# This file was produced by bcftools stats (1.23.1+htslib-1.23) and can be plotted using plot-vcfstats.
# The command line was:	bcftools stats  --threads 50 freebayes.BC1.v4.filter4.0.95.vcf
#
# Definition of sets:
# ID	[2]id	[3]tab-separated file names
ID	0	freebayes.BC1.v4.filter4.0.95.vcf
# 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:	94
SN	0	number of records:	1574
SN	0	number of no-ALTs:	0
SN	0	number of SNPs:	1406
SN	0	number of MNPs:	349
SN	0	number of indels:	59
SN	0	number of others:	41
SN	0	number of multiallelic sites:	390
SN	0	number of multiallelic SNP sites:	36
# 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	806	457	1.76	767	415	1.85
# 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	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	0.030000	0	0	0	1	0	0	1
AF	0	0.050000	2	2	0	1	0	0	1
AF	0	0.060000	1	0	1	0	0	0	0
AF	0	0.080000	2	1	1	1	0	0	1
AF	0	0.090000	0	0	0	1	0	0	1
AF	0	0.110000	15	9	6	0	0	0	0
AF	0	0.120000	9	6	3	0	0	0	0
AF	0	0.130000	6	3	3	1	0	0	1
AF	0	0.140000	9	5	4	1	0	0	1
AF	0	0.150000	18	9	9	0	0	0	0
AF	0	0.160000	43	30	13	1	0	0	1
AF	0	0.170000	21	14	7	0	0	0	0
AF	0	0.180000	36	23	13	7	0	0	7
AF	0	0.190000	7	3	4	1	0	0	1
AF	0	0.200000	24	18	6	1	0	0	1
AF	0	0.210000	53	36	17	1	0	0	1
AF	0	0.220000	28	14	14	1	0	0	1
AF	0	0.230000	73	43	30	8	0	0	8
AF	0	0.240000	64	45	19	3	0	0	3
AF	0	0.250000	82	54	28	1	0	0	1
AF	0	0.260000	33	26	7	4	0	0	4
AF	0	0.270000	36	22	14	1	0	0	1
AF	0	0.280000	15	9	6	2	0	0	2
AF	0	0.290000	14	7	7	0	0	0	0
AF	0	0.300000	13	8	5	0	0	0	0
AF	0	0.310000	8	5	3	1	0	0	1
AF	0	0.320000	3	2	1	0	0	0	0
AF	0	0.330000	6	5	1	0	0	0	0
AF	0	0.340000	3	2	1	0	0	0	0
AF	0	0.360000	3	2	1	0	0	0	0
AF	0	0.370000	0	0	0	1	0	0	1
AF	0	0.380000	1	0	1	0	0	0	0
AF	0	0.390000	1	0	1	0	0	0	0
AF	0	0.410000	1	0	1	0	0	0	0
AF	0	0.420000	3	2	1	0	0	0	0
AF	0	0.430000	4	3	1	0	0	0	0
AF	0	0.440000	6	2	4	0	0	0	0
AF	0	0.450000	4	2	2	0	0	0	0
AF	0	0.470000	12	8	4	1	0	0	1
AF	0	0.480000	27	18	9	1	0	0	1
AF	0	0.490000	29	17	12	0	0	0	0
AF	0	0.500000	17	6	11	1	0	0	1
AF	0	0.510000	3	3	0	0	0	0	0
AF	0	0.520000	2	1	1	0	0	0	0
AF	0	0.530000	3	1	2	1	0	0	1
AF	0	0.540000	1	1	0	0	0	0	0
AF	0	0.560000	1	0	1	0	0	0	0
AF	0	0.570000	2	1	1	0	0	0	0
AF	0	0.580000	1	1	0	0	0	0	0
AF	0	0.590000	1	1	0	0	0	0	0
AF	0	0.600000	1	1	0	0	0	0	0
AF	0	0.650000	4	2	2	0	0	0	0
AF	0	0.660000	10	4	6	0	0	0	0
AF	0	0.670000	12	11	1	0	0	0	0
AF	0	0.680000	5	3	2	1	0	0	1
AF	0	0.690000	4	1	3	0	0	0	0
AF	0	0.700000	23	17	6	1	0	0	1
AF	0	0.710000	35	25	10	2	0	0	2
AF	0	0.720000	33	23	10	3	0	0	3
AF	0	0.730000	56	30	26	2	0	0	2
AF	0	0.740000	48	33	15	2	0	0	2
AF	0	0.750000	66	45	21	2	0	0	2
AF	0	0.760000	32	21	11	2	0	0	2
AF	0	0.770000	50	30	20	0	0	0	0
AF	0	0.780000	27	20	7	0	0	0	0
AF	0	0.790000	3	3	0	0	0	0	0
AF	0	0.800000	33	20	13	3	0	0	3
AF	0	0.810000	12	8	4	0	0	0	0
AF	0	0.820000	19	11	8	0	0	0	0
AF	0	0.830000	14	7	7	1	0	0	1
AF	0	0.840000	3	3	0	0	0	0	0
AF	0	0.850000	7	4	3	1	0	0	1
AF	0	0.860000	6	5	1	0	0	0	0
AF	0	0.870000	10	5	5	1	0	0	1
AF	0	0.900000	4	4	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	0.0	12	9	3	0
QUAL	0	146.9	1	0	1	0
QUAL	0	260.1	1	1	0	0
QUAL	0	651.7	1	1	0	0
QUAL	0	727.5	1	1	0	0
QUAL	0	826.1	1	0	1	0
QUAL	0	1050.7	0	0	0	1
QUAL	0	1661.0	1	0	1	0
QUAL	0	2570.0	1	0	1	0
QUAL	0	3370.0	1	1	0	0
QUAL	0	4353.5	1	1	0	0
QUAL	0	4771.9	1	1	0	0
QUAL	0	5229.3	1	1	0	0
QUAL	0	5608.5	0	0	0	1
QUAL	0	5721.1	1	1	0	0
QUAL	0	7100.3	1	1	0	0
QUAL	0	7149.5	1	1	0	0
QUAL	0	7495.1	1	0	1	0
QUAL	0	7529.5	1	0	1	0
QUAL	0	7836.7	1	0	1	0
QUAL	0	8078.7	1	1	0	0
QUAL	0	9291.4	1	1	0	0
QUAL	0	9569.9	1	1	0	0
QUAL	0	9988.0	1	0	1	0
QUAL	0	10092.9	1	0	1	0
QUAL	0	10176.9	1	0	1	0
QUAL	0	10339.9	1	1	0	0
QUAL	0	10395.9	0	0	0	1
QUAL	0	10515.9	1	0	1	0
QUAL	0	10871.9	1	1	0	0
QUAL	0	10986.9	1	1	0	0
QUAL	0	10993.9	0	0	0	1
QUAL	0	11347.9	1	1	0	0
QUAL	0	11482.9	1	0	1	0
QUAL	0	11489.9	0	0	0	1
QUAL	0	11846.9	1	1	0	0
QUAL	0	12627.9	1	0	1	0
QUAL	0	12773.9	1	0	1	0
QUAL	0	12997.9	1	1	0	0
QUAL	0	13026.9	1	1	0	0
QUAL	0	13033.9	1	1	0	0
QUAL	0	13189.9	1	0	1	0
QUAL	0	13225.9	1	1	0	0
QUAL	0	13287.9	1	1	0	0
QUAL	0	13415.9	1	1	0	0
QUAL	0	13578.9	1	0	1	0
QUAL	0	14322.9	0	0	0	1
QUAL	0	14465.9	1	1	0	0
QUAL	0	14575.9	1	0	1	0
QUAL	0	14679.9	1	1	0	0
QUAL	0	14946.9	1	1	0	0
QUAL	0	14951.9	1	1	0	0
QUAL	0	15019.9	1	1	0	0
QUAL	0	15096.9	1	1	0	0
QUAL	0	15114.9	1	1	0	0
QUAL	0	15124.9	1	1	0	0
QUAL	0	15173.9	1	1	0	0
QUAL	0	15193.9	1	1	0	0
QUAL	0	15255.9	1	0	1	0
QUAL	0	15288.9	1	1	0	0
QUAL	0	15433.9	1	1	0	0
QUAL	0	15497.9	1	1	0	0
QUAL	0	15787.9	1	0	1	0
QUAL	0	15790.9	1	1	0	0
QUAL	0	16127.9	1	1	0	0
QUAL	0	16287.9	1	0	1	0
QUAL	0	16440.9	1	1	0	0
QUAL	0	16611.9	1	0	1	0
QUAL	0	16678.9	1	1	0	0
QUAL	0	16728.9	1	1	0	0
QUAL	0	16823.9	1	0	1	0
QUAL	0	16929.9	1	1	0	0
QUAL	0	17169.9	1	1	0	0
QUAL	0	17635.9	1	0	1	0
QUAL	0	17832.9	1	0	1	0
QUAL	0	17844.9	1	1	0	0
QUAL	0	18080.9	1	1	0	0
QUAL	0	18135.9	1	1	0	0
QUAL	0	18312.9	1	0	1	0
QUAL	0	18313.9	0	0	0	1
QUAL	0	18444.9	1	0	1	0
QUAL	0	18629.9	1	1	0	0
QUAL	0	18716.9	1	0	1	0
QUAL	0	18751.9	1	1	0	0
QUAL	0	18810.9	1	0	1	0
QUAL	0	18965.9	1	0	1	0
QUAL	0	19116.9	1	0	1	0
QUAL	0	19158.9	1	1	0	0
QUAL	0	19374.9	1	0	1	0
QUAL	0	19415.9	1	1	0	0
QUAL	0	19544.9	1	1	0	0
QUAL	0	19739.9	1	1	0	0
QUAL	0	20015.9	1	0	1	0
QUAL	0	20133.9	1	0	1	0
QUAL	0	20152.9	1	1	0	0
QUAL	0	20342.9	1	1	0	0
QUAL	0	20496.9	1	1	0	0
QUAL	0	20517.9	0	0	0	1
QUAL	0	20661.9	1	1	0	0
QUAL	0	20712.9	1	0	1	0
QUAL	0	20932.9	1	1	0	0
QUAL	0	21433.9	1	1	0	0
QUAL	0	21478.9	1	1	0	0
QUAL	0	21573.9	1	0	1	0
QUAL	0	21663.9	1	1	0	0
QUAL	0	21745.9	1	0	1	0
QUAL	0	21929.9	1	1	0	0
QUAL	0	22025.9	1	0	1	0
QUAL	0	22199.9	1	0	1	0
QUAL	0	22529.9	1	1	0	0
QUAL	0	22579.9	1	1	0	0
QUAL	0	22760.9	1	0	1	0
QUAL	0	22819.9	1	0	1	0
QUAL	0	22896.9	0	0	0	1
QUAL	0	22963.9	1	0	1	0
QUAL	0	22967.9	1	1	0	0
QUAL	0	23272.9	1	0	1	0
QUAL	0	23324.9	1	1	0	0
QUAL	0	23465.9	1	0	1	0
QUAL	0	23491.9	1	1	0	0
QUAL	0	24046.9	1	1	0	0
QUAL	0	24200.9	1	0	1	0
QUAL	0	24287.9	1	1	0	0
QUAL	0	24289.9	1	1	0	0
QUAL	0	24292.9	1	0	1	0
QUAL	0	24395.9	1	1	0	0
QUAL	0	24449.9	1	1	0	0
QUAL	0	24676.9	0	0	0	1
QUAL	0	24686.9	1	0	1	0
QUAL	0	24730.9	1	1	0	0
QUAL	0	24777.9	0	0	0	1
QUAL	0	24819.9	1	1	0	0
QUAL	0	24842.9	1	1	0	0
QUAL	0	24910.9	1	1	0	0
QUAL	0	25007.9	1	0	1	0
QUAL	0	25065.9	1	1	0	0
QUAL	0	25091.9	1	1	0	0
QUAL	0	25114.9	1	0	1	0
QUAL	0	25128.9	1	1	0	0
QUAL	0	25153.9	1	1	0	0
QUAL	0	25169.9	1	1	0	0
QUAL	0	25385.9	1	0	1	0
QUAL	0	25502.9	1	1	0	0
QUAL	0	25518.9	1	0	1	0
QUAL	0	25699.9	1	1	0	0
QUAL	0	25725.9	1	0	1	0
QUAL	0	25843.9	1	0	1	0
QUAL	0	25893.9	1	0	1	0
QUAL	0	25934.9	1	1	0	0
QUAL	0	25970.9	1	1	0	0
QUAL	0	26005.9	1	1	0	0
QUAL	0	26009.9	1	0	1	0
QUAL	0	26234.9	1	1	0	0
QUAL	0	26236.9	1	1	0	0
QUAL	0	26301.9	1	0	1	0
QUAL	0	26362.9	1	1	0	0
QUAL	0	26379.9	1	0	1	0
QUAL	0	26443.9	1	1	0	0
QUAL	0	26468.9	1	0	1	0
QUAL	0	26754.9	1	0	1	0
QUAL	0	26791.9	1	0	1	0
QUAL	0	26801.9	1	0	1	0
QUAL	0	26809.9	1	0	1	0
QUAL	0	26823.9	1	0	1	0
QUAL	0	26869.9	1	1	0	0
QUAL	0	26920.9	1	1	0	0
QUAL	0	26958.9	0	0	0	1
QUAL	0	26986.9	1	1	0	0
QUAL	0	27254.9	1	0	1	0
QUAL	0	27311.9	0	0	0	1
QUAL	0	27327.9	1	1	0	0
QUAL	0	27470.9	1	0	1	0
QUAL	0	27795.9	0	0	0	1
QUAL	0	27815.9	1	0	1	0
QUAL	0	27841.9	1	1	0	0
QUAL	0	27881.9	1	1	0	0
QUAL	0	27976.9	1	1	0	0
QUAL	0	27994.9	1	0	1	0
QUAL	0	28048.9	1	0	1	0
QUAL	0	28089.9	1	1	0	0
QUAL	0	28199.9	1	1	0	0
QUAL	0	28444.9	1	1	0	0
QUAL	0	28577.9	1	1	0	0
QUAL	0	28712.9	1	0	1	0
QUAL	0	28723.9	1	1	0	0
QUAL	0	28789.9	1	1	0	0
QUAL	0	28790.9	1	1	0	0
QUAL	0	28915.9	1	1	0	0
QUAL	0	28998.9	1	0	1	0
QUAL	0	29222.9	1	1	0	0
QUAL	0	29368.9	1	1	0	0
QUAL	0	29397.9	1	1	0	0
QUAL	0	29506.9	1	1	0	0
QUAL	0	29585.9	1	1	0	0
QUAL	0	29629.9	1	1	0	0
QUAL	0	29648.9	1	0	1	0
QUAL	0	29665.9	1	1	0	0
QUAL	0	29699.9	1	1	0	0
QUAL	0	29824.9	1	0	1	0
QUAL	0	29845.9	1	1	0	0
QUAL	0	29891.9	1	1	0	0
QUAL	0	29899.9	1	1	0	0
QUAL	0	30104.9	1	1	0	0
QUAL	0	30127.9	1	0	1	0
QUAL	0	30160.9	1	1	0	0
QUAL	0	30338.9	1	1	0	0
QUAL	0	30397.9	1	1	0	0
QUAL	0	30432.9	1	0	1	0
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QUAL	0	31291.9	1	0	1	0
QUAL	0	31292.9	1	1	0	0
QUAL	0	31343.9	1	1	0	0
QUAL	0	31427.9	1	1	0	0
QUAL	0	31767.9	1	1	0	0
QUAL	0	31870.9	1	1	0	0
QUAL	0	31909.9	1	1	0	0
QUAL	0	32086.9	1	0	1	0
QUAL	0	32139.9	1	1	0	0
QUAL	0	32142.9	1	1	0	0
QUAL	0	32230.9	1	1	0	0
QUAL	0	32259.9	1	1	0	0
QUAL	0	32341.9	1	0	1	0
QUAL	0	32380.9	1	1	0	0
QUAL	0	32396.9	1	1	0	0
QUAL	0	32427.9	1	1	0	0
QUAL	0	32704.9	1	1	0	0
QUAL	0	32730.9	1	0	1	0
QUAL	0	33045.9	1	0	1	0
QUAL	0	33229.9	1	1	0	0
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QUAL	0	33616.9	1	1	0	0
QUAL	0	33712.9	1	1	0	0
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QUAL	0	33770.9	1	1	0	0
QUAL	0	33898.9	1	1	0	0
QUAL	0	33929.9	1	0	1	0
QUAL	0	34050.9	1	1	0	0
QUAL	0	34140.9	1	1	0	0
QUAL	0	34164.9	1	1	0	0
QUAL	0	34172.9	1	1	0	0
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QUAL	0	35325.9	1	1	0	0
QUAL	0	35497.9	1	1	0	0
QUAL	0	35534.9	1	1	0	0
QUAL	0	35548.9	0	0	0	1
QUAL	0	35565.9	1	1	0	0
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QUAL	0	37029.9	1	1	0	0
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QUAL	0	37186.9	1	0	1	0
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QUAL	0	37571.9	1	1	0	0
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QUAL	0	37894.9	1	1	0	0
QUAL	0	37905.9	1	1	0	0
QUAL	0	38024.9	1	1	0	0
QUAL	0	38091.9	1	1	0	0
QUAL	0	38101.9	1	1	0	0
QUAL	0	38317.9	1	1	0	0
QUAL	0	38463.9	1	0	1	0
QUAL	0	38478.9	1	1	0	0
QUAL	0	38565.9	1	1	0	0
QUAL	0	38805.9	1	1	0	0
QUAL	0	39013.9	1	0	1	0
QUAL	0	39017.9	1	0	1	0
QUAL	0	39086.9	1	1	0	0
QUAL	0	39330.9	1	1	0	0
QUAL	0	39339.9	1	0	1	0
QUAL	0	39355.9	1	0	1	0
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QUAL	0	519209.9	0	0	0	1
QUAL	0	522799.9	1	1	0	0
QUAL	0	525299.9	1	0	1	0
QUAL	0	525329.9	1	1	0	0
QUAL	0	525629.9	1	1	0	0
QUAL	0	540449.9	1	1	0	0
QUAL	0	544049.9	1	1	0	0
QUAL	0	545769.9	1	0	1	0
QUAL	0	558209.9	1	1	0	0
QUAL	0	561339.9	1	0	1	0
QUAL	0	570039.9	1	1	0	0
QUAL	0	573919.9	1	0	1	0
QUAL	0	575879.9	1	1	0	0
QUAL	0	584989.9	1	0	1	0
QUAL	0	587799.9	1	0	1	0
QUAL	0	590399.9	1	0	1	0
QUAL	0	590839.9	1	0	1	0
QUAL	0	603959.9	1	1	0	0
QUAL	0	621999.9	1	0	1	0
QUAL	0	623949.9	0	0	0	1
QUAL	0	626789.9	1	0	1	0
QUAL	0	629579.9	1	0	1	0
QUAL	0	639239.9	1	1	0	0
QUAL	0	650139.9	1	1	0	0
QUAL	0	650329.9	1	1	0	0
QUAL	0	665389.9	1	1	0	0
QUAL	0	667719.9	1	1	0	0
QUAL	0	674209.9	1	1	0	0
QUAL	0	693599.9	1	1	0	0
QUAL	0	699919.9	1	0	1	0
QUAL	0	702859.9	1	0	1	0
QUAL	0	772849.9	1	1	0	0
QUAL	0	802459.9	0	0	0	1
QUAL	0	929329.9	1	0	1	0
QUAL	0	946859.9	1	1	0	0
QUAL	0	1033099.9	1	1	0	0
QUAL	0	2179900.0	1	1	0	0
# IDD, InDel distribution:
# IDD	[2]id	[3]length (deletions negative)	[4]number of sites	[5]number of genotypes	[6]mean VAF
IDD	0	-9	1	0	.
IDD	0	-6	1	0	.
IDD	0	-5	1	0	.
IDD	0	-4	1	0	.
IDD	0	-3	7	0	.
IDD	0	-2	7	0	.
IDD	0	-1	23	0	.
IDD	0	1	15	0	.
IDD	0	2	5	0	.
IDD	0	3	2	0	.
IDD	0	7	1	0	.
# ST, Substitution types:
# ST	[2]id	[3]type	[4]count
ST	0	A>C	65
ST	0	A>G	200
ST	0	A>T	84
ST	0	C>A	51
ST	0	C>G	39
ST	0	C>T	218
ST	0	G>A	213
ST	0	G>C	53
ST	0	G>T	69
ST	0	T>A	61
ST	0	T>C	175
ST	0	T>G	35
# 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	>500	0	0.000000	1574	100.000000