;SRR=21;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|PA14_69310|PA14_69310|transcript|ABJ14632.1|protein_coding|1/1|c.294G>T|p.Leu98Phe|294/630|294/630|98/209||,A|upstream_gene_variant|MODIFIER|PA14_69280|PA14_69280|transcript|ABJ14630.1|protein_coding||c.-2409G>T|||||2409|,A|upstream_gene_variant|MODIFIER|PA14_69300|PA14_69300|transcript|ABJ14631.1|protein_coding||c.-441G>T|||||441|,A|upstream_gene_variant|MODIFIER|PA14_69350|PA14_69350|transcript|ABJ14636.1|protein_coding||c.-3828C>A|||||3828|,A|downstream_gene_variant|MODIFIER|PA14_69250|PA14_69250|transcript|ABJ14627.1|protein_coding||c.*4278C>A|||||4278|,A|downstream_gene_variant|MODIFIER|elbB|PA14_69260|transcript|ABJ14628.1|protein_coding||c.*3445C>A|||||3445|,A|downstream_gene_variant|MODIFIER|PA14_69270|PA14_69270|transcript|ABJ14629.1|protein_coding||c.*2876C>A|||||2876|,A|downstream_gene_variant|MODIFIER|PA14_69320|PA14_69320|transcript|ABJ14633.1|protein_coding||c.*523G>T|||||523|,A|downstream_gene_variant|MODIFIER|PA14_69330|PA14_69330|transcript|ABJ14634.1|protein_coding||c.*1288G>T|||||1288|,A|downstream_gene_variant|MODIFIER|PA14_69340|PA14_69340|transcript|ABJ14635.1|protein_coding||c.*1866G>T|||||1866|,A|downstream_gene_variant|MODIFIER|algP|PA14_69370|transcript|ABJ14637.1|protein_coding||c.*4304G>T|||||4304| GT:DP:DPR:RO:QR:AO:QA:GL 0:13:13,1:12:344:1:15:0,-29.7316 0:9:9,3:6:119:3:47:0,-6.51848 0:12:12,1:11:331:1:2:0,-29.873 0:11:11,0:11:329:0:0:0,-29.8925 +Chromosome 6203118 . T C 2.92335E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=36;DPB=36;DPRA=1.76923;EPP=3.73412;EPPR=6.23461;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=56.4477;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=93;QR=1144;RO=33;RPL=2;RPP=3.73412;RPPR=10.9724;RPR=1;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=23;SRP=14.1309;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_69540|PA14_69540|transcript|ABJ14650.1|protein_coding|1/1|c.746A>G|p.Glu249Gly|746/882|746/882|249/293||,C|upstream_gene_variant|MODIFIER|PA14_69510|PA14_69510|transcript|ABJ14648.1|protein_coding||c.-3710A>G|||||3710|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_69520|PA14_69520|transcript|ABJ14649.1|protein_coding||c.-133A>G|||||133|,C|upstream_gene_variant|MODIFIER|PA14_69580|PA14_69580|transcript|ABJ14654.1|protein_coding||c.-4867T>C|||||4867|,C|downstream_gene_variant|MODIFIER|argH|PA14_69500|transcript|ABJ14647.1|protein_coding||c.*4914T>C|||||4914|,C|downstream_gene_variant|MODIFIER|PA14_69550|PA14_69550|transcript|ABJ14651.1|protein_coding||c.*735A>G|||||735|,C|downstream_gene_variant|MODIFIER|hcpB|PA14_69560|transcript|ABJ14652.1|protein_coding||c.*2974A>G|||||2974|,C|downstream_gene_variant|MODIFIER|corA|PA14_69570|transcript|ABJ14653.1|protein_coding||c.*3785A>G|||||3785| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:265:0:0:0,-24.2086 0:14:14,1:13:432:1:39:0,-35.2918 0:6:6,0:6:186:0:0:0,-17.0372 0:9:9,2:7:261:2:54:0,-18.7183 +Chromosome 6217921 . G C 1.9496E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=31;DPB=31;DPRA=0.606061;EPP=11.6962;EPPR=3.34437;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=30.7616;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=948;RO=26;RPL=4;RPP=11.6962;RPPR=4.34659;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=13;SRP=3.0103;SRR=13;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|sss|PA14_69710|transcript|ABJ14665.1|protein_coding|1/1|c.395G>C|p.Arg132Pro|395/912|395/912|132/303||,C|upstream_gene_variant|MODIFIER|rnk|PA14_69630|transcript|ABJ14659.1|protein_coding||c.-4297C>G|||||4297|,C|upstream_gene_variant|MODIFIER|cyaY|PA14_69640|transcript|ABJ14660.1|protein_coding||c.-3639C>G|||||3639|,C|upstream_gene_variant|MODIFIER|PA14_69720|PA14_69720|transcript|ABJ14666.1|protein_coding||c.-514G>C|||||514|,C|upstream_gene_variant|MODIFIER|PA14_69750|PA14_69750|transcript|ABJ14668.1|protein_coding||c.-2575G>C|||||2575|,C|downstream_gene_variant|MODIFIER|PA14_69620|PA14_69620|transcript|ABJ14658.1|protein_coding||c.*4745G>C|||||4745|,C|downstream_gene_variant|MODIFIER|rnk_pseudo|EBG00001225014|transcript|EBT00001793472.1|lincRNA||n.*4136G>C|||||4136|,C|downstream_gene_variant|MODIFIER|lppL|PA14_69660|transcript|ABJ14661.1|protein_coding||c.*3245G>C|||||3245|,C|downstream_gene_variant|MODIFIER|lysA|PA14_69670|transcript|ABJ14662.1|protein_coding||c.*1987G>C|||||1987|,C|downstream_gene_variant|MODIFIER|dapF|PA14_69690|transcript|ABJ14663.1|protein_coding||c.*1146G>C|||||1146|,C|downstream_gene_variant|MODIFIER|PA14_69700|PA14_69700|transcript|ABJ14664.1|protein_coding||c.*414G>C|||||414|,C|downstream_gene_variant|MODIFIER|PA14_69740|PA14_69740|transcript|ABJ14667.1|protein_coding||c.*1243C>G|||||1243|,C|downstream_gene_variant|MODIFIER|PA14_69760|PA14_69760|transcript|ABJ14669.1|protein_coding||c.*3976C>G|||||3976| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,1:2:75:1:2:0,-6.91959 0:7:7,1:6:212:1:2:0,-19.2151 0:10:10,2:8:295:2:4:0,-26.5191 0:11:11,0:10:366:0:0:0,-33.2306 +Chromosome 6223771 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=57;DPB=57;DPRA=0.965517;EPP=9.52472;EPPR=3.6537;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=55.2652;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=48;QR=1525;RO=54;RPL=0;RPP=9.52472;RPPR=7.03155;RPR=3;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=45;SRP=55.1256;SRR=9;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_69780|PA14_69780|transcript|ABJ14671.1|protein_coding|1/1|c.298C>A|p.Gln100Lys|298/426|298/426|100/141||,T|upstream_gene_variant|MODIFIER|PA14_69740|PA14_69740|transcript|ABJ14667.1|protein_coding||c.-3438C>A|||||3438|,T|upstream_gene_variant|MODIFIER|PA14_69760|PA14_69760|transcript|ABJ14669.1|protein_coding||c.-960C>A|||||960|,T|upstream_gene_variant|MODIFIER|PA14_69770|PA14_69770|transcript|ABJ14670.1|protein_coding||c.-206C>A|||||206|,T|upstream_gene_variant|MODIFIER|PA14_69820|PA14_69820|transcript|ABJ14673.1|protein_coding||c.-2704G>T|||||2704|,T|upstream_gene_variant|MODIFIER|PA14_69840|PA14_69840|transcript|ABJ14674.1|protein_coding||c.-3005G>T|||||3005|,T|upstream_gene_variant|MODIFIER|betT|PA14_69850|transcript|ABJ14675.1|protein_coding||c.-4623G>T|||||4623|,T|downstream_gene_variant|MODIFIER|PA14_69720|PA14_69720|transcript|ABJ14666.1|protein_coding||c.*4638G>T|||||4638|,T|downstream_gene_variant|MODIFIER|PA14_69750|PA14_69750|transcript|ABJ14668.1|protein_coding||c.*1899G>T|||||1899|,T|downstream_gene_variant|MODIFIER|amtB|PA14_69795|transcript|ABJ15656.1|protein_coding||c.*558C>A|||||558|,T|downstream_gene_variant|MODIFIER|glnK|PA14_69810|transcript|ABJ14672.1|protein_coding||c.*1926C>A|||||1926| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,2:8:210:2:32:0,-16.1137 0:18:18,1:17:478:1:16:0,-41.6831 0:15:15,0:15:445:0:0:0,-40.327 0:14:14,0:14:392:0:0:0,-35.544 +Chromosome 6227171 . A C 4.30852E-12 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=20;DPB=20;DPRA=2;EPP=7.35324;EPPR=10.7311;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=27.6405;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=23;QR=603;RO=18;RPL=2;RPP=7.35324;RPPR=10.7311;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=10;SRP=3.49285;SRR=8;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|PA14_69840|PA14_69840|transcript|ABJ14674.1|protein_coding|1/1|c.396A>C|p.Ala132Ala|396/1494|396/1494|132/497||,C|upstream_gene_variant|MODIFIER|PA14_69760|PA14_69760|transcript|ABJ14669.1|protein_coding||c.-4360T>G|||||4360|,C|upstream_gene_variant|MODIFIER|PA14_69770|PA14_69770|transcript|ABJ14670.1|protein_coding||c.-3606T>G|||||3606|,C|upstream_gene_variant|MODIFIER|PA14_69780|PA14_69780|transcript|ABJ14671.1|protein_coding||c.-3103T>G|||||3103|,C|upstream_gene_variant|MODIFIER|amtB|PA14_69795|transcript|ABJ15656.1|protein_coding||c.-1514T>G|||||1514|,C|upstream_gene_variant|MODIFIER|glnK|PA14_69810|transcript|ABJ14672.1|protein_coding||c.-1136T>G|||||1136|,C|upstream_gene_variant|MODIFIER|betT|PA14_69850|transcript|ABJ14675.1|protein_coding||c.-1223A>C|||||1223|,C|downstream_gene_variant|MODIFIER|PA14_69820|PA14_69820|transcript|ABJ14673.1|protein_coding||c.*436A>C|||||436|,C|downstream_gene_variant|MODIFIER|pchP|PA14_69870|transcript|ABJ14676.1|protein_coding||c.*3251T>G|||||3251|,C|downstream_gene_variant|MODIFIER|PA14_69880|PA14_69880|transcript|ABJ14677.1|protein_coding||c.*4451T>G|||||4451| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:117:0:0:0,-10.9104 0:3:3,0:3:78:0:0:0,-7.27658 0:6:6,0:6:230:0:0:0,-21.0656 0:8:8,2:6:178:2:23:0,-14.1197 +Chromosome 6244944 . T C 5.61973E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=19;DPB=19;DPRA=0.9;EPP=9.52472;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=20.4655;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=534;RO=16;RPL=3;RPP=9.52472;RPPR=3.55317;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=13;SRP=16.582;SRR=3;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|dadX|PA14_69990|transcript|ABJ14685.1|protein_coding|1/1|c.65A>G|p.Glu22Gly|65/1074|65/1074|22/357||,C|upstream_gene_variant|MODIFIER|PA14_69950|PA14_69950|transcript|ABJ14682.1|protein_coding||c.-2550A>G|||||2550|,C|upstream_gene_variant|MODIFIER|cycB|PA14_69970|transcript|ABJ14683.1|protein_coding||c.-1930A>G|||||1930|,C|upstream_gene_variant|MODIFIER|PA14_69980|PA14_69980|transcript|ABJ14684.1|protein_coding||c.-1160A>G|||||1160|,C|downstream_gene_variant|MODIFIER|xpt|PA14_69940|transcript|ABJ14681.1|protein_coding||c.*4417T>C|||||4417|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_70010|PA14_70010|transcript|ABJ14686.1|protein_coding||c.*155A>G|||||155|,C|downstream_gene_variant|MODIFIER|dadA|PA14_70040|transcript|ABJ14687.1|protein_coding||c.*483A>G|||||483|,C|downstream_gene_variant|MODIFIER|PA14_70050|PA14_70050|transcript|ABJ14688.1|protein_coding||c.*2138A>G|||||2138|,C|downstream_gene_variant|MODIFIER|PA14_70060|PA14_70060|transcript|ABJ14689.1|protein_coding||c.*2495A>G|||||2495|,C|downstream_gene_variant|MODIFIER|PA14_70070|PA14_70070|transcript|ABJ14690.1|protein_coding||c.*2707A>G|||||2707| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:239:0:0:0,-21.8384 0:3:3,1:2:51:1:15:0,-3.34294 0:6:6,2:4:135:2:4:0,-12.1023 0:3:3,0:3:109:0:0:0,-10.1657 +Chromosome 6277129 . T C 7.3982E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=35;DPB=35;DPRA=1.03846;EPP=3.0103;EPPR=5.45321;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=57.7008;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=41;QR=1059;RO=32;RPL=2;RPP=7.35324;RPPR=7.35324;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=21;SRP=9.79615;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=C|upstream_gene_variant|MODIFIER|PA14_70330|PA14_70330|transcript|ABJ14710.1|protein_coding||c.-4534A>G|||||4534|,C|upstream_gene_variant|MODIFIER|PA14_70340|PA14_70340|transcript|ABJ14711.1|protein_coding||c.-4067A>G|||||4067|,C|upstream_gene_variant|MODIFIER|PA14_70360|PA14_70360|transcript|ABJ14713.1|protein_coding||c.-2832A>G|||||2832|,C|upstream_gene_variant|MODIFIER|pyrE|PA14_70370|transcript|ABJ14714.1|protein_coding||c.-2170A>G|||||2170|,C|upstream_gene_variant|MODIFIER|PA14_70400|PA14_70400|transcript|ABJ14716.1|protein_coding||c.-880A>G|||||880|,C|upstream_gene_variant|MODIFIER|rph|PA14_70420|transcript|ABJ14717.1|protein_coding||c.-114A>G|||||114|,C|upstream_gene_variant|MODIFIER|yicC|PA14_70430|transcript|ABJ14718.1|protein_coding||c.-67T>C|||||67|,C|upstream_gene_variant|MODIFIER|gmk|PA14_70440|transcript|ABJ14719.1|protein_coding||c.-989T>C|||||989|,C|upstream_gene_variant|MODIFIER|rpoZ|PA14_70450|transcript|ABJ14720.1|protein_coding||c.-1689T>C|||||1689|,C|upstream_gene_variant|MODIFIER|spoT|PA14_70470|transcript|ABJ14721.1|protein_coding||c.-2021T>C|||||2021|,C|upstream_gene_variant|MODIFIER|PA14_70480|PA14_70480|transcript|ABJ14722.1|protein_coding||c.-4188T>C|||||4188|,C|upstream_gene_variant|MODIFIER|PA14_70490|PA14_70490|transcript|ABJ14723.1|protein_coding||c.-4623T>C|||||4623|,C|downstream_gene_variant|MODIFIER|PA14_70350|PA14_70350|transcript|ABJ14712.1|protein_coding||c.*3429T>C|||||3429|,C|downstream_gene_variant|MODIFIER|crc|PA14_70390|transcript|ABJ14715.1|protein_coding||c.*1310T>C|||||1310|,C|intergenic_region|MODIFIER|rph-yicC|PA14_70420-PA14_70430|intergenic_region|PA14_70420-PA14_70430|||n.6277129T>C|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,2:7:247:2:41:0,-18.6724 0:7:7,0:6:206:0:0:0,-18.6882 0:8:8,0:8:212:0:0:0,-19.3285 0:11:11,0:11:394:0:0:0,-35.7892 +Chromosome 6282558 . C A 9.87477E-4 . AB=0;ABP=0;AC=0;AF=0;AN=3;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=5;EPP=7.35324;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=8.62549;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=57;RO=5;RPL=0;RPP=7.35324;RPPR=3.44459;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=13.8677;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|PA14_70510|PA14_70510|transcript|ABJ14724.1|protein_coding|1/1|c.553G>T|p.Ala185Ser|553/621|553/621|185/206||,A|upstream_gene_variant|MODIFIER|PA14_70560|PA14_70560|transcript|ABJ14727.1|protein_coding||c.-2408C>A|||||2408|,A|upstream_gene_variant|MODIFIER|recG|PA14_70570|transcript|ABJ14728.1|protein_coding||c.-3337C>A|||||3337|,A|downstream_gene_variant|MODIFIER|yicC|PA14_70430|transcript|ABJ14718.1|protein_coding||c.*4499C>A|||||4499|,A|downstream_gene_variant|MODIFIER|gmk|PA14_70440|transcript|ABJ14719.1|protein_coding||c.*3829C>A|||||3829|,A|downstream_gene_variant|MODIFIER|rpoZ|PA14_70450|transcript|ABJ14720.1|protein_coding||c.*3474C>A|||||3474|,A|downstream_gene_variant|MODIFIER|spoT|PA14_70470|transcript|ABJ14721.1|protein_coding||c.*1303C>A|||||1303|,A|downstream_gene_variant|MODIFIER|PA14_70480|PA14_70480|transcript|ABJ14722.1|protein_coding||c.*861C>A|||||861|,A|downstream_gene_variant|MODIFIER|PA14_70490|PA14_70490|transcript|ABJ14723.1|protein_coding||c.*75C>A|||||75|,A|downstream_gene_variant|MODIFIER|PA14_70530|PA14_70530|transcript|ABJ14725.1|protein_coding||c.*619G>T|||||619|,A|downstream_gene_variant|MODIFIER|PA14_70550|PA14_70550|transcript|ABJ14726.1|protein_coding||c.*1419G>T|||||1419| GT:DP:DPR:RO:QR:AO:QA:GL . 0:1:1,0:1:16:0:0:0,-1.59998 0:1:1,0:1:2:0:0:0,-0.2 0:5:5,2:3:39:2:4:0,-3.25872 +Chromosome 6283327 . C A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=50;DPB=50;DPRA=1.27273;EPP=3.44459;EPPR=3.05855;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=42.9923;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=61;QR=1402;RO=45;RPL=2;RPP=3.44459;RPPR=8.84915;RPR=3;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=10;SRP=33.1696;SRR=35;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|PA14_70530|PA14_70530|transcript|ABJ14725.1|protein_coding|1/1|c.651G>T|p.Val217Val|651/801|651/801|217/266||,A|upstream_gene_variant|MODIFIER|PA14_70510|PA14_70510|transcript|ABJ14724.1|protein_coding||c.-217G>T|||||217|,A|upstream_gene_variant|MODIFIER|PA14_70560|PA14_70560|transcript|ABJ14727.1|protein_coding||c.-1639C>A|||||1639|,A|upstream_gene_variant|MODIFIER|recG|PA14_70570|transcript|ABJ14728.1|protein_coding||c.-2568C>A|||||2568|,A|upstream_gene_variant|MODIFIER|PA14_70580|PA14_70580|transcript|ABJ14729.1|protein_coding||c.-4733C>A|||||4733|,A|downstream_gene_variant|MODIFIER|gmk|PA14_70440|transcript|ABJ14719.1|protein_coding||c.*4598C>A|||||4598|,A|downstream_gene_variant|MODIFIER|rpoZ|PA14_70450|transcript|ABJ14720.1|protein_coding||c.*4243C>A|||||4243|,A|downstream_gene_variant|MODIFIER|spoT|PA14_70470|transcript|ABJ14721.1|protein_coding||c.*2072C>A|||||2072|,A|downstream_gene_variant|MODIFIER|PA14_70480|PA14_70480|transcript|ABJ14722.1|protein_coding||c.*1630C>A|||||1630|,A|downstream_gene_variant|MODIFIER|PA14_70490|PA14_70490|transcript|ABJ14723.1|protein_coding||c.*844C>A|||||844|,A|downstream_gene_variant|MODIFIER|PA14_70550|PA14_70550|transcript|ABJ14726.1|protein_coding||c.*650G>T|||||650| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:137:0:0:0,-12.6661 0:20:20,3:17:541:3:31:0,-46.0859 0:18:18,0:18:585:0:0:0,-52.9478 0:8:8,2:6:139:2:30:0,-9.88916 +Chromosome 6289057 . T G 1.72571E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=32;DPB=32;DPRA=1.36364;EPP=7.35324;EPPR=7.64277;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=65.0169;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=29;QR=1162;RO=30;RPL=0;RPP=7.35324;RPPR=5.61607;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=25;SRP=31.9633;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_70580|PA14_70580|transcript|ABJ14729.1|protein_coding|1/1|c.998T>G|p.Leu333Arg|998/1410|998/1410|333/469||,G|upstream_gene_variant|MODIFIER|PA14_70550|PA14_70550|transcript|ABJ14726.1|protein_coding||c.-4229A>C|||||4229|,G|downstream_gene_variant|MODIFIER|PA14_70560|PA14_70560|transcript|ABJ14727.1|protein_coding||c.*3159T>G|||||3159|,G|downstream_gene_variant|MODIFIER|recG|PA14_70570|transcript|ABJ14728.1|protein_coding||c.*1087T>G|||||1087|,G|downstream_gene_variant|MODIFIER|PA14_70590|PA14_70590|transcript|ABJ14730.1|protein_coding||c.*484A>C|||||484|,G|downstream_gene_variant|MODIFIER|hupA|PA14_70600|transcript|ABJ14731.1|protein_coding||c.*1012A>C|||||1012|,G|downstream_gene_variant|MODIFIER|rubB|PA14_70620|transcript|ABJ14732.1|protein_coding||c.*1486A>C|||||1486|,G|downstream_gene_variant|MODIFIER|rubA2|PA14_70630|transcript|ABJ14733.1|protein_coding||c.*2692A>C|||||2692|,G|downstream_gene_variant|MODIFIER|rubA1|PA14_70640|transcript|ABJ14734.1|protein_coding||c.*3043A>C|||||3043|,G|downstream_gene_variant|MODIFIER|glcG|PA14_70650|transcript|ABJ14735.1|protein_coding||c.*3344A>C|||||3344|,G|downstream_gene_variant|MODIFIER|glcF|PA14_70670|transcript|ABJ14736.1|protein_coding||c.*3750A>C|||||3750|,G|downstream_gene_variant|MODIFIER|glcE|PA14_70680|transcript|ABJ14737.1|protein_coding||c.*4986A>C|||||4986| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:305:0:0:0,-27.8064 0:8:8,0:8:313:0:0:0,-28.534 0:10:10,2:8:314:2:29:0,-25.8695 0:6:6,0:6:230:0:0:0,-21.0631 +Chromosome 6308510 . C A 1.69139E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=22;DPB=22;DPRA=1.125;EPP=7.35324;EPPR=9.95901;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=38.7186;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=703;RO=20;RPL=0;RPP=7.35324;RPPR=13.8677;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=17;SRP=24.2907;SRR=3;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|pstA|PA14_70830|transcript|ABJ14750.1|protein_coding|1/1|c.146G>T|p.Trp49Leu|146/1677|146/1677|49/558||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|PA14_70780|PA14_70780|transcript|ABJ14746.1|protein_coding||c.-4342G>T|||||4342|,A|upstream_gene_variant|MODIFIER|PA14_70790|PA14_70790|transcript|ABJ14747.1|protein_coding||c.-3323G>T|||||3323|,A|upstream_gene_variant|MODIFIER|phoU|PA14_70800|transcript|ABJ14748.1|protein_coding||c.-2476G>T|||||2476|,A|upstream_gene_variant|MODIFIER|pstB|PA14_70810|transcript|ABJ14749.1|protein_coding||c.-1547G>T|||||1547|,A|upstream_gene_variant|MODIFIER|5S_rRNA|EBG00001225130|transcript|EBT00001793430.1|rRNA||n.-3996C>A|||||3996|,A|upstream_gene_variant|MODIFIER|LSU_rRNA_bacteria|EBG00001225047|transcript|EBT00001793475.1|rRNA||n.-4256C>A|||||4256|,A|upstream_gene_variant|MODIFIER|PK-G12rRNA|EBG00001225028|transcript|EBT00001793370.1|rRNA||n.-4770C>A|||||4770|,A|downstream_gene_variant|MODIFIER|pstC|PA14_70850|transcript|ABJ14751.1|protein_coding||c.*165G>T|||||165|,A|downstream_gene_variant|MODIFIER|PA14_70860|PA14_70860|transcript|ABJ14752.1|protein_coding||c.*2621G>T|||||2621|,A|downstream_gene_variant|MODIFIER|PA14_70870|PA14_70870|transcript|PA14_70870-1.1|rRNA||n.*3988G>T|||||3988|,A|downstream_gene_variant|MODIFIER|PA14_70880|PA14_70880|transcript|PA14_70880-1.1|rRNA||n.*4256G>T|||||4256| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,2:4:139:2:18:0,-11.14 0:4:4,0:4:135:0:0:0,-12.4755 0:6:6,0:6:220:0:0:0,-20.1526 0:6:6,0:6:209:0:0:0,-19.1423 +Chromosome 6321041 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=7;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=18.2106;EPPR=31.7922;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=98.7964;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=1981;RO=55;RPL=0;RPP=18.2106;RPPR=40.9518;RPR=7;RUN=1;SAF=0;SAP=18.2106;SAR=7;SRF=4;SRP=90.2245;SRR=51;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|betA|PA14_70940|transcript|ABJ14755.1|protein_coding|1/1|c.928T>C|p.Cys310Arg|928/1686|928/1686|310/561||,G|upstream_gene_variant|MODIFIER|PA14_70900|PA14_70900|transcript|PA14_70900-1.1|protein_coding||c.-4978T>C|||||4978|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,G|upstream_gene_variant|MODIFIER|PA14_70910|PA14_70910|transcript|PA14_70910-1.1|rRNA||n.-3387T>C|||||3387|,G|upstream_gene_variant|MODIFIER|PA14_70920|PA14_70920|transcript|ABJ14753.1|protein_coding||c.-1496T>C|||||1496|,G|upstream_gene_variant|MODIFIER|betT1|PA14_70980|transcript|ABJ14758.1|protein_coding||c.-3522A>G|||||3522|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|tRNA|EBG00001225079|transcript|EBT00001793417.1|protein_coding||c.*4978A>G|||||4978|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|SSU_rRNA_archaea|EBG00001225021|transcript|EBT00001793395.1|rRNA||n.*3383A>G|||||3383|,G|downstream_gene_variant|MODIFIER|PA14_70930|PA14_70930|transcript|ABJ14754.1|protein_coding||c.*804A>G|||||804|,G|downstream_gene_variant|MODIFIER|betB|PA14_70950|transcript|ABJ14756.1|protein_coding||c.*1063T>C|||||1063|,G|downstream_gene_variant|MODIFIER|betI|PA14_70970|transcript|ABJ14757.1|protein_coding||c.*2596T>C|||||2596| GT:DP:DPR:RO:QR:AO:QA:GL 0:14:14,2:12:448:2:4:0,-40.2762 0:19:19,1:18:666:1:2:0,-60.0658 0:14:14,1:13:467:1:2:0,-42.1564 0:15:15,3:12:400:3:6:0,-35.7502 +Chromosome 6342165 . C A 1.36216E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=19;DPB=19;DPRA=2.18182;EPP=7.35324;EPPR=9.26925;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=21.8827;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=543;RO=17;RPL=0;RPP=7.35324;RPPR=4.1599;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=7;SRP=4.1599;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|PA14_71190|PA14_71190|transcript|ABJ14774.1|protein_coding|1/1|c.584G>T|p.Trp195Leu|584/675|584/675|195/224||,A|upstream_gene_variant|MODIFIER|PA14_71140|PA14_71140|transcript|ABJ14769.1|protein_coding||c.-4399G>T|||||4399|,A|upstream_gene_variant|MODIFIER|PA14_71150|PA14_71150|transcript|ABJ14770.1|protein_coding||c.-3464G>T|||||3464|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|PA14_71160|PA14_71160|transcript|ABJ14771.1|protein_coding||c.-2453G>T|||||2453|,A|upstream_gene_variant|MODIFIER|PA14_71180|PA14_71180|transcript|ABJ14773.1|protein_coding||c.-148G>T|||||148|,A|upstream_gene_variant|MODIFIER|PA14_71230|PA14_71230|transcript|ABJ14778.1|protein_coding||c.-4290C>A|||||4290|,A|upstream_gene_variant|MODIFIER|PA14_71240|PA14_71240|transcript|ABJ14779.1|protein_coding||c.-4982C>A|||||4982|,A|downstream_gene_variant|MODIFIER|PA14_71170|PA14_71170|transcript|ABJ14772.1|protein_coding||c.*1232C>A|||||1232|,A|downstream_gene_variant|MODIFIER|PA14_71200|PA14_71200|transcript|ABJ14775.1|protein_coding||c.*597G>T|||||597|,A|downstream_gene_variant|MODIFIER|PA14_71210|PA14_71210|transcript|ABJ14776.1|protein_coding||c.*1019G>T|||||1019|,A|downstream_gene_variant|MODIFIER|cls|PA14_71220|transcript|ABJ14777.1|protein_coding||c.*2665G>T|||||2665| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:49:0:0:0,-4.57281 0:4:4,0:4:157:0:0:0,-14.5088 0:4:4,0:4:147:0:0:0,-13.5887 0:8:8,2:6:190:2:31:0,-14.46 +Chromosome 6342746 . C A 1.11614E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=22;DPB=22;DPRA=0.666667;EPP=7.35324;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=22.3675;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=745;RO=20;RPL=0;RPP=7.35324;RPPR=4.74748;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=15;SRP=13.8677;SRR=5;TYPE=snp;technology.ILLUMINA=1;ANN=A|start_lost|HIGH|PA14_71190|PA14_71190|transcript|ABJ14774.1|protein_coding|1/1|c.3G>T|p.Met1?|3/675|3/675|1/224||,A|upstream_gene_variant|MODIFIER|PA14_71140|PA14_71140|transcript|ABJ14769.1|protein_coding||c.-4980G>T|||||4980|,A|upstream_gene_variant|MODIFIER|PA14_71150|PA14_71150|transcript|ABJ14770.1|protein_coding||c.-4045G>T|||||4045|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|PA14_71160|PA14_71160|transcript|ABJ14771.1|protein_coding||c.-3034G>T|||||3034|,A|upstream_gene_variant|MODIFIER|PA14_71180|PA14_71180|transcript|ABJ14773.1|protein_coding||c.-729G>T|||||729|,A|upstream_gene_variant|MODIFIER|PA14_71230|PA14_71230|transcript|ABJ14778.1|protein_coding||c.-3709C>A|||||3709|,A|upstream_gene_variant|MODIFIER|PA14_71240|PA14_71240|transcript|ABJ14779.1|protein_coding||c.-4401C>A|||||4401|,A|downstream_gene_variant|MODIFIER|PA14_71170|PA14_71170|transcript|ABJ14772.1|protein_coding||c.*1813C>A|||||1813|,A|downstream_gene_variant|MODIFIER|PA14_71200|PA14_71200|transcript|ABJ14775.1|protein_coding||c.*16G>T|||||16|,A|downstream_gene_variant|MODIFIER|PA14_71210|PA14_71210|transcript|ABJ14776.1|protein_coding||c.*438G>T|||||438|,A|downstream_gene_variant|MODIFIER|cls|PA14_71220|transcript|ABJ14777.1|protein_coding||c.*2084G>T|||||2084|;LOF=(PA14_71190|PA14_71190|1|1.00) GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:39:0:0:0,-3.89656 0:9:9,0:9:347:0:0:0,-31.5878 0:4:4,2:2:71:2:31:0,-3.79541 0:8:8,0:8:288:0:0:0,-26.2643 +Chromosome 6343302 . T G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=38;DPB=38;DPRA=1.23529;EPP=11.6962;EPPR=12.2071;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=62.2976;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1247;RO=34;RPL=0;RPP=11.6962;RPPR=7.09778;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=8;SRP=23.7032;SRR=26;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_71210|PA14_71210|transcript|ABJ14776.1|protein_coding|1/1|c.1235A>C|p.His412Pro|1235/1353|1235/1353|412/450||,G|upstream_gene_variant|MODIFIER|PA14_71150|PA14_71150|transcript|ABJ14770.1|protein_coding||c.-4601A>C|||||4601|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_71160|PA14_71160|transcript|ABJ14771.1|protein_coding||c.-3590A>C|||||3590|,G|upstream_gene_variant|MODIFIER|PA14_71180|PA14_71180|transcript|ABJ14773.1|protein_coding||c.-1285A>C|||||1285|,G|upstream_gene_variant|MODIFIER|PA14_71190|PA14_71190|transcript|ABJ14774.1|protein_coding||c.-554A>C|||||554|,G|upstream_gene_variant|MODIFIER|PA14_71200|PA14_71200|transcript|ABJ14775.1|protein_coding||c.-118A>C|||||118|,G|upstream_gene_variant|MODIFIER|PA14_71230|PA14_71230|transcript|ABJ14778.1|protein_coding||c.-3153T>G|||||3153|,G|upstream_gene_variant|MODIFIER|PA14_71240|PA14_71240|transcript|ABJ14779.1|protein_coding||c.-3845T>G|||||3845|,G|upstream_gene_variant|MODIFIER|PA14_71250|PA14_71250|transcript|ABJ14780.1|protein_coding||c.-4949T>G|||||4949|,G|downstream_gene_variant|MODIFIER|PA14_71170|PA14_71170|transcript|ABJ14772.1|protein_coding||c.*2369T>G|||||2369|,G|downstream_gene_variant|MODIFIER|cls|PA14_71220|transcript|ABJ14777.1|protein_coding||c.*1528A>C|||||1528| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:233:0:0:0,-21.3389 0:11:11,0:11:424:0:0:0,-38.5123 0:12:12,3:9:343:3:6:0,-30.666 0:9:9,1:8:247:1:2:0,-22.3197 +Chromosome 6343671 . A C 3.11225E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=18;DPB=18;DPRA=2;EPP=9.52472;EPPR=4.31318;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=21.0609;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=502;RO=15;RPL=3;RPP=9.52472;RPPR=6.62942;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=11;SRP=10.1038;SRR=4;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_71210|PA14_71210|transcript|ABJ14776.1|protein_coding|1/1|c.866T>G|p.Leu289Arg|866/1353|866/1353|289/450||,C|upstream_gene_variant|MODIFIER|PA14_71150|PA14_71150|transcript|ABJ14770.1|protein_coding||c.-4970T>G|||||4970|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_71160|PA14_71160|transcript|ABJ14771.1|protein_coding||c.-3959T>G|||||3959|,C|upstream_gene_variant|MODIFIER|PA14_71180|PA14_71180|transcript|ABJ14773.1|protein_coding||c.-1654T>G|||||1654|,C|upstream_gene_variant|MODIFIER|PA14_71190|PA14_71190|transcript|ABJ14774.1|protein_coding||c.-923T>G|||||923|,C|upstream_gene_variant|MODIFIER|PA14_71200|PA14_71200|transcript|ABJ14775.1|protein_coding||c.-487T>G|||||487|,C|upstream_gene_variant|MODIFIER|PA14_71230|PA14_71230|transcript|ABJ14778.1|protein_coding||c.-2784A>C|||||2784|,C|upstream_gene_variant|MODIFIER|PA14_71240|PA14_71240|transcript|ABJ14779.1|protein_coding||c.-3476A>C|||||3476|,C|upstream_gene_variant|MODIFIER|PA14_71250|PA14_71250|transcript|ABJ14780.1|protein_coding||c.-4580A>C|||||4580|,C|downstream_gene_variant|MODIFIER|PA14_71170|PA14_71170|transcript|ABJ14772.1|protein_coding||c.*2738A>C|||||2738|,C|downstream_gene_variant|MODIFIER|cls|PA14_71220|transcript|ABJ14777.1|protein_coding||c.*1159T>G|||||1159| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,1:2:69:1:2:0,-6.35266 0:2:2,0:2:43:0:0:0,-4.08458 0:9:9,2:7:235:2:15:0,-20.0476 0:4:4,0:4:155:0:0:0,-14.3247 +Chromosome 6356937 . C A 9.84104E-17 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=27;DPB=27;DPRA=1.76471;EPP=3.0103;EPPR=7.26639;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=52.1162;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=29;QR=842;RO=25;RPL=1;RPP=3.0103;RPPR=3.09716;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=7;SRP=13.5202;SRR=18;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|PA14_71360|PA14_71360|transcript|ABJ14789.1|protein_coding|1/1|c.270C>A|p.Gly90Gly|270/333|270/333|90/110||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|PA14_71370|PA14_71370|transcript|ABJ14790.1|protein_coding||c.-60C>A|||||60|,A|upstream_gene_variant|MODIFIER|PA14_71420|PA14_71420|transcript|ABJ14795.1|protein_coding||c.-3090C>A|||||3090|,A|downstream_gene_variant|MODIFIER|PA14_71280|PA14_71280|transcript|ABJ14782.1|protein_coding||c.*4017C>A|||||4017|,A|downstream_gene_variant|MODIFIER|etfA-1|PA14_71300|transcript|ABJ14783.1|protein_coding||c.*2666C>A|||||2666|,A|downstream_gene_variant|MODIFIER|etfB-1|PA14_71310|transcript|ABJ14784.1|protein_coding||c.*1857C>A|||||1857|,A|downstream_gene_variant|MODIFIER|PA14_71320|PA14_71320|transcript|ABJ14785.1|protein_coding||c.*1163C>A|||||1163|,A|downstream_gene_variant|MODIFIER|PA14_71330|PA14_71330|transcript|ABJ14786.1|protein_coding||c.*949C>A|||||949|,A|downstream_gene_variant|MODIFIER|PA14_71340|PA14_71340|transcript|ABJ14787.1|protein_coding||c.*513C>A|||||513|,A|downstream_gene_variant|MODIFIER|PA14_71350|PA14_71350|transcript|ABJ14788.1|protein_coding||c.*266C>A|||||266|,A|downstream_gene_variant|MODIFIER|PA14_71380|PA14_71380|transcript|ABJ14791.1|protein_coding||c.*347G>T|||||347|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_71390|PA14_71390|transcript|ABJ14792.1|protein_coding||c.*528G>T|||||528|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_71400|PA14_71400|transcript|ABJ14793.1|protein_coding||c.*1215G>T|||||1215|,A|downstream_gene_variant|MODIFIER|PA14_71410|PA14_71410|transcript|ABJ14794.1|protein_coding||c.*1373G>T|||||1373|,A|downstream_gene_variant|MODIFIER|PA14_71430|PA14_71430|transcript|ABJ14796.1|protein_coding||c.*4184G>T|||||4184| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,2:8:249:2:29:0,-19.954 0:5:5,0:5:193:0:0:0,-17.741 0:6:6,0:6:211:0:0:0,-19.3296 0:6:6,0:6:189:0:0:0,-17.3155 +Chromosome 6357795 . G C 1.23658E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=28;DPB=28;DPRA=0.866667;EPP=9.52472;EPPR=7.26639;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=21.9795;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=916;RO=25;RPL=3;RPP=9.52472;RPPR=17.6895;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=7;SRP=13.5202;SRR=18;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|PA14_71390|PA14_71390|transcript|ABJ14792.1|protein_coding|1/1|c.231C>G|p.Val77Val|231/561|231/561|77/186||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_71380|PA14_71380|transcript|ABJ14791.1|protein_coding||c.-335C>G|||||335|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_71420|PA14_71420|transcript|ABJ14795.1|protein_coding||c.-2232G>C|||||2232|,C|downstream_gene_variant|MODIFIER|PA14_71280|PA14_71280|transcript|ABJ14782.1|protein_coding||c.*4875G>C|||||4875|,C|downstream_gene_variant|MODIFIER|etfA-1|PA14_71300|transcript|ABJ14783.1|protein_coding||c.*3524G>C|||||3524|,C|downstream_gene_variant|MODIFIER|etfB-1|PA14_71310|transcript|ABJ14784.1|protein_coding||c.*2715G>C|||||2715|,C|downstream_gene_variant|MODIFIER|PA14_71320|PA14_71320|transcript|ABJ14785.1|protein_coding||c.*2021G>C|||||2021|,C|downstream_gene_variant|MODIFIER|PA14_71330|PA14_71330|transcript|ABJ14786.1|protein_coding||c.*1807G>C|||||1807|,C|downstream_gene_variant|MODIFIER|PA14_71340|PA14_71340|transcript|ABJ14787.1|protein_coding||c.*1371G>C|||||1371|,C|downstream_gene_variant|MODIFIER|PA14_71350|PA14_71350|transcript|ABJ14788.1|protein_coding||c.*1124G>C|||||1124|,C|downstream_gene_variant|MODIFIER|PA14_71360|PA14_71360|transcript|ABJ14789.1|protein_coding||c.*795G>C|||||795|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_71370|PA14_71370|transcript|ABJ14790.1|protein_coding||c.*508G>C|||||508|,C|downstream_gene_variant|MODIFIER|PA14_71400|PA14_71400|transcript|ABJ14793.1|protein_coding||c.*357C>G|||||357|,C|downstream_gene_variant|MODIFIER|PA14_71410|PA14_71410|transcript|ABJ14794.1|protein_coding||c.*515C>G|||||515|,C|downstream_gene_variant|MODIFIER|PA14_71430|PA14_71430|transcript|ABJ14796.1|protein_coding||c.*3326C>G|||||3326| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:148:0:0:0,-13.6805 0:11:11,0:11:378:0:0:0,-34.3455 0:3:3,2:1:34:2:4:0,-3.01891 0:10:10,1:9:356:1:2:0,-32.2034 +Chromosome 6373456 . T C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=6;CIGAR=1X;DP=44;DPB=44;DPRA=1.7619;EPP=16.0391;EPPR=3.23888;GTI=0;LEN=1;MEANALT=1;MQM=55;MQMR=60;NS=4;NUMALT=1;ODDS=53.2249;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=54;QR=1140;RO=38;RPL=6;RPP=16.0391;RPPR=5.06748;RPR=0;RUN=1;SAF=6;SAP=16.0391;SAR=0;SRF=22;SRP=5.06748;SRR=16;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|soxG|PA14_71510|transcript|ABJ14803.1|protein_coding|1/1|c.398T>C|p.Leu133Pro|398/636|398/636|133/211||,C|upstream_gene_variant|MODIFIER|purU2|PA14_71530|transcript|ABJ14804.1|protein_coding||c.-288T>C|||||288|,C|upstream_gene_variant|MODIFIER|fdhA|PA14_71560|transcript|ABJ14805.1|protein_coding||c.-1352T>C|||||1352|,C|upstream_gene_variant|MODIFIER|PA14_71570|PA14_71570|transcript|ABJ14806.1|protein_coding||c.-2635T>C|||||2635|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|soxB|PA14_71470|transcript|ABJ14800.1|protein_coding||c.*3919T>C|||||3919|,C|downstream_gene_variant|MODIFIER|soxD|PA14_71490|transcript|ABJ14801.1|protein_coding||c.*3505T>C|||||3505|,C|downstream_gene_variant|MODIFIER|soxA|PA14_71500|transcript|ABJ14802.1|protein_coding||c.*491T>C|||||491|,C|downstream_gene_variant|MODIFIER|PA14_71580|PA14_71580|transcript|ABJ14807.1|protein_coding||c.*3656A>G|||||3656|,C|downstream_gene_variant|MODIFIER|PA14_71590|PA14_71590|transcript|ABJ14808.1|protein_coding||c.*4266A>G|||||4266|,C|downstream_gene_variant|MODIFIER|purK|PA14_71600|transcript|ABJ14809.1|protein_coding||c.*4626A>G|||||4626| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:176:0:0:0,-16.0822 0:11:11,1:10:327:1:2:0,-29.5369 0:12:12,4:8:281:4:36:0,-22.2959 0:14:14,1:13:356:1:16:0,-30.6952 +Chromosome 6379749 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=60;DPB=60;DPRA=1;EPP=5.18177;EPPR=8.59409;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=87.8681;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=56;QR=1703;RO=56;RPL=1;RPP=5.18177;RPPR=12.937;RPR=3;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=8;SRP=65.0524;SRR=48;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|PA14_71580|PA14_71580|transcript|ABJ14807.1|protein_coding||c.-2089T>C|||||2089|,G|upstream_gene_variant|MODIFIER|PA14_71590|PA14_71590|transcript|ABJ14808.1|protein_coding||c.-1782T>C|||||1782|,G|upstream_gene_variant|MODIFIER|purK|PA14_71600|transcript|ABJ14809.1|protein_coding||c.-585T>C|||||585|,G|upstream_gene_variant|MODIFIER|purE|PA14_71620|transcript|ABJ14810.1|protein_coding||c.-63T>C|||||63|,G|upstream_gene_variant|MODIFIER|adhA|PA14_71630|transcript|ABJ14811.1|protein_coding||c.-285A>G|||||285|,G|upstream_gene_variant|MODIFIER|aspA|PA14_71650|transcript|ABJ14813.1|protein_coding||c.-2434A>G|||||2434|,G|downstream_gene_variant|MODIFIER|fdhA|PA14_71560|transcript|ABJ14805.1|protein_coding||c.*3742A>G|||||3742|,G|downstream_gene_variant|MODIFIER|PA14_71570|PA14_71570|transcript|ABJ14806.1|protein_coding||c.*2702A>G|||||2702|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_71640|PA14_71640|transcript|ABJ14812.1|protein_coding||c.*1350T>C|||||1350|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_71670|PA14_71670|transcript|ABJ14814.1|protein_coding||c.*4222T>C|||||4222|,G|intergenic_region|MODIFIER|purE-adhA|PA14_71620-PA14_71630|intergenic_region|PA14_71620-PA14_71630|||n.6379749A>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:15:15,1:14:402:1:14:0,-35.0488 0:14:14,0:14:391:0:0:0,-35.4514 0:15:15,3:12:402:3:42:0,-32.5731 0:16:16,0:16:508:0:0:0,-46.0089 +Chromosome 6393684 . C A 4.92005E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=27;DPB=27;DPRA=1.5;EPP=3.0103;EPPR=7.26639;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=44.7633;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=917;RO=25;RPL=1;RPP=3.0103;RPPR=10.0459;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=7;SRP=13.5202;SRR=18;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|PA14_71750|PA14_71750|transcript|ABJ14821.1|protein_coding|1/1|c.801C>A|p.Arg267Arg|801/936|801/936|267/311||,A|upstream_gene_variant|MODIFIER|mtr|PA14_71710|transcript|ABJ14818.1|protein_coding||c.-4449G>T|||||4449|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|oadA|PA14_71720|transcript|ABJ14819.1|protein_coding||c.-2445G>T|||||2445|,A|upstream_gene_variant|MODIFIER|accC|PA14_71740|transcript|ABJ14820.1|protein_coding||c.-1014G>T|||||1014|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|zwf|PA14_71800|transcript|ABJ14824.1|protein_coding||c.-1378C>A|||||1378|,A|upstream_gene_variant|MODIFIER|yegQ|PA14_71820|transcript|ABJ14825.1|protein_coding||c.-2925C>A|||||2925|,A|downstream_gene_variant|MODIFIER|PA14_71760|PA14_71760|transcript|ABJ14822.1|protein_coding||c.*89G>T|||||89|,A|downstream_gene_variant|MODIFIER|PA14_71780|PA14_71780|transcript|ABJ14823.1|protein_coding||c.*411G>T|||||411|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_71830|PA14_71830|transcript|ABJ14826.1|protein_coding||c.*4313G>T|||||4313| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,2:7:247:2:31:0,-19.6241 0:7:7,0:7:267:0:0:0,-24.3904 0:7:7,0:7:262:0:0:0,-23.9363 0:4:4,0:4:141:0:0:0,-13.0343 +Chromosome 6398805 . G T 6.57725E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=47;DPB=47;DPRA=1.13636;EPP=9.52472;EPPR=4.78696;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=59.0609;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=1338;RO=44;RPL=3;RPP=9.52472;RPPR=3.79993;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=33;SRP=26.8965;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_71840|PA14_71840|transcript|ABJ14827.1|protein_coding|1/1|c.2116C>A|p.Gln706Lys|2116/2202|2116/2202|706/733||,T|upstream_gene_variant|MODIFIER|PA14_71760|PA14_71760|transcript|ABJ14822.1|protein_coding||c.-4817C>A|||||4817|,T|upstream_gene_variant|MODIFIER|PA14_71780|PA14_71780|transcript|ABJ14823.1|protein_coding||c.-3829C>A|||||3829|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|PA14_71830|PA14_71830|transcript|ABJ14826.1|protein_coding||c.-17C>A|||||17|,T|downstream_gene_variant|MODIFIER|PA14_71750|PA14_71750|transcript|ABJ14821.1|protein_coding||c.*4986G>T|||||4986|,T|downstream_gene_variant|MODIFIER|zwf|PA14_71800|transcript|ABJ14824.1|protein_coding||c.*2277G>T|||||2277|,T|downstream_gene_variant|MODIFIER|yegQ|PA14_71820|transcript|ABJ14825.1|protein_coding||c.*802G>T|||||802|,T|downstream_gene_variant|MODIFIER|PA14_71850|PA14_71850|transcript|ABJ14828.1|protein_coding||c.*2174C>A|||||2174| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,2:7:218:2:17:0,-18.305 0:11:11,0:11:359:0:0:0,-32.6189 0:11:11,0:11:316:0:0:0,-28.708 0:16:16,1:15:445:1:16:0,-38.7189 +Chromosome 6400019 . A G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=52;DPB=52;DPRA=0.925926;EPP=9.52472;EPPR=3.40914;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=74.6509;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=28;QR=1708;RO=49;RPL=0;RPP=9.52472;RPPR=4.11819;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=22;SRP=4.11819;SRR=27;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_71840|PA14_71840|transcript|ABJ14827.1|protein_coding|1/1|c.902T>C|p.Leu301Pro|902/2202|902/2202|301/733||,G|upstream_gene_variant|MODIFIER|PA14_71830|PA14_71830|transcript|ABJ14826.1|protein_coding||c.-1231T>C|||||1231|,G|upstream_gene_variant|MODIFIER|uvrD|PA14_71870|transcript|ABJ14829.1|protein_coding||c.-3989A>G|||||3989|,G|downstream_gene_variant|MODIFIER|zwf|PA14_71800|transcript|ABJ14824.1|protein_coding||c.*3491A>G|||||3491|,G|downstream_gene_variant|MODIFIER|yegQ|PA14_71820|transcript|ABJ14825.1|protein_coding||c.*2016A>G|||||2016|,G|downstream_gene_variant|MODIFIER|PA14_71850|PA14_71850|transcript|ABJ14828.1|protein_coding||c.*960T>C|||||960| GT:DP:DPR:RO:QR:AO:QA:GL 0:12:12,0:12:426:0:0:0,-38.6644 0:10:10,2:8:276:2:15:0,-23.7485 0:15:15,0:15:543:0:0:0,-49.1952 0:15:15,1:14:463:1:13:0,-40.671 +Chromosome 6403960 . T G 1.74636E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=31;DPB=31;DPRA=0.9375;EPP=9.52472;EPPR=18.2106;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=33.8358;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=51;QR=976;RO=28;RPL=0;RPP=9.52472;RPPR=10.7656;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=8;SRP=14.1779;SRR=20;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|PA14_71840|PA14_71840|transcript|ABJ14827.1|protein_coding||c.-3040A>C|||||3040|,G|upstream_gene_variant|MODIFIER|PA14_71850|PA14_71850|transcript|ABJ14828.1|protein_coding||c.-129A>C|||||129|,G|upstream_gene_variant|MODIFIER|uvrD|PA14_71870|transcript|ABJ14829.1|protein_coding||c.-48T>G|||||48|,G|upstream_gene_variant|MODIFIER|PA14_71880|PA14_71880|transcript|ABJ14830.1|protein_coding||c.-2272T>G|||||2272|,G|upstream_gene_variant|MODIFIER|psecoA|PA14_71890|transcript|ABJ14831.1|protein_coding||c.-2798T>G|||||2798|,G|upstream_gene_variant|MODIFIER|PA14_71900|PA14_71900|transcript|ABJ14832.1|protein_coding||c.-4669T>G|||||4669|,G|downstream_gene_variant|MODIFIER|wbpZ|PA14_71910|transcript|ABJ14833.1|protein_coding||c.*4928A>C|||||4928|,G|intergenic_region|MODIFIER|PA14_71850-uvrD|PA14_71850-PA14_71870|intergenic_region|PA14_71850-PA14_71870|||n.6403960T>G|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:9:9,0:9:283:0:0:0,-25.7674 0:7:7,0:7:263:0:0:0,-24.0279 0:5:5,1:4:124:1:22:0,-9.26402 0:10:10,2:8:306:2:29:0,-25.1442 +Chromosome 6423194 . A G 3.64385E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=15;DPB=15;DPRA=2;EPP=7.35324;EPPR=7.18621;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=20.8991;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=26;QR=369;RO=13;RPL=0;RPP=7.35324;RPPR=3.17734;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=4;SRP=7.18621;SRR=9;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_72040|PA14_72040|transcript|ABJ14844.1|protein_coding|1/1|c.1096A>G|p.Ser366Gly|1096/1143|1096/1143|366/380||,G|upstream_gene_variant|MODIFIER|PA14_72050|PA14_72050|transcript|ABJ14845.1|protein_coding||c.-41A>G|||||41|,G|upstream_gene_variant|MODIFIER|PA14_72060|PA14_72060|transcript|ABJ14846.1|protein_coding||c.-1040A>G|||||1040|,G|upstream_gene_variant|MODIFIER|PA14_72070|PA14_72070|transcript|ABJ14847.1|protein_coding||c.-1348A>G|||||1348|,G|upstream_gene_variant|MODIFIER|PA14_72080|PA14_72080|transcript|ABJ14848.1|protein_coding||c.-1790A>G|||||1790|,G|upstream_gene_variant|MODIFIER|PA14_72090|PA14_72090|transcript|ABJ14849.1|protein_coding||c.-2112A>G|||||2112|,G|upstream_gene_variant|MODIFIER|PA14_72110|PA14_72110|transcript|ABJ14850.1|protein_coding||c.-2441A>G|||||2441|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_72140|PA14_72140|transcript|ABJ14852.1|protein_coding||c.-4994A>G|||||4994|,G|downstream_gene_variant|MODIFIER|PA14_72010|PA14_72010|transcript|ABJ14841.1|protein_coding||c.*3247A>G|||||3247|,G|downstream_gene_variant|MODIFIER|PA14_72020|PA14_72020|transcript|ABJ14842.1|protein_coding||c.*1952A>G|||||1952|,G|downstream_gene_variant|MODIFIER|PA14_72030|PA14_72030|transcript|ABJ14843.1|protein_coding||c.*1092A>G|||||1092|,G|downstream_gene_variant|MODIFIER|PA14_72130|PA14_72130|transcript|ABJ14851.1|protein_coding||c.*4507T>C|||||4507| GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:40:0:0:0,-3.99568 0:4:4,0:4:95:0:0:0,-8.78547 0:4:4,0:4:123:0:0:0,-11.3715 0:6:6,2:4:111:2:26:0,-7.79173 +Chromosome 6423591 . G T 4.09873E-13 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=29;DPB=29;DPRA=1.9;EPP=3.73412;EPPR=8.35546;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=30.0073;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=826;RO=26;RPL=2;RPP=3.73412;RPPR=4.34659;RPR=1;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=12;SRP=3.34437;SRR=14;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_72050|PA14_72050|transcript|ABJ14845.1|protein_coding|1/1|c.357G>T|p.Leu119Phe|357/837|357/837|119/278||,T|upstream_gene_variant|MODIFIER|PA14_72060|PA14_72060|transcript|ABJ14846.1|protein_coding||c.-643G>T|||||643|,T|upstream_gene_variant|MODIFIER|PA14_72070|PA14_72070|transcript|ABJ14847.1|protein_coding||c.-951G>T|||||951|,T|upstream_gene_variant|MODIFIER|PA14_72080|PA14_72080|transcript|ABJ14848.1|protein_coding||c.-1393G>T|||||1393|,T|upstream_gene_variant|MODIFIER|PA14_72090|PA14_72090|transcript|ABJ14849.1|protein_coding||c.-1715G>T|||||1715|,T|upstream_gene_variant|MODIFIER|PA14_72110|PA14_72110|transcript|ABJ14850.1|protein_coding||c.-2044G>T|||||2044|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|PA14_72140|PA14_72140|transcript|ABJ14852.1|protein_coding||c.-4597G>T|||||4597|,T|downstream_gene_variant|MODIFIER|PA14_72010|PA14_72010|transcript|ABJ14841.1|protein_coding||c.*3644G>T|||||3644|,T|downstream_gene_variant|MODIFIER|PA14_72020|PA14_72020|transcript|ABJ14842.1|protein_coding||c.*2349G>T|||||2349|,T|downstream_gene_variant|MODIFIER|PA14_72030|PA14_72030|transcript|ABJ14843.1|protein_coding||c.*1489G>T|||||1489|,T|downstream_gene_variant|MODIFIER|PA14_72040|PA14_72040|transcript|ABJ14844.1|protein_coding||c.*350G>T|||||350|,T|downstream_gene_variant|MODIFIER|PA14_72130|PA14_72130|transcript|ABJ14851.1|protein_coding||c.*4110C>A|||||4110| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:70:0:0:0,-6.52928 0:10:10,1:9:268:1:16:0,-22.8047 0:7:7,0:7:258:0:0:0,-23.5697 0:9:9,2:7:230:2:18:0,-19.3067 +Chromosome 6434747 . G C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=52;DPB=52;DPRA=1.08;EPP=9.52472;EPPR=12.9813;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=43.2963;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=1692;RO=49;RPL=3;RPP=9.52472;RPPR=30.7077;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=21;SRP=5.18177;SRR=28;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_72220|PA14_72220|transcript|ABJ14858.1|protein_coding|1/1|c.38C>G|p.Ser13Trp|38/801|38/801|13/266||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|prfH|PA14_72200|transcript|ABJ14856.1|protein_coding||c.-2267C>G|||||2267|,C|upstream_gene_variant|MODIFIER|PA14_72210|PA14_72210|transcript|ABJ14857.1|protein_coding||c.-1131C>G|||||1131|,C|upstream_gene_variant|MODIFIER|PA14_72230|PA14_72230|transcript|ABJ14859.1|protein_coding||c.-391G>C|||||391|,C|upstream_gene_variant|MODIFIER|PA14_72250|PA14_72250|transcript|ABJ14860.1|protein_coding||c.-2208G>C|||||2208|,C|downstream_gene_variant|MODIFIER|citM|PA14_72170|transcript|ABJ14854.1|protein_coding||c.*3672G>C|||||3672|,C|downstream_gene_variant|MODIFIER|PA14_72180|PA14_72180|transcript|ABJ14855.1|protein_coding||c.*2887G>C|||||2887|,C|downstream_gene_variant|MODIFIER|PA14_72260|PA14_72260|transcript|ABJ14861.1|protein_coding||c.*3587C>G|||||3587|,C|downstream_gene_variant|MODIFIER|citA|PA14_72280|transcript|ABJ14862.1|protein_coding||c.*4290C>G|||||4290| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:271:0:0:0,-24.755 0:8:8,2:6:122:2:4:0,-10.7987 0:19:19,1:18:667:1:2:0,-60.1513 0:18:18,0:18:632:0:0:0,-57.1912 +Chromosome 6451084 . C T 1.46667E-11 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=30;DPB=30;DPRA=0.75;EPP=7.35324;EPPR=28.1373;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=26.4137;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=960;RO=28;RPL=1;RPP=3.0103;RPPR=5.80219;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=16;SRP=4.25114;SRR=12;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_72420|PA14_72420|transcript|ABJ14873.1|protein_coding|1/1|c.1879G>A|p.Glu627Lys|1879/2016|1879/2016|627/671||,T|upstream_gene_variant|MODIFIER|PA14_72400|PA14_72400|transcript|ABJ14871.1|protein_coding||c.-878G>A|||||878|,T|upstream_gene_variant|MODIFIER|PA14_72410|PA14_72410|transcript|ABJ14872.1|protein_coding||c.-255G>A|||||255|,T|upstream_gene_variant|MODIFIER|engB|PA14_72480|transcript|ABJ14878.1|protein_coding||c.-4700C>T|||||4700|,T|downstream_gene_variant|MODIFIER|algB|PA14_72380|transcript|ABJ14869.1|protein_coding||c.*3476C>T|||||3476|,T|downstream_gene_variant|MODIFIER|kinB|PA14_72390|transcript|ABJ14870.1|protein_coding||c.*1692C>T|||||1692|,T|downstream_gene_variant|MODIFIER|PA14_72430|PA14_72430|transcript|ABJ14874.1|protein_coding||c.*1875G>A|||||1875|,T|downstream_gene_variant|MODIFIER|dsbA|PA14_72450|transcript|ABJ14875.1|protein_coding||c.*2769G>A|||||2769|,T|downstream_gene_variant|MODIFIER|cc4|PA14_72460|transcript|ABJ14876.1|protein_coding||c.*3572G>A|||||3572|,T|downstream_gene_variant|MODIFIER|PA14_72470|PA14_72470|transcript|ABJ14877.1|protein_coding||c.*4223G>A|||||4223| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:250:0:0:0,-22.8429 0:10:10,0:10:333:0:0:0,-30.2865 0:6:6,2:4:130:2:75:0,-4.90012 0:7:7,0:7:247:0:0:0,-22.5697 +Chromosome 6456703 . C T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=12;CIGAR=1X;DP=86;DPB=86;DPRA=0;EPP=29.068;EPPR=7.23587;GTI=0;LEN=1;MEANALT=1;MQM=52.4167;MQMR=59.8514;NS=4;NUMALT=1;ODDS=85.3584;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=102;QR=2312;RO=74;RPL=0;RPP=29.068;RPPR=4.06669;RPR=12;RUN=1;SAF=0;SAP=29.068;SAR=12;SRF=51;SRP=26.0162;SRR=23;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|polA|PA14_72490|transcript|ABJ14879.1|protein_coding|1/1|c.2734G>A|p.Ala912Thr|2734/2742|2734/2742|912/913||,T|upstream_gene_variant|MODIFIER|PA14_72420|PA14_72420|transcript|ABJ14873.1|protein_coding||c.-3741G>A|||||3741|,T|upstream_gene_variant|MODIFIER|PA14_72430|PA14_72430|transcript|ABJ14874.1|protein_coding||c.-2866G>A|||||2866|,T|upstream_gene_variant|MODIFIER|dsbA|PA14_72450|transcript|ABJ14875.1|protein_coding||c.-2215G>A|||||2215|,T|upstream_gene_variant|MODIFIER|cc4|PA14_72460|transcript|ABJ14876.1|protein_coding||c.-1442G>A|||||1442|,T|upstream_gene_variant|MODIFIER|PA14_72470|PA14_72470|transcript|ABJ14877.1|protein_coding||c.-1103G>A|||||1103|,T|upstream_gene_variant|MODIFIER|PA14_72500|PA14_72500|transcript|ABJ14880.1|protein_coding||c.-2811C>T|||||2811|,T|upstream_gene_variant|MODIFIER|thrB|PA14_72510|transcript|ABJ14881.1|protein_coding||c.-3135C>T|||||3135|,T|downstream_gene_variant|MODIFIER|engB|PA14_72480|transcript|ABJ14878.1|protein_coding||c.*272C>T|||||272|,T|downstream_gene_variant|MODIFIER|Pseudomon-1|EBG00001225059|transcript|EBT00001793460.1|sRNA||n.*155C>T|||||155|,T|downstream_gene_variant|MODIFIER|PA14_72520|PA14_72520|transcript|ABJ14882.1|protein_coding||c.*4701G>A|||||4701| GT:DP:DPR:RO:QR:AO:QA:GL 0:22:22,2:20:666:2:17:0,-58.6094 0:16:16,5:11:334:5:49:0,-25.8345 0:25:25,2:23:607:2:4:0,-54.4784 0:23:23,3:20:705:3:32:0,-60.7638 +Chromosome 6473485 . A C 2.97761E-7 . AB=0;ABP=0;AC=0;AF=0;AN=3;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=2.66667;EPP=7.35324;EPPR=6.91895;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=16.5618;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=29;QR=172;RO=5;RPL=2;RPP=7.35324;RPPR=13.8677;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=1;SRP=6.91895;SRR=4;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|PA14_72690|PA14_72690|transcript|ABJ14894.1|protein_coding|1/1|c.681A>C|p.Ala227Ala|681/1332|681/1332|227/443||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_72700|PA14_72700|transcript|ABJ14895.1|protein_coding||c.-719A>C|||||719|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_72710|PA14_72710|transcript|ABJ14896.1|protein_coding||c.-1489A>C|||||1489|,C|downstream_gene_variant|MODIFIER|abc|PA14_72620|transcript|ABJ14889.1|protein_coding||c.*3931A>C|||||3931|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|yaeE|PA14_72630|transcript|ABJ14890.1|protein_coding||c.*3254A>C|||||3254|,C|downstream_gene_variant|MODIFIER|PA14_72640|PA14_72640|transcript|ABJ14891.1|protein_coding||c.*2395A>C|||||2395|,C|downstream_gene_variant|MODIFIER|PA14_72650|PA14_72650|transcript|ABJ14892.1|protein_coding||c.*1335A>C|||||1335|,C|downstream_gene_variant|MODIFIER|PA14_72660|PA14_72660|transcript|ABJ14893.1|protein_coding||c.*677A>C|||||677|,C|downstream_gene_variant|MODIFIER|dctD|PA14_72720|transcript|ABJ14897.1|protein_coding||c.*2857T>G|||||2857|,C|downstream_gene_variant|MODIFIER|dctB|PA14_72740|transcript|ABJ14898.1|protein_coding||c.*4197T>G|||||4197| GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:39:0:0:0,-3.89656 . 0:4:4,2:2:80:2:29:0,-4.837 0:2:2,0:2:53:0:0:0,-5.03089 +Chromosome 6488392 . T C 2.84448E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=13.8677;EPPR=8.34028;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=48.0982;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1181;RO=33;RPL=0;RPP=13.8677;RPPR=3.60252;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=13;SRP=6.23461;SRR=20;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_72850|PA14_72850|transcript|ABJ14909.1|protein_coding|1/1|c.644A>G|p.Glu215Gly|644/1368|644/1368|215/455||,C|upstream_gene_variant|MODIFIER|rosB|PA14_72800|transcript|ABJ14904.1|protein_coding||c.-3385A>G|||||3385|,C|upstream_gene_variant|MODIFIER|PA14_72810|PA14_72810|transcript|ABJ14905.1|protein_coding||c.-2440A>G|||||2440|,C|upstream_gene_variant|MODIFIER|PA14_72840|PA14_72840|transcript|ABJ14908.1|protein_coding||c.-819A>G|||||819|,C|upstream_gene_variant|MODIFIER|fabG|PA14_72880|transcript|ABJ14911.1|protein_coding||c.-2155T>C|||||2155|,C|upstream_gene_variant|MODIFIER|PA14_72890|PA14_72890|transcript|ABJ14912.1|protein_coding||c.-2948T>C|||||2948|,C|downstream_gene_variant|MODIFIER|PA14_72820|PA14_72820|transcript|ABJ14906.1|protein_coding||c.*1662T>C|||||1662|,C|downstream_gene_variant|MODIFIER|PA14_72830|PA14_72830|transcript|ABJ14907.1|protein_coding||c.*1625T>C|||||1625|,C|downstream_gene_variant|MODIFIER|PA14_72870|PA14_72870|transcript|ABJ14910.1|protein_coding||c.*645A>G|||||645|,C|downstream_gene_variant|MODIFIER|PA14_72900|PA14_72900|transcript|ABJ14913.1|protein_coding||c.*3699A>G|||||3699|,C|downstream_gene_variant|MODIFIER|PA14_72920|PA14_72920|transcript|ABJ14914.1|protein_coding||c.*4129A>G|||||4129|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_72930|PA14_72930|transcript|ABJ14915.1|protein_coding||c.*4726A>G|||||4726| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,1:4:157:1:2:0,-14.309 0:15:15,1:14:510:1:2:0,-46.0259 0:8:8,1:7:231:1:2:0,-20.9034 0:10:10,2:8:283:2:4:0,-25.4261 +Chromosome 6491720 . G T 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=33;DPB=33;DPRA=1.30435;EPP=7.35324;EPPR=3.08035;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=46.7157;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1190;RO=31;RPL=2;RPP=7.35324;RPPR=23.254;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=17;SRP=3.64073;SRR=14;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|PA14_72890|PA14_72890|transcript|ABJ14912.1|protein_coding|1/1|c.381G>T|p.Leu127Leu|381/735|381/735|127/244||,T|upstream_gene_variant|MODIFIER|PA14_72840|PA14_72840|transcript|ABJ14908.1|protein_coding||c.-4147C>A|||||4147|,T|upstream_gene_variant|MODIFIER|PA14_72850|PA14_72850|transcript|ABJ14909.1|protein_coding||c.-2685C>A|||||2685|,T|upstream_gene_variant|MODIFIER|PA14_72870|PA14_72870|transcript|ABJ14910.1|protein_coding||c.-1331C>A|||||1331|,T|upstream_gene_variant|MODIFIER|PA14_72940|PA14_72940|transcript|ABJ14916.1|protein_coding||c.-2619G>T|||||2619|,T|upstream_gene_variant|MODIFIER|kgtP|PA14_72960|transcript|ABJ14917.1|protein_coding||c.-4692G>T|||||4692|,T|downstream_gene_variant|MODIFIER|PA14_72820|PA14_72820|transcript|ABJ14906.1|protein_coding||c.*4990G>T|||||4990|,T|downstream_gene_variant|MODIFIER|PA14_72830|PA14_72830|transcript|ABJ14907.1|protein_coding||c.*4953G>T|||||4953|,T|downstream_gene_variant|MODIFIER|fabG|PA14_72880|transcript|ABJ14911.1|protein_coding||c.*391G>T|||||391|,T|downstream_gene_variant|MODIFIER|PA14_72900|PA14_72900|transcript|ABJ14913.1|protein_coding||c.*371C>A|||||371|,T|downstream_gene_variant|MODIFIER|PA14_72920|PA14_72920|transcript|ABJ14914.1|protein_coding||c.*801C>A|||||801|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|PA14_72930|PA14_72930|transcript|ABJ14915.1|protein_coding||c.*1398C>A|||||1398| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:148:0:0:0,-13.6805 0:10:10,0:10:382:0:0:0,-34.7331 0:9:9,0:9:355:0:0:0,-32.313 0:10:10,2:8:305:2:17:0,-26.1939 +Chromosome 6495573 . A C 1.04767E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=46;DPB=46;DPRA=1.55556;EPP=11.6962;EPPR=10.4553;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=68.4981;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1477;RO=42;RPL=4;RPP=11.6962;RPPR=3.83753;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=32;SRP=28.0339;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_72940|PA14_72940|transcript|ABJ14916.1|protein_coding|1/1|c.1235A>C|p.Gln412Pro|1235/1758|1235/1758|412/585||,C|upstream_gene_variant|MODIFIER|PA14_72900|PA14_72900|transcript|ABJ14913.1|protein_coding||c.-3270T>G|||||3270|,C|upstream_gene_variant|MODIFIER|PA14_72920|PA14_72920|transcript|ABJ14914.1|protein_coding||c.-2651T>G|||||2651|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_72930|PA14_72930|transcript|ABJ14915.1|protein_coding||c.-1598T>G|||||1598|,C|upstream_gene_variant|MODIFIER|kgtP|PA14_72960|transcript|ABJ14917.1|protein_coding||c.-839A>C|||||839|,C|upstream_gene_variant|MODIFIER|PA14_72990|PA14_72990|transcript|ABJ14920.1|protein_coding||c.-4754A>C|||||4754|,C|downstream_gene_variant|MODIFIER|fabG|PA14_72880|transcript|ABJ14911.1|protein_coding||c.*4244A>C|||||4244|,C|downstream_gene_variant|MODIFIER|PA14_72890|PA14_72890|transcript|ABJ14912.1|protein_coding||c.*3499A>C|||||3499|,C|downstream_gene_variant|MODIFIER|tonB|PA14_72970|transcript|ABJ14918.1|protein_coding||c.*2562T>G|||||2562|,C|downstream_gene_variant|MODIFIER|PA14_72980|PA14_72980|transcript|ABJ14919.1|protein_coding||c.*3683T>G|||||3683| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:254:0:0:0,-23.1634 0:10:10,0:10:336:0:0:0,-30.5512 0:14:14,3:11:412:3:6:0,-36.8625 0:14:14,1:13:475:1:2:0,-42.8852 +Chromosome 6505016 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=60;DPB=60;DPRA=0.818182;EPP=11.6962;EPPR=16.0391;GTI=0;LEN=1;MEANALT=1.5;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=77.4257;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1527;RO=54;RPL=4;RPP=11.6962;RPPR=5.5839;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=11;SRP=44.1879;SRR=43;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_73050|PA14_73050|transcript|ABJ14926.1|protein_coding|1/1|c.110A>C|p.Gln37Pro|110/897|110/897|37/298||,C|upstream_gene_variant|MODIFIER|PA14_72980|PA14_72980|transcript|ABJ14919.1|protein_coding||c.-4792T>G|||||4792|,C|upstream_gene_variant|MODIFIER|PA14_73000|PA14_73000|transcript|ABJ14921.1|protein_coding||c.-3527T>G|||||3527|,C|upstream_gene_variant|MODIFIER|PA14_73010|PA14_73010|transcript|ABJ14922.1|protein_coding||c.-2328T>G|||||2328|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_73020|PA14_73020|transcript|ABJ14923.1|protein_coding||c.-1909T>G|||||1909|,C|upstream_gene_variant|MODIFIER|amiA|PA14_73040|transcript|ABJ14925.1|protein_coding||c.-209T>G|||||209|,C|upstream_gene_variant|MODIFIER|cynT|PA14_73060|transcript|ABJ14927.1|protein_coding||c.-784A>C|||||784|,C|upstream_gene_variant|MODIFIER|pyrQ|PA14_73070|transcript|ABJ14928.1|protein_coding||c.-1347A>C|||||1347|,C|downstream_gene_variant|MODIFIER|PA14_72990|PA14_72990|transcript|ABJ14920.1|protein_coding||c.*4321A>C|||||4321|,C|downstream_gene_variant|MODIFIER|PA14_73030|PA14_73030|transcript|ABJ14924.1|protein_coding||c.*1380A>C|||||1380|,C|downstream_gene_variant|MODIFIER|PA14_73090|PA14_73090|transcript|ABJ14929.1|protein_coding||c.*2729T>G|||||2729|,C|downstream_gene_variant|MODIFIER|PA14_73100|PA14_73100|transcript|ABJ14930.1|protein_coding||c.*4060T>G|||||4060|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_73110|PA14_73110|transcript|ABJ14931.1|protein_coding||c.*4455T>G|||||4455| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,2:8:292:2:4:0,-26.2478 0:17:17,2:13:400:2:4:0,-35.8697 0:16:16,0:16:333:0:0:0,-30.1719 0:17:17,0:17:502:0:0:0,-45.4513 +Chromosome 6506150 . C G 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=4;CIGAR=1X;DP=43;DPB=43;DPRA=2.30769;EPP=11.6962;EPPR=3.06598;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=59.9855;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=1286;RO=39;RPL=0;RPP=11.6962;RPPR=9.74743;RPR=4;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=20;SRP=3.06598;SRR=19;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|cynT|PA14_73060|transcript|ABJ14927.1|protein_coding|1/1|c.351C>G|p.Gly117Gly|351/561|351/561|117/186||,G|upstream_gene_variant|MODIFIER|PA14_73000|PA14_73000|transcript|ABJ14921.1|protein_coding||c.-4661G>C|||||4661|,G|upstream_gene_variant|MODIFIER|PA14_73010|PA14_73010|transcript|ABJ14922.1|protein_coding||c.-3462G>C|||||3462|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_73020|PA14_73020|transcript|ABJ14923.1|protein_coding||c.-3043G>C|||||3043|,G|upstream_gene_variant|MODIFIER|amiA|PA14_73040|transcript|ABJ14925.1|protein_coding||c.-1343G>C|||||1343|,G|upstream_gene_variant|MODIFIER|pyrQ|PA14_73070|transcript|ABJ14928.1|protein_coding||c.-213C>G|||||213|,G|downstream_gene_variant|MODIFIER|PA14_73030|PA14_73030|transcript|ABJ14924.1|protein_coding||c.*2514C>G|||||2514|,G|downstream_gene_variant|MODIFIER|PA14_73050|PA14_73050|transcript|ABJ14926.1|protein_coding||c.*347C>G|||||347|,G|downstream_gene_variant|MODIFIER|PA14_73090|PA14_73090|transcript|ABJ14929.1|protein_coding||c.*1595G>C|||||1595|,G|downstream_gene_variant|MODIFIER|PA14_73100|PA14_73100|transcript|ABJ14930.1|protein_coding||c.*2926G>C|||||2926|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_73110|PA14_73110|transcript|ABJ14931.1|protein_coding||c.*3321G>C|||||3321| GT:DP:DPR:RO:QR:AO:QA:GL 0:7:7,0:7:240:0:0:0,-21.9277 0:10:10,2:8:236:2:30:0,-18.6665 0:6:6,0:6:218:0:0:0,-19.9705 0:20:20,2:18:592:2:28:0,-50.9072 +Chromosome 6511841 . T G 2.08686E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=8;CIGAR=1X;DP=57;DPB=57;DPRA=0;EPP=20.3821;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=49.1036;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=81;QR=1442;RO=49;RPL=3;RPP=4.09604;RPPR=3.05462;RPR=5;RUN=1;SAF=3;SAP=4.09604;SAR=5;SRF=33;SRP=15.8176;SRR=16;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_73120|PA14_73120|transcript|ABJ14932.1|protein_coding|1/1|c.689A>C|p.His230Pro|689/960|689/960|230/319||,G|upstream_gene_variant|MODIFIER|PA14_73090|PA14_73090|transcript|ABJ14929.1|protein_coding||c.-2852A>C|||||2852|,G|upstream_gene_variant|MODIFIER|PA14_73100|PA14_73100|transcript|ABJ14930.1|protein_coding||c.-2367A>C|||||2367|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|PA14_73110|PA14_73110|transcript|ABJ14931.1|protein_coding||c.-346A>C|||||346|,G|upstream_gene_variant|MODIFIER|PA14_73150|PA14_73150|transcript|ABJ14934.1|protein_coding||c.-2274T>G|||||2274|,G|upstream_gene_variant|MODIFIER|PA14_73160|PA14_73160|transcript|ABJ14935.1|protein_coding||c.-3257T>G|||||3257|,G|downstream_gene_variant|MODIFIER|pyrQ|PA14_73070|transcript|ABJ14928.1|protein_coding||c.*4141T>G|||||4141|,G|downstream_gene_variant|MODIFIER|PA14_73140|PA14_73140|transcript|ABJ14933.1|protein_coding||c.*852A>C|||||852|,G|downstream_gene_variant|MODIFIER|glmS|PA14_73170|transcript|ABJ14936.1|protein_coding||c.*4526A>C|||||4526| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,2:6:172:2:30:0,-12.9098 0:20:20,3:17:525:3:19:0,-45.7575 0:11:11,1:10:295:1:15:0,-25.3328 0:18:18,2:16:450:2:17:0,-39.1385 +Chromosome 6514951 . G T 2.59187E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=20;CIGAR=1X;DP=124;DPB=124;DPRA=0;EPP=46.4397;EPPR=59.4686;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=126.602;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=94;QR=2584;RO=104;RPL=0;RPP=46.4397;RPPR=15.0369;RPR=20;RUN=1;SAF=0;SAP=46.4397;SAR=20;SRF=40;SRP=15.0369;SRR=64;TYPE=snp;technology.ILLUMINA=1;ANN=T|upstream_gene_variant|MODIFIER|PA14_73110|PA14_73110|transcript|ABJ14931.1|protein_coding||c.-3456C>A|||||3456|,T|upstream_gene_variant|MODIFIER|PA14_73120|PA14_73120|transcript|ABJ14932.1|protein_coding||c.-2422C>A|||||2422|,T|upstream_gene_variant|MODIFIER|PA14_73140|PA14_73140|transcript|ABJ14933.1|protein_coding||c.-1074C>A|||||1074|,T|upstream_gene_variant|MODIFIER|PA14_73160|PA14_73160|transcript|ABJ14935.1|protein_coding||c.-147G>T|||||147|,T|downstream_gene_variant|MODIFIER|PA14_73150|PA14_73150|transcript|ABJ14934.1|protein_coding||c.*213G>T|||||213|,T|downstream_gene_variant|MODIFIER|glmS|PA14_73170|transcript|ABJ14936.1|protein_coding||c.*1416C>A|||||1416|,T|downstream_gene_variant|MODIFIER|glmR|PA14_73190|transcript|ABJ14937.1|protein_coding||c.*3267C>A|||||3267|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|PA14_73200|PA14_73200|transcript|ABJ14938.1|protein_coding||c.*4108C>A|||||4108|,T|downstream_gene_variant|MODIFIER|glmU|PA14_73220|transcript|ABJ14939.1|protein_coding||c.*4631C>A|||||4631|,T|intergenic_region|MODIFIER|PA14_73150-PA14_73160|PA14_73150-PA14_73160|intergenic_region|PA14_73150-PA14_73160|||n.6514951G>T|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:23:23,4:19:502:4:34:0,-42.2712 0:27:27,4:23:625:4:8:0,-55.7508 0:34:34,9:25:639:9:46:0,-53.541 0:40:40,3:37:818:3:6:0,-73.2516 +Chromosome 6514965 . T C 1.26568E-14 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=26;CIGAR=1X;DP=139;DPB=139;DPRA=0;EPP=19.3799;EPPR=41.9239;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=130.587;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=333;QR=2703;RO=113;RPL=6;RPP=19.3799;RPPR=6.2579;RPR=20;RUN=1;SAF=0;SAP=59.4686;SAR=26;SRF=48;SRP=8.56389;SRR=65;TYPE=snp;technology.ILLUMINA=1;ANN=C|upstream_gene_variant|MODIFIER|PA14_73110|PA14_73110|transcript|ABJ14931.1|protein_coding||c.-3470A>G|||||3470|,C|upstream_gene_variant|MODIFIER|PA14_73120|PA14_73120|transcript|ABJ14932.1|protein_coding||c.-2436A>G|||||2436|,C|upstream_gene_variant|MODIFIER|PA14_73140|PA14_73140|transcript|ABJ14933.1|protein_coding||c.-1088A>G|||||1088|,C|upstream_gene_variant|MODIFIER|PA14_73160|PA14_73160|transcript|ABJ14935.1|protein_coding||c.-133T>C|||||133|,C|downstream_gene_variant|MODIFIER|PA14_73150|PA14_73150|transcript|ABJ14934.1|protein_coding||c.*227T>C|||||227|,C|downstream_gene_variant|MODIFIER|glmS|PA14_73170|transcript|ABJ14936.1|protein_coding||c.*1402A>G|||||1402|,C|downstream_gene_variant|MODIFIER|glmR|PA14_73190|transcript|ABJ14937.1|protein_coding||c.*3253A>G|||||3253|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_73200|PA14_73200|transcript|ABJ14938.1|protein_coding||c.*4094A>G|||||4094|,C|downstream_gene_variant|MODIFIER|glmU|PA14_73220|transcript|ABJ14939.1|protein_coding||c.*4617A>G|||||4617|,C|intergenic_region|MODIFIER|PA14_73150-PA14_73160|PA14_73150-PA14_73160|intergenic_region|PA14_73150-PA14_73160|||n.6514965T>C|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:25:25,4:21:531:4:53:0,-43.1132 0:33:33,8:25:731:8:95:0,-57.3754 0:38:38,5:33:760:5:67:0,-62.4363 0:43:43,9:34:681:9:118:0,-50.7239 +Chromosome 6515567 . C A 6.72039E-15 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=59;DPB=59;DPRA=0.84375;EPP=9.52472;EPPR=3.63072;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=65.0537;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=48;QR=1946;RO=56;RPL=0;RPP=9.52472;RPPR=3.63072;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=16;SRP=25.3454;SRR=40;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|PA14_73160|PA14_73160|transcript|ABJ14935.1|protein_coding|1/1|c.470C>A|p.Ala157Glu|470/1206|470/1206|157/401||,A|upstream_gene_variant|MODIFIER|PA14_73110|PA14_73110|transcript|ABJ14931.1|protein_coding||c.-4072G>T|||||4072|,A|upstream_gene_variant|MODIFIER|PA14_73120|PA14_73120|transcript|ABJ14932.1|protein_coding||c.-3038G>T|||||3038|,A|upstream_gene_variant|MODIFIER|PA14_73140|PA14_73140|transcript|ABJ14933.1|protein_coding||c.-1690G>T|||||1690|,A|downstream_gene_variant|MODIFIER|PA14_73150|PA14_73150|transcript|ABJ14934.1|protein_coding||c.*829C>A|||||829|,A|downstream_gene_variant|MODIFIER|glmS|PA14_73170|transcript|ABJ14936.1|protein_coding||c.*800G>T|||||800|,A|downstream_gene_variant|MODIFIER|glmR|PA14_73190|transcript|ABJ14937.1|protein_coding||c.*2651G>T|||||2651|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_73200|PA14_73200|transcript|ABJ14938.1|protein_coding||c.*3492G>T|||||3492|,A|downstream_gene_variant|MODIFIER|glmU|PA14_73220|transcript|ABJ14939.1|protein_coding||c.*4015G>T|||||4015| GT:DP:DPR:RO:QR:AO:QA:GL 0:6:6,0:6:204:0:0:0,-18.6872 0:10:10,2:8:292:2:32:0,-23.5864 0:17:17,1:16:560:1:16:0,-49.1192 0:26:26,0:26:890:0:0:0,-80.3856 +Chromosome 6520795 . A C 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=31;DPB=31;DPRA=1.04348;EPP=7.35324;EPPR=19.8579;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=51.0466;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=29;QR=1015;RO=29;RPL=2;RPP=7.35324;RPPR=15.6647;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=20;SRP=12.0706;SRR=9;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|glmU|PA14_73220|transcript|ABJ14939.1|protein_coding|1/1|c.152T>G|p.Val51Gly|152/1365|152/1365|51/454||,C|upstream_gene_variant|MODIFIER|glmS|PA14_73170|transcript|ABJ14936.1|protein_coding||c.-2593T>G|||||2593|,C|upstream_gene_variant|MODIFIER|glmR|PA14_73190|transcript|ABJ14937.1|protein_coding||c.-1804T>G|||||1804|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_73200|PA14_73200|transcript|ABJ14938.1|protein_coding||c.-1227T>G|||||1227|,C|downstream_gene_variant|MODIFIER|PA14_73160|PA14_73160|transcript|ABJ14935.1|protein_coding||c.*4492A>C|||||4492|,C|downstream_gene_variant|MODIFIER|atpC|PA14_73230|transcript|ABJ14940.1|protein_coding||c.*272T>G|||||272|,C|downstream_gene_variant|MODIFIER|atpD|PA14_73240|transcript|ABJ14941.1|protein_coding||c.*739T>G|||||739|,C|downstream_gene_variant|MODIFIER|atpG|PA14_73250|transcript|ABJ14942.1|protein_coding||c.*2146T>G|||||2146|,C|downstream_gene_variant|MODIFIER|atpA|PA14_73260|transcript|ABJ14943.1|protein_coding||c.*3057T>G|||||3057|,C|downstream_gene_variant|MODIFIER|atpH|PA14_73280|transcript|ABJ14944.1|protein_coding||c.*4620T>G|||||4620| GT:DP:DPR:RO:QR:AO:QA:GL 0:8:8,0:8:259:0:0:0,-23.6197 0:8:8,0:8:299:0:0:0,-27.2643 0:8:8,2:6:210:2:29:0,-16.4841 0:7:7,0:7:247:0:0:0,-22.5643
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lest1.vcf Wed Oct 10 18:53:14 2018 -0400 @@ -0,0 +1,52 @@ +##fileformat=VCFv4.2 +##fileDate=20180104 +##reference= +##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> +##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> +##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> +##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)"> +##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"> +##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants"> +##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants"> +##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants"> +##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants"> +##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends"> +##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend"> +##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants"> +##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples"> +##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples"> +##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples"> +##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples"> +##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call"> +##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend"> +##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend"> +##ALT=<ID=DEL,Description="Deletion"> +##ALT=<ID=DUP,Description="Duplication"> +##ALT=<ID=INV,Description="Inversion"> +##ALT=<ID=DUP:TANDEM,Description="Tandem duplication"> +##ALT=<ID=INS,Description="Insertion of novel sequence"> +##ALT=<ID=CNV,Description="Copy number variable region"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant"> +##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant"> +##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant"> +##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality"> +##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Phred-scaled probability that this site is variant (non-reference in this sample"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth"> +##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally"> +##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of reference observations"> +##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of alternate observations"> +##FORMAT=<ID=RS,Number=1,Type=Integer,Description="Reference allele split-read observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=AS,Number=A,Type=Integer,Description="Alternate allele split-read observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=ASC,Number=A,Type=Integer,Description="Alternate allele clipped-read observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Reference allele paired-end observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)"> +##source=LUMPY +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT JSS-Qmut-07__Read JSS-Qmut-08__Read JSS-Vmut-01__Read JSS-Vmut-03__Read JSS-Vmut-05__Read JSS-Vmut-06__Read JSS-Vmut-07__Read JSS-Vmut-08__Read JSS-Vmut-09__Read JSS-Vmut-10__Read JSS-Vmut-11__Read JSS-Vmut-12__Read JSS-Vmut-13__Read JSS-Vmut-14__Read VP882-c2__Read VP882-c24__Read VP882-parent__Read JSS-Qmut-01__Read JSS-Qmut-02__Read JSS-Qmut-03__Read JSS-Qmut-04__Read JSS-Qmut-05__Read JSS-Qmut-06__Read JSS-Qmut-09__Read JSS-Qmut-10__Read JSS-Vmut-02__Read JSS-Vmut-04__Read +NC_009016.1 9156 1 N <DUP> 0.00 . 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lest2.vcf Wed Oct 10 18:53:14 2018 -0400 @@ -0,0 +1,71 @@ +##fileformat=VCFv4.2 +##fileDate=20180104 +##reference= +##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> +##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> +##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> +##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)"> +##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"> +##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants"> +##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants"> +##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants"> +##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants"> +##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends"> +##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend"> +##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants"> +##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples"> +##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples"> +##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples"> +##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples"> +##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call"> +##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend"> +##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend"> +##ALT=<ID=DEL,Description="Deletion"> +##ALT=<ID=DUP,Description="Duplication"> +##ALT=<ID=INV,Description="Inversion"> +##ALT=<ID=DUP:TANDEM,Description="Tandem duplication"> +##ALT=<ID=INS,Description="Insertion of novel sequence"> +##ALT=<ID=CNV,Description="Copy number variable region"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant"> +##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant"> +##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant"> +##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality"> +##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Phred-scaled probability that this site is variant (non-reference in this sample"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth"> +##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally"> +##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of reference observations"> +##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of alternate observations"> +##FORMAT=<ID=RS,Number=1,Type=Integer,Description="Reference allele split-read observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=AS,Number=A,Type=Integer,Description="Alternate allele split-read observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=ASC,Number=A,Type=Integer,Description="Alternate allele clipped-read observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Reference allele paired-end observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)"> +##source=LUMPY +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 195 213 +chr1 668399 1_1 N N]chr1:674472] 86.29 . 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SVTYPE=DUP;SVLEN=298;END=1734162;STRANDS=-+:38;IMPRECISE;CIPOS=-240,9;CIEND=-6,251;CIPOS95=-52,1;CIEND95=-2,64;SU=38;PE=38;SR=0 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/1:16:16:0:122:267.06:-32,-5,-17:182:147:35:146:34:63:0:3:83:31:0.19 0/1:22:22:0:146:516.81:-58,-7,-26:302:241:61:240:61:112:0:9:128:52:0.2 +chr1 2206996 9 N <DEL> 502.28 . SVTYPE=DEL;SVLEN=-26;END=2207022;STRANDS=+-:18;CIPOS=-2,1;CIEND=-6,9;CIPOS95=0,0;CIEND95=0,0;SU=18;PE=0;SR=18 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 1/1:9:0:9:22:265.90:-27,-3,-0:9:0:9:0:9:0:0:9:0:0:1 1/1:9:0:9:20:236.38:-24,-2,-0:8:0:8:0:8:0:0:8:0:0:1 +chr1 431018 10 N <DUP> 0.00 . SVTYPE=DUP;SVLEN=1900013;END=2331031;STRANDS=-+:4;IMPRECISE;CIPOS=-10,8;CIEND=-10,9;CIPOS95=-1,0;CIEND95=-1,1;SU=4;PE=2;SR=2 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:0:0:0:156:0.00:-1,-32,-55:184:184:0:183:0:85:0:0:98:0:0 0/0:4:2:2:156:0.00:-1,-25,-44:162:158:3:157:2:81:1:0:76:1:0.013 +chr1 2687759 11 N <DEL> 1942.68 . SVTYPE=DEL;SVLEN=-215;END=2687974;STRANDS=+-:68;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=68;PE=0;SR=68 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/1:38:0:38:200:1025.29:-104,-1,-22:89:45:43:45:43:45:37:5:0:0:0.49 0/1:30:0:30:153:917.39:-93,-1,-17:75:36:38:36:38:36:29:8:0:0:0.51 +chr1 2687860 12 N <DUP> 1665.77 . SVTYPE=DUP;SVLEN=210;END=2688070;STRANDS=-+:8;IMPRECISE;CIPOS=-546,6;CIEND=-6,532;CIPOS95=-130,0;CIEND95=0,134;SU=8;PE=8;SR=0 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/1:5:5:0:17:642.58:-66,-1,-3:141:88:53:87:52:27:11:24:60:16:0.37 1/1:3:3:0:5:1023.19:-104,-3,-2:190:109:80:108:79:44:24:28:64:26:0.42 +chr1 2687860 13 N <DUP> 1668.43 . SVTYPE=DUP;SVLEN=211;END=2688071;STRANDS=-+:37;CIPOS=-1,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=37;PE=0;SR=37 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/1:12:0:12:17:642.58:-66,-1,-3:142:88:53:87:52:27:11:24:60:16:0.37 1/1:25:0:25:6:1025.85:-105,-3,-2:188:108:80:107:79:43:24:29:64:25:0.42 +chr1 907970 14 N <DUP> 0.00 . SVTYPE=DUP;SVLEN=1931107;END=2839077;STRANDS=-+:4;IMPRECISE;CIPOS=-10,8;CIEND=-10,9;CIPOS95=-1,0;CIEND95=-1,1;SU=4;PE=2;SR=2 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:4:2:2:156:0.00:-1,-25,-45:166:162:3:161:2:72:1:0:89:1:0.012 0/0:0:0:0:200:0.00:-1,-29,-49:163:163:0:162:0:75:0:0:87:0:0 +chr1 10 15 N <DUP> 3194.06 . SVTYPE=DUP;SVLEN=3288548;END=3288558;STRANDS=-+:212;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=212;PE=88;SR=124 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 1/1:122:55:67:200:1817.90:-214,-51,-32:108:0:108:0:107:0:32:11:0:63:1 1/1:90:33:57:140:1376.17:-162,-39,-24:82:0:82:0:81:0:28:11:0:42:1 +chr2 786218 16 N <DUP> 0.00 . SVTYPE=DUP;SVLEN=413;END=786631;STRANDS=-+:4;IMPRECISE;CIPOS=-10,8;CIEND=-10,9;CIPOS95=-1,0;CIEND95=-1,1;SU=4;PE=2;SR=2 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:0:0:0:156:0.00:-1,-32,-54:181:181:0:180:0:94:0:0:86:0:0 0/0:4:2:2:200:0.00:-1,-33,-61:232:226:5:225:4:129:1:0:96:3:0.017 +chr2 1636681 17 N <DUP> 0.00 . SVTYPE=DUP;SVLEN=30926;END=1667607;STRANDS=-+:4;IMPRECISE;CIPOS=-10,8;CIEND=-10,9;CIPOS95=-1,0;CIEND95=-1,1;SU=4;PE=2;SR=2 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:4:2:2:156:0.00:-1,-40,-72:264:259:4:258:3:128:1:0:130:1:0.011 0/0:0:0:0:151:0.00:-1,-48,-82:272:272:0:271:0:130:0:0:141:0:0 +chr2 1846648 18_1 N N]chr2:1847584] 910.74 . SVTYPE=BND;STRANDS=++:24;IMPRECISE;CIPOS=-2,249;CIEND=-10,618;CIPOS95=0,69;CIEND95=-1,60;MATEID=18_2;EVENT=18;SU=24;PE=24;SR=0 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/1:7:7:0:200:362.51:-40,-4,-34:70:50:19:50:19:50:19:0:0:0:0.28 0/1:17:17:0:146:548.24:-61,-6,-53:108:78:29:78:29:78:29:0:0:0:0.27 +chr2 1847584 18_2 N N]chr2:1846648] 910.74 . SVTYPE=BND;STRANDS=++:24;IMPRECISE;CIPOS=-10,618;CIEND=-2,249;CIPOS95=-1,60;CIEND95=0,69;MATEID=18_1;EVENT=18;SECONDARY;SU=24;PE=24;SR=0 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/1:7:7:0:200:362.51:-40,-4,-34:70:50:19:50:19:50:19:0:0:0:0.28 0/1:17:17:0:146:548.24:-61,-6,-53:108:78:29:78:29:78:29:0:0:0:0.27 +chr2 1846649 19 N <DEL> 8567.30 . SVTYPE=DEL;SVLEN=-882;END=1847531;STRANDS=+-:193;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=193;PE=109;SR=84 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 1/1:84:51:33:146:3574.63:-363,-36,-6:122:0:122:0:121:0:32:17:0:71:1 1/1:109:58:51:200:4992.67:-507,-51,-8:170:0:170:0:169:0:50:20:0:98:1 +chr2 10 20 N <DUP> 4604.21 . SVTYPE=DUP;SVLEN=1877202;END=1877212;STRANDS=-+:241;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=241;PE=188;SR=53 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 1/1:146:119:27:200:2769.32:-326,-78,-49:164:0:164:0:163:0:13:12:0:137:1 1/1:95:69:26:200:1834.89:-216,-52,-33:109:0:109:0:108:0:12:11:0:84:1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test10.in3.s0.d0.af.a6.hy.fy.gy.rvcf Wed Oct 10 18:53:14 2018 -0400 @@ -0,0 +1,2 @@ +#CHROM POS ID REF ALT BEST_PAIR BEST_SEP_SCORE BEST_AVEDP PAIR_NUM PAIR_SEP_SCORE PAIR_AVEDP STATE(S)_USED PAIR1_MEMBERS PAIR1_SCORE_DATA PAIR2_MEMBERS PAIR2_SCORE_DATA +chr1 1659220 6 N <DUP> 1 0.8910 490 1 0.8910 490 0 195 97/890 213 90/90
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test10.in3.s0.d0.af.a6.hy.fy.gy.vcf Wed Oct 10 18:53:14 2018 -0400 @@ -0,0 +1,50 @@ +##fileformat=VCFv4.2 +##fileDate=20180104 +##reference= +##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> +##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> +##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> +##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)"> +##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"> +##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants"> +##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants"> +##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants"> +##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants"> +##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends"> +##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend"> +##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants"> +##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples"> +##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples"> +##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples"> +##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples"> +##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call"> +##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend"> +##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend"> +##ALT=<ID=DEL,Description="Deletion"> +##ALT=<ID=DUP,Description="Duplication"> +##ALT=<ID=INV,Description="Inversion"> +##ALT=<ID=DUP:TANDEM,Description="Tandem duplication"> +##ALT=<ID=INS,Description="Insertion of novel sequence"> +##ALT=<ID=CNV,Description="Copy number variable region"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant"> +##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant"> +##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant"> +##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality"> +##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Phred-scaled probability that this site is variant (non-reference in this sample"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth"> +##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally"> +##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of reference observations"> +##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of alternate observations"> +##FORMAT=<ID=RS,Number=1,Type=Integer,Description="Reference allele split-read observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=AS,Number=A,Type=Integer,Description="Alternate allele split-read observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=ASC,Number=A,Type=Integer,Description="Alternate allele clipped-read observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Reference allele paired-end observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)"> +##source=LUMPY +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 195 213 +chr1 1659220 6 N <DUP> 13154.05 . SVTYPE=DUP;SVLEN=6530;END=1665750;STRANDS=-+:627;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=627;PE=482;SR=145 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 1/1:627:482:145:200:13154.05:-1452,-264,-136:890:97:792:96:791:43:144:129:53:517:0.89 0/0:0:0:0:151:0.00:-0,-16,-27:90:90:0:89:0:42:0:0:47:0:0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test7.in1.s1.s3.d1.d1.af.a6.nh.fy.gy.rvcf Wed Oct 10 18:53:14 2018 -0400 @@ -0,0 +1,17 @@ +#CHROM POS ID REF ALT BEST_PAIR BEST_SEP_SCORE BEST_AVEDP PAIR_NUM PAIR_SEP_SCORE PAIR_AVEDP STATE(S)_USED PAIR1_MEMBERS PAIR1_SCORE_DATA PAIR2_MEMBERS PAIR2_SCORE_DATA +Chromosome 4521011 . G T 1 1 3 1 1 3 1 gDNA-PA14 0/3 205w3 2/2 +Chromosome 1881807 . C A 1 1 2 1 1 2 1 gDNA-PA14 2/2 205w1,205w2,205w3 0/3,0/1,0/3 +Chromosome 3103618 . G T 1 1 2 1 1 2 1 gDNA-PA14 2/2 205w2 0/2 +Chromosome 4980019 . A C 1 0.8333 4 1 0.8333 4 1 gDNA-PA14 0/2 205w1 5/6 +Chromosome 1165356 . A G 1 0.75 4 1 0.75 4 1 gDNA-PA14 0/4 205w2 3/4 +Chromosome 3022790 . A C 1 0.6667 7 1 0.6667 7 1 gDNA-PA14 2/3 205w1,205w3,205w2 0/5,0/8,0/13 +Chromosome 1757873 . G C 1 0.6667 5 1 0.6667 5 1 gDNA-PA14 2/3 205w1,205w2,205w3 0/7,0/7,0/3 +Chromosome 6357795 . G C 1 0.6667 4 1 0.6667 4 1 gDNA-PA14 0/4 205w2 2/3 +Chromosome 3864628 . TCCT CCCC 1 0.6667 3 1 0.6667 3 1 gDNA-PA14 2/3 205w1,205w2 0/4,0/2 +Chromosome 19337 . C A 1 0.6667 3 1 0.6667 3 1 gDNA-PA14 2/3 205w1,205w2,205w3 0/5,0/2,0/1 +Chromosome 3000510 . C G 1 0.6667 3 1 0.6667 3 1 gDNA-PA14 0/2 205w2 2/3 +Chromosome 4969672 . A C 1 0.6667 3 1 0.6667 3 1 gDNA-PA14 0/2 205w3 2/3 +Chromosome 287074 . T C 1 0.6667 2 1 0.6667 2 1 gDNA-PA14 2/3 205w1 0/1 +Chromosome 1899851 . T G 1 0.6667 2 1 0.6667 2 1 gDNA-PA14 0/1 205w2 2/3 +Chromosome 2835395 . C G 1 0.6 5 1 0.6 5 1 gDNA-PA14 0/5 205w1 3/5 +Chromosome 4265157 . T C 1 0.6 4 1 0.6 4 1 gDNA-PA14 0/2 205w3 3/5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test7.in1.s1.s3.d1.d1.af.a6.nh.fy.gy.vcf Wed Oct 10 18:53:14 2018 -0400 @@ -0,0 +1,83 @@ +##fileformat=VCFv4.1 +##fileDate=20170620 +##source=freeBayes v1.0.2-29-g41c1313 +##reference=localref.fa +##contig=<ID=Chromosome,length=6537648> +##phasing=none +##commandline="freebayes --region Chromosome:0..6537648 --bam b_0.bam --bam b_1.bam --bam b_2.bam --bam b_3.bam --fasta-reference localref.fa --vcf ./vcf_output/part_Chromosome:0..6537648.vcf --theta 0.001 --ploidy 1" +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> +##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype"> +##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]"> +##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally"> +##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally"> +##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally"> +##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally"> +##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> +##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred"> +##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations"> +##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations"> +##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand"> +##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand"> +##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand"> +##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand"> +##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous"> +##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome"> +##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele"> +##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele"> +##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without."> +##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best."> +##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout."> +##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> +##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR."> +##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position."> +##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles."> +##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length"> +##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles"> +##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles"> +##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments"> +##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments"> +##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> +##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record."> +##INFO=<ID=technology.ILLUMINA,Number=A,Type=Float,Description="Fraction of observations supporting the alternate observed in reads from ILLUMINA"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=DPR,Number=A,Type=Integer,Description="Number of observation for each allele"> +##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> +##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> +##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> +##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> +##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> +##SnpEffVersion="4.3i (build 2016-12-15 22:33), by Pablo Cingolani" +##SnpEffCmd="SnpEff Pseudomonas_aeruginosa_ucbpp_pa14 /Users/rleach/PROJECT/NINA/PA14DNASEQ-20170601/SNPsSmallIndels/FreeBayes_ploidy1_filtering_FreeBayes_variants.vcf.fixed " +##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' "> +##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' "> +##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' "> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT gDNA-PA14 205w3 205w2 205w1 +Chromosome 4521011 . G T 0.00639626 . AB=0;ABP=0;AC=1;AF=0.25;AN=4;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=0.666667;EPP=7.35324;EPPR=3.25157;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=6.51986;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=208;RO=9;RPL=2;RPP=7.35324;RPPR=3.25157;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=8;SRP=14.8328;SRR=1;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_50850|PA14_50850|transcript|ABJ10208.1|protein_coding|1/1|c.403G>T|p.Gly135Cys|403/465|403/465|135/154||,T|upstream_gene_variant|MODIFIER|PA14_50830|PA14_50830|transcript|ABJ10210.1|protein_coding||c.-2755C>A|||||2755|,T|upstream_gene_variant|MODIFIER|PA14_50840|PA14_50840|transcript|ABJ10209.1|protein_coding||c.-532C>A|||||532|,T|upstream_gene_variant|MODIFIER|PA14_50890|PA14_50890|transcript|ABJ10204.1|protein_coding||c.-2081G>T|||||2081|,T|upstream_gene_variant|MODIFIER|PA14_50900|PA14_50900|transcript|ABJ10203.1|protein_coding||c.-2581G>T|||||2581|,T|upstream_gene_variant|MODIFIER|PA14_50910|PA14_50910|transcript|ABJ10202.1|protein_coding||c.-3054G>T|||||3054|,T|upstream_gene_variant|MODIFIER|PA14_50920|PA14_50920|transcript|ABJ10201.1|protein_coding||c.-3454G>T|||||3454|,T|downstream_gene_variant|MODIFIER|PA14_50860|PA14_50860|transcript|ABJ10207.1|protein_coding||c.*101C>A|||||101|,T|downstream_gene_variant|MODIFIER|PA14_50870|PA14_50870|transcript|ABJ10206.1|protein_coding||c.*903C>A|||||903|,T|downstream_gene_variant|MODIFIER|PA14_50880|PA14_50880|transcript|ABJ10205.1|protein_coding||c.*1318C>A|||||1318|,T|downstream_gene_variant|MODIFIER|PA14_50930|PA14_50930|transcript|ABJ10200.1|protein_coding||c.*4192C>A|||||4192| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:74:0:0:0,-6.90589 1:2:2,2:0:0:2:32:-3.03997,0 0:2:2,0:2:49:0:0:0,-4.65395 0:4:4,0:4:85:0:0:0,-7.85997 +Chromosome 1881807 . C A 1.66784E-5 . AB=0;ABP=0;AC=1;AF=0.25;AN=4;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0.857143;EPP=7.35324;EPPR=18.2106;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=12.4931;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=262;RO=7;RPL=0;RPP=7.35324;RPPR=10.7656;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=10.7656;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|lhr1|PA14_21690|transcript|ABJ12522.1|protein_coding|1/1|c.2440C>A|p.Gln814Lys|2440/4347|2440/4347|814/1448||,A|upstream_gene_variant|MODIFIER|PA14_21670|PA14_21670|transcript|ABJ12523.1|protein_coding||c.-3058G>T|||||3058|,A|downstream_gene_variant|MODIFIER|PA14_21640|PA14_21640|transcript|ABJ12527.1|protein_coding||c.*4405C>A|||||4405|,A|downstream_gene_variant|MODIFIER|PA14_21650|PA14_21650|transcript|ABJ12526.1|protein_coding||c.*3750C>A|||||3750|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_21660|PA14_21660|transcript|ABJ12525.1|protein_coding||c.*3424C>A|||||3424|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_21680|PA14_21680|transcript|ABJ12524.1|protein_coding||c.*2508C>A|||||2508|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_21700|PA14_21700|transcript|ABJ12521.1|protein_coding||c.*1915G>T|||||1915| GT:DP:DPR:RO:QR:AO:QA:GL 1:2:2,2:0:0:2:4:-0.38,0 0:3:3,0:3:109:0:0:0,-10.1657 0:1:1,0:1:36:0:0:0,-3.59827 0:3:3,0:3:117:0:0:0,-10.9104 +Chromosome 3103618 . G T 0.0227988 . AB=0;ABP=0;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=1;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=2;NUMALT=1;ODDS=5.74083;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=54;RO=2;RPL=0;RPP=7.35324;RPPR=7.35324;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_34850|PA14_34850|transcript|ABJ11481.1|protein_coding|1/1|c.387G>T|p.Leu129Phe|387/543|387/543|129/180||,T|upstream_gene_variant|MODIFIER|chiC|PA14_34870|transcript|ABJ11480.1|protein_coding||c.-375G>T|||||375|,T|upstream_gene_variant|MODIFIER|PA14_34880|PA14_34880|transcript|ABJ11479.1|protein_coding||c.-2003G>T|||||2003|,T|upstream_gene_variant|MODIFIER|PA14_34900|PA14_34900|transcript|ABJ11478.1|protein_coding||c.-2749G>T|||||2749|,T|upstream_gene_variant|MODIFIER|PA14_34920|PA14_34920|transcript|ABJ11477.1|protein_coding||c.-4559G>T|||||4559|,T|downstream_gene_variant|MODIFIER|PA14_34840|PA14_34840|transcript|ABJ11482.1|protein_coding||c.*454G>T|||||454| GT:DP:DPR:RO:QR:AO:QA:GL 1:2:2,2:0:0:2:32:-3.03997,0 . 0:2:2,0:2:54:0:0:0,-5.12589 . +Chromosome 4980019 . A C 5.0981E-11 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=18;DPB=18;DPRA=1.5;EPP=13.8677;EPPR=4.51363;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=25.298;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=433;RO=13;RPL=0;RPP=13.8677;RPPR=4.51363;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=6;SRP=3.17734;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=C|upstream_gene_variant|MODIFIER|PA14_55750|PA14_55750|transcript|ABJ13561.1|protein_coding||c.-2360T>G|||||2360|,C|upstream_gene_variant|MODIFIER|PA14_55800|PA14_55800|transcript|ABJ13565.1|protein_coding||c.-3355A>C|||||3355|,C|upstream_gene_variant|MODIFIER|PA14_55810|PA14_55810|transcript|ABJ13566.1|protein_coding||c.-3958A>C|||||3958|,C|downstream_gene_variant|MODIFIER|chrA|PA14_55740|transcript|ABJ13559.1|protein_coding||c.*3973A>C|||||3973|,C|downstream_gene_variant|MODIFIER|PA14_55760|PA14_55760|transcript|ABJ13560.1|protein_coding||c.*1675A>C|||||1675|,C|downstream_gene_variant|MODIFIER|pitA|PA14_55770|transcript|ABJ13562.1|protein_coding||c.*61A>C|||||61|,C|downstream_gene_variant|MODIFIER|PA14_55780|PA14_55780|transcript|ABJ13563.1|protein_coding||c.*7T>G|||||7|,C|downstream_gene_variant|MODIFIER|PA14_55790|PA14_55790|transcript|ABJ13564.1|protein_coding||c.*2785T>G|||||2785|,C|downstream_gene_variant|MODIFIER|PA14_55820|PA14_55820|transcript|ABJ13567.1|protein_coding||c.*4811T>G|||||4811|,C|intergenic_region|MODIFIER|pitA-PA14_55780|PA14_55770-PA14_55780|intergenic_region|PA14_55770-PA14_55780|||n.4980019A>C|||||| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:62:0:0:0,-5.88849 0:5:5,0:5:162:0:0:0,-14.8962 0:5:5,0:5:169:0:0:0,-15.5407 0:6:6,5:1:40:5:10:0,-3.07568 +Chromosome 1165356 . A G 7.47539E-8 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=5;CIGAR=1X;DP=19;DPB=19;DPRA=2.8;EPP=13.8677;EPPR=5.49198;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=17.9526;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=360;RO=14;RPL=5;RPP=13.8677;RPPR=3.63072;RPR=0;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=7;SRP=3.0103;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_13530|PA14_13530|transcript|ABJ13166.1|protein_coding|1/1|c.1198A>G|p.Met400Val|1198/2196|1198/2196|400/731||,G|upstream_gene_variant|MODIFIER|PA14_13500|PA14_13500|transcript|ABJ13169.1|protein_coding||c.-3978T>C|||||3978|,G|upstream_gene_variant|MODIFIER|PA14_13510|PA14_13510|transcript|ABJ13168.1|protein_coding||c.-2930T>C|||||2930|,G|upstream_gene_variant|MODIFIER|PA14_13560|PA14_13560|transcript|ABJ13165.1|protein_coding||c.-1225A>G|||||1225|,G|downstream_gene_variant|MODIFIER|PA14_13490|PA14_13490|transcript|ABJ13170.1|protein_coding||c.*4973A>G|||||4973|,G|downstream_gene_variant|MODIFIER|PA14_13520|PA14_13520|transcript|ABJ13167.1|protein_coding||c.*1194A>G|||||1194|,G|downstream_gene_variant|MODIFIER|PA14_13580|PA14_13580|transcript|ABJ13164.1|protein_coding||c.*2261T>C|||||2261|,G|downstream_gene_variant|MODIFIER|PA14_13590|PA14_13590|transcript|ABJ13163.1|protein_coding||c.*3437T>C|||||3437|,G|downstream_gene_variant|MODIFIER|PA14_13600|PA14_13600|transcript|ABJ13162.1|protein_coding||c.*4099T>C|||||4099| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:69:0:0:0,-6.38099 0:1:1,0:1:36:0:0:0,-3.59827 0:4:4,3:1:14:3:6:0,-0.83999 0:10:10,2:8:241:2:4:0,-21.5966 +Chromosome 3022790 . A C 4.57364E-10 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=29;DPB=29;DPRA=0.346154;EPP=7.35324;EPPR=6.01695;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=22.9741;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=873;RO=26;RPL=2;RPP=7.35324;RPPR=3.0103;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=17;SRP=8.35546;SRR=9;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_33990|PA14_33990|transcript|ABJ11547.1|protein_coding|1/1|c.1100T>G|p.Leu367Arg|1100/2550|1100/2550|367/849||,C|upstream_gene_variant|MODIFIER|PA14_33960|PA14_33960|transcript|ABJ11550.1|protein_coding||c.-3200T>G|||||3200|,C|upstream_gene_variant|MODIFIER|PA14_33970|PA14_33970|transcript|ABJ11549.1|protein_coding||c.-2096T>G|||||2096|,C|upstream_gene_variant|MODIFIER|PA14_33980|PA14_33980|transcript|ABJ11548.1|protein_coding||c.-1524T>G|||||1524|,C|downstream_gene_variant|MODIFIER|PA14_34000|PA14_34000|transcript|ABJ11546.1|protein_coding||c.*1101T>G|||||1101|,C|downstream_gene_variant|MODIFIER|PA14_34010|PA14_34010|transcript|ABJ11545.1|protein_coding||c.*2081T>G|||||2081|,C|downstream_gene_variant|MODIFIER|PA14_34020|PA14_34020|transcript|ABJ11544.1|protein_coding||c.*3858T>G|||||3858|,C|downstream_gene_variant|MODIFIER|PA14_34030|PA14_34030|transcript|ABJ11543.1|protein_coding||c.*4296T>G|||||4296|,C|downstream_gene_variant|MODIFIER|PA14_34050|PA14_34050|transcript|ABJ11542.1|protein_coding||c.*4867T>G|||||4867| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,2:1:35:2:4:0,-3.11863 0:8:8,0:8:255:0:0:0,-23.2533 0:13:13,0:12:401:0:0:0,-36.2399 0:5:5,0:5:182:0:0:0,-16.7345 +Chromosome 1757873 . G C 2.24648E-7 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=20;DPB=20;DPRA=0.529412;EPP=7.35324;EPPR=4.9405;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=16.7773;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=653;RO=18;RPL=2;RPP=7.35324;RPPR=7.35324;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=9;SRP=3.0103;SRR=9;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|phnN|PA14_20440|transcript|ABJ12627.1|protein_coding|1/1|c.277G>C|p.Asp93His|277/558|277/558|93/185||,C|upstream_gene_variant|MODIFIER|phnP|PA14_20450|transcript|ABJ12626.1|protein_coding||c.-272G>C|||||272|,C|upstream_gene_variant|MODIFIER|PA14_20500|PA14_20500|transcript|PA14_20500-1.1|protein_coding||c.-2662G>C|||||2662|WARNING_TRANSCRIPT_INCOMPLETE,C|upstream_gene_variant|MODIFIER|PA14_20510|PA14_20510|transcript|ABJ12621.1|protein_coding||c.-4635G>C|||||4635|,C|downstream_gene_variant|MODIFIER|phnH|PA14_20370|transcript|ABJ12633.1|protein_coding||c.*4989G>C|||||4989|,C|downstream_gene_variant|MODIFIER|phnI|PA14_20380|transcript|ABJ12632.1|protein_coding||c.*3889G>C|||||3889|,C|downstream_gene_variant|MODIFIER|phnJ|PA14_20390|transcript|ABJ12631.1|protein_coding||c.*3008G>C|||||3008|,C|downstream_gene_variant|MODIFIER|phnK|PA14_20400|transcript|ABJ12630.1|protein_coding||c.*2196G>C|||||2196|,C|downstream_gene_variant|MODIFIER|phnL|PA14_20420|transcript|ABJ12629.1|protein_coding||c.*1429G>C|||||1429|,C|downstream_gene_variant|MODIFIER|phnM|PA14_20430|transcript|ABJ12628.1|protein_coding||c.*276G>C|||||276|,C|downstream_gene_variant|MODIFIER|PA14_20460|PA14_20460|transcript|ABJ12625.1|protein_coding||c.*1081C>G|||||1081|,C|downstream_gene_variant|MODIFIER|PA14_20470|PA14_20470|transcript|ABJ12624.1|protein_coding||c.*1318C>G|||||1318|,C|downstream_gene_variant|MODIFIER|PA14_20480|PA14_20480|transcript|ABJ12623.1|protein_coding||c.*1553C>G|||||1553|,C|downstream_gene_variant|MODIFIER|PA14_20491|PA14_20491|transcript|ABJ12622.1|protein_coding||c.*2024C>G|||||2024|,C|downstream_gene_variant|MODIFIER|tRNA|EBG00001225096|transcript|EBT00001793400.1|protein_coding||c.*2662C>G|||||2662|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,2:1:15:2:4:0,-1.11999 0:3:3,0:3:105:0:0:0,-9.795 0:7:7,0:7:268:0:0:0,-24.4822 0:7:7,0:7:265:0:0:0,-24.207 +Chromosome 6357795 . G C 1.23658E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=28;DPB=28;DPRA=0.866667;EPP=9.52472;EPPR=7.26639;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=21.9795;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=916;RO=25;RPL=3;RPP=9.52472;RPPR=17.6895;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=7;SRP=13.5202;SRR=18;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|PA14_71390|PA14_71390|transcript|ABJ14792.1|protein_coding|1/1|c.231C>G|p.Val77Val|231/561|231/561|77/186||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_71380|PA14_71380|transcript|ABJ14791.1|protein_coding||c.-335C>G|||||335|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_71420|PA14_71420|transcript|ABJ14795.1|protein_coding||c.-2232G>C|||||2232|,C|downstream_gene_variant|MODIFIER|PA14_71280|PA14_71280|transcript|ABJ14782.1|protein_coding||c.*4875G>C|||||4875|,C|downstream_gene_variant|MODIFIER|etfA-1|PA14_71300|transcript|ABJ14783.1|protein_coding||c.*3524G>C|||||3524|,C|downstream_gene_variant|MODIFIER|etfB-1|PA14_71310|transcript|ABJ14784.1|protein_coding||c.*2715G>C|||||2715|,C|downstream_gene_variant|MODIFIER|PA14_71320|PA14_71320|transcript|ABJ14785.1|protein_coding||c.*2021G>C|||||2021|,C|downstream_gene_variant|MODIFIER|PA14_71330|PA14_71330|transcript|ABJ14786.1|protein_coding||c.*1807G>C|||||1807|,C|downstream_gene_variant|MODIFIER|PA14_71340|PA14_71340|transcript|ABJ14787.1|protein_coding||c.*1371G>C|||||1371|,C|downstream_gene_variant|MODIFIER|PA14_71350|PA14_71350|transcript|ABJ14788.1|protein_coding||c.*1124G>C|||||1124|,C|downstream_gene_variant|MODIFIER|PA14_71360|PA14_71360|transcript|ABJ14789.1|protein_coding||c.*795G>C|||||795|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_71370|PA14_71370|transcript|ABJ14790.1|protein_coding||c.*508G>C|||||508|,C|downstream_gene_variant|MODIFIER|PA14_71400|PA14_71400|transcript|ABJ14793.1|protein_coding||c.*357C>G|||||357|,C|downstream_gene_variant|MODIFIER|PA14_71410|PA14_71410|transcript|ABJ14794.1|protein_coding||c.*515C>G|||||515|,C|downstream_gene_variant|MODIFIER|PA14_71430|PA14_71430|transcript|ABJ14796.1|protein_coding||c.*3326C>G|||||3326| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:148:0:0:0,-13.6805 0:11:11,0:11:378:0:0:0,-34.3455 0:3:3,2:1:34:2:4:0,-3.01891 0:10:10,1:9:356:1:2:0,-32.2034 +Chromosome 3864628 . TCCT CCCC 1.0009E-6 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X2M1X;DP=11;DPB=11.75;DPRA=0.833333;EPP=9.52472;EPPR=12.7819;GTI=0;LEN=4;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=15.3564;PAIRED=0;PAIREDR=0;PAO=1;PQA=11;PQR=0;PRO=0;QA=28;QR=255;RO=8;RPL=3;RPP=9.52472;RPPR=7.35324;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=1;SRP=12.7819;SRR=7;TYPE=complex;technology.ILLUMINA=1;ANN=CCCC|missense_variant|MODERATE|kdpB|PA14_43380|transcript|ABJ10814.1|protein_coding|1/1|c.1118_1121delAGGAinsGGGG|p.GluGlu373GlyGly|1121/2073|1118/2073|373/690||,CCCC|upstream_gene_variant|MODIFIER|kdpE|PA14_43340|transcript|ABJ10817.1|protein_coding||c.-4426_-4423delAGGAinsGGGG|||||4423|,CCCC|upstream_gene_variant|MODIFIER|kdpD|PA14_43350|transcript|ABJ10816.1|protein_coding||c.-1668_-1665delAGGAinsGGGG|||||1665|,CCCC|upstream_gene_variant|MODIFIER|kdpC|PA14_43370|transcript|ABJ10815.1|protein_coding||c.-1009_-1006delAGGAinsGGGG|||||1006|,CCCC|downstream_gene_variant|MODIFIER|kdpA|PA14_43400|transcript|ABJ10813.1|protein_coding||c.*1129_*1132delAGGAinsGGGG|||||1132|,CCCC|downstream_gene_variant|MODIFIER|kdpF|PA14_43405|transcript|ABJ15698.1|protein_coding||c.*2834_*2837delAGGAinsGGGG|||||2837|,CCCC|downstream_gene_variant|MODIFIER|PA14_43420|PA14_43420|transcript|ABJ10812.1|protein_coding||c.*3111_*3114delAGGAinsGGGG|||||3114|,CCCC|downstream_gene_variant|MODIFIER|PA14_43430|PA14_43430|transcript|ABJ10811.1|protein_coding||c.*4320_*4323delAGGAinsGGGG|||||4323| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,2:1:40:2:26:0,-1.52569 0:2:2,1:1:37:1:2:0,-3.49783 0:2:2,0:2:66:0:0:0,-6.26573 0:4:4,0:4:112:0:0:0,-9.25301 +Chromosome 19337 . C A 3.84232E-6 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=1.125;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=14.361;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=220;RO=9;RPL=0;RPP=7.35324;RPPR=5.18177;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=9.04217;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|sun|PA14_00180|transcript|ABJ14973.1|protein_coding|1/1|c.757G>T|p.Ala253Ser|757/1305|757/1305|253/434||,A|upstream_gene_variant|MODIFIER|PA14_00150|PA14_00150|transcript|ABJ14970.1|protein_coding||c.-2729G>T|||||2729|,A|upstream_gene_variant|MODIFIER|PA14_00160|PA14_00160|transcript|ABJ14971.1|protein_coding||c.-2097G>T|||||2097|,A|upstream_gene_variant|MODIFIER|trkA|PA14_00170|transcript|ABJ14972.1|protein_coding||c.-575G>T|||||575|,A|upstream_gene_variant|MODIFIER|PA14_00210|PA14_00210|transcript|ABJ14976.1|protein_coding||c.-2396C>A|||||2396|,A|upstream_gene_variant|MODIFIER|smf|PA14_00230|transcript|ABJ14977.1|protein_coding||c.-3556C>A|||||3556|,A|upstream_gene_variant|MODIFIER|PA14_00240|PA14_00240|transcript|ABJ14978.1|protein_coding||c.-4685C>A|||||4685|,A|downstream_gene_variant|MODIFIER|PA14_00120|PA14_00120|transcript|ABJ14967.1|protein_coding||c.*4214C>A|||||4214|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_00130|PA14_00130|transcript|ABJ14968.1|protein_coding||c.*3863C>A|||||3863|,A|downstream_gene_variant|MODIFIER|PA14_00140|PA14_00140|transcript|ABJ14969.1|protein_coding||c.*3063C>A|||||3063|,A|downstream_gene_variant|MODIFIER|fmt|PA14_00190|transcript|ABJ14974.1|protein_coding||c.*753G>T|||||753|,A|downstream_gene_variant|MODIFIER|def|PA14_00200|transcript|ABJ14975.1|protein_coding||c.*1751G>T|||||1751| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,2:1:36:2:17:0,-1.98329 0:1:1,0:1:16:0:0:0,-1.59998 0:2:2,0:2:32:0:0:0,-3.03997 0:5:5,0:5:136:0:0:0,-12.5017 +Chromosome 3000510 . C G 5.39191E-5 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=1.125;EPP=3.0103;EPPR=3.25157;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=11.2967;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=41;QR=280;RO=9;RPL=2;RPP=7.35324;RPPR=9.04217;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=2;SRP=9.04217;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_33770|PA14_33770|transcript|ABJ11566.1|protein_coding|1/1|c.1153G>C|p.Ala385Pro|1153/1176|1153/1176|385/391||,G|upstream_gene_variant|MODIFIER|opmQ|PA14_33750|transcript|ABJ11568.1|protein_coding||c.-2020G>C|||||2020|,G|upstream_gene_variant|MODIFIER|PA14_33760|PA14_33760|transcript|ABJ11567.1|protein_coding||c.-23G>C|||||23|,G|upstream_gene_variant|MODIFIER|PA14_33800|PA14_33800|transcript|ABJ11564.1|protein_coding||c.-2412C>G|||||2412|,G|upstream_gene_variant|MODIFIER|pvdA|PA14_33810|transcript|ABJ11563.1|protein_coding||c.-3024C>G|||||3024|,G|upstream_gene_variant|MODIFIER|pvdQ|PA14_33820|transcript|ABJ11562.1|protein_coding||c.-4478C>G|||||4478|,G|downstream_gene_variant|MODIFIER|pvdP|PA14_33740|transcript|ABJ11569.1|protein_coding||c.*3493C>G|||||3493|,G|downstream_gene_variant|MODIFIER|PA14_33780|PA14_33780|transcript|ABJ11565.1|protein_coding||c.*1253G>C|||||1253| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:79:0:0:0,-7.49763 0:4:4,0:4:120:0:0:0,-11.0896 0:3:3,2:1:40:2:41:0,-0.103943 0:2:2,0:2:41:0:0:0,-3.89478 +Chromosome 4969672 . A C 2.53434E-9 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=16;DPB=16;DPRA=2.2;EPP=9.52472;EPPR=11.1951;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=21.2638;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=500;RO=13;RPL=3;RPP=9.52472;RPPR=4.51363;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=7;SRP=3.17734;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|recC|PA14_55690|transcript|ABJ13555.1|protein_coding|1/1|c.2485T>G|p.Trp829Gly|2485/3516|2485/3516|829/1171||,C|upstream_gene_variant|MODIFIER|recD|PA14_55660|transcript|ABJ13553.1|protein_coding||c.-4762T>G|||||4762|,C|upstream_gene_variant|MODIFIER|recB|PA14_55670|transcript|ABJ13554.1|protein_coding||c.-1028T>G|||||1028|,C|upstream_gene_variant|MODIFIER|PA14_55730|PA14_55730|transcript|ABJ13558.1|protein_coding||c.-4311A>C|||||4311|,C|downstream_gene_variant|MODIFIER|PA14_55710|PA14_55710|transcript|ABJ13556.1|protein_coding||c.*2525T>G|||||2525|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_55720|PA14_55720|transcript|ABJ13557.1|protein_coding||c.*3321T>G|||||3321| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:74:0:0:0,-7.02486 0:3:3,2:1:39:2:4:0,-3.51656 0:3:3,0:3:115:0:0:0,-10.724 0:8:8,1:7:272:1:2:0,-24.6464 +Chromosome 287074 . T C 0.288088 . AB=0;ABP=0;AC=1;AF=0.25;AN=4;AO=4;CIGAR=1X;DP=7;DPB=7;DPRA=2;EPP=11.6962;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=7.25;MQMR=5;NS=4;NUMALT=1;ODDS=2.68773;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=109;RO=3;RPL=4;RPP=11.6962;RPPR=9.52472;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=3;SRP=9.52472;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_03220|PA14_03220|transcript|ABJ15211.1|protein_coding|1/1|c.1199A>G|p.Glu400Gly|1199/3060|1199/3060|400/1019||,C|upstream_gene_variant|MODIFIER|PA14_03190|PA14_03190|transcript|ABJ15208.1|protein_coding||c.-4659A>G|||||4659|,C|upstream_gene_variant|MODIFIER|PA14_03200|PA14_03200|transcript|ABJ15209.1|protein_coding||c.-2359A>G|||||2359|,C|upstream_gene_variant|MODIFIER|PA14_03210|PA14_03210|transcript|ABJ15210.1|protein_coding||c.-1865A>G|||||1865|,C|upstream_gene_variant|MODIFIER|PA14_03250|PA14_03250|transcript|ABJ15213.1|protein_coding||c.-4494T>C|||||4494|,C|downstream_gene_variant|MODIFIER|hcpC|PA14_03240|transcript|ABJ15212.1|protein_coding||c.*1380A>G|||||1380| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,2:1:39:2:4:0,-0.0192772 0:2:2,1:1:36:1:2:0,-0.459207 1:1:1,1:0:0:1:15:-0.813795,0 0:1:1,0:1:34:0:0:0,-0.599485 +Chromosome 1899851 . T G 9.29372E-7 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=11;DPB=11;DPRA=1.75;EPP=9.52472;EPPR=5.80219;GTI=0;LEN=1;MEANALT=1.5;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=15.9309;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=29;QR=225;RO=7;RPL=0;RPP=9.52472;RPPR=10.7656;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=4;SRP=3.32051;SRR=3;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|PA14_21860|PA14_21860|transcript|ABJ12508.1|protein_coding|1/1|c.26T>G|p.Leu9Arg|26/480|26/480|9/159||,G|upstream_gene_variant|MODIFIER|PA14_21780|PA14_21780|transcript|ABJ12514.1|protein_coding||c.-4691A>C|||||4691|,G|upstream_gene_variant|MODIFIER|rdgC|PA14_21790|transcript|ABJ12513.1|protein_coding||c.-3684A>C|||||3684|,G|upstream_gene_variant|MODIFIER|tRNA|EBG00001225062|transcript|EBT00001793441.1|protein_coding||c.-3447A>C|||||3447|WARNING_TRANSCRIPT_INCOMPLETE,G|upstream_gene_variant|MODIFIER|tRNA|EBG00001225157|transcript|EBT00001793503.1|protein_coding||c.-3354A>C|||||3354|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,G|upstream_gene_variant|MODIFIER|PA14_21840|PA14_21840|transcript|ABJ12510.1|protein_coding||c.-798A>C|||||798|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|qor|PA14_21890|transcript|ABJ12505.1|protein_coding||c.-4538T>G|||||4538|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|PA14_21800|PA14_21800|transcript|PA14_21800-1.1|protein_coding||c.*3447T>G|||||3447|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|PA14_21810|PA14_21810|transcript|PA14_21810-1.1|protein_coding||c.*3354T>G|||||3354|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|PA14_21820|PA14_21820|transcript|ABJ12512.1|protein_coding||c.*2333T>G|||||2333|,G|downstream_gene_variant|MODIFIER|PA14_21830|PA14_21830|transcript|ABJ12511.1|protein_coding||c.*1532T>G|||||1532|,G|downstream_gene_variant|MODIFIER|PA14_21850|PA14_21850|transcript|ABJ12509.1|protein_coding||c.*383T>G|||||383|,G|downstream_gene_variant|MODIFIER|PA14_21870|PA14_21870|transcript|ABJ12507.1|protein_coding||c.*468A>C|||||468|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|tsp|PA14_21880|transcript|ABJ12506.1|protein_coding||c.*2312A>C|||||2312| GT:DP:DPR:RO:QR:AO:QA:GL 0:1:1,0:1:39:0:0:0,-3.89656 0:3:3,0:3:117:0:0:0,-10.9104 0:3:3,2:1:27:2:15:0,-1.27479 0:4:4,1:2:42:1:14:0,-2.58264 +Chromosome 2835395 . C G 2.9588E-8 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=17;DPB=17;DPRA=1.25;EPP=9.52472;EPPR=5.49198;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=18.8045;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=28;QR=522;RO=14;RPL=0;RPP=9.52472;RPPR=8.59409;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=13;SRP=25.3454;SRR=1;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|PA14_32640|PA14_32640|transcript|ABJ11654.1|protein_coding|1/1|c.72G>C|p.Ala24Ala|72/912|72/912|24/303||,G|upstream_gene_variant|MODIFIER|PA14_32700|PA14_32700|transcript|ABJ11649.1|protein_coding||c.-4091C>G|||||4091|,G|downstream_gene_variant|MODIFIER|dipZ2|PA14_32590|transcript|ABJ11658.1|protein_coding||c.*3832C>G|||||3832|,G|downstream_gene_variant|MODIFIER|PA14_32600|PA14_32600|transcript|ABJ11657.1|protein_coding||c.*2996C>G|||||2996|,G|downstream_gene_variant|MODIFIER|dsbG|PA14_32610|transcript|ABJ11656.1|protein_coding||c.*2229C>G|||||2229|,G|downstream_gene_variant|MODIFIER|PA14_32630|PA14_32630|transcript|ABJ11655.1|protein_coding||c.*822C>G|||||822|,G|downstream_gene_variant|MODIFIER|PA14_32650|PA14_32650|transcript|ABJ11653.1|protein_coding||c.*113G>C|||||113|,G|downstream_gene_variant|MODIFIER|PA14_32660|PA14_32660|transcript|ABJ11652.1|protein_coding||c.*770G>C|||||770|,G|downstream_gene_variant|MODIFIER|PA14_32670|PA14_32670|transcript|ABJ11651.1|protein_coding||c.*2194G>C|||||2194|,G|downstream_gene_variant|MODIFIER|gtdA|PA14_32690|transcript|ABJ11650.1|protein_coding||c.*2905G>C|||||2905| GT:DP:DPR:RO:QR:AO:QA:GL 0:5:5,0:5:197:0:0:0,-18.1066 0:1:1,0:1:36:0:0:0,-3.59827 0:6:6,0:6:209:0:0:0,-19.1415 0:5:5,3:2:80:3:28:0,-4.97856 +Chromosome 4265157 . T C 4.70121E-11 . AB=0;ABP=0;AC=0;AF=0;AN=4;AO=3;CIGAR=1X;DP=15;DPB=15;DPRA=1.5;EPP=9.52472;EPPR=5.9056;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=25.9168;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6;QR=375;RO=12;RPL=0;RPP=9.52472;RPPR=3.73412;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=5;SRP=3.73412;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=C|synonymous_variant|LOW|PA14_47910|PA14_47910|transcript|ABJ10449.1|protein_coding|1/1|c.654T>C|p.His218His|654/675|654/675|218/224||,C|upstream_gene_variant|MODIFIER|PA14_47870|PA14_47870|transcript|ABJ10453.1|protein_coding||c.-4506A>G|||||4506|,C|upstream_gene_variant|MODIFIER|PA14_47890|PA14_47890|transcript|ABJ10451.1|protein_coding||c.-2299A>G|||||2299|,C|upstream_gene_variant|MODIFIER|PA14_47920|PA14_47920|transcript|ABJ10448.1|protein_coding||c.-278T>C|||||278|,C|upstream_gene_variant|MODIFIER|PA14_47930|PA14_47930|transcript|ABJ10447.1|protein_coding||c.-1158T>C|||||1158|,C|upstream_gene_variant|MODIFIER|PA14_47940|PA14_47940|transcript|ABJ10446.1|protein_coding||c.-2900T>C|||||2900|,C|upstream_gene_variant|MODIFIER|PA14_47950|PA14_47950|transcript|ABJ10445.1|protein_coding||c.-3576T>C|||||3576|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|glnQ|PA14_47960|transcript|ABJ10444.1|protein_coding||c.-4217T>C|||||4217|,C|upstream_gene_variant|MODIFIER|PA14_47970|PA14_47970|transcript|ABJ10443.1|protein_coding||c.-4965T>C|||||4965|,C|downstream_gene_variant|MODIFIER|PA14_47880|PA14_47880|transcript|ABJ10452.1|protein_coding||c.*3540T>C|||||3540|,C|downstream_gene_variant|MODIFIER|PA14_47900|PA14_47900|transcript|ABJ10450.1|protein_coding||c.*818T>C|||||818| GT:DP:DPR:RO:QR:AO:QA:GL 0:2:2,0:2:65:0:0:0,-6.1722 0:5:5,3:2:74:3:6:0,-6.46543 0:5:5,0:5:161:0:0:0,-14.7969 0:3:3,0:3:75:0:0:0,-6.99617
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test8.in1.s1.s3.d1.d1.gt.nh.fy.gy.rvcf Wed Oct 10 18:53:14 2018 -0400 @@ -0,0 +1,8 @@ +#CHROM POS ID REF ALT BEST_PAIR BEST_SEP_SCORE BEST_AVEDP PAIR_NUM PAIR_SEP_SCORE PAIR_AVEDP STATE(S)_USED PAIR1_MEMBERS PAIR1_SCORE_DATA PAIR2_MEMBERS PAIR2_SCORE_DATA +Chromosome 4823634 . C A 1 1 7 1 1 7 0;1 gDNA-PA14 0 205w3 1 +Chromosome 5734941 . G T 1 1 5 1 1 5 0;1 gDNA-PA14 0 205w2 1 +Chromosome 1805739 . T C 1 1 4 1 1 4 0;1 gDNA-PA14 0 205w2 1 +Chromosome 4521011 . G T 1 1 3 1 1 3 0;1 gDNA-PA14 0 205w3 1 +Chromosome 1881807 . C A 1 1 2 1 1 2 1;0 gDNA-PA14 1 205w1,205w2,205w3 0,0,0 +Chromosome 287074 . T C 1 1 2 1 1 2 0;1 gDNA-PA14 0 205w2 1 +Chromosome 3103618 . G T 1 1 2 1 1 2 1;0 gDNA-PA14 1 205w2 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test8.in1.s1.s3.d1.d1.gt.nh.fy.gy.vcf Wed Oct 10 18:53:14 2018 -0400 @@ -0,0 +1,74 @@ +##fileformat=VCFv4.1 +##fileDate=20170620 +##source=freeBayes v1.0.2-29-g41c1313 +##reference=localref.fa +##contig=<ID=Chromosome,length=6537648> +##phasing=none +##commandline="freebayes --region Chromosome:0..6537648 --bam b_0.bam --bam b_1.bam --bam b_2.bam --bam b_3.bam --fasta-reference localref.fa --vcf ./vcf_output/part_Chromosome:0..6537648.vcf --theta 0.001 --ploidy 1" +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> +##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype"> +##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]"> +##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally"> +##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally"> +##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally"> +##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally"> +##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> +##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred"> +##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations"> +##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations"> +##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand"> +##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand"> +##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand"> +##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand"> +##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous"> +##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome"> +##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele"> +##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele"> +##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without."> +##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best."> +##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout."> +##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> +##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR."> +##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position."> +##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles."> +##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length"> +##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles"> +##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles"> +##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments"> +##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments"> +##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> +##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record."> +##INFO=<ID=technology.ILLUMINA,Number=A,Type=Float,Description="Fraction of observations supporting the alternate observed in reads from ILLUMINA"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=DPR,Number=A,Type=Integer,Description="Number of observation for each allele"> +##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> +##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> +##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> +##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> +##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> +##SnpEffVersion="4.3i (build 2016-12-15 22:33), by Pablo Cingolani" +##SnpEffCmd="SnpEff Pseudomonas_aeruginosa_ucbpp_pa14 /Users/rleach/PROJECT/NINA/PA14DNASEQ-20170601/SNPsSmallIndels/FreeBayes_ploidy1_filtering_FreeBayes_variants.vcf.fixed " +##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' "> +##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' "> +##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' "> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT gDNA-PA14 205w3 205w2 205w1 +Chromosome 4823634 . C A 9.86082E-8 . AB=0;ABP=0;AC=1;AF=0.25;AN=4;AO=3;CIGAR=1X;DP=35;DPB=35;DPRA=0.590909;EPP=3.73412;EPPR=4.09604;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=17.6007;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1016;RO=32;RPL=1;RPP=3.73412;RPPR=4.09604;RPR=2;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=16;SRP=3.0103;SRR=16;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|mucD|PA14_54390|transcript|ABJ09918.1|protein_coding|1/1|c.372G>T|p.Val124Val|372/1425|372/1425|124/474||,A|upstream_gene_variant|MODIFIER|rnc|PA14_54330|transcript|ABJ09922.1|protein_coding||c.-4406G>T|||||4406|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|PA14_54340|PA14_54340|transcript|ABJ09921.1|protein_coding||c.-4032G>T|||||4032|,A|upstream_gene_variant|MODIFIER|lepB|PA14_54350|transcript|ABJ09920.1|protein_coding||c.-3008G>T|||||3008|,A|upstream_gene_variant|MODIFIER|lepA|PA14_54370|transcript|ABJ09919.1|protein_coding||c.-1203G>T|||||1203|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|nadB|PA14_54450|transcript|ABJ09913.1|protein_coding||c.-3428C>A|||||3428|,A|downstream_gene_variant|MODIFIER|mucC|PA14_54400|transcript|ABJ09917.1|protein_coding||c.*411G>T|||||411|,A|downstream_gene_variant|MODIFIER|mucB|PA14_54410|transcript|ABJ09916.1|protein_coding||c.*863G>T|||||863|,A|downstream_gene_variant|MODIFIER|mucA|PA14_54420|transcript|ABJ09915.1|protein_coding||c.*1822G>T|||||1822|,A|downstream_gene_variant|MODIFIER|algU|PA14_54430|transcript|ABJ09914.1|protein_coding||c.*2438G>T|||||2438| GT:DP:DPR:RO:QR:AO:QA:GL 0:10:10,1:9:270:1:16:0,-22.9897 1:3:3,2:1:16:2:18:-0.110001,0 0:9:9,0:9:308:0:0:0,-28.0447 0:13:13,0:13:422:0:0:0,-38.2837 +Chromosome 5734941 . G T 8.00079E-6 . AB=0;ABP=0;AC=1;AF=0.25;AN=4;AO=4;CIGAR=1X;DP=16;DPB=16;DPRA=1.28571;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=13.7369;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=64;QR=268;RO=12;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=3;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=10;SRP=14.5915;SRR=2;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|yncA|PA14_64360|transcript|ABJ14250.1|protein_coding|1/1|c.360G>T|p.Val120Val|360/519|360/519|120/172||,T|upstream_gene_variant|MODIFIER|ureB|PA14_64370|transcript|ABJ14251.1|protein_coding||c.-176G>T|||||176|,T|upstream_gene_variant|MODIFIER|ureC|PA14_64390|transcript|ABJ14252.1|protein_coding||c.-544G>T|||||544|,T|upstream_gene_variant|MODIFIER|5_ureB_sRNA|EBG00001225143|transcript|EBT00001793474.1|sRNA||n.-690G>T|||||690|,T|upstream_gene_variant|MODIFIER|PA14_64400|PA14_64400|transcript|ABJ14253.1|protein_coding||c.-2513G>T|||||2513|,T|upstream_gene_variant|MODIFIER|PA14_64420|PA14_64420|transcript|ABJ14255.1|protein_coding||c.-4132G>T|||||4132|,T|upstream_gene_variant|MODIFIER|PA14_64430|PA14_64430|transcript|ABJ14256.1|protein_coding||c.-4898G>T|||||4898|,T|downstream_gene_variant|MODIFIER|PA14_64280|PA14_64280|transcript|ABJ14244.1|protein_coding||c.*4824G>T|||||4824|,T|downstream_gene_variant|MODIFIER|PA14_64290|PA14_64290|transcript|ABJ14245.1|protein_coding||c.*3748G>T|||||3748|,T|downstream_gene_variant|MODIFIER|PA14_64300|PA14_64300|transcript|ABJ14246.1|protein_coding||c.*2894G>T|||||2894|,T|downstream_gene_variant|MODIFIER|PA14_64310|PA14_64310|transcript|ABJ14247.1|protein_coding||c.*2059G>T|||||2059|,T|downstream_gene_variant|MODIFIER|PA14_64320|PA14_64320|transcript|ABJ14248.1|protein_coding||c.*1523G>T|||||1523|,T|downstream_gene_variant|MODIFIER|ureD|PA14_64335|transcript|ABJ15649.1|protein_coding||c.*672G>T|||||672|,T|downstream_gene_variant|MODIFIER|ureA|PA14_64350|transcript|ABJ14249.1|protein_coding||c.*368G>T|||||368|,T|downstream_gene_variant|MODIFIER|ybiI|PA14_64410|transcript|ABJ14254.1|protein_coding||c.*3740C>A|||||3740| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,0:4:102:0:0:0,-9.43129 0:3:3,1:2:32:1:16:0,-1.43998 1:6:6,3:3:47:3:48:-0.09333,0 0:3:3,0:3:87:0:0:0,-8.11544 +Chromosome 1805739 . T C 1.50676E-4 . AB=0;ABP=0;AC=1;AF=0.25;AN=4;AO=4;CIGAR=1X;DP=15;DPB=15;DPRA=4.66667;EPP=5.18177;EPPR=7.94546;GTI=0;LEN=1;MEANALT=1;MQM=56;MQMR=60;NS=4;NUMALT=1;ODDS=10.2882;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=44;QR=242;RO=11;RPL=3;RPP=5.18177;RPPR=4.78696;RPR=1;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=7;SRP=4.78696;SRR=4;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|cyp23|PA14_20970|transcript|ABJ12582.1|protein_coding|1/1|c.482A>G|p.Glu161Gly|482/1257|482/1257|161/418||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_20900|PA14_20900|transcript|ABJ12587.1|protein_coding||c.-3408A>G|||||3408|,C|upstream_gene_variant|MODIFIER|PA14_20920|PA14_20920|transcript|ABJ12586.1|protein_coding||c.-2564A>G|||||2564|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|PA14_20940|PA14_20940|transcript|ABJ12585.1|protein_coding||c.-2207A>G|||||2207|,C|upstream_gene_variant|MODIFIER|fabH2|PA14_20950|transcript|ABJ12584.1|protein_coding||c.-1201A>G|||||1201|,C|upstream_gene_variant|MODIFIER|PA14_20960|PA14_20960|transcript|ABJ12583.1|protein_coding||c.-772A>G|||||772|,C|downstream_gene_variant|MODIFIER|rfaD|PA14_20890|transcript|ABJ12588.1|protein_coding||c.*4585T>C|||||4585|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|PA14_20980|PA14_20980|transcript|ABJ12581.1|protein_coding||c.*474A>G|||||474|,C|downstream_gene_variant|MODIFIER|PA14_21000|PA14_21000|transcript|ABJ12580.1|protein_coding||c.*1390A>G|||||1390|,C|downstream_gene_variant|MODIFIER|PA14_21010|PA14_21010|transcript|ABJ12579.1|protein_coding||c.*2715A>G|||||2715|,C|downstream_gene_variant|MODIFIER|PA14_21020|PA14_21020|transcript|ABJ12578.1|protein_coding||c.*3878A>G|||||3878| GT:DP:DPR:RO:QR:AO:QA:GL 0:4:4,1:3:56:1:14:0,-3.82263 0:1:1,0:1:14:0:0:0,-1.39999 1:3:3,2:1:2:2:16:-1.31998,0 0:7:7,1:6:170:1:14:0,-14.1769 +Chromosome 4521011 . G T 0.00639626 . AB=0;ABP=0;AC=1;AF=0.25;AN=4;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=0.666667;EPP=7.35324;EPPR=3.25157;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=6.51986;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=208;RO=9;RPL=2;RPP=7.35324;RPPR=3.25157;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=8;SRP=14.8328;SRR=1;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_50850|PA14_50850|transcript|ABJ10208.1|protein_coding|1/1|c.403G>T|p.Gly135Cys|403/465|403/465|135/154||,T|upstream_gene_variant|MODIFIER|PA14_50830|PA14_50830|transcript|ABJ10210.1|protein_coding||c.-2755C>A|||||2755|,T|upstream_gene_variant|MODIFIER|PA14_50840|PA14_50840|transcript|ABJ10209.1|protein_coding||c.-532C>A|||||532|,T|upstream_gene_variant|MODIFIER|PA14_50890|PA14_50890|transcript|ABJ10204.1|protein_coding||c.-2081G>T|||||2081|,T|upstream_gene_variant|MODIFIER|PA14_50900|PA14_50900|transcript|ABJ10203.1|protein_coding||c.-2581G>T|||||2581|,T|upstream_gene_variant|MODIFIER|PA14_50910|PA14_50910|transcript|ABJ10202.1|protein_coding||c.-3054G>T|||||3054|,T|upstream_gene_variant|MODIFIER|PA14_50920|PA14_50920|transcript|ABJ10201.1|protein_coding||c.-3454G>T|||||3454|,T|downstream_gene_variant|MODIFIER|PA14_50860|PA14_50860|transcript|ABJ10207.1|protein_coding||c.*101C>A|||||101|,T|downstream_gene_variant|MODIFIER|PA14_50870|PA14_50870|transcript|ABJ10206.1|protein_coding||c.*903C>A|||||903|,T|downstream_gene_variant|MODIFIER|PA14_50880|PA14_50880|transcript|ABJ10205.1|protein_coding||c.*1318C>A|||||1318|,T|downstream_gene_variant|MODIFIER|PA14_50930|PA14_50930|transcript|ABJ10200.1|protein_coding||c.*4192C>A|||||4192| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,0:3:74:0:0:0,-6.90589 1:2:2,2:0:0:2:32:-3.03997,0 0:2:2,0:2:49:0:0:0,-4.65395 0:4:4,0:4:85:0:0:0,-7.85997 +Chromosome 1881807 . C A 1.66784E-5 . AB=0;ABP=0;AC=1;AF=0.25;AN=4;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0.857143;EPP=7.35324;EPPR=18.2106;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=4;NUMALT=1;ODDS=12.4931;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4;QR=262;RO=7;RPL=0;RPP=7.35324;RPPR=10.7656;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=10.7656;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=A|missense_variant|MODERATE|lhr1|PA14_21690|transcript|ABJ12522.1|protein_coding|1/1|c.2440C>A|p.Gln814Lys|2440/4347|2440/4347|814/1448||,A|upstream_gene_variant|MODIFIER|PA14_21670|PA14_21670|transcript|ABJ12523.1|protein_coding||c.-3058G>T|||||3058|,A|downstream_gene_variant|MODIFIER|PA14_21640|PA14_21640|transcript|ABJ12527.1|protein_coding||c.*4405C>A|||||4405|,A|downstream_gene_variant|MODIFIER|PA14_21650|PA14_21650|transcript|ABJ12526.1|protein_coding||c.*3750C>A|||||3750|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_21660|PA14_21660|transcript|ABJ12525.1|protein_coding||c.*3424C>A|||||3424|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_21680|PA14_21680|transcript|ABJ12524.1|protein_coding||c.*2508C>A|||||2508|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|PA14_21700|PA14_21700|transcript|ABJ12521.1|protein_coding||c.*1915G>T|||||1915| GT:DP:DPR:RO:QR:AO:QA:GL 1:2:2,2:0:0:2:4:-0.38,0 0:3:3,0:3:109:0:0:0,-10.1657 0:1:1,0:1:36:0:0:0,-3.59827 0:3:3,0:3:117:0:0:0,-10.9104 +Chromosome 287074 . T C 0.288088 . AB=0;ABP=0;AC=1;AF=0.25;AN=4;AO=4;CIGAR=1X;DP=7;DPB=7;DPRA=2;EPP=11.6962;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=7.25;MQMR=5;NS=4;NUMALT=1;ODDS=2.68773;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=109;RO=3;RPL=4;RPP=11.6962;RPPR=9.52472;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=3;SRP=9.52472;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|PA14_03220|PA14_03220|transcript|ABJ15211.1|protein_coding|1/1|c.1199A>G|p.Glu400Gly|1199/3060|1199/3060|400/1019||,C|upstream_gene_variant|MODIFIER|PA14_03190|PA14_03190|transcript|ABJ15208.1|protein_coding||c.-4659A>G|||||4659|,C|upstream_gene_variant|MODIFIER|PA14_03200|PA14_03200|transcript|ABJ15209.1|protein_coding||c.-2359A>G|||||2359|,C|upstream_gene_variant|MODIFIER|PA14_03210|PA14_03210|transcript|ABJ15210.1|protein_coding||c.-1865A>G|||||1865|,C|upstream_gene_variant|MODIFIER|PA14_03250|PA14_03250|transcript|ABJ15213.1|protein_coding||c.-4494T>C|||||4494|,C|downstream_gene_variant|MODIFIER|hcpC|PA14_03240|transcript|ABJ15212.1|protein_coding||c.*1380A>G|||||1380| GT:DP:DPR:RO:QR:AO:QA:GL 0:3:3,2:1:39:2:4:0,-0.0192772 0:2:2,1:1:36:1:2:0,-0.459207 1:1:1,1:0:0:1:15:-0.813795,0 0:1:1,0:1:34:0:0:0,-0.599485 +Chromosome 3103618 . G T 0.0227988 . AB=0;ABP=0;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=1;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=2;NUMALT=1;ODDS=5.74083;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=54;RO=2;RPL=0;RPP=7.35324;RPPR=7.35324;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.ILLUMINA=1;ANN=T|missense_variant|MODERATE|PA14_34850|PA14_34850|transcript|ABJ11481.1|protein_coding|1/1|c.387G>T|p.Leu129Phe|387/543|387/543|129/180||,T|upstream_gene_variant|MODIFIER|chiC|PA14_34870|transcript|ABJ11480.1|protein_coding||c.-375G>T|||||375|,T|upstream_gene_variant|MODIFIER|PA14_34880|PA14_34880|transcript|ABJ11479.1|protein_coding||c.-2003G>T|||||2003|,T|upstream_gene_variant|MODIFIER|PA14_34900|PA14_34900|transcript|ABJ11478.1|protein_coding||c.-2749G>T|||||2749|,T|upstream_gene_variant|MODIFIER|PA14_34920|PA14_34920|transcript|ABJ11477.1|protein_coding||c.-4559G>T|||||4559|,T|downstream_gene_variant|MODIFIER|PA14_34840|PA14_34840|transcript|ABJ11482.1|protein_coding||c.*454G>T|||||454| GT:DP:DPR:RO:QR:AO:QA:GL 1:2:2,2:0:0:2:32:-3.03997,0 . 0:2:2,0:2:54:0:0:0,-5.12589 .
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test9.in2.s0.d0.gt.hy.fy.gy.rvcf Wed Oct 10 18:53:14 2018 -0400 @@ -0,0 +1,1 @@ +#CHROM POS ID REF ALT BEST_PAIR BEST_SEP_SCORE BEST_AVEDP PAIR_NUM PAIR_SEP_SCORE PAIR_AVEDP STATE(S)_USED PAIR1_MEMBERS PAIR1_SCORE_DATA PAIR2_MEMBERS PAIR2_SCORE_DATA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test9.in2.s0.d0.gt.hy.fy.gy.vcf Wed Oct 10 18:53:14 2018 -0400 @@ -0,0 +1,49 @@ +##fileformat=VCFv4.2 +##fileDate=20180104 +##reference= +##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> +##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> +##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> +##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)"> +##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"> +##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants"> +##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants"> +##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants"> +##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants"> +##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends"> +##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend"> +##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants"> +##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples"> +##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples"> +##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples"> +##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples"> +##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call"> +##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend"> +##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend"> +##ALT=<ID=DEL,Description="Deletion"> +##ALT=<ID=DUP,Description="Duplication"> +##ALT=<ID=INV,Description="Inversion"> +##ALT=<ID=DUP:TANDEM,Description="Tandem duplication"> +##ALT=<ID=INS,Description="Insertion of novel sequence"> +##ALT=<ID=CNV,Description="Copy number variable region"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant"> +##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant"> +##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant"> +##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality"> +##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Phred-scaled probability that this site is variant (non-reference in this sample"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth"> +##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally"> +##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of reference observations"> +##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of alternate observations"> +##FORMAT=<ID=RS,Number=1,Type=Integer,Description="Reference allele split-read observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=AS,Number=A,Type=Integer,Description="Alternate allele split-read observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=ASC,Number=A,Type=Integer,Description="Alternate allele clipped-read observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Reference allele paired-end observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)"> +##source=LUMPY +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT JSS-Qmut-07__Read JSS-Qmut-08__Read JSS-Vmut-01__Read JSS-Vmut-03__Read JSS-Vmut-05__Read JSS-Vmut-06__Read JSS-Vmut-07__Read JSS-Vmut-08__Read JSS-Vmut-09__Read JSS-Vmut-10__Read JSS-Vmut-11__Read JSS-Vmut-12__Read JSS-Vmut-13__Read JSS-Vmut-14__Read VP882-c2__Read VP882-c24__Read VP882-parent__Read JSS-Qmut-01__Read JSS-Qmut-02__Read JSS-Qmut-03__Read JSS-Qmut-04__Read JSS-Qmut-05__Read JSS-Qmut-06__Read JSS-Qmut-09__Read JSS-Qmut-10__Read JSS-Vmut-02__Read JSS-Vmut-04__Read
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcfsamplecompare.xml Wed Oct 10 18:53:14 2018 -0400 @@ -0,0 +1,236 @@ +<tool id="vcfsamplecompare" + name="vcfsamplecompare" + version="0.1.0"> + + <description>sort/filter variants that differ between sample groups</description> + + <requirements> + <requirement type="package" version="v2.006">vcfsamplecompare</requirement> + </requirements> + + <version_command>vcfSampleCompare.pl --version</version_command> + + <command detect_errors="aggressive"> + <![CDATA[ + vcfSampleCompare.pl + '$infile' + + #for $comp in $rep_comparisons: + -s '$comp.groupone' + -d '$comp.minone' + -s '$comp.grouptwo' + -d '$comp.mintwo' + #end for + + $genotypemode + $filtermode + $growmode + $header + -u '.vsc' + -o '.vsc.vcf' && + mv '${infile}.vsc.vcf' '$vcfoutfile' && + mv '${infile}.vsc' '$rvcfoutfile' + ]]> + </command> + + <inputs> + <param format="vcf" + name="infile" + label="VCF file" + argument="-i" + type="data" + + help="A VCF file that has more than 1 sample column."/> + + <repeat name="rep_comparisons" title="Sample Comparison" min="0"> + <param name="groupone" + type="text" + label="Sample Group 1" + help="Space delimited list of sample names (exactly as they appear in the column headers of the VCF file), e.g. 'wt1 wt2 wt3'."/> + <param name="minone" + type="integer" + min="1" + value="1" + label="Minimum size of Sample Group 1" + help="The minimum size of sample group 1 must be an integer between 1 and the number of samples in sample group 1. The minimum of 1 of the 2 sample groups must represent a majority of that group (to produce meaningful results). Use-case: If you have 3 wild type replicate samples in group 1 and you want to find at least 2 of 10 mutant samples from group 2 that differ from all of the wildtype samples, you would specify `-d 3` for group 1 and `-d 2` for group 2"/> + <param name="grouptwo" + type="text" + label="Sample Group 2" + help="Space delimited list of sample names (exactly as they appear in the column headers of the VCF file), e.g. 'mutant1 mutant2 mutant3'."/> + <param name="mintwo" + type="integer" + min="1" + value="1" + label="Minimum size of Sample Group 2" + help="The minimum size of sample group 2 must be an integer between 1 and the number of samples in sample group 2. The minimum of 1 of the 2 sample groups must represent a majority of that group (to produce meaningful results). Use-case: If you have 3 wild type replicate samples in group 1 and you want to find at least 2 of 10 mutant samples from group 2 that differ from all of the wildtype samples, you would specify `-d 3` for group 1 and `-d 2` for group 2"/> + </repeat> + + <param name="obsrat" + label="Allelic frequency difference gap" + argument="-a" + type="float" + value="0.6" + + help="A decimal value between 0.0 and 1.0 (inclusive) indicating the minimum difference in the observation ratio averages of a particular variant state (e.g. 'AO/DP') in the sample groups being compared. Not used in genotype mode." /> + + <param name="genotypemode" + label="Comparison mode" + argument="--genotype|--nogenotype" + type="select" + + help="The basis for the degree of difference between the 2 sample groups can be either the genotype calls or allelic frequency (i.e. observation ratios (AO/DP))."> + <option value="--genotype" selected="true">Genotype calls</option> + <option value="--nogenotype">Allelic Frequencies</option> + </param> + + <param name="filtermode" + label="Comparison mode" + argument="--filter|--nofilter" + type="select" + + help="Filtering will omit rows based on the comparison mode. If the comparison mode is based on genotype calls, the sample groups must not share any genotype calls in common. If the comparison mode is allelic frequencies, the difference between the average observation ratios in the sample groups must be greater than (or equal to) the allelic frequency difference gap (-a)."> + <option value="--filter" selected="true">Filter</option> + <option value="--nofilter">Do not filter</option> + </param> + + <param name="growmode" + label="Grow mode" + argument="--grow|--nogrow" + type="select" + + help="Sample groups will initially be greedily created using their minimum size (-d). If the minimum sample group size is less than the number of samples available for a group, samples will be added when in grow mode (in a way consistent with the comparison mode). If the comparison mode is based on genotype calls, as long as the sample groups do not share any genotype calls in common, samples will be greedily added to each group. If the comparison mode is allelic frequencies, as long as the difference between the average observation ratios in the sample groups is greater than (or equal to) the allelic frequency difference gap (-a), samples will be greedily added to each group. Note, grow mode may lower the sort order of a variant in allelic frequency mode."> + <option value="--grow" selected="true">Grow sample groups from the minimum size (-d)</option> + <option value="--nogrow">Do not grow sample groups</option> + </param> + + <param name="header" + label="Header" + argument="--header|--noheader" + type="hidden" + value="--noheader"/> + </inputs> + + <outputs> + <data format="vcf" name="vcfoutfile" /> + <data format="tabular" name="rvcfoutfile" /> + </outputs> + + <tests> + <test> + <param name="infile" value="fbse1.vcf"/> + <repeat name="rep_comparisons"> + <param name="groupone" value="gDNA-PA14"/> + <param name="minone" value="1"/> + <param name="grouptwo" value="205w3 205w2 205w1"/> + <param name="mintwo" value="1"/> + </repeat> + <param name="obsrat" value="0.6"/> + <param name="genotypemode" value="--nogenotype"/> + <param name="filtermode" value="--filter"/> + <param name="growmode" value="--grow"/> + <param name="header" value="--noheader"/> + <output name="vcfoutfile" file="test7.in1.s1.s3.d1.d1.af.a6.nh.fy.gy.vcf"/> + <output name="rvcfoutfile" file="test7.in1.s1.s3.d1.d1.af.a6.nh.fy.gy.rvcf"/> + </test> + <test> + <param name="infile" value="fbse1.vcf"/> + <repeat name="rep_comparisons"> + <param name="groupone" value="gDNA-PA14"/> + <param name="minone" value="1"/> + <param name="grouptwo" value="205w3 205w2 205w1"/> + <param name="mintwo" value="1"/> + </repeat> + <param name="obsrat" value="0.6"/> + <param name="genotypemode" value="--genotype"/> + <param name="filtermode" value="--filter"/> + <param name="growmode" value="--grow"/> + <param name="header" value="--noheader"/> + <output name="vcfoutfile" file="test8.in1.s1.s3.d1.d1.gt.nh.fy.gy.vcf"/> + <output name="rvcfoutfile" file="test8.in1.s1.s3.d1.d1.gt.nh.fy.gy.rvcf"/> + </test> + <test> + <param name="infile" value="lest1.vcf"/> + <param name="obsrat" value="0.6"/> + <param name="genotypemode" value="--genotype"/> + <param name="filtermode" value="--filter"/> + <param name="growmode" value="--grow"/> + <param name="header" value="--noheader"/> + <output name="vcfoutfile" file="test9.in2.s0.d0.gt.hy.fy.gy.vcf"/> + <output name="rvcfoutfile" file="test9.in2.s0.d0.gt.hy.fy.gy.rvcf"/> + </test> + <test> + <param name="infile" value="lest2.vcf"/> + <param name="obsrat" value="0.6"/> + <param name="genotypemode" value="--nogenotype"/> + <param name="filtermode" value="--filter"/> + <param name="growmode" value="--grow"/> + <param name="header" value="--noheader"/> + <output name="vcfoutfile" file="test10.in3.s0.d0.af.a6.hy.fy.gy.vcf"/> + <output name="rvcfoutfile" file="test10.in3.s0.d0.af.a6.hy.fy.gy.rvcf"/> + </test> + </tests> + + <help> + <![CDATA[ + +This script sorts and (optionally) filters the rows/variants of a VCF file (containing data for 2 or more samples) based on the differences in the variant data between samples or sample groups. Degree of "difference" is determined by either the ratio of group-specific genotype calls over group size or the difference in average allelic frequency (with a gap size threshold). The the pair of samples or sample groups used to represent the difference for a variant row is the one leading to the greatest difference in consistent genotype or average allelic frequencies (i.e. observation ratios, e.g. AO/DP) of the same variant state. + +This script works with VCF files generated by freeBayes (for SNP and small nucleotide variants) or svTyper (for structural variants). It will work with any other VCF data that includes GT or AO, RO, and DP tags in the FORMAT string. + +Each row in a VCF file will be assumed to represent a variant (or variant position). In the context of this script, there are two ways to look at differences among the samples: genotype calls and the ratio of observations of a particular variant out of the total observatons. We'll refer to this as either "allelic frequency" or "observation ratios" throughout the documentation. + +DEFAULT SORTING BEHAVIOR + +VCF rows/variants are sorted by the (maximum) degree of difference that exists between the pairs of sample groups you define. If multiple pairs are defined, the maximum difference computed among those pairs is used in the sort. How the degree of difference is calculated depends on whether the --genotype or --nogenotype flag is supplied. + +If --genotype is supplied, sorting will be based on the degree of difference in genotype calls between the 2 sample groups. Put simply, variants where all the genotype calls differ between sample group 1 and sample group 2 will be at the top of the results. If the genotype calls within a group are not consistent, the rank of the row falls and it will appear lower in the results. If all of the genotype calls between 2 sample groups are the same, the row will be at the bottom of the results. If samples do not have genotype calls, the rank falls even lower. The very bottom of the results will contain variant which have no genotype calls among any samples in the 2 groups. + +If --nogenotype is supplied, sorting will be based on the degree of difference in allelic frequencies between the 2 samples groups. The degree of difference between allelic frequencies will be the maximum difference in observation ratios among the samples, e.g. an 'A' in sample 1 is seen in 1 out of 10 reads that map over the variant position whereas an 'A' is seen in sample 2 in 10 out of 10 reads. The difference in those observation ratios is 9/10 or 0.9. The variant state (among all the observations in the 2 sample groups) with the largest difference in observation ratios between the samples in the 2 sample groups is selected to represent the row. The difference in average ratios of each group is what is used in the sort. + +SETTING A MINIMUM GROUP SIZE + +Supplying a --min-group-size affects sorting and allows you to find which samples among 2 sample groups differ (by bringing them to the top of the sorted results). By default, all group members are used to compute maximum difference between 2 sample groups as described above. + +When --min-group-size is supplied with --nogentotype, the maximum difference between the sample groups' average observation ratios is computed twice, between N members of sample group 1 and M members of sample group 2. When comparing sample groups, the maximum difference is determined by taking the greater difference of 2 comparisons: 1. the top N observation ratios of sample group 1 versus the bottom M (inverse) observation ratios of sample group 2. 2. the bottom N observation ratios of sample group 1 versus top M observation ratios of sample group 2. In order to avoid meaningless results, either N or M must represent a majority of their respective sample groups. It is recommended to always set -d to the group size for 1 of the 2 groups. --min-group-size should only be used when the groups being compared are not 2 sets of replicates. + +When --min-group-size is supplied with --gentotype, the maximum difference between the sample groups' is computed in the same manner as described above for --genotype, except calls within a sample group are allowed to differ as long as there exists a subgroup of at least size --min-group-size with a consistent genotype call. + +DYNAMIC CREATION OF SAMPLE GROUPS + +When pairs of sample groups are not supplied, sample groups are greedily determined on each row independently. Up to 2 --min-group-size's can be supplied, but must not sum to more than the number of samples. The default minimum group sizes are both 1. Sorting is performed in the same manner, except (in the case of --nogenotype) the top N and bottom M samples compared are selected from a single list. In the case of --genotype, the samples are ordered by genotype call abundance and assigned to the groups from either end (omitting those with no-calls). + +GROWING SAMPLE GROUPS FROM THE MINIMUM GROUP SIZE + +If you have supplied a --min-group-size that is less than the number of samples defined in the group, you can allow sample groups to grow using the --grow parameter. This allows you to identify groups of different (i.e. non-replicate) samples that share a difference with the comparison group. Growing groups behaves differently depending on whether --genotype or --nogenotype is supplied. + +If --nogenotype is supplied, grow groups is done using the --separation-gap threshold. It uses the difference in the obervation ratio of 1 group and its inverse observation ratio in the comparison group. For example, if you supply `--grow --nogenotype --separation-gap 0.5`, samples will be greedily* added to the 2 groups in order of their difference with the current group's observation ratio average and stops just before the difference in the averages crosses the threshold of 0.5. + +If --genotype is supplied, all members of a sample group matching a genotype call in the sample group of size --min-group-size are added to the group. If sample groups are being created dynamically and the groups have genotype calls in common, no other samples of the common genotype call will be added. + +\* Sample groups are seeded with members from either the bottom or top set of observation ratios. Samples in different groups are seeded from opposite ends (top or bottom). Samples are then traversed top-down or bottom-up and greedily added to the respective sample group in order of ascending difference from the current group average. + +FILTERING + +There are 2 threshold options that can be used to filter variants that do not contain differences between the sample groups that meet the thresholds. In --genotype mode, the threshold is --min-group-size. In --nogenotype mode the threshold is the combination of --separation-gap and --min-group-size. + + n --nogenotype mode, if the difference between the observation ratios between (all of the*) pairs of sample groups is less than the separation gap threshold, the row will not be printed. + +In --genotype mode, if the (all of the*) pairs of sample groups share a common genotypoe call, the row will not be printed. + +\* In either case, if any pair of sample groups meets the threshold(s), the row will be printed regardless of whether or not any other pair fails the threshold(s). + + EXAMPLE + +To sort based on the difference between specific samples or groups of samples, those groups can be defined on the command line using -s. You can specify a minimum number of samples in the groups to differ. So for example, say you have 3 wildtype (WT) replicates and you would like to see differences that all 3 WT samples have with any one of a set of 10 mutant samples. You would do that on the command line using the sample names: + + -s "wt1 wt2 wt3" -d 3 -s "m1 m2 m3 m4 m5 m6 m7 m8 m9 m10" -d 1 + +The largest difference that the average observation ratio of the WT samples has with 1 of the mutant samples will be at the top of the results. + ]]> + </help> + + <citations> + <citation type="doi">10.5072/zenodo.245784</citation> + </citations> + +</tool> \ No newline at end of file