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#
# Definition of sets:
# ID [2]id [3]tab-separated file names
# SN, Summary numbers:
# number of records .. number of data rows in the VCF
# number of no-ALTs .. reference-only sites, ALT is either "." or identical to REF
# number of SNPs .. number of rows with a SNP
# number of MNPs .. number of rows with a MNP, such as CC>TT
# number of indels .. number of rows with an indel
# number of others .. number of rows with other type, for example a symbolic allele or
# a complex substitution, such as ACT>TCGA
# number of multiallelic sites .. number of rows with multiple alternate alleles
# number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs
#
# Note that rows containing multiple types will be counted multiple times, in each
# counter. For example, a row with a SNP and an indel increments both the SNP and
# the indel counter.
#
# SN [2]id [3]key [4]value
SN 0 number of samples: 2
SN 0 number of records: 18
SN 0 number of no-ALTs: 1
SN 0 number of SNPs: 5
SN 0 number of MNPs: 1
SN 0 number of indels: 9
SN 0 number of others: 2
SN 0 number of multiallelic sites: 6
SN 0 number of multiallelic SNP sites: 1
# TSTV, transitions/transversions:
# TSTV [2]id [3]ts [4]tv [5]ts/tv [6]ts (1st ALT) [7]tv (1st ALT) [8]ts/tv (1st ALT)
TSTV 0 3 2 1.50 3 1 3.00
# SiS, Singleton stats:
# SiS [2]id [3]allele count [4]number of SNPs [5]number of transitions [6]number of transversions [7]number of indels [8]repeat-consistent [9]repeat-inconsistent [10]not applicable
SiS 0 1 3 1 2 0 0 0 0
# AF, Stats by non-reference allele frequency:
# AF [2]id [3]allele frequency [4]number of SNPs [5]number of transitions [6]number of transversions [7]number of indels [8]repeat-consistent [9]repeat-inconsistent [10]not applicable
AF 0 0.000000 3 1 2 2 0 0 2
AF 0 0.490000 0 0 0 12 0 0 12
AF 0 0.740000 1 1 0 0 0 0 0
AF 0 0.990000 1 1 0 0 0 0 0
# QUAL, Stats by quality
# QUAL [2]id [3]Quality [4]number of SNPs [5]number of transitions (1st ALT) [6]number of transversions (1st ALT) [7]number of indels
QUAL 0 12.6 1 0 1 0
QUAL 0 12.9 0 0 0 1
QUAL 0 45.0 0 0 0 1
QUAL 0 59.2 1 1 0 0
QUAL 0 59.9 0 0 0 3
QUAL 0 60.2 1 1 0 0
QUAL 0 61.5 0 0 0 1
QUAL 0 79.0 0 0 0 1
QUAL 0 82.7 0 0 0 1
QUAL 0 90.6 1 1 0 0
QUAL 0 342.0 0 0 0 1
# IDD, InDel distribution:
# IDD [2]id [3]length (deletions negative) [4]number of sites [5]number of genotypes [6]mean VAF
IDD 0 -10 1 0 .
IDD 0 -8 1 0 .
IDD 0 -4 3 0 .
IDD 0 -3 4 0 .
IDD 0 -2 1 0 .
IDD 0 -1 2 0 .
IDD 0 1 1 0 .
IDD 0 2 1 0 .
# ST, Substitution types:
# ST [2]id [3]type [4]count
ST 0 A>C 0
ST 0 A>G 0
ST 0 A>T 0
ST 0 C>A 0
ST 0 C>G 0
ST 0 C>T 0
ST 0 G>A 3
ST 0 G>C 1
ST 0 G>T 1
ST 0 T>A 0
ST 0 T>C 0
ST 0 T>G 0
# DP, Depth distribution
# DP [2]id [3]bin [4]number of genotypes [5]fraction of genotypes (%) [6]number of sites [7]fraction of sites (%)
DP 0 10 2 5.555556 0 0.000000
DP 0 21 2 5.555556 0 0.000000
DP 0 22 2 5.555556 0 0.000000
DP 0 26 4 11.111111 0 0.000000
DP 0 30 2 5.555556 0 0.000000
DP 0 31 16 44.444444 0 0.000000
DP 0 32 4 11.111111 0 0.000000
DP 0 35 4 11.111111 0 0.000000
DP 0 60 0 0.000000 1 33.333333
DP 0 62 0 0.000000 2 66.666667
# PSC, Per-sample counts. Note that the ref/het/hom counts include only SNPs, for indels see PSI. The rest include both SNPs and indels.
# PSC [2]id [3]sample [4]nRefHom [5]nNonRefHom [6]nHets [7]nTransitions [8]nTransversions [9]nIndels [10]average depth [11]nSingletons [12]nHapRef [13]nHapAlt [14]nMissing
PSC 0 A 0 2 4 3 2 9 28.7 1 0 0 0
PSC 0 B 1 1 4 2 2 9 28.7 0 0 0 0
# PSI, Per-Sample Indels. Note that alt-het genotypes with both ins and del allele are counted twice, in both nInsHets and nDelHets.
# PSI [2]id [3]sample [4]in-frame [5]out-frame [6]not applicable [7]out/(in+out) ratio [8]nInsHets [9]nDelHets [10]nInsAltHoms [11]nDelAltHoms
PSI 0 A 0 0 0 0.00 1 8 0 0
PSI 0 B 0 0 0 0.00 1 8 0 0
# HWE
# HWE [2]id [3]1st ALT allele frequency [4]Number of observations [5]25th percentile [6]median [7]75th percentile
HWE 0 0.000000 2 0.490000 0.490000 0.990000
HWE 0 0.490000 14 0.990000 0.990000 0.990000
HWE 0 0.740000 1 0.490000 0.490000 0.490000
HWE 0 0.990000 1 0.000000 0.000000 0.000000
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