-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathvelvet.samtools.vcf
More file actions
46 lines (46 loc) · 5 KB
/
velvet.samtools.vcf
File metadata and controls
46 lines (46 loc) · 5 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
##fileformat=VCFv4.1
##samtoolsVersion=0.1.19-44428cd
##reference=file://../velvetLinear.fasta
##contig=<ID=ordered_SL1344,length=4882670>
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=IS,Number=2,Type=Float,Description="Maximum number of reads supporting an indel and fraction of indel reads">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint">
##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio">
##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio">
##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
##INFO=<ID=QBD,Number=1,Type=Float,Description="Quality by Depth: QUAL/#reads">
##INFO=<ID=RPB,Number=1,Type=Float,Description="Read Position Bias">
##INFO=<ID=MDV,Number=1,Type=Integer,Description="Maximum number of high-quality nonRef reads in samples">
##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias (v2) for filtering splice-site artefacts in RNA-seq data. Note: this version may be broken.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality non-reference bases">
##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ../align/velvet_bowtie2_very_sensitive_local_k4.sorted.bam
ordered_SL1344 302866 . C T 8.64 . DP=100;VDB=1.952161e-01;RPB=-8.459357e-02;AF1=0.5;AC1=1;DP4=37,33,7,16;MQ=15;FQ=11.3;PV4=0.091,1,1,1 GT:PL:DP:GQ 0/1:38,0,57:93:40
ordered_SL1344 302948 . A G 20 . DP=98;VDB=4.560235e-02;RPB=-2.113137e-02;AF1=0.5;AC1=1;DP4=34,34,17,9;MQ=15;FQ=16.9;PV4=0.25,0.13,1,1 GT:PL:DP:GQ 0/1:50,0,45:94:47
ordered_SL1344 1002440 . C T 4.77 . DP=92;VDB=9.986689e-02;RPB=-4.717792e-01;AF1=0.4999;AC1=1;DP4=32,35,5,18;MQ=21;FQ=6.99;PV4=0.048,0.031,0.43,1 GT:PL:DP:GQ 0/1:33,0,216:90:33
ordered_SL1344 1554131 . G A 36 . DP=100;VDB=2.752249e-01;RPB=1.171129e+00;AF1=0.5;AC1=1;DP4=28,34,21,8;MQ=29;FQ=39;PV4=0.023,0.00019,2.2e-10,1 GT:PL:DP:GQ 0/1:66,0,255:91:69
ordered_SL1344 1554140 . C G 25 . DP=100;VDB=2.589062e-01;RPB=8.606900e-01;AF1=0.5;AC1=1;DP4=34,33,18,9;MQ=29;FQ=28;PV4=0.18,0.086,1.9e-09,1 GT:PL:DP:GQ 0/1:55,0,255:94:58
ordered_SL1344 1554141 . A G 19.1 . DP=100;VDB=1.877230e-01;RPB=1.261163e+00;AF1=0.5;AC1=1;DP4=32,33,17,8;MQ=29;FQ=22;PV4=0.16,0.002,2.1e-09,1 GT:PL:DP:GQ 0/1:49,0,255:90:52
ordered_SL1344 1754538 . G A 3.01 . DP=100;VDB=1.605872e-01;RPB=-4.688577e-01;AF1=0.4997;AC1=1;DP4=32,36,2,27;MQ=25;FQ=4.77;PV4=0.00013,0.0076,0.00044,1 GT:PL:DP:GQ 0/1:30,0,253:97:28
ordered_SL1344 2282766 . C T 52 . DP=97;VDB=5.118387e-06;RPB=-3.905295e+00;AF1=0.5;AC1=1;DP4=14,47,21,12;MQ=19;FQ=55;PV4=0.00014,0.031,0.43,1 GT:PL:DP:GQ 0/1:82,0,159:94:85
ordered_SL1344 2282822 . A ACGCAGCAGCTACCCGCCGCGGCGGTTATCCTCCGGGTCGGACGAGCGCGTCAGC 109 . INDEL;IS=13,0.224138;DP=58;VDB=4.019414e-04;AF1=1;AC1=2;DP4=0,0,4,9;MQ=19;FQ=-73.5 GT:PL:DP:GQ 1/1:150,39,0:13:75