# This file was produced by bcftools stats (1.20+htslib-1.20) and can be plotted using plot-vcfstats.
# The command line was: bcftools stats Sig_18_tissue_vs_Sig_18_Blood.tnseq.filtered.vcf.gz
#
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 Sig_18_tissue_vs_Sig_18_Blood.tnseq.filtered.vcf.gz
# 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: 363
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 314
SN 0 number of MNPs: 5
SN 0 number of indels: 47
SN 0 number of others: 0
SN 0 number of multiallelic sites: 14
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 0 238 77 3.09 234 77 3.04
# 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 1 315 238 77 84 0 0 84
# 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 315 238 77 84 0 0 84
# 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 . 311 234 77 47
# IDD, InDel distribution:
# IDD [2]id [3]length (deletions negative) [4]number of sites [5]number of genotypes [6]mean VAF
IDD 0 -60 1 0 .
IDD 0 -42 1 0 .
IDD 0 -21 1 0 .
IDD 0 -12 1 0 .
IDD 0 -10 2 0 .
IDD 0 -9 1 0 .
IDD 0 -8 1 0 .
IDD 0 -6 5 0 .
IDD 0 -5 1 0 .
IDD 0 -4 4 0 .
IDD 0 -3 16 0 .
IDD 0 -2 11 0 .
IDD 0 -1 10 0 .
IDD 0 1 12 0 .
IDD 0 2 9 0 .
IDD 0 3 3 0 .
IDD 0 4 2 0 .
IDD 0 5 1 0 .
IDD 0 6 1 0 .
IDD 0 39 1 0 .
# ST, Substitution types:
# ST [2]id [3]type [4]count
ST 0 A>C 8
ST 0 A>G 54
ST 0 A>T 5
ST 0 C>A 8
ST 0 C>G 13
ST 0 C>T 60
ST 0 G>A 66
ST 0 G>C 19
ST 0 G>T 12
ST 0 T>A 5
ST 0 T>C 58
ST 0 T>G 7
# 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 0 313 0 0.000000 1 0.275482
DP 0 410 0 0.000000 1 0.275482
DP 0 412 0 0.000000 1 0.275482
DP 0 430 0 0.000000 1 0.275482
DP 0 439 0 0.000000 1 0.275482
DP 0 457 0 0.000000 1 0.275482
DP 0 492 0 0.000000 1 0.275482
DP 0 499 0 0.000000 1 0.275482
DP 0 >500 0 0.000000 355 97.796143