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Sig_18_Blood.entropy.entropy.bcftools_stats.txt
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s3://natera-rnd-pltf-dev-nextflow-data-01/users/mipeters/semiproductionize/sarek/698115e9/test_regression_dev_b0193075/reports/raw_qc/bcftools/haplotypecaller/Sig_18_Blood/Sig_18_Blood.entropy.entropy.bcftools_stats.txt
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Feb 02, 2026 1:41 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  Sig_18_Blood.entropy.entropy.vcf.gz
#
# Definition of sets:
# ID	[2]id	[3]tab-separated file names
ID	0	Sig_18_Blood.entropy.entropy.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:	1
SN	0	number of records:	397
SN	0	number of no-ALTs:	0
SN	0	number of SNPs:	371
SN	0	number of MNPs:	0
SN	0	number of indels:	26
SN	0	number of others:	0
SN	0	number of multiallelic sites:	0
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	277	94	2.95	277	94	2.95
# 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	226	171	55	17	0	0	17
# 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	226	171	55	17	0	0	17
AF	0	0.990000	145	106	39	9	0	0	9
# 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	47.6	1	1	0	0
QUAL	0	111.6	1	0	1	0
QUAL	0	184.6	0	0	0	1
QUAL	0	187.6	0	0	0	1
QUAL	0	257.0	1	1	0	0
QUAL	0	338.6	1	0	1	0
QUAL	0	491.6	1	0	1	0
QUAL	0	494.6	1	1	0	0
QUAL	0	515.6	1	1	0	0
QUAL	0	571.6	1	0	1	0
QUAL	0	801.0	1	1	0	0
QUAL	0	846.6	1	1	0	0
QUAL	0	894.6	1	1	0	0
QUAL	0	1195.6	1	1	0	0
QUAL	0	1250.6	1	1	0	0
QUAL	0	1289.6	1	1	0	0
QUAL	0	1308.6	1	1	0	0
QUAL	0	1337.6	1	0	1	0
QUAL	0	1386.6	1	1	0	0
QUAL	0	1390.6	1	0	1	0
QUAL	0	1396.6	1	1	0	0
QUAL	0	1417.6	1	1	0	0
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QUAL	0	1634.6	1	1	0	0
QUAL	0	1668.0	0	0	0	1
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QUAL	0	1742.6	1	0	1	0
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QUAL	0	1986.6	1	0	1	0
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QUAL	0	2005.6	1	0	1	0
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QUAL	0	2184.6	0	0	0	1
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QUAL	0	5854.0	1	1	0	0
QUAL	0	5920.0	1	1	0	0
QUAL	0	6011.6	2	2	0	0
QUAL	0	6112.6	1	1	0	0
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QUAL	0	6199.6	1	1	0	0
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QUAL	0	8177.0	1	1	0	0
QUAL	0	8213.0	1	0	1	0
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QUAL	0	9854.0	1	1	0	0
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QUAL	0	10130.9	1	1	0	0
QUAL	0	10242.9	1	1	0	0
QUAL	0	10248.9	1	0	1	0
QUAL	0	10314.9	1	0	1	0
QUAL	0	10424.9	1	1	0	0
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QUAL	0	11248.9	1	1	0	0
QUAL	0	11393.9	1	1	0	0
QUAL	0	11531.9	1	1	0	0
QUAL	0	11705.9	1	1	0	0
QUAL	0	11708.9	1	0	1	0
QUAL	0	11721.9	1	1	0	0
QUAL	0	11728.9	1	1	0	0
QUAL	0	11839.9	1	1	0	0
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QUAL	0	16173.9	1	1	0	0
QUAL	0	16495.9	1	1	0	0
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QUAL	0	16921.9	2	2	0	0
QUAL	0	17479.9	1	1	0	0
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QUAL	0	19795.9	1	1	0	0
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QUAL	0	22166.9	1	0	1	0
QUAL	0	22188.9	1	0	1	0
QUAL	0	22218.9	1	1	0	0
QUAL	0	23099.9	1	1	0	0
QUAL	0	23619.9	1	0	1	0
QUAL	0	23913.9	1	1	0	0
QUAL	0	24427.9	1	1	0	0
QUAL	0	24497.9	1	0	1	0
QUAL	0	25137.9	1	0	1	0
QUAL	0	25403.9	0	0	0	1
QUAL	0	25435.9	1	1	0	0
QUAL	0	25554.9	1	1	0	0
QUAL	0	25645.9	1	0	1	0
QUAL	0	25806.9	1	1	0	0
QUAL	0	25873.9	1	1	0	0
QUAL	0	25984.9	1	0	1	0
QUAL	0	26157.9	0	0	0	1
QUAL	0	26477.9	1	1	0	0
QUAL	0	26665.9	1	1	0	0
QUAL	0	26669.9	1	1	0	0
QUAL	0	27374.9	1	1	0	0
QUAL	0	27376.9	1	0	1	0
QUAL	0	27408.9	1	1	0	0
QUAL	0	27458.9	1	1	0	0
QUAL	0	27728.9	1	1	0	0
QUAL	0	28175.9	0	0	0	1
QUAL	0	28308.9	1	1	0	0
QUAL	0	28440.9	1	1	0	0
QUAL	0	28974.9	1	1	0	0
QUAL	0	29024.9	1	0	1	0
QUAL	0	30098.9	1	0	1	0
QUAL	0	31109.9	1	1	0	0
QUAL	0	31389.9	1	1	0	0
QUAL	0	32171.9	1	1	0	0
QUAL	0	32439.9	0	0	0	1
QUAL	0	32502.9	1	1	0	0
QUAL	0	34607.9	0	0	0	1
QUAL	0	34631.9	1	1	0	0
QUAL	0	35594.9	1	1	0	0
QUAL	0	35996.9	1	1	0	0
QUAL	0	36591.9	1	0	1	0
QUAL	0	37218.9	1	1	0	0
QUAL	0	39171.9	1	1	0	0
QUAL	0	45487.9	1	1	0	0
QUAL	0	46017.9	1	1	0	0
QUAL	0	48844.9	1	1	0	0
QUAL	0	49400.9	1	0	1	0
QUAL	0	55338.9	1	1	0	0
QUAL	0	59773.9	1	1	0	0
QUAL	0	60672.9	1	1	0	0
QUAL	0	62240.9	1	0	1	0
QUAL	0	63050.9	1	0	1	0
QUAL	0	63942.9	1	1	0	0
QUAL	0	68839.9	1	0	1	0
QUAL	0	71440.9	1	0	1	0
QUAL	0	76676.9	1	1	0	0
QUAL	0	78118.9	0	0	0	1
QUAL	0	80747.9	1	0	1	0
# IDD, InDel distribution:
# IDD	[2]id	[3]length (deletions negative)	[4]number of sites	[5]number of genotypes	[6]mean VAF
IDD	0	-15	1	0	.
IDD	0	-10	1	0	.
IDD	0	-9	1	0	.
IDD	0	-6	1	0	.
IDD	0	-5	1	0	.
IDD	0	-3	1	0	.
IDD	0	-2	2	0	.
IDD	0	-1	6	0	.
IDD	0	1	4	0	.
IDD	0	2	3	0	.
IDD	0	3	1	0	.
IDD	0	5	1	0	.
IDD	0	6	1	0	.
IDD	0	39	1	0	.
IDD	0	40	1	0	.
# ST, Substitution types:
# ST	[2]id	[3]type	[4]count
ST	0	A>C	13
ST	0	A>G	64
ST	0	A>T	9
ST	0	C>A	10
ST	0	C>G	13
ST	0	C>T	75
ST	0	G>A	71
ST	0	G>C	24
ST	0	G>T	8
ST	0	T>A	7
ST	0	T>C	67
ST	0	T>G	10
# 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	21	0	0.000000	1	0.251889
DP	0	32	0	0.000000	1	0.251889
DP	0	38	0	0.000000	1	0.251889
DP	0	68	0	0.000000	1	0.251889
DP	0	76	0	0.000000	1	0.251889
DP	0	87	0	0.000000	1	0.251889
DP	0	92	0	0.000000	1	0.251889
DP	0	94	0	0.000000	1	0.251889
DP	0	102	0	0.000000	1	0.251889
DP	0	105	0	0.000000	1	0.251889
DP	0	110	0	0.000000	1	0.251889
DP	0	113	0	0.000000	1	0.251889
DP	0	118	0	0.000000	1	0.251889
DP	0	120	0	0.000000	1	0.251889
DP	0	121	0	0.000000	1	0.251889
DP	0	122	0	0.000000	2	0.503778
DP	0	124	0	0.000000	1	0.251889
DP	0	126	0	0.000000	2	0.503778
DP	0	133	0	0.000000	2	0.503778
DP	0	134	0	0.000000	2	0.503778
DP	0	135	0	0.000000	2	0.503778
DP	0	136	0	0.000000	1	0.251889
DP	0	137	0	0.000000	1	0.251889
DP	0	138	0	0.000000	1	0.251889
DP	0	140	0	0.000000	1	0.251889
DP	0	141	0	0.000000	1	0.251889
DP	0	144	0	0.000000	2	0.503778
DP	0	146	0	0.000000	1	0.251889
DP	0	148	0	0.000000	1	0.251889
DP	0	149	0	0.000000	1	0.251889
DP	0	151	0	0.000000	1	0.251889
DP	0	152	0	0.000000	2	0.503778
DP	0	153	0	0.000000	2	0.503778
DP	0	154	0	0.000000	1	0.251889
DP	0	155	0	0.000000	1	0.251889
DP	0	157	0	0.000000	2	0.503778
DP	0	158	0	0.000000	1	0.251889
DP	0	159	0	0.000000	1	0.251889
DP	0	161	0	0.000000	1	0.251889
DP	0	162	0	0.000000	2	0.503778
DP	0	166	0	0.000000	1	0.251889
DP	0	169	0	0.000000	1	0.251889
DP	0	170	0	0.000000	1	0.251889
DP	0	174	0	0.000000	3	0.755668
DP	0	175	0	0.000000	1	0.251889
DP	0	177	0	0.000000	3	0.755668
DP	0	180	0	0.000000	4	1.007557
DP	0	182	0	0.000000	2	0.503778
DP	0	183	0	0.000000	3	0.755668
DP	0	184	0	0.000000	3	0.755668
DP	0	185	0	0.000000	3	0.755668
DP	0	186	0	0.000000	1	0.251889
DP	0	187	0	0.000000	2	0.503778
DP	0	190	0	0.000000	2	0.503778
DP	0	191	0	0.000000	1	0.251889
DP	0	192	0	0.000000	3	0.755668
DP	0	193	0	0.000000	1	0.251889
DP	0	194	0	0.000000	1	0.251889
DP	0	195	0	0.000000	1	0.251889
DP	0	196	0	0.000000	1	0.251889
DP	0	197	0	0.000000	2	0.503778
DP	0	198	0	0.000000	1	0.251889
DP	0	199	0	0.000000	1	0.251889
DP	0	200	0	0.000000	1	0.251889
DP	0	201	0	0.000000	2	0.503778
DP	0	202	0	0.000000	2	0.503778
DP	0	203	0	0.000000	2	0.503778
DP	0	205	0	0.000000	1	0.251889
DP	0	206	0	0.000000	1	0.251889
DP	0	207	0	0.000000	1	0.251889
DP	0	208	0	0.000000	1	0.251889
DP	0	209	0	0.000000	2	0.503778
DP	0	210	0	0.000000	1	0.251889
DP	0	211	0	0.000000	1	0.251889
DP	0	212	0	0.000000	2	0.503778
DP	0	214	0	0.000000	2	0.503778
DP	0	215	0	0.000000	2	0.503778
DP	0	216	0	0.000000	2	0.503778
DP	0	217	0	0.000000	2	0.503778
DP	0	218	0	0.000000	1	0.251889
DP	0	219	0	0.000000	2	0.503778
DP	0	220	0	0.000000	1	0.251889
DP	0	222	0	0.000000	1	0.251889
DP	0	223	0	0.000000	4	1.007557
DP	0	225	0	0.000000	2	0.503778
DP	0	226	0	0.000000	2	0.503778
DP	0	229	0	0.000000	2	0.503778
DP	0	231	0	0.000000	1	0.251889
DP	0	232	0	0.000000	1	0.251889
DP	0	235	0	0.000000	2	0.503778
DP	0	236	0	0.000000	1	0.251889
DP	0	237	0	0.000000	1	0.251889
DP	0	238	0	0.000000	1	0.251889
DP	0	239	0	0.000000	2	0.503778
DP	0	241	0	0.000000	1	0.251889
DP	0	245	0	0.000000	4	1.007557
DP	0	246	0	0.000000	1	0.251889
DP	0	247	0	0.000000	2	0.503778
DP	0	248	0	0.000000	2	0.503778
DP	0	249	0	0.000000	2	0.503778
DP	0	251	0	0.000000	1	0.251889
DP	0	253	0	0.000000	1	0.251889
DP	0	254	0	0.000000	3	0.755668
DP	0	255	0	0.000000	1	0.251889
DP	0	258	0	0.000000	2	0.503778
DP	0	259	0	0.000000	1	0.251889
DP	0	262	0	0.000000	2	0.503778
DP	0	263	0	0.000000	1	0.251889
DP	0	265	0	0.000000	2	0.503778
DP	0	266	0	0.000000	3	0.755668
DP	0	267	0	0.000000	3	0.755668
DP	0	268	0	0.000000	5	1.259446
DP	0	269	0	0.000000	1	0.251889
DP	0	270	0	0.000000	1	0.251889
DP	0	272	0	0.000000	2	0.503778
DP	0	273	0	0.000000	3	0.755668
DP	0	276	0	0.000000	1	0.251889
DP	0	277	0	0.000000	1	0.251889
DP	0	278	0	0.000000	1	0.251889
DP	0	279	0	0.000000	3	0.755668
DP	0	280	0	0.000000	2	0.503778
DP	0	281	0	0.000000	1	0.251889
DP	0	283	0	0.000000	1	0.251889
DP	0	284	0	0.000000	2	0.503778
DP	0	286	0	0.000000	1	0.251889
DP	0	288	0	0.000000	1	0.251889
DP	0	289	0	0.000000	1	0.251889
DP	0	290	0	0.000000	1	0.251889
DP	0	291	0	0.000000	1	0.251889
DP	0	292	0	0.000000	1	0.251889
DP	0	295	0	0.000000	1	0.251889
DP	0	297	0	0.000000	2	0.503778
DP	0	298	0	0.000000	1	0.251889
DP	0	299	0	0.000000	1	0.251889
DP	0	301	0	0.000000	1	0.251889
DP	0	302	0	0.000000	1	0.251889
DP	0	303	0	0.000000	2	0.503778
DP	0	304	0	0.000000	2	0.503778
DP	0	306	0	0.000000	1	0.251889
DP	0	307	0	0.000000	1	0.251889
DP	0	308	0	0.000000	1	0.251889
DP	0	312	0	0.000000	2	0.503778
DP	0	319	0	0.000000	2	0.503778
DP	0	324	0	0.000000	2	0.503778
DP	0	326	0	0.000000	1	0.251889
DP	0	327	0	0.000000	3	0.755668
DP	0	330	0	0.000000	2	0.503778
DP	0	331	0	0.000000	2	0.503778
DP	0	334	0	0.000000	4	1.007557
DP	0	335	0	0.000000	1	0.251889
DP	0	337	0	0.000000	2	0.503778
DP	0	342	0	0.000000	1	0.251889
DP	0	345	0	0.000000	1	0.251889
DP	0	348	0	0.000000	2	0.503778
DP	0	350	0	0.000000	1	0.251889
DP	0	351	0	0.000000	1	0.251889
DP	0	352	0	0.000000	1	0.251889
DP	0	354	0	0.000000	1	0.251889
DP	0	355	0	0.000000	1	0.251889
DP	0	358	0	0.000000	1	0.251889
DP	0	359	0	0.000000	1	0.251889
DP	0	360	0	0.000000	1	0.251889
DP	0	361	0	0.000000	2	0.503778
DP	0	362	0	0.000000	1	0.251889
DP	0	366	0	0.000000	1	0.251889
DP	0	367	0	0.000000	1	0.251889
DP	0	374	0	0.000000	1	0.251889
DP	0	375	0	0.000000	1	0.251889
DP	0	376	0	0.000000	2	0.503778
DP	0	378	0	0.000000	1	0.251889
DP	0	380	0	0.000000	1	0.251889
DP	0	381	0	0.000000	1	0.251889
DP	0	382	0	0.000000	1	0.251889
DP	0	383	0	0.000000	1	0.251889
DP	0	389	0	0.000000	1	0.251889
DP	0	391	0	0.000000	1	0.251889
DP	0	394	0	0.000000	1	0.251889
DP	0	395	0	0.000000	1	0.251889
DP	0	397	0	0.000000	1	0.251889
DP	0	399	0	0.000000	1	0.251889
DP	0	400	0	0.000000	1	0.251889
DP	0	406	0	0.000000	2	0.503778
DP	0	413	0	0.000000	1	0.251889
DP	0	416	0	0.000000	1	0.251889
DP	0	417	0	0.000000	1	0.251889
DP	0	423	0	0.000000	1	0.251889
DP	0	427	0	0.000000	2	0.503778
DP	0	431	0	0.000000	1	0.251889
DP	0	437	0	0.000000	1	0.251889
DP	0	440	0	0.000000	1	0.251889
DP	0	445	0	0.000000	1	0.251889
DP	0	455	0	0.000000	2	0.503778
DP	0	456	0	0.000000	1	0.251889
DP	0	463	0	0.000000	2	0.503778
DP	0	471	0	0.000000	2	0.503778
DP	0	472	0	0.000000	2	0.503778
DP	0	487	0	0.000000	2	0.503778
DP	0	497	0	0.000000	1	0.251889
DP	0	>500	0	0.000000	102	25.692695