Mercurial > repos > iuc > snpfreqplot

view test-data/snpeff.123.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/009/430/9430166/working/pp-tmp/lofreq2_call_parallelpfou9vt9/0.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_52,Description="Minimum Indel Quality (Phred) 52">
##FILTER=<ID=min_snvqual_70,Description="Minimum SNV Quality (Phred) 70">
##FILTER=<ID=min_indelqual_57,Description="Minimum Indel Quality (Phred) 57">
##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/009/430/9430172/galaxy_dataset_24243789.dat NC_045512.2 /data/dnb02/galaxy_db/files/022/094/dataset_22094491.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	13172.0	PASS	DP=363;AF=0.980716;SB=0;DP4=1,1,167,193
NC_045512.2	424	.	AGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTT	A	6194.0	PASS	DP=283;AF=0.565371;SB=0;DP4=76,47,98,62;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gtagaagttgaaaaaggcgttttgcctcaacttgaa/gaa|VEVEKGVLPQLE54E|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gtagaagttgaaaaaggcgttttgcctcaacttgaa/gaa|VEVEKGVLPQLE54E|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gtagaagttgaaaaaggcgttttgcctcaacttgaa/gaa|VEVEKGVLPQLE54E|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gtagaagttgaaaaaggcgttttgcctcaacttgaa/gaa|VEVEKGVLPQLE54E|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME)
NC_045512.2	457	.	T	TA	577.0	PASS	DP=184;AF=0.114130;SB=0;DP4=100,63,14,7;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||gaa/Agaa|E65R?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|TA),FRAME_SHIFT(HIGH||gaa/Agaa|E65R?|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|TA|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||gaa/Agaa|E65R?|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|TA|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||gaa/Agaa|E65R?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|TA);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2	518	.	ATGGTT	A	126.0	min_af_0.050000	DP=553;AF=0.010850;SB=0;DP4=262,283,3,3;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||atggtt/|MV85|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),FRAME_SHIFT(HIGH||atggtt/|MV85|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||atggtt/|MV85|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||atggtt/|MV85|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2	3037	.	C	T	4542.0	PASS	DP=127;AF=0.960630;SB=0;DP4=0,0,70,57;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	83.0	min_af_0.050000	DP=220;AF=0.031818;SB=11;DP4=122,88,2,6;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	6373	.	GGATA	G	92.0	min_af_0.050000	DP=238;AF=0.016807;SB=0;DP4=123,111,2,2;INDEL;HRUN=2;EFF=FRAME_SHIFT(HIGH||gataat/|DN2037|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),FRAME_SHIFT(HIGH||gataat/|DN2037|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),FRAME_SHIFT(HIGH||gataat/|DN1219|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),FRAME_SHIFT(HIGH||gataat/|DN1219|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2	6906	.	C	T	6592.0	PASS	DP=175;AF=0.988571;SB=0;DP4=0,0,69,106;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2214L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2214L|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S1396L|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S1396L|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	10450	.	C	T	161.0	min_af_0.050000	DP=302;AF=0.046358;SB=0;DP4=178,105,9,5;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P3395|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P3395|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P132|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P132|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	10451	.	A	G	110.0	min_af_0.050000	DP=233;AF=0.047210;SB=19;DP4=161,55,4,7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N3396D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N3396D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N133D|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N133D|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	10620	.	A	G	239.0	PASS	DP=347;AF=0.051873;SB=2;DP4=139,189,9,9;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	12835	.	T	G	115.0	min_af_0.050000	DP=423;AF=0.023641;SB=0;DP4=180,232,5,6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaT/gaG|D4190E|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaT/gaG|D4190E|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaT/gaG|D50E|112|ORF1ab|protein_coding|CODING|YP_009725305.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaT/gaG|D50E|112|ORF1ab|protein_coding|CODING|YP_009742616.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	13123	.	T	C	163.0	min_af_0.050000	DP=775;AF=0.015484;SB=4;DP4=312,451,3,9;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	134.0	min_af_0.050000	DP=389;AF=0.048843;SB=0;DP4=165,197,9,11;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	13815	.	A	G	95.0	min_af_0.050000	DP=551;AF=0.014519;SB=0;DP4=246,297,4,4;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A4517|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A125|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	14408	.	C	T	6433.0	PASS	DP=186;AF=0.962366;SB=0;DP4=1,1,96,86;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	15324	.	C	T	9790.0	PASS	DP=273;AF=0.992674;SB=0;DP4=0,0,140,133;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N5020|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N628|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	18108	.	A	G	72.0	min_af_0.050000	DP=376;AF=0.015957;SB=3;DP4=211,158,2,4;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	22487	.	GA	G	64.0	min_af_0.050000	DP=200;AF=0.015000;SB=0;DP4=101,100,1,2;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||aaa/|K310|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2	22573	.	T	C	71.0	min_af_0.050000	DP=256;AF=0.015625;SB=0;DP4=122,130,2,2;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P337|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2	23403	.	A	G	14383.0	PASS	DP=391;AF=0.969309;SB=0;DP4=0,0,227,164;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2	24108	.	T	C	71.0	min_af_0.050000	DP=410;AF=0.014634;SB=3;DP4=210,192,2,4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cCc|L849P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2	25207	.	C	T	152.0	min_af_0.050000	DP=307;AF=0.026059;SB=2;DP4=148,151,5,3;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1215|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2	25453	.	A	C	106.0	min_af_0.050000	DP=291;AF=0.020619;SB=1;DP4=139,144,4,3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Cag|K21Q|275|ORF3a|protein_coding|CODING|GU280_gp03|1|C)
NC_045512.2	29270	.	TAC	T	72.0	min_af_0.050000	DP=813;AF=0.004920;SB=0;DP4=450,363,2,2;INDEL;HRUN=1;EFF=FRAME_SHIFT(HIGH||aca/|T334|419|N|protein_coding|CODING|GU280_gp10|1|T|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00)
NC_045512.2	29564	.	T	G	81.0	min_af_0.050000	DP=762;AF=0.010499;SB=5;DP4=424,325,3,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Gat|Y3D|38|ORF10|protein_coding|CODING|GU280_gp11|1|G)
NC_045512.2	29765	.	T	C	370.0	min_af_0.050000	DP=581;AF=0.034423;SB=1;DP4=291,267,9,11