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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit c062eb1cd00ce9d565f3e2f3b042b3dd90d78ce4"
author iuc
date Wed, 06 Jan 2021 10:55:53 +0000
parents 1062d6ad6503
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##fileformat=VCFv4.0
##fileDate=20200707
##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512.2:1-14951 -o /data/dnb02/galaxy_db/job_working_directory/009/430/9430167/working/pp-tmp/lofreq2_call_paralleleu47zedc/0.vcf.gz reads.bam 
##reference=reference.fa
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
##FILTER=<ID=min_snvqual_64,Description="Minimum SNV Quality (Phred) 64">
##FILTER=<ID=min_indelqual_47,Description="Minimum Indel Quality (Phred) 47">
##FILTER=<ID=min_snvqual_68,Description="Minimum SNV Quality (Phred) 68">
##FILTER=<ID=min_indelqual_53,Description="Minimum Indel Quality (Phred) 53">
##FILTER=<ID=min_af_0.050000,Description="Minimum allele frequency 0.050000">
##FILTER=<ID=min_dp_5,Description="Minimum Coverage 5">
##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
##SnpEffVersion="4.5covid19 (build 2020-04-15 22:26), by Pablo Cingolani"
##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-upstream -no-utr -stats /data/dnb02/galaxy_db/job_working_directory/009/430/9430173/galaxy_dataset_24243791.dat NC_045512.2 /data/dnb02/galaxy_db/files/022/094/dataset_22094492.dat "
##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype [ | ERRORS | WARNINGS ] )' ">
##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
NC_045512.2	241	.	C	T	7565.0	PASS	DP=202;AF=1.000000;SB=0;DP4=0,0,94,108
NC_045512.2	3037	.	C	T	2399.0	PASS	DP=64;AF=0.984375;SB=0;DP4=0,0,33,31;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	4291	.	A	G	87.0	PASS	DP=127;AF=0.055118;SB=1;DP4=68,52,3,4;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1342|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1342|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A524|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A524|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	5806	.	C	T	203.0	min_af_0.050000	DP=260;AF=0.038462;SB=1;DP4=172,78,8,2;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C1847|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C1847|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C1029|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C1029|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	8554	.	T	C	95.0	PASS	DP=116;AF=0.068966;SB=0;DP4=57,51,4,4;EFF=SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G1945|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SPLICE_SITE_REGION+SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G1945|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G2763|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G2763|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C)
NC_045512.2	10620	.	A	G	78.0	min_af_0.050000	DP=214;AF=0.028037;SB=0;DP4=88,120,2,4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q3452R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q3452R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q189R|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q189R|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	12297	.	A	G	118.0	min_af_0.050000	DP=314;AF=0.028662;SB=0;DP4=131,174,4,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q4011R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q4011R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q69R|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q69R|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	13123	.	T	C	186.0	min_af_0.050000	DP=573;AF=0.020942;SB=0;DP4=241,319,6,7;EFF=SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S4286|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S4286|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S33|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S33|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	13129	.	A	G	78.0	min_af_0.050000	DP=283;AF=0.035336;SB=2;DP4=126,144,4,7;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G4288|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G4288|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G35|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G35|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	13993	.	G	T	215.0	PASS	DP=99;AF=0.090909;SB=11;DP4=60,30,3,6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A4577S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A185S|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	15830	.	CA	C	74.0	min_af_0.050000	DP=587;AF=0.006814;SB=0;DP4=256,327,2,2;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||aaa/|K5190|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K798|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2	15958	.	G	A	73.0	min_af_0.050000	DP=148;AF=0.027027;SB=2;DP4=92,52,2,2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A5232T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A840T|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	16695	.	T	G	117.0	min_af_0.050000	DP=202;AF=0.029703;SB=0;DP4=93,103,3,3;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acG|T5477|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),SYNONYMOUS_CODING(LOW|SILENT|acT/acG|T153|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	17999	.	C	T	1226.0	PASS	DP=483;AF=0.103520;SB=3;DP4=195,236,26,25;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T5912I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T588I|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	18108	.	A	G	74.0	min_af_0.050000	DP=193;AF=0.031088;SB=1;DP4=108,79,3,3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A5948|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A23|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	21147	.	T	C	77.0	min_af_0.050000	DP=150;AF=0.026667;SB=0;DP4=77,69,2,2;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L6961|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L163|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	23403	.	A	G	8550.0	PASS	DP=229;AF=0.982533;SB=0;DP4=0,0,136,93;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2	23582	.	TATCAGACTCAGACTA	T	238.0	min_af_0.050000	DP=448;AF=0.022321;SB=2;DP4=177,263,5,5;INDEL;HRUN=1;EFF=CODON_DELETION(MODERATE||cagactcagactaat/|QTQTN675|1273|S|protein_coding|CODING|GU280_gp02|1|T|INFO_REALIGN_3_PRIME)
NC_045512.2	23595	.	CTAATTCTCCTCGGCGGGCACG	C	571.0	PASS	DP=408;AF=0.051471;SB=4;DP4=167,227,11,10;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattctcctcggcgggcacgtagt/agt|NSPRRARS679S|1273|S|protein_coding|CODING|GU280_gp02|1|C|INFO_REALIGN_3_PRIME)
NC_045512.2	26256	.	CGTTTCGGAAGAGACAGGTACGTTAATA	C	963.0	PASS	DP=196;AF=0.153061;SB=1;DP4=76,90,12,18;INDEL;HRUN=1;EFF=CODON_DELETION(MODERATE||tcggaagagacaggtacgttaatagtt/|SEETGTLIV6|75|E|protein_coding|CODING|GU280_gp04|1|C|INFO_REALIGN_3_PRIME)
NC_045512.2	26259	.	TTCGGAAGAGACAGGTACGTTAATA	T	2451.0	PASS	DP=133;AF=0.511278;SB=1;DP4=57,69,29,39;INDEL;HRUN=3;EFF=CODON_DELETION(MODERATE||tcggaagagacaggtacgttaata/|SEETGTLI6|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512.2	26895	.	C	T	240.0	min_af_0.050000	DP=557;AF=0.025135;SB=0;DP4=246,297,6,8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H125Y|222|M|protein_coding|CODING|GU280_gp05|1|T)
NC_045512.2	28868	.	C	T	446.0	PASS	DP=236;AF=0.084746;SB=0;DP4=101,115,10,10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P199S|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512.2	29361	.	TC	T	71.0	min_af_0.050000	DP=862;AF=0.004640;SB=0;DP4=424,456,2,2;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||cca/|P364|419|N|protein_coding|CODING|GU280_gp10|1|T|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00)
NC_045512.2	29855	.	T	C	212.0	PASS	DP=183;AF=0.054645;SB=1;DP4=89,84,6,4
NC_045512.2	29859	.	T	C	72.0	min_af_0.050000	DP=164;AF=0.024390;SB=12;DP4=77,82,4,0