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HCC1395_tumor_vs_HCC1395_BL.tnseq.filtered.bcftools_stats.txt
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Feb 02, 2026 1:38 PM

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# 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  HCC1395_tumor_vs_HCC1395_BL.tnseq.filtered.vcf.gz
#
# Definition of sets:
# ID	[2]id	[3]tab-separated file names
ID	0	HCC1395_tumor_vs_HCC1395_BL.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:	305
SN	0	number of no-ALTs:	0
SN	0	number of SNPs:	275
SN	0	number of MNPs:	6
SN	0	number of indels:	25
SN	0	number of others:	0
SN	0	number of multiallelic sites:	9
SN	0	number of multiallelic SNP sites:	0
# 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	213	62	3.44	213	62	3.44
# 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	275	213	62	48	0	0	48
# 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	275	213	62	48	0	0	48
# 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	.	275	213	62	25
# 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	-24	1	0	.
IDD	0	-9	1	0	.
IDD	0	-8	1	0	.
IDD	0	-6	2	0	.
IDD	0	-4	3	0	.
IDD	0	-3	8	0	.
IDD	0	-2	8	0	.
IDD	0	-1	6	0	.
IDD	0	1	6	0	.
IDD	0	2	7	0	.
IDD	0	3	2	0	.
IDD	0	4	1	0	.
IDD	0	6	1	0	.
# ST, Substitution types:
# ST	[2]id	[3]type	[4]count
ST	0	A>C	5
ST	0	A>G	48
ST	0	A>T	4
ST	0	C>A	9
ST	0	C>G	10
ST	0	C>T	55
ST	0	G>A	59
ST	0	G>C	18
ST	0	G>T	10
ST	0	T>A	1
ST	0	T>C	51
ST	0	T>G	5
# 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	6	0	0.000000	1	0.327869
DP	0	10	0	0.000000	1	0.327869
DP	0	124	0	0.000000	1	0.327869
DP	0	143	0	0.000000	1	0.327869
DP	0	196	0	0.000000	1	0.327869
DP	0	202	0	0.000000	1	0.327869
DP	0	210	0	0.000000	1	0.327869
DP	0	212	0	0.000000	1	0.327869
DP	0	240	0	0.000000	1	0.327869
DP	0	243	0	0.000000	1	0.327869
DP	0	244	0	0.000000	1	0.327869
DP	0	249	0	0.000000	1	0.327869
DP	0	263	0	0.000000	1	0.327869
DP	0	273	0	0.000000	1	0.327869
DP	0	275	0	0.000000	1	0.327869
DP	0	276	0	0.000000	1	0.327869
DP	0	277	0	0.000000	1	0.327869
DP	0	286	0	0.000000	1	0.327869
DP	0	288	0	0.000000	1	0.327869
DP	0	294	0	0.000000	2	0.655738
DP	0	295	0	0.000000	1	0.327869
DP	0	305	0	0.000000	1	0.327869
DP	0	317	0	0.000000	1	0.327869
DP	0	318	0	0.000000	1	0.327869
DP	0	319	0	0.000000	1	0.327869
DP	0	327	0	0.000000	1	0.327869
DP	0	331	0	0.000000	1	0.327869
DP	0	335	0	0.000000	1	0.327869
DP	0	350	0	0.000000	1	0.327869
DP	0	355	0	0.000000	1	0.327869
DP	0	356	0	0.000000	1	0.327869
DP	0	359	0	0.000000	1	0.327869
DP	0	360	0	0.000000	1	0.327869
DP	0	361	0	0.000000	1	0.327869
DP	0	363	0	0.000000	1	0.327869
DP	0	364	0	0.000000	1	0.327869
DP	0	372	0	0.000000	1	0.327869
DP	0	375	0	0.000000	1	0.327869
DP	0	377	0	0.000000	1	0.327869
DP	0	379	0	0.000000	1	0.327869
DP	0	380	0	0.000000	2	0.655738
DP	0	382	0	0.000000	1	0.327869
DP	0	384	0	0.000000	2	0.655738
DP	0	403	0	0.000000	1	0.327869
DP	0	405	0	0.000000	1	0.327869
DP	0	412	0	0.000000	2	0.655738
DP	0	420	0	0.000000	1	0.327869
DP	0	421	0	0.000000	1	0.327869
DP	0	422	0	0.000000	1	0.327869
DP	0	423	0	0.000000	1	0.327869
DP	0	424	0	0.000000	1	0.327869
DP	0	431	0	0.000000	1	0.327869
DP	0	433	0	0.000000	1	0.327869
DP	0	437	0	0.000000	1	0.327869
DP	0	438	0	0.000000	1	0.327869
DP	0	439	0	0.000000	2	0.655738
DP	0	440	0	0.000000	1	0.327869
DP	0	442	0	0.000000	1	0.327869
DP	0	443	0	0.000000	1	0.327869
DP	0	448	0	0.000000	1	0.327869
DP	0	453	0	0.000000	1	0.327869
DP	0	458	0	0.000000	1	0.327869
DP	0	459	0	0.000000	1	0.327869
DP	0	461	0	0.000000	1	0.327869
DP	0	462	0	0.000000	1	0.327869
DP	0	471	0	0.000000	1	0.327869
DP	0	472	0	0.000000	1	0.327869
DP	0	473	0	0.000000	2	0.655738
DP	0	475	0	0.000000	1	0.327869
DP	0	478	0	0.000000	2	0.655738
DP	0	479	0	0.000000	1	0.327869
DP	0	489	0	0.000000	1	0.327869
DP	0	494	0	0.000000	1	0.327869
DP	0	>500	0	0.000000	225	73.770492