Mercurial > repos > iuc > snpfreqplot

view test-data/snpeff.456.vcf @ 3:3d0adeee3f2b draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
children
line wrap: on
line source

##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/009/430/9430165/working/pp-tmp/lofreq2_call_parallel147y6wii/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_66,Description="Minimum SNV Quality (Phred) 66">
##FILTER=<ID=min_indelqual_51,Description="Minimum Indel Quality (Phred) 51">
##FILTER=<ID=min_snvqual_70,Description="Minimum SNV Quality (Phred) 70">
##FILTER=<ID=min_indelqual_56,Description="Minimum Indel Quality (Phred) 56">
##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/009/430/9430171/galaxy_dataset_24243787.dat NC_045512.2 /data/dnb02/galaxy_db/files/022/094/dataset_22094490.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	222	.	C	T	292.0	min_af_0.050000	DP=304;AF=0.046053;SB=1;DP4=130,160,7,7
NC_045512.2	241	.	C	T	11451.0	PASS	DP=311;AF=0.983923;SB=0;DP4=0,0,138,171
NC_045512.2	520	.	GGTT	G	83.0	min_af_0.050000	DP=424;AF=0.009434;SB=0;DP4=216,206,2,2;INDEL;HRUN=2;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttgag/gag|VE86E|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttgag/gag|VE86E|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttgag/gag|VE86E|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttgag/gag|VE86E|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME)
NC_045512.2	1059	.	C	T	6195.0	PASS	DP=201;AF=0.860696;SB=0;DP4=12,14,83,92;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T265I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T265I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T85I|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T85I|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	3037	.	C	T	4662.0	PASS	DP=124;AF=0.983871;SB=0;DP4=0,0,63,61;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	3307	.	G	A	124.0	min_af_0.050000	DP=353;AF=0.019830;SB=1;DP4=245,101,6,1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M1014I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M1014I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M196I|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M196I|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	3373	.	C	A	3249.0	PASS	DP=732;AF=0.166667;SB=1;DP4=288,319,57,68;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaA|D1036E|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaA|D1036E|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaA|D218E|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaA|D218E|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	4456	.	C	T	79.0	min_af_0.050000	DP=476;AF=0.010504;SB=0;DP4=203,268,2,3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1397|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1397|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A579|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A579|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	5138	.	G	T	154.0	min_af_0.050000	DP=506;AF=0.017787;SB=0;DP4=226,270,5,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Tac|D1625Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Tac|D1625Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Tac|D807Y|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Tac|D807Y|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	7388	.	GC	G	86.0	min_af_0.050000	DP=223;AF=0.017937;SB=0;DP4=103,117,2,2;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||ccg/|P2376|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ccg/|P2376|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ccg/|P1558|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ccg/|P1558|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2	10620	.	A	G	185.0	min_af_0.050000	DP=290;AF=0.048276;SB=0;DP4=126,150,6,8;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	13123	.	T	C	225.0	min_af_0.050000	DP=764;AF=0.019634;SB=0;DP4=302,446,7,9;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	145.0	PASS	DP=395;AF=0.055696;SB=1;DP4=167,195,9,13;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	14408	.	C	T	7389.0	PASS	DP=202;AF=0.995049;SB=0;DP4=0,0,103,99;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4715L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P323L|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	15380	.	G	T	276.0	min_af_0.050000	DP=286;AF=0.045455;SB=1;DP4=132,141,7,6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aTc|S5039I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aTc|S647I|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	15385	.	TCA	T	90.0	min_af_0.050000	DP=292;AF=0.013699;SB=0;DP4=141,147,2,2;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||cac/|H5042|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||cac/|H650|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2	15689	.	G	A	2771.0	PASS	DP=273;AF=0.344322;SB=0;DP4=113,65,61,34;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R5142H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R750H|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	23403	.	A	G	10124.0	PASS	DP=285;AF=0.943860;SB=0;DP4=0,0,166,119;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2	24826	.	CT	C	83.0	min_af_0.050000	DP=451;AF=0.008869;SB=0;DP4=232,216,2,2;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||ttt/|F1089|1273|S|protein_coding|CODING|GU280_gp02|1|C|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2	25563	.	G	T	4454.0	PASS	DP=173;AF=0.751445;SB=0;DP4=21,20,64,68;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q57H|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512.2	26259	.	TTCGGAAGAGACAGGTACGTTAATA	T	1183.0	PASS	DP=201;AF=0.184080;SB=0;DP4=97,112,17,20;INDEL;HRUN=3;EFF=CODON_DELETION(MODERATE||tcggaagagacaggtacgttaata/|SEETGTLI6|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512.2	26753	.	C	T	137.0	min_af_0.050000	DP=592;AF=0.016892;SB=0;DP4=314,267,6,5;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T77|222|M|protein_coding|CODING|GU280_gp05|1|T)
NC_045512.2	27883	.	C	A	7166.0	PASS	DP=413;AF=0.554479;SB=2;DP4=84,94,118,117;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gAc|A43D|43|ORF7b|protein_coding|CODING|GU280_gp08|1|A)
NC_045512.2	27916	.	G	T	1336.0	PASS	DP=374;AF=0.139037;SB=6;DP4=147,173,30,24;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G8V|121|ORF8|protein_coding|CODING|GU280_gp09|1|T)
NC_045512.2	28134	.	G	GT	80.0	min_af_0.050000	DP=531;AF=0.007533;SB=0;DP4=295,232,2,2;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||tcc/tTcc|S82F?|121|ORF8|protein_coding|CODING|GU280_gp09|1|GT|INFO_REALIGN_3_PRIME);LOF=(ORF8|GU280_gp09|1|1.00)
NC_045512.2	28254	.	A	C	139.0	min_af_0.050000	DP=618;AF=0.017799;SB=2;DP4=297,309,7,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Ctc|I121L|121|ORF8|protein_coding|CODING|GU280_gp09|1|C)
NC_045512.2	28881	.	G	A	925.0	PASS	DP=368;AF=0.108696;SB=0;DP4=159,166,21,21;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2	28882	.	G	A	929.0	PASS	DP=391;AF=0.104859;SB=0;DP4=175,174,21,21;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2	28883	.	G	C	945.0	PASS	DP=391;AF=0.107417;SB=0;DP4=177,172,21,21;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
NC_045512.2	29659	.	C	T	70.0	min_af_0.050000	DP=1375;AF=0.004364;SB=0;DP4=614,755,3,3;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N34|38|ORF10|protein_coding|CODING|GU280_gp11|1|T)
NC_045512.2	29800	.	G	A	629.0	PASS	DP=505;AF=0.057426;SB=0;DP4=245,229,16,13
NC_045512.2	29859	.	T	C	80.0	min_af_0.050000	DP=299;AF=0.016722;SB=20;DP4=129,164,6,0