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comparison test-data/.svn/text-base/result.vcf.svn-base @ 2:15319113c0a5 draft

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author dereeper
date Thu, 12 Feb 2015 15:54:24 -0500
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1:b058193a71d0 2:15319113c0a5
1 ##fileformat=VCFv4.1
2 ##FILTER=<ID=LowQual,Description="Low quality">
3 ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
4 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
5 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
6 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
7 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
8 ##GATKCommandLine=<ID=UnifiedGenotyper,Version=2.7-4-g6f46d11,Date="Fri Nov 01 16:17:42 CET 2013",Epoch=1383319062999,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/scratch/hueber-35211/CATB1.RG.sorted.indelrealigned.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[BadCigar] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data/projects/coffee_snp/donnees_genomiques/pseudomolecules.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=4 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=SNP pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 allSitePLs=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false output_mode=EMIT_VARIANTS_ONLY heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=10.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub onlyEmitSamples=[] debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
9 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
10 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
11 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
12 ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
13 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
14 ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
15 ##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
16 ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
17 ##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
18 ##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
19 ##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
20 ##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
21 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
22 ##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
23 ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
24 ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
25 ##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
26 ##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
27 ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
28 ##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
29 ##contig=<ID=chr1,length=38193400>
30 ##contig=<ID=chr10,length=27624748>
31 ##contig=<ID=chr11,length=33540656>
32 ##contig=<ID=chr2,length=54522928>
33 ##contig=<ID=chr3,length=32030951>
34 ##contig=<ID=chr4,length=28191985>
35 ##contig=<ID=chr5,length=29137935>
36 ##contig=<ID=chr6,length=37293965>
37 ##contig=<ID=chr7,length=29833120>
38 ##contig=<ID=chr8,length=31585744>
39 ##contig=<ID=chr9,length=22352177>
40 ##contig=<ID=chr0,length=205603396>
41 ##reference=file:///data/projects/coffee_snp/donnees_genomiques/pseudomolecules.fasta
42 ##SnpEffVersion="2.0.5d (build 2012-01-19), by Pablo Cingolani"
43 ##SnpEffCmd="SnpEff eff coffea /apps/www/sniplay.cirad.fr/data/Coffee/Argemo_genomic.nonannotated.vcf.2 -i VCF -o VCF -c snpEff.config "
44 ##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effefct_Impact | Functional_Class | Codon_Change | Amino_Acid_change | Gene_Name | Gene_BioType | Coding | Transcript | Exon [ | ERRORS | WARNINGS ] )' ">
45 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1
46 chr1 5059 . C G 146.84 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=24.14;MQ0=1;QD=18.35;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,8:8:18:175,18,0
47 chr1 5110 . A G 94.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.328;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.75;MQ0=3;MQRankSum=-0.421;QD=4.51;ReadPosRankSum=-1.826;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:12,9:21:99:123,0,278
48 chr1 5170 . A G 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.817;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=25.23;MQ0=2;MQRankSum=0.212;QD=3.65;ReadPosRankSum=0.533;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:8,7:15:83:83,0,127
49 chr1 5171 . T G 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.978;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=26.11;MQ0=1;MQRankSum=0.212;QD=3.91;ReadPosRankSum=0.533;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:8,6:14:83:83,0,122
50 chr1 5284 . A C 76.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.784;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=1.9827;MLEAC=1;MLEAF=0.500;MQ=34.72;MQ0=1;MQRankSum=-0.784;QD=3.49;ReadPosRankSum=-1.445;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:16,6:22:99:105,0,410
51 chr1 5324 . C T 208.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.780;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=28.74;MQ0=3;MQRankSum=1.491;QD=10.44;ReadPosRankSum=-0.818;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:10,10:20:99:237,0,166
52 chr1 5361 . A G 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.919;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=24.40;MQ0=2;MQRankSum=1.412;QD=11.41;ReadPosRankSum=0.688;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:9,14:24:44:302,0,44
53 chr1 5557 . A G 298.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=25.74;MQ0=5;QD=18.67;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,16:16:30:327,30,0
54 chr1 5648 . T C 59.28 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=14.66;MQ0=3;QD=6.59;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:1,8:9:9:87,9,0
55 chr1 5834 . G T 15.88 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.714;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=3.3843;MLEAC=1;MLEAF=0.500;MQ=27.17;MQ0=1;MQRankSum=1.191;QD=0.93;ReadPosRankSum=0.714;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:15,2:17:44:44,0,279
56 chr1 5889 . T G 147.1 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.488;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=21.23;MQ0=4;MQRankSum=-0.248;QD=8.17;ReadPosRankSum=-0.744;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:4,14:18:11:175,0,11
57 chr1 5890 . T G 229.78 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.5784;MLEAC=2;MLEAF=1.00;MQ=21.11;MQ0=4;QD=12.09;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,19:19:24:258,24,0
58 chr1 5938 . C G 64.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.520;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=14.73;MQ0=10;MQRankSum=1.034;QD=3.08;ReadPosRankSum=0.597;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:15,6:21:69:93,0,69
59 chr1 5968 . A T 115.9 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=14.07;MQ0=8;QD=7.24;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,16:16:15:144,15,0
60 chr1 5974 . A G 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.818;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=18.51;MQ0=8;MQRankSum=0.296;QD=1.88;ReadPosRankSum=1.580;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:14,4:18:62:62,0,114
61 chr1 6010 . A T 490.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.66;MQ0=2;QD=21.34;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,23:23:45:519,45,0
62 chr1 6041 . T A 311.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.00;MQ=28.89;MQ0=0;QD=14.85;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,21:21:33:340,33,0
63 chr1 6209 . A G 273.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=19.61;MQ0=6;QD=13.04;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,20:21:30:302,30,0
64 chr1 6350 . T G 134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.311;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=16.20;MQ0=21;MQRankSum=1.670;QD=2.93;ReadPosRankSum=-0.085;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:163,0,206
65 chr1 6426 . T C 272.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.580;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=25.78;MQ0=2;MQRankSum=-1.099;QD=5.25;ReadPosRankSum=0.859;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:31,21:52:99:301,0,677
66 chr1 6486 . A G 511.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.248;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=24.11;MQ0=16;MQRankSum=-0.330;QD=8.00;ReadPosRankSum=0.268;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:39,25:64:99:540,0,604
67 chr1 6532 . C T 117.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.087;DP=53;Dels=0.00;FS=4.619;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=17.32;MQ0=28;MQRankSum=0.087;QD=2.22;ReadPosRankSum=-0.379;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:146,0,419
68 chr1 6577 . G A 201.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=15.35;MQ0=17;MQRankSum=-1.883;QD=6.11;ReadPosRankSum=0.269;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:8,25:33:28:230,0,28
69 chr1 6607 . T C 88.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.160;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=5.9778;MLEAC=1;MLEAF=0.500;MQ=18.87;MQ0=12;MQRankSum=-1.702;QD=2.28;ReadPosRankSum=0.321;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:22,17:39:99:117,0,385
70 chr1 6609 . G T 89.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.087;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=5.9778;MLEAC=1;MLEAF=0.500;MQ=18.87;MQ0=12;MQRankSum=0.904;QD=2.30;ReadPosRankSum=-0.204;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:32,7:39:99:118,0,377
71 chr1 6675 . G A 58.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.540;DP=52;Dels=0.00;FS=8.076;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=21.45;MQ0=15;MQRankSum=-1.788;QD=1.13;ReadPosRankSum=-0.973;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:36,16:52:87:87,0,729
72 chr1 6691 . G T 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.208;DP=49;Dels=0.00;FS=8.321;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=21.34;MQ0=17;MQRankSum=-0.467;QD=0.71;ReadPosRankSum=-0.311;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:36,13:49:63:63,0,703
73 chr1 6725 . G A 193.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.122;DP=26;Dels=0.00;FS=1.957;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=22.03;MQ0=9;MQRankSum=-0.927;QD=7.45;ReadPosRankSum=-0.146;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:13,13:26:99:222,0,183
74 chr1 6752 . T C 113.9 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=16.88;MQ0=6;QD=10.35;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,11:11:15:142,15,0
75 chr1 6942 . G C 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.400;DP=21;Dels=0.00;FS=13.222;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=17.08;MQ0=7;MQRankSum=0.267;QD=2.66;ReadPosRankSum=-1.067;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:14,7:21:84:84,0,137
76 chr1 7107 . C T 262.74 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.283;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=17.07;MQ0=9;MQRankSum=1.189;QD=10.11;ReadPosRankSum=-1.302;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:7,19:26:6:290,6,0
77 chr1 7384 . T G 58.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.259;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=10.91;MQ0=30;MQRankSum=0.259;QD=1.40;ReadPosRankSum=0.583;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:26,16:42:87:87,0,93
78 chr1 8682 . T G 266.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.674;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=20.57;MQ0=23;MQRankSum=-1.898;QD=7.02;ReadPosRankSum=0.429;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:8,30:38:99:295,0,141
79 chr1 8738 . A G 850.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=23.36;MQ0=29;QD=15.75;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,54:54:72:879,72,0
80 chr1 8785 . C G 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.453;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=15.27;MQ0=40;MQRankSum=-2.450;QD=1.48;ReadPosRankSum=1.668;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:22,28:50:99:102,0,173
81 chr1 8936 . C T 263.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.372;DP=47;Dels=0.00;FS=11.458;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=29.37;MQ0=14;MQRankSum=2.448;QD=5.61;ReadPosRankSum=1.430;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:35,12:47:99:292,0,700
82 chr1 8946 . A G 231.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.028;DP=39;Dels=0.00;FS=15.108;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=30.14;MQ0=13;MQRankSum=1.417;QD=5.94;ReadPosRankSum=0.472;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:29,10:39:99:260,0,533
83 chr1 14025 . A G 1167.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.743;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=4.5620;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=0.490;QD=19.14;ReadPosRankSum=0.702;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:24,36:61:99:1196,0,669
84 chr1 14039 . C T 781.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.305;DP=61;Dels=0.00;FS=1.002;HaplotypeScore=2.6609;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=0.839;QD=12.82;ReadPosRankSum=-1.116;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:35,26:61:99:810,0,1140
85 chr1 14053 . A G 1002.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.152;DP=61;Dels=0.00;FS=3.495;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=1.107;QD=16.44;ReadPosRankSum=1.469;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:28,33:61:99:1031,0,874
86 chr1 14525 . C T 1169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.228;DP=57;Dels=0.00;FS=7.529;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.92;MQ0=0;MQRankSum=-0.041;QD=20.52;ReadPosRankSum=0.447;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:23,34:57:99:1198,0,732
87 chr1 14531 . A G 1030.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.821;DP=54;Dels=0.00;FS=7.625;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=-0.153;QD=19.09;ReadPosRankSum=0.045;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:22,31:54:99:1059,0,726
88 chr1 14540 . C T 1109.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.716;DP=56;Dels=0.00;FS=9.774;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=-0.899;QD=19.82;ReadPosRankSum=-0.716;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:23,33:56:99:1138,0,754
89 chr1 14569 . T C 927.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.152;DP=57;Dels=0.00;FS=3.724;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=0.646;QD=16.28;ReadPosRankSum=0.519;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:28,29:57:99:956,0,955
90 chr1 14614 . T G 929.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.643;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.68;MQ0=0;MQRankSum=-0.395;QD=17.88;ReadPosRankSum=-0.174;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:24,28:52:99:958,0,770
91 chr1 14674 . G T 923.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.540;DP=54;Dels=0.00;FS=3.828;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=1.419;QD=17.11;ReadPosRankSum=1.228;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:27,27:54:99:952,0,875
92 chr1 14720 . C A 2453.77 . AC=2;AF=1.00;AN=2;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.53;MQ0=0;QD=32.86;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,64:64:99:2482,187,0
93 chr1 14957 . C T 730.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.581;DP=43;Dels=0.00;FS=2.756;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.60;MQ0=1;MQRankSum=-0.253;QD=16.99;ReadPosRankSum=-0.758;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:20,23:43:99:759,0,646
94 chr1 15110 . T A 822.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.328;DP=65;Dels=0.00;FS=0.970;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.78;MQ0=0;MQRankSum=-0.569;QD=12.66;ReadPosRankSum=0.261;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:39,26:65:99:851,0,1349
95 chr1 15135 . A G 1010.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.804;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-0.364;QD=16.04;ReadPosRankSum=-1.767;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:32,31:63:99:1039,0,1093
96 chr1 15338 . C T 1812.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.74;MQ0=1;QD=24.29;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,48:48:99:1841,138,0
97 chr1 15597 . C A 464.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.595;DP=47;Dels=0.00;FS=6.639;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-0.617;QD=9.89;ReadPosRankSum=-0.797;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:31,16:47:99:493,0,1065
98 chr1 15875 . A C 541.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.537;DP=42;Dels=0.00;FS=1.222;HaplotypeScore=1.9330;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=1;MQRankSum=-0.066;QD=12.90;ReadPosRankSum=1.064;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:23,19:42:99:570,0,798
99 chr1 15977 . A T 707.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.672;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=53.37;MQ0=3;MQRankSum=-3.958;QD=12.64;ReadPosRankSum=-1.385;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:24,32:56:99:736,0,832
100 chr1 16014 . C G 2424.77 . AC=2;AF=1.00;AN=2;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=10.8438;MLEAC=2;MLEAF=1.00;MQ=52.58;MQ0=3;QD=33.68;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,69:72:99:2453,187,0
101 chr1 16017 . T G 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.483;DP=72;Dels=0.00;FS=1.018;HaplotypeScore=11.7597;MLEAC=1;MLEAF=0.500;MQ=52.21;MQ0=3;MQRankSum=-3.104;QD=11.80;ReadPosRankSum=-0.109;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:36,28:72:99:878,0,1143
102 chr1 16621 . C T 1196.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.059;DP=65;Dels=0.00;FS=3.448;HaplotypeScore=2.7337;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.323;QD=18.41;ReadPosRankSum=-1.247;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:29,36:65:99:1225,0,946
103 chr1 16671 . C T 1029.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.317;DP=52;Dels=0.00;FS=2.477;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-0.746;QD=19.80;ReadPosRankSum=0.075;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:21,31:52:99:1058,0,684
104 chr1 16700 . C G 864.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.439;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=1.092;QD=18.80;ReadPosRankSum=-0.912;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:18,28:46:99:893,0,570
105 chr1 16782 . C T 1114.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.227;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=1.9279;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=1.342;QD=17.69;ReadPosRankSum=-0.791;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:30,33:63:99:1143,0,988
106 chr1 16844 . C A 2131.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.55;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2160,160,0
107 chr1 16871 . T C 870.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.251;DP=59;Dels=0.00;FS=5.468;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=0.494;QD=14.76;ReadPosRankSum=-0.373;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:32,27:59:99:899,0,1075
108 chr1 16912 . T A 808.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.631;DP=51;Dels=0.00;FS=7.963;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.556;QD=15.86;ReadPosRankSum=-1.724;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:26,25:51:99:837,0,878
109 chr1 16926 . A G 688.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.660;DP=48;Dels=0.00;FS=6.044;HaplotypeScore=2.7745;MLEAC=1;MLEAF=0.500;MQ=59.05;MQ0=0;MQRankSum=0.042;QD=14.35;ReadPosRankSum=-0.249;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:717,0,884
110 chr1 17027 . T C 939.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.218;DP=65;Dels=0.00;FS=4.856;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.944;QD=14.46;ReadPosRankSum=-0.495;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:36,29:65:99:968,0,1247
111 chr1 17324 . T G 856.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.562;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=-0.432;QD=18.63;ReadPosRankSum=0.875;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:20,26:46:99:885,0,675