# This file was produced by bcftools stats (1.14+htslib-1.14) and can be plotted using plot-vcfstats.
# The command line was:	bcftools stats  --threads 1 --samples AAP-07 --fasta-ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/human_GRCh38_no_alt_analysis_set.fasta /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/AAP-07.hap1.asm.GRCh38.paftools.vcf.gz
#
# Definition of sets:
# ID	[2]id	[3]tab-separated file names
ID	0	/mnt/miniwdl_task_container/work/_miniwdl_inputs/0/AAP-07.hap1.asm.GRCh38.paftools.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:	3247737
SN	0	number of no-ALTs:	0
SN	0	number of SNPs:	2566559
SN	0	number of MNPs:	0
SN	0	number of indels:	681178
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	1704182	862377	1.98	1704182	862377	1.98
# ICS, Indel context summary:
# ICS	[2]id	[3]repeat-consistent	[4]repeat-inconsistent	[5]not applicable	[6]c/(c+i) ratio
ICS	0	143068	19869	518241	0.8781
# ICL, Indel context by length:
# ICL	[2]id	[3]length of repeat element	[4]repeat-consistent deletions)	[5]repeat-inconsistent deletions	[6]consistent insertions	[7]inconsistent insertions	[8]c/(c+i) ratio
ICL	0	2	45828	3395	40660	4812	0.9133
ICL	0	3	9087	1475	5652	1993	0.8095
ICL	0	4	16456	2161	13600	2464	0.8666
ICL	0	5	4403	773	3214	773	0.8313
ICL	0	6	1293	430	750	433	0.7030
ICL	0	7	503	192	137	174	0.6362
ICL	0	8	568	190	149	170	0.6657
ICL	0	9	340	112	85	101	0.6661
ICL	0	10	278	113	65	108	0.6082
# 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	0	0	0	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	0.990000	2566559	1704182	862377	681178	143068	19869	518241
# 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	5.0	4663	1939	2724	219
QUAL	0	6.0	3013	1404	1609	198
QUAL	0	7.0	4817	1962	2855	176
QUAL	0	8.0	782	336	446	42
QUAL	0	9.0	1834	860	974	63
QUAL	0	10.0	1133	607	526	136
QUAL	0	11.0	1078	457	621	76
QUAL	0	12.0	3505	1642	1863	69
QUAL	0	13.0	360	235	125	76
QUAL	0	14.0	1092	549	543	96
QUAL	0	15.0	204	101	103	12
QUAL	0	16.0	456	270	186	63
QUAL	0	18.0	148	71	77	8
QUAL	0	19.0	34	20	14	4
QUAL	0	20.0	441	208	233	49
QUAL	0	21.0	360	168	192	65
QUAL	0	22.0	26	21	5	15
QUAL	0	23.0	971	490	481	52
QUAL	0	24.0	403	155	248	15
QUAL	0	25.0	345	141	204	19
QUAL	0	26.0	134	84	50	10
QUAL	0	27.0	1262	592	670	51
QUAL	0	28.0	537	332	205	70
QUAL	0	30.0	124	74	50	21
QUAL	0	31.0	148	92	56	25
QUAL	0	32.0	252	110	142	19
QUAL	0	33.0	272	164	108	49
QUAL	0	34.0	196	117	79	42
QUAL	0	35.0	1233	557	676	50
QUAL	0	36.0	342	152	190	15
QUAL	0	37.0	951	478	473	76
QUAL	0	38.0	195	78	117	9
QUAL	0	39.0	56	32	24	22
QUAL	0	40.0	5	2	3	4
QUAL	0	41.0	1548	755	793	128
QUAL	0	42.0	882	505	377	74
QUAL	0	43.0	571	308	263	61
QUAL	0	44.0	743	379	364	32
QUAL	0	45.0	155	72	83	4
QUAL	0	46.0	462	246	216	39
QUAL	0	47.0	618	251	367	21
QUAL	0	48.0	593	331	262	64
QUAL	0	49.0	1057	484	573	30
QUAL	0	50.0	677	343	334	42
QUAL	0	51.0	1813	860	953	41
QUAL	0	52.0	998	564	434	85
QUAL	0	53.0	285	159	126	14
QUAL	0	54.0	839	383	456	18
QUAL	0	55.0	491	265	226	40
QUAL	0	56.0	145	103	42	25
QUAL	0	58.0	99	22	77	6
QUAL	0	59.0	391	198	193	10
QUAL	0	60.0	2522820	1683454	839366	678528
# IDD, InDel distribution:
# IDD	[2]id	[3]length (deletions negative)	[4]number of sites	[5]number of genotypes	[6]mean VAF
IDD	0	-60	5063	0	.
IDD	0	-59	38	0	.
IDD	0	-58	61	0	.
IDD	0	-57	43	0	.
IDD	0	-56	86	0	.
IDD	0	-55	58	0	.
IDD	0	-54	81	0	.
IDD	0	-53	46	0	.
IDD	0	-52	106	0	.
IDD	0	-51	67	0	.
IDD	0	-50	132	0	.
IDD	0	-49	109	0	.
IDD	0	-48	152	0	.
IDD	0	-47	67	0	.
IDD	0	-46	126	0	.
IDD	0	-45	89	0	.
IDD	0	-44	135	0	.
IDD	0	-43	81	0	.
IDD	0	-42	158	0	.
IDD	0	-41	99	0	.
IDD	0	-40	257	0	.
IDD	0	-39	127	0	.
IDD	0	-38	207	0	.
IDD	0	-37	134	0	.
IDD	0	-36	295	0	.
IDD	0	-35	170	0	.
IDD	0	-34	256	0	.
IDD	0	-33	183	0	.
IDD	0	-32	406	0	.
IDD	0	-31	203	0	.
IDD	0	-30	480	0	.
IDD	0	-29	240	0	.
IDD	0	-28	615	0	.
IDD	0	-27	315	0	.
IDD	0	-26	585	0	.
IDD	0	-25	385	0	.
IDD	0	-24	923	0	.
IDD	0	-23	367	0	.
IDD	0	-22	794	0	.
IDD	0	-21	461	0	.
IDD	0	-20	1513	0	.
IDD	0	-19	549	0	.
IDD	0	-18	1369	0	.
IDD	0	-17	719	0	.
IDD	0	-16	2339	0	.
IDD	0	-15	1396	0	.
IDD	0	-14	2279	0	.
IDD	0	-13	1280	0	.
IDD	0	-12	4684	0	.
IDD	0	-11	1558	0	.
IDD	0	-10	4480	0	.
IDD	0	-9	2532	0	.
IDD	0	-8	8108	0	.
IDD	0	-7	3345	0	.
IDD	0	-6	9674	0	.
IDD	0	-5	9029	0	.
IDD	0	-4	30252	0	.
IDD	0	-3	21229	0	.
IDD	0	-2	59384	0	.
IDD	0	-1	177249	0	.
IDD	0	1	151699	0	.
IDD	0	2	54003	0	.
IDD	0	3	20089	0	.
IDD	0	4	29285	0	.
IDD	0	5	8622	0	.
IDD	0	6	9224	0	.
IDD	0	7	3163	0	.
IDD	0	8	7850	0	.
IDD	0	9	2578	0	.
IDD	0	10	4293	0	.
IDD	0	11	1642	0	.
IDD	0	12	4382	0	.
IDD	0	13	1258	0	.
IDD	0	14	1966	0	.
IDD	0	15	1330	0	.
IDD	0	16	2219	0	.
IDD	0	17	728	0	.
IDD	0	18	1258	0	.
IDD	0	19	554	0	.
IDD	0	20	1420	0	.
IDD	0	21	506	0	.
IDD	0	22	707	0	.
IDD	0	23	390	0	.
IDD	0	24	929	0	.
IDD	0	25	362	0	.
IDD	0	26	509	0	.
IDD	0	27	294	0	.
IDD	0	28	582	0	.
IDD	0	29	227	0	.
IDD	0	30	451	0	.
IDD	0	31	203	0	.
IDD	0	32	386	0	.
IDD	0	33	174	0	.
IDD	0	34	237	0	.
IDD	0	35	169	0	.
IDD	0	36	257	0	.
IDD	0	37	124	0	.
IDD	0	38	172	0	.
IDD	0	39	118	0	.
IDD	0	40	247	0	.
IDD	0	41	103	0	.
IDD	0	42	165	0	.
IDD	0	43	86	0	.
IDD	0	44	133	0	.
IDD	0	45	87	0	.
IDD	0	46	116	0	.
IDD	0	47	70	0	.
IDD	0	48	160	0	.
IDD	0	49	104	0	.
IDD	0	50	110	0	.
IDD	0	51	80	0	.
IDD	0	52	94	0	.
IDD	0	53	48	0	.
IDD	0	54	98	0	.
IDD	0	55	75	0	.
IDD	0	56	97	0	.
IDD	0	57	57	0	.
IDD	0	58	89	0	.
IDD	0	59	60	0	.
IDD	0	60	7571	0	.
# ST, Substitution types:
# ST	[2]id	[3]type	[4]count
ST	0	A>C	110850
ST	0	A>G	424799
ST	0	A>T	96367
ST	0	C>A	110065
ST	0	C>G	112801
ST	0	C>T	426614
ST	0	G>A	426332
ST	0	G>C	113067
ST	0	G>T	111015
ST	0	T>A	96819
ST	0	T>C	426437
ST	0	T>G	111393
# DP, Depth distribution
# DP	[2]id	[3]bin	[4]number of genotypes	[5]fraction of genotypes (%)	[6]number of sites	[7]fraction of sites (%)
# 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	AAP-07	0	2566559	0	1704182	862377	681178	0.0	3247737	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	AAP-07	0	0	0	0.00	0	0	324010	357168
# HWE
# HWE	[2]id	[3]1st ALT allele frequency	[4]Number of observations	[5]25th percentile	[6]median	[7]75th percentile
HWE	0	0.990000	3247737	0.000000	0.000000	0.000000