#
# 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
#   - transitions, see https://en.wikipedia.org/wiki/Transition_(genetics)
#   - transversions, see https://en.wikipedia.org/wiki/Transversion
# 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:
#   - allele count, i.e. the number of singleton genotypes (AC=1)
#   - number of transitions, see above
#   - number of transversions, see above
#   - repeat-consistent, inconsistent and n/a: experimental and useless stats [DEPRECATED]
# 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:
#   - set id, see above
#   - the depth bin, corresponds to the depth (unless --depth was given)
#   - number of genotypes with this depth (zero unless -s/-S was given)
#   - fraction of genotypes with this depth (zero unless -s/-S was given)
#   - number of sites with this depth
#   - fraction of sites with this depth
# 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
