# This file was produced by bcftools stats (1.9+htslib-1.9) and can be plotted using plot-vcfstats. # The command line was: bcftools stats chr8_filtered.vcf # # Definition of sets: # ID [2]id [3]tab-separated file names ID 0 chr8_filtered.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: 1 SN 0 number of records: 19758 SN 0 number of no-ALTs: 0 SN 0 number of SNPs: 19512 SN 0 number of MNPs: 0 SN 0 number of indels: 246 SN 0 number of others: 0 SN 0 number of multiallelic sites: 162 SN 0 number of multiallelic SNP sites: 161 # 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 13356 6317 2.11 13315 6197 2.15 # 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 17098 11801 5297 227 0 0 227 # 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 17098 11801 5297 227 0 0 227 AF 0 0.990000 2575 1555 1020 20 0 0 20 # 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 30 67 46 21 2 QUAL 0 31 60 43 17 0 QUAL 0 32 40 25 15 1 QUAL 0 33 60 39 21 2 QUAL 0 34 51 34 17 1 QUAL 0 35 46 35 11 2 QUAL 0 36 50 36 14 1 QUAL 0 37 67 40 27 1 QUAL 0 38 56 36 20 2 QUAL 0 39 32 20 12 0 QUAL 0 40 65 41 24 2 QUAL 0 41 60 43 17 1 QUAL 0 42 59 41 18 0 QUAL 0 43 46 26 20 1 QUAL 0 44 51 31 20 1 QUAL 0 45 45 26 19 1 QUAL 0 46 48 29 19 1 QUAL 0 47 60 36 24 3 QUAL 0 48 63 33 30 1 QUAL 0 49 59 37 22 2 QUAL 0 50 30 15 15 1 QUAL 0 51 46 30 16 1 QUAL 0 52 51 37 14 0 QUAL 0 53 50 26 24 2 QUAL 0 54 47 34 13 0 QUAL 0 55 48 31 17 1 QUAL 0 56 45 39 6 0 QUAL 0 57 48 36 12 1 QUAL 0 58 45 31 14 1 QUAL 0 59 55 40 15 2 QUAL 0 60 56 35 21 1 QUAL 0 61 49 30 19 1 QUAL 0 62 52 38 14 0 QUAL 0 63 56 37 19 2 QUAL 0 64 48 25 23 1 QUAL 0 65 52 35 17 0 QUAL 0 66 57 43 14 0 QUAL 0 67 42 33 9 0 QUAL 0 68 46 34 12 1 QUAL 0 69 50 34 16 0 QUAL 0 70 51 32 19 1 QUAL 0 71 47 35 12 1 QUAL 0 72 54 37 17 1 QUAL 0 73 54 38 16 1 QUAL 0 74 58 31 27 2 QUAL 0 75 43 32 11 0 QUAL 0 76 47 31 16 0 QUAL 0 77 46 30 16 1 QUAL 0 78 39 27 12 0 QUAL 0 79 50 35 15 0 QUAL 0 80 38 32 6 1 QUAL 0 81 54 40 14 0 QUAL 0 82 44 22 22 2 QUAL 0 83 46 31 15 0 QUAL 0 84 55 36 19 0 QUAL 0 85 47 31 16 0 QUAL 0 86 43 30 13 0 QUAL 0 87 40 24 16 0 QUAL 0 88 51 36 15 2 QUAL 0 89 53 35 18 1 QUAL 0 90 50 31 19 1 QUAL 0 91 44 28 16 0 QUAL 0 92 52 35 17 2 QUAL 0 93 58 40 18 1 QUAL 0 94 49 37 12 0 QUAL 0 95 53 32 21 1 QUAL 0 96 51 30 21 0 QUAL 0 97 52 35 17 0 QUAL 0 98 46 29 17 2 QUAL 0 99 42 32 10 0 QUAL 0 100 51 35 16 0 QUAL 0 101 62 50 12 0 QUAL 0 102 48 31 17 0 QUAL 0 103 53 32 21 1 QUAL 0 104 51 32 19 0 QUAL 0 105 55 43 12 2 QUAL 0 106 61 38 23 0 QUAL 0 107 51 33 18 1 QUAL 0 108 49 39 10 0 QUAL 0 109 55 33 22 1 QUAL 0 110 52 36 16 1 QUAL 0 111 33 26 7 1 QUAL 0 112 56 39 17 1 QUAL 0 113 62 42 20 0 QUAL 0 114 55 35 20 2 QUAL 0 115 58 38 20 0 QUAL 0 116 44 29 15 0 QUAL 0 117 51 37 14 2 QUAL 0 118 52 35 17 0 QUAL 0 119 53 37 16 3 QUAL 0 120 59 36 23 1 QUAL 0 121 60 42 18 0 QUAL 0 122 45 26 19 0 QUAL 0 123 45 23 22 1 QUAL 0 124 42 27 15 1 QUAL 0 125 63 45 18 0 QUAL 0 126 47 27 20 1 QUAL 0 127 58 40 18 0 QUAL 0 128 49 37 12 0 QUAL 0 129 55 38 17 0 QUAL 0 130 69 49 20 0 QUAL 0 131 56 41 15 2 QUAL 0 132 64 43 21 0 QUAL 0 133 53 30 23 3 QUAL 0 134 54 37 17 1 QUAL 0 135 56 38 18 0 QUAL 0 136 71 46 25 2 QUAL 0 137 58 43 15 1 QUAL 0 138 57 30 27 0 QUAL 0 139 61 41 20 1 QUAL 0 140 59 40 19 0 QUAL 0 141 42 27 15 0 QUAL 0 142 51 28 23 1 QUAL 0 143 66 39 27 1 QUAL 0 144 70 52 18 0 QUAL 0 145 57 40 17 1 QUAL 0 146 60 40 20 1 QUAL 0 147 58 43 15 1 QUAL 0 148 62 42 20 1 QUAL 0 149 61 37 24 0 QUAL 0 150 86 52 34 0 QUAL 0 151 71 52 19 0 QUAL 0 152 66 48 18 0 QUAL 0 153 52 36 16 1 QUAL 0 154 53 42 11 1 QUAL 0 155 54 34 20 0 QUAL 0 156 56 37 19 0 QUAL 0 157 54 33 21 1 QUAL 0 158 42 23 19 1 QUAL 0 159 41 25 16 0 QUAL 0 160 63 38 25 1 QUAL 0 161 56 33 23 2 QUAL 0 162 39 29 10 1 QUAL 0 163 57 42 15 0 QUAL 0 164 55 36 19 1 QUAL 0 165 52 37 15 0 QUAL 0 166 43 23 20 0 QUAL 0 167 51 43 8 0 QUAL 0 168 41 29 12 0 QUAL 0 169 47 33 14 0 QUAL 0 170 50 34 16 0 QUAL 0 171 50 32 18 0 QUAL 0 172 51 37 14 1 QUAL 0 173 58 39 19 0 QUAL 0 174 58 35 23 1 QUAL 0 175 41 30 11 0 QUAL 0 176 57 36 21 1 QUAL 0 177 60 42 18 0 QUAL 0 178 58 35 23 0 QUAL 0 179 55 40 15 1 QUAL 0 180 55 32 23 1 QUAL 0 181 49 34 15 0 QUAL 0 182 42 28 14 2 QUAL 0 183 38 30 8 1 QUAL 0 184 45 32 13 2 QUAL 0 185 56 40 16 0 QUAL 0 186 52 43 9 1 QUAL 0 187 63 39 24 0 QUAL 0 188 38 26 12 1 QUAL 0 189 39 25 14 1 QUAL 0 190 50 36 14 0 QUAL 0 191 53 35 18 0 QUAL 0 192 54 36 18 1 QUAL 0 193 50 33 17 1 QUAL 0 194 92 43 49 1 QUAL 0 195 134 56 78 0 QUAL 0 196 75 43 32 0 QUAL 0 197 47 29 18 1 QUAL 0 198 70 46 24 1 QUAL 0 199 41 34 7 1 QUAL 0 200 56 40 16 0 QUAL 0 201 39 24 15 1 QUAL 0 202 53 34 19 1 QUAL 0 203 43 33 10 1 QUAL 0 204 49 30 19 2 QUAL 0 205 57 39 18 0 QUAL 0 206 48 32 16 0 QUAL 0 207 45 34 11 0 QUAL 0 208 49 38 11 0 QUAL 0 209 49 37 12 1 QUAL 0 210 45 35 10 1 QUAL 0 211 53 37 16 0 QUAL 0 212 48 33 15 0 QUAL 0 213 43 33 10 0 QUAL 0 214 56 37 19 1 QUAL 0 215 41 36 5 0 QUAL 0 216 43 30 13 1 QUAL 0 217 53 37 16 1 QUAL 0 218 81 57 24 4 QUAL 0 219 191 131 60 1 QUAL 0 220 601 399 202 2 QUAL 0 221 1156 777 379 9 QUAL 0 222 5933 4318 1615 88 QUAL 0 223 17 6 11 0 QUAL 0 224 13 8 5 0 QUAL 0 225 366 251 115 0 QUAL 0 226 14 10 4 0 QUAL 0 227 8 3 5 1 QUAL 0 228 1227 750 477 8 # IDD, InDel distribution: # IDD [2]id [3]length (deletions negative) [4]count IDD 0 -16 1 IDD 0 -13 1 IDD 0 -9 2 IDD 0 -7 2 IDD 0 -6 5 IDD 0 -5 5 IDD 0 -4 15 IDD 0 -3 21 IDD 0 -2 12 IDD 0 -1 27 IDD 0 1 48 IDD 0 2 19 IDD 0 3 31 IDD 0 4 25 IDD 0 5 10 IDD 0 6 3 IDD 0 7 9 IDD 0 8 6 IDD 0 9 2 IDD 0 11 1 IDD 0 18 1 IDD 0 19 1 # ST, Substitution types: # ST [2]id [3]type [4]count ST 0 A>C 874 ST 0 A>G 3707 ST 0 A>T 753 ST 0 C>A 705 ST 0 C>G 840 ST 0 C>T 3102 ST 0 G>A 2993 ST 0 G>C 837 ST 0 G>T 715 ST 0 T>A 728 ST 0 T>C 3554 ST 0 T>G 865 # 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 51 0 0.000000 220 1.113473 DP 0 52 0 0.000000 252 1.275433 DP 0 53 0 0.000000 222 1.123596 DP 0 54 0 0.000000 208 1.052738 DP 0 55 0 0.000000 216 1.093228 DP 0 56 0 0.000000 216 1.093228 DP 0 57 0 0.000000 200 1.012248 DP 0 58 0 0.000000 236 1.194453 DP 0 59 0 0.000000 197 0.997064 DP 0 60 0 0.000000 210 1.062861 DP 0 61 0 0.000000 185 0.936330 DP 0 62 0 0.000000 227 1.148902 DP 0 63 0 0.000000 197 0.997064 DP 0 64 0 0.000000 175 0.885717 DP 0 65 0 0.000000 177 0.895840 DP 0 66 0 0.000000 181 0.916085 DP 0 67 0 0.000000 181 0.916085 DP 0 68 0 0.000000 171 0.865472 DP 0 69 0 0.000000 170 0.860411 DP 0 70 0 0.000000 156 0.789554 DP 0 71 0 0.000000 157 0.794615 DP 0 72 0 0.000000 177 0.895840 DP 0 73 0 0.000000 162 0.819921 DP 0 74 0 0.000000 144 0.728819 DP 0 75 0 0.000000 170 0.860411 DP 0 76 0 0.000000 165 0.835105 DP 0 77 0 0.000000 131 0.663023 DP 0 78 0 0.000000 148 0.749064 DP 0 79 0 0.000000 137 0.693390 DP 0 80 0 0.000000 131 0.663023 DP 0 81 0 0.000000 160 0.809799 DP 0 82 0 0.000000 138 0.698451 DP 0 83 0 0.000000 127 0.642778 DP 0 84 0 0.000000 148 0.749064 DP 0 85 0 0.000000 123 0.622533 DP 0 86 0 0.000000 134 0.678206 DP 0 87 0 0.000000 134 0.678206 DP 0 88 0 0.000000 141 0.713635 DP 0 89 0 0.000000 126 0.637716 DP 0 90 0 0.000000 108 0.546614 DP 0 91 0 0.000000 125 0.632655 DP 0 92 0 0.000000 125 0.632655 DP 0 93 0 0.000000 148 0.749064 DP 0 94 0 0.000000 101 0.511185 DP 0 95 0 0.000000 121 0.612410 DP 0 96 0 0.000000 126 0.637716 DP 0 97 0 0.000000 114 0.576981 DP 0 98 0 0.000000 107 0.541553 DP 0 99 0 0.000000 124 0.627594 DP 0 100 0 0.000000 123 0.622533 DP 0 101 0 0.000000 117 0.592165 DP 0 102 0 0.000000 91 0.460573 DP 0 103 0 0.000000 96 0.485879 DP 0 104 0 0.000000 111 0.561798 DP 0 105 0 0.000000 95 0.480818 DP 0 106 0 0.000000 114 0.576981 DP 0 107 0 0.000000 87 0.440328 DP 0 108 0 0.000000 112 0.566859 DP 0 109 0 0.000000 92 0.465634 DP 0 110 0 0.000000 102 0.516247 DP 0 111 0 0.000000 109 0.551675 DP 0 112 0 0.000000 93 0.470695 DP 0 113 0 0.000000 105 0.531430 DP 0 114 0 0.000000 94 0.475757 DP 0 115 0 0.000000 84 0.425144 DP 0 116 0 0.000000 79 0.399838 DP 0 117 0 0.000000 100 0.506124 DP 0 118 0 0.000000 77 0.389716 DP 0 119 0 0.000000 87 0.440328 DP 0 120 0 0.000000 87 0.440328 DP 0 121 0 0.000000 87 0.440328 DP 0 122 0 0.000000 94 0.475757 DP 0 123 0 0.000000 87 0.440328 DP 0 124 0 0.000000 93 0.470695 DP 0 125 0 0.000000 76 0.384654 DP 0 126 0 0.000000 82 0.415022 DP 0 127 0 0.000000 90 0.455512 DP 0 128 0 0.000000 71 0.359348 DP 0 129 0 0.000000 92 0.465634 DP 0 130 0 0.000000 79 0.399838 DP 0 131 0 0.000000 73 0.369471 DP 0 132 0 0.000000 65 0.328981 DP 0 133 0 0.000000 89 0.450450 DP 0 134 0 0.000000 77 0.389716 DP 0 135 0 0.000000 85 0.430205 DP 0 136 0 0.000000 71 0.359348 DP 0 137 0 0.000000 75 0.379593 DP 0 138 0 0.000000 68 0.344164 DP 0 139 0 0.000000 58 0.293552 DP 0 140 0 0.000000 69 0.349226 DP 0 141 0 0.000000 65 0.328981 DP 0 142 0 0.000000 72 0.364409 DP 0 143 0 0.000000 72 0.364409 DP 0 144 0 0.000000 75 0.379593 DP 0 145 0 0.000000 79 0.399838 DP 0 146 0 0.000000 65 0.328981 DP 0 147 0 0.000000 74 0.374532 DP 0 148 0 0.000000 63 0.318858 DP 0 149 0 0.000000 67 0.339103 DP 0 150 0 0.000000 54 0.273307 DP 0 151 0 0.000000 59 0.298613 DP 0 152 0 0.000000 64 0.323919 DP 0 153 0 0.000000 83 0.420083 DP 0 154 0 0.000000 70 0.354287 DP 0 155 0 0.000000 54 0.273307 DP 0 156 0 0.000000 55 0.278368 DP 0 157 0 0.000000 62 0.313797 DP 0 158 0 0.000000 68 0.344164 DP 0 159 0 0.000000 54 0.273307 DP 0 160 0 0.000000 50 0.253062 DP 0 161 0 0.000000 65 0.328981 DP 0 162 0 0.000000 68 0.344164 DP 0 163 0 0.000000 50 0.253062 DP 0 164 0 0.000000 52 0.263185 DP 0 165 0 0.000000 65 0.328981 DP 0 166 0 0.000000 65 0.328981 DP 0 167 0 0.000000 52 0.263185 DP 0 168 0 0.000000 56 0.283429 DP 0 169 0 0.000000 50 0.253062 DP 0 170 0 0.000000 50 0.253062 DP 0 171 0 0.000000 51 0.258123 DP 0 172 0 0.000000 59 0.298613 DP 0 173 0 0.000000 54 0.273307 DP 0 174 0 0.000000 56 0.283429 DP 0 175 0 0.000000 52 0.263185 DP 0 176 0 0.000000 41 0.207511 DP 0 177 0 0.000000 64 0.323919 DP 0 178 0 0.000000 57 0.288491 DP 0 179 0 0.000000 51 0.258123 DP 0 180 0 0.000000 45 0.227756 DP 0 181 0 0.000000 56 0.283429 DP 0 182 0 0.000000 47 0.237878 DP 0 183 0 0.000000 61 0.308736 DP 0 184 0 0.000000 46 0.232817 DP 0 185 0 0.000000 53 0.268246 DP 0 186 0 0.000000 52 0.263185 DP 0 187 0 0.000000 47 0.237878 DP 0 188 0 0.000000 52 0.263185 DP 0 189 0 0.000000 46 0.232817 DP 0 190 0 0.000000 46 0.232817 DP 0 191 0 0.000000 43 0.217633 DP 0 192 0 0.000000 34 0.172082 DP 0 193 0 0.000000 58 0.293552 DP 0 194 0 0.000000 51 0.258123 DP 0 195 0 0.000000 40 0.202450 DP 0 196 0 0.000000 50 0.253062 DP 0 197 0 0.000000 43 0.217633 DP 0 198 0 0.000000 56 0.283429 DP 0 199 0 0.000000 52 0.263185 DP 0 200 0 0.000000 44 0.222695 DP 0 201 0 0.000000 60 0.303674 DP 0 202 0 0.000000 58 0.293552 DP 0 203 0 0.000000 47 0.237878 DP 0 204 0 0.000000 55 0.278368 DP 0 205 0 0.000000 55 0.278368 DP 0 206 0 0.000000 44 0.222695 DP 0 207 0 0.000000 57 0.288491 DP 0 208 0 0.000000 44 0.222695 DP 0 209 0 0.000000 57 0.288491 DP 0 210 0 0.000000 39 0.197388 DP 0 211 0 0.000000 59 0.298613 DP 0 212 0 0.000000 58 0.293552 DP 0 213 0 0.000000 62 0.313797 DP 0 214 0 0.000000 56 0.283429 DP 0 215 0 0.000000 57 0.288491 DP 0 216 0 0.000000 45 0.227756 DP 0 217 0 0.000000 56 0.283429 DP 0 218 0 0.000000 65 0.328981 DP 0 219 0 0.000000 50 0.253062 DP 0 220 0 0.000000 63 0.318858 DP 0 221 0 0.000000 61 0.308736 DP 0 222 0 0.000000 60 0.303674 DP 0 223 0 0.000000 54 0.273307 DP 0 224 0 0.000000 56 0.283429 DP 0 225 0 0.000000 55 0.278368 DP 0 226 0 0.000000 61 0.308736 DP 0 227 0 0.000000 63 0.318858 DP 0 228 0 0.000000 63 0.318858 DP 0 229 0 0.000000 82 0.415022 DP 0 230 0 0.000000 56 0.283429 DP 0 231 0 0.000000 73 0.369471 DP 0 232 0 0.000000 76 0.384654 DP 0 233 0 0.000000 65 0.328981 DP 0 234 0 0.000000 92 0.465634 DP 0 235 0 0.000000 82 0.415022 DP 0 236 0 0.000000 84 0.425144 DP 0 237 0 0.000000 95 0.480818 DP 0 238 0 0.000000 97 0.490940 DP 0 239 0 0.000000 102 0.516247 DP 0 240 0 0.000000 99 0.501063 DP 0 241 0 0.000000 103 0.521308 DP 0 242 0 0.000000 138 0.698451 DP 0 243 0 0.000000 142 0.718696 DP 0 244 0 0.000000 156 0.789554 DP 0 245 0 0.000000 209 1.057799 DP 0 246 0 0.000000 159 0.804737 DP 0 247 0 0.000000 243 1.229882 DP 0 248 0 0.000000 224 1.133718 DP 0 249 0 0.000000 243 1.229882 DP 0 250 0 0.000000 172 0.870533 DP 0 251 0 0.000000 77 0.389716 DP 0 252 0 0.000000 52 0.263185 DP 0 253 0 0.000000 56 0.283429 DP 0 254 0 0.000000 38 0.192327 DP 0 255 0 0.000000 36 0.182205 DP 0 256 0 0.000000 29 0.146776 DP 0 257 0 0.000000 25 0.126531 DP 0 258 0 0.000000 22 0.111347 DP 0 259 0 0.000000 19 0.096164 DP 0 260 0 0.000000 13 0.065796 DP 0 261 0 0.000000 12 0.060735 DP 0 262 0 0.000000 11 0.055674 DP 0 263 0 0.000000 4 0.020245 DP 0 264 0 0.000000 7 0.035429 DP 0 265 0 0.000000 7 0.035429 DP 0 266 0 0.000000 6 0.030367 DP 0 267 0 0.000000 5 0.025306 DP 0 268 0 0.000000 4 0.020245 DP 0 269 0 0.000000 4 0.020245 DP 0 270 0 0.000000 5 0.025306 DP 0 272 0 0.000000 1 0.005061 DP 0 274 0 0.000000 1 0.005061 DP 0 276 0 0.000000 1 0.005061 DP 0 279 0 0.000000 1 0.005061