# 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 2.vcf # # Definition of sets: # ID [2]id [3]tab-separated file names ID 0 2.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: 23432 SN 0 number of no-ALTs: 0 SN 0 number of SNPs: 23094 SN 0 number of MNPs: 0 SN 0 number of indels: 338 SN 0 number of others: 0 SN 0 number of multiallelic sites: 182 SN 0 number of multiallelic SNP sites: 177 # 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 15590 7681 2.03 15560 7534 2.07 # 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 19958 13587 6371 320 0 0 320 # 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 19958 13587 6371 320 0 0 320 AF 0 0.990000 3313 2003 1310 23 0 0 23 # 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 71 48 23 2 QUAL 0 31 56 41 15 2 QUAL 0 32 68 48 20 1 QUAL 0 33 59 38 21 3 QUAL 0 34 71 47 24 1 QUAL 0 35 70 42 28 1 QUAL 0 36 74 50 24 2 QUAL 0 37 64 48 16 2 QUAL 0 38 72 49 23 0 QUAL 0 39 56 40 16 2 QUAL 0 40 56 42 14 0 QUAL 0 41 68 44 24 0 QUAL 0 42 74 49 25 1 QUAL 0 43 67 36 31 2 QUAL 0 44 73 47 26 2 QUAL 0 45 69 45 24 4 QUAL 0 46 59 36 23 2 QUAL 0 47 80 55 25 0 QUAL 0 48 70 42 28 0 QUAL 0 49 56 39 17 2 QUAL 0 50 30 22 8 0 QUAL 0 51 65 44 21 1 QUAL 0 52 70 45 25 1 QUAL 0 53 66 43 23 0 QUAL 0 54 75 46 29 3 QUAL 0 55 62 38 24 1 QUAL 0 56 68 36 32 1 QUAL 0 57 62 42 20 1 QUAL 0 58 50 38 12 6 QUAL 0 59 56 38 18 2 QUAL 0 60 64 41 23 0 QUAL 0 61 76 53 23 0 QUAL 0 62 58 38 20 1 QUAL 0 63 58 41 17 0 QUAL 0 64 67 43 24 1 QUAL 0 65 76 54 22 0 QUAL 0 66 54 37 17 1 QUAL 0 67 58 35 23 1 QUAL 0 68 49 29 20 0 QUAL 0 69 64 42 22 3 QUAL 0 70 80 52 28 2 QUAL 0 71 68 46 22 1 QUAL 0 72 72 48 24 1 QUAL 0 73 46 32 14 4 QUAL 0 74 54 30 24 1 QUAL 0 75 52 36 16 0 QUAL 0 76 57 44 13 3 QUAL 0 77 58 44 14 1 QUAL 0 78 58 36 22 1 QUAL 0 79 61 41 20 0 QUAL 0 80 56 42 14 1 QUAL 0 81 73 52 21 2 QUAL 0 82 70 47 23 0 QUAL 0 83 62 40 22 1 QUAL 0 84 55 38 17 0 QUAL 0 85 56 38 18 3 QUAL 0 86 64 40 24 0 QUAL 0 87 65 51 14 1 QUAL 0 88 60 39 21 0 QUAL 0 89 63 44 19 4 QUAL 0 90 68 43 25 2 QUAL 0 91 56 36 20 0 QUAL 0 92 57 39 18 4 QUAL 0 93 58 41 17 1 QUAL 0 94 55 35 20 0 QUAL 0 95 59 42 17 1 QUAL 0 96 61 35 26 1 QUAL 0 97 65 45 20 0 QUAL 0 98 63 39 24 0 QUAL 0 99 65 42 23 0 QUAL 0 100 65 43 22 0 QUAL 0 101 68 42 26 0 QUAL 0 102 67 38 29 0 QUAL 0 103 65 42 23 3 QUAL 0 104 55 40 15 0 QUAL 0 105 58 37 21 2 QUAL 0 106 68 46 22 0 QUAL 0 107 48 28 20 1 QUAL 0 108 49 24 25 2 QUAL 0 109 66 53 13 0 QUAL 0 110 59 43 16 0 QUAL 0 111 69 50 19 0 QUAL 0 112 65 36 29 1 QUAL 0 113 72 46 26 2 QUAL 0 114 61 38 23 1 QUAL 0 115 57 40 17 0 QUAL 0 116 75 50 25 0 QUAL 0 117 58 33 25 0 QUAL 0 118 77 53 24 0 QUAL 0 119 53 35 18 1 QUAL 0 120 56 38 18 1 QUAL 0 121 61 38 23 0 QUAL 0 122 56 29 27 1 QUAL 0 123 70 45 25 1 QUAL 0 124 64 47 17 2 QUAL 0 125 71 47 24 0 QUAL 0 126 54 40 14 1 QUAL 0 127 63 43 20 0 QUAL 0 128 61 29 32 1 QUAL 0 129 67 42 25 0 QUAL 0 130 60 39 21 0 QUAL 0 131 83 49 34 0 QUAL 0 132 66 49 17 0 QUAL 0 133 67 48 19 0 QUAL 0 134 75 55 20 0 QUAL 0 135 77 47 30 0 QUAL 0 136 76 54 22 3 QUAL 0 137 73 45 28 0 QUAL 0 138 60 35 25 0 QUAL 0 139 83 62 21 0 QUAL 0 140 58 39 19 1 QUAL 0 141 68 40 28 0 QUAL 0 142 70 50 20 0 QUAL 0 143 73 52 21 2 QUAL 0 144 67 45 22 0 QUAL 0 145 68 43 25 1 QUAL 0 146 78 58 20 2 QUAL 0 147 72 48 24 1 QUAL 0 148 74 48 26 1 QUAL 0 149 79 51 28 2 QUAL 0 150 78 56 22 1 QUAL 0 151 75 50 25 0 QUAL 0 152 73 48 25 3 QUAL 0 153 51 29 22 1 QUAL 0 154 65 47 18 1 QUAL 0 155 53 34 19 2 QUAL 0 156 60 42 18 1 QUAL 0 157 46 29 17 2 QUAL 0 158 59 41 18 0 QUAL 0 159 61 43 18 1 QUAL 0 160 51 36 15 3 QUAL 0 161 65 41 24 2 QUAL 0 162 59 38 21 1 QUAL 0 163 52 35 17 1 QUAL 0 164 55 34 21 1 QUAL 0 165 52 29 23 2 QUAL 0 166 42 30 12 0 QUAL 0 167 57 37 20 1 QUAL 0 168 51 34 17 0 QUAL 0 169 60 29 31 0 QUAL 0 170 70 51 19 1 QUAL 0 171 59 35 24 1 QUAL 0 172 60 38 22 0 QUAL 0 173 67 47 20 1 QUAL 0 174 54 39 15 2 QUAL 0 175 63 43 20 0 QUAL 0 176 49 31 18 1 QUAL 0 177 35 25 10 0 QUAL 0 178 57 42 15 0 QUAL 0 179 52 31 21 0 QUAL 0 180 62 37 25 0 QUAL 0 181 60 45 15 0 QUAL 0 182 46 31 15 0 QUAL 0 183 63 47 16 1 QUAL 0 184 50 35 15 1 QUAL 0 185 62 44 18 1 QUAL 0 186 65 45 20 0 QUAL 0 187 60 38 22 2 QUAL 0 188 52 38 14 1 QUAL 0 189 53 40 13 1 QUAL 0 190 61 42 19 0 QUAL 0 191 54 41 13 0 QUAL 0 192 67 40 27 2 QUAL 0 193 59 37 22 1 QUAL 0 194 97 48 49 3 QUAL 0 195 134 44 90 1 QUAL 0 196 61 39 22 1 QUAL 0 197 57 42 15 5 QUAL 0 198 62 38 24 2 QUAL 0 199 60 39 21 3 QUAL 0 200 46 34 12 1 QUAL 0 201 70 45 25 1 QUAL 0 202 65 37 28 0 QUAL 0 203 64 45 19 1 QUAL 0 204 51 31 20 1 QUAL 0 205 46 33 13 0 QUAL 0 206 69 42 27 0 QUAL 0 207 55 40 15 0 QUAL 0 208 70 46 24 0 QUAL 0 209 67 37 30 0 QUAL 0 210 64 45 19 1 QUAL 0 211 58 45 13 0 QUAL 0 212 57 37 20 0 QUAL 0 213 55 37 18 0 QUAL 0 214 58 39 19 2 QUAL 0 215 62 43 19 1 QUAL 0 216 84 57 27 0 QUAL 0 217 73 50 23 1 QUAL 0 218 74 53 21 1 QUAL 0 219 254 167 87 2 QUAL 0 220 528 350 178 5 QUAL 0 221 1179 798 381 17 QUAL 0 222 6865 4953 1912 116 QUAL 0 223 17 5 12 0 QUAL 0 224 17 12 5 0 QUAL 0 225 652 408 244 3 QUAL 0 226 11 7 4 0 QUAL 0 227 14 12 2 1 QUAL 0 228 1650 998 652 10 # IDD, InDel distribution: # IDD [2]id [3]length (deletions negative) [4]count IDD 0 -13 1 IDD 0 -12 2 IDD 0 -10 1 IDD 0 -9 2 IDD 0 -8 5 IDD 0 -7 1 IDD 0 -6 5 IDD 0 -5 5 IDD 0 -4 22 IDD 0 -3 23 IDD 0 -2 24 IDD 0 -1 48 IDD 0 1 69 IDD 0 2 32 IDD 0 3 46 IDD 0 4 21 IDD 0 5 16 IDD 0 6 7 IDD 0 7 4 IDD 0 10 4 IDD 0 11 2 IDD 0 13 1 IDD 0 15 1 IDD 0 16 1 # ST, Substitution types: # ST [2]id [3]type [4]count ST 0 A>C 1035 ST 0 A>G 4137 ST 0 A>T 875 ST 0 C>A 912 ST 0 C>G 989 ST 0 C>T 3683 ST 0 G>A 3723 ST 0 G>C 1072 ST 0 G>T 930 ST 0 T>A 874 ST 0 T>C 4047 ST 0 T>G 994 # 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 278 1.186412 DP 0 52 0 0.000000 279 1.190679 DP 0 53 0 0.000000 281 1.199215 DP 0 54 0 0.000000 276 1.177876 DP 0 55 0 0.000000 256 1.092523 DP 0 56 0 0.000000 257 1.096791 DP 0 57 0 0.000000 250 1.066917 DP 0 58 0 0.000000 238 1.015705 DP 0 59 0 0.000000 266 1.135200 DP 0 60 0 0.000000 243 1.037043 DP 0 61 0 0.000000 240 1.024240 DP 0 62 0 0.000000 262 1.118129 DP 0 63 0 0.000000 227 0.968761 DP 0 64 0 0.000000 235 1.002902 DP 0 65 0 0.000000 219 0.934619 DP 0 66 0 0.000000 215 0.917549 DP 0 67 0 0.000000 225 0.960225 DP 0 68 0 0.000000 225 0.960225 DP 0 69 0 0.000000 186 0.793786 DP 0 70 0 0.000000 224 0.955958 DP 0 71 0 0.000000 196 0.836463 DP 0 72 0 0.000000 217 0.926084 DP 0 73 0 0.000000 201 0.857801 DP 0 74 0 0.000000 200 0.853534 DP 0 75 0 0.000000 189 0.806589 DP 0 76 0 0.000000 188 0.802322 DP 0 77 0 0.000000 187 0.798054 DP 0 78 0 0.000000 204 0.870604 DP 0 79 0 0.000000 170 0.725504 DP 0 80 0 0.000000 198 0.844998 DP 0 81 0 0.000000 161 0.687095 DP 0 82 0 0.000000 191 0.815125 DP 0 83 0 0.000000 143 0.610277 DP 0 84 0 0.000000 152 0.648686 DP 0 85 0 0.000000 154 0.657221 DP 0 86 0 0.000000 157 0.670024 DP 0 87 0 0.000000 139 0.593206 DP 0 88 0 0.000000 154 0.657221 DP 0 89 0 0.000000 161 0.687095 DP 0 90 0 0.000000 140 0.597474 DP 0 91 0 0.000000 155 0.661489 DP 0 92 0 0.000000 132 0.563332 DP 0 93 0 0.000000 138 0.588938 DP 0 94 0 0.000000 148 0.631615 DP 0 95 0 0.000000 141 0.601741 DP 0 96 0 0.000000 117 0.499317 DP 0 97 0 0.000000 148 0.631615 DP 0 98 0 0.000000 107 0.456640 DP 0 99 0 0.000000 131 0.559065 DP 0 100 0 0.000000 122 0.520656 DP 0 101 0 0.000000 142 0.606009 DP 0 102 0 0.000000 116 0.495050 DP 0 103 0 0.000000 124 0.529191 DP 0 104 0 0.000000 112 0.477979 DP 0 105 0 0.000000 116 0.495050 DP 0 106 0 0.000000 110 0.469443 DP 0 107 0 0.000000 99 0.422499 DP 0 108 0 0.000000 115 0.490782 DP 0 109 0 0.000000 127 0.541994 DP 0 110 0 0.000000 104 0.443837 DP 0 111 0 0.000000 103 0.439570 DP 0 112 0 0.000000 139 0.593206 DP 0 113 0 0.000000 124 0.529191 DP 0 114 0 0.000000 84 0.358484 DP 0 115 0 0.000000 98 0.418231 DP 0 116 0 0.000000 92 0.392625 DP 0 117 0 0.000000 80 0.341413 DP 0 118 0 0.000000 113 0.482247 DP 0 119 0 0.000000 109 0.465176 DP 0 120 0 0.000000 106 0.452373 DP 0 121 0 0.000000 110 0.469443 DP 0 122 0 0.000000 104 0.443837 DP 0 123 0 0.000000 101 0.431034 DP 0 124 0 0.000000 111 0.473711 DP 0 125 0 0.000000 86 0.367019 DP 0 126 0 0.000000 85 0.362752 DP 0 127 0 0.000000 93 0.396893 DP 0 128 0 0.000000 95 0.405428 DP 0 129 0 0.000000 86 0.367019 DP 0 130 0 0.000000 80 0.341413 DP 0 131 0 0.000000 84 0.358484 DP 0 132 0 0.000000 85 0.362752 DP 0 133 0 0.000000 73 0.311540 DP 0 134 0 0.000000 89 0.379822 DP 0 135 0 0.000000 88 0.375555 DP 0 136 0 0.000000 73 0.311540 DP 0 137 0 0.000000 74 0.315807 DP 0 138 0 0.000000 89 0.379822 DP 0 139 0 0.000000 82 0.349949 DP 0 140 0 0.000000 86 0.367019 DP 0 141 0 0.000000 74 0.315807 DP 0 142 0 0.000000 72 0.307272 DP 0 143 0 0.000000 64 0.273131 DP 0 144 0 0.000000 74 0.315807 DP 0 145 0 0.000000 84 0.358484 DP 0 146 0 0.000000 86 0.367019 DP 0 147 0 0.000000 60 0.256060 DP 0 148 0 0.000000 88 0.375555 DP 0 149 0 0.000000 71 0.303004 DP 0 150 0 0.000000 58 0.247525 DP 0 151 0 0.000000 73 0.311540 DP 0 152 0 0.000000 71 0.303004 DP 0 153 0 0.000000 73 0.311540 DP 0 154 0 0.000000 63 0.268863 DP 0 155 0 0.000000 62 0.264595 DP 0 156 0 0.000000 57 0.243257 DP 0 157 0 0.000000 68 0.290201 DP 0 158 0 0.000000 59 0.251792 DP 0 159 0 0.000000 71 0.303004 DP 0 160 0 0.000000 68 0.290201 DP 0 161 0 0.000000 84 0.358484 DP 0 162 0 0.000000 54 0.230454 DP 0 163 0 0.000000 67 0.285934 DP 0 164 0 0.000000 68 0.290201 DP 0 165 0 0.000000 68 0.290201 DP 0 166 0 0.000000 61 0.260328 DP 0 167 0 0.000000 75 0.320075 DP 0 168 0 0.000000 51 0.217651 DP 0 169 0 0.000000 77 0.328610 DP 0 170 0 0.000000 46 0.196313 DP 0 171 0 0.000000 57 0.243257 DP 0 172 0 0.000000 56 0.238989 DP 0 173 0 0.000000 48 0.204848 DP 0 174 0 0.000000 57 0.243257 DP 0 175 0 0.000000 63 0.268863 DP 0 176 0 0.000000 58 0.247525 DP 0 177 0 0.000000 65 0.277398 DP 0 178 0 0.000000 59 0.251792 DP 0 179 0 0.000000 61 0.260328 DP 0 180 0 0.000000 69 0.294469 DP 0 181 0 0.000000 61 0.260328 DP 0 182 0 0.000000 72 0.307272 DP 0 183 0 0.000000 64 0.273131 DP 0 184 0 0.000000 61 0.260328 DP 0 185 0 0.000000 56 0.238989 DP 0 186 0 0.000000 64 0.273131 DP 0 187 0 0.000000 49 0.209116 DP 0 188 0 0.000000 61 0.260328 DP 0 189 0 0.000000 62 0.264595 DP 0 190 0 0.000000 61 0.260328 DP 0 191 0 0.000000 80 0.341413 DP 0 192 0 0.000000 74 0.315807 DP 0 193 0 0.000000 45 0.192045 DP 0 194 0 0.000000 53 0.226186 DP 0 195 0 0.000000 43 0.183510 DP 0 196 0 0.000000 57 0.243257 DP 0 197 0 0.000000 61 0.260328 DP 0 198 0 0.000000 60 0.256060 DP 0 199 0 0.000000 61 0.260328 DP 0 200 0 0.000000 57 0.243257 DP 0 201 0 0.000000 44 0.187777 DP 0 202 0 0.000000 61 0.260328 DP 0 203 0 0.000000 73 0.311540 DP 0 204 0 0.000000 50 0.213383 DP 0 205 0 0.000000 61 0.260328 DP 0 206 0 0.000000 56 0.238989 DP 0 207 0 0.000000 55 0.234722 DP 0 208 0 0.000000 65 0.277398 DP 0 209 0 0.000000 76 0.324343 DP 0 210 0 0.000000 61 0.260328 DP 0 211 0 0.000000 58 0.247525 DP 0 212 0 0.000000 45 0.192045 DP 0 213 0 0.000000 58 0.247525 DP 0 214 0 0.000000 79 0.337146 DP 0 215 0 0.000000 65 0.277398 DP 0 216 0 0.000000 68 0.290201 DP 0 217 0 0.000000 63 0.268863 DP 0 218 0 0.000000 82 0.349949 DP 0 219 0 0.000000 80 0.341413 DP 0 220 0 0.000000 67 0.285934 DP 0 221 0 0.000000 72 0.307272 DP 0 222 0 0.000000 60 0.256060 DP 0 223 0 0.000000 73 0.311540 DP 0 224 0 0.000000 62 0.264595 DP 0 225 0 0.000000 70 0.298737 DP 0 226 0 0.000000 67 0.285934 DP 0 227 0 0.000000 69 0.294469 DP 0 228 0 0.000000 70 0.298737 DP 0 229 0 0.000000 82 0.349949 DP 0 230 0 0.000000 75 0.320075 DP 0 231 0 0.000000 96 0.409696 DP 0 232 0 0.000000 107 0.456640 DP 0 233 0 0.000000 102 0.435302 DP 0 234 0 0.000000 102 0.435302 DP 0 235 0 0.000000 98 0.418231 DP 0 236 0 0.000000 107 0.456640 DP 0 237 0 0.000000 112 0.477979 DP 0 238 0 0.000000 127 0.541994 DP 0 239 0 0.000000 135 0.576135 DP 0 240 0 0.000000 141 0.601741 DP 0 241 0 0.000000 159 0.678559 DP 0 242 0 0.000000 175 0.746842 DP 0 243 0 0.000000 203 0.866337 DP 0 244 0 0.000000 221 0.943155 DP 0 245 0 0.000000 266 1.135200 DP 0 246 0 0.000000 285 1.216285 DP 0 247 0 0.000000 318 1.357118 DP 0 248 0 0.000000 315 1.344315 DP 0 249 0 0.000000 320 1.365654 DP 0 250 0 0.000000 160 0.682827 DP 0 251 0 0.000000 80 0.341413 DP 0 252 0 0.000000 61 0.260328 DP 0 253 0 0.000000 41 0.174974 DP 0 254 0 0.000000 25 0.106692 DP 0 255 0 0.000000 26 0.110959 DP 0 256 0 0.000000 23 0.098156 DP 0 257 0 0.000000 18 0.076818 DP 0 258 0 0.000000 15 0.064015 DP 0 259 0 0.000000 19 0.081086 DP 0 260 0 0.000000 11 0.046944 DP 0 261 0 0.000000 6 0.025606 DP 0 262 0 0.000000 9 0.038409 DP 0 263 0 0.000000 10 0.042677 DP 0 264 0 0.000000 2 0.008535 DP 0 265 0 0.000000 4 0.017071 DP 0 266 0 0.000000 2 0.008535 DP 0 267 0 0.000000 4 0.017071 DP 0 268 0 0.000000 3 0.012803 DP 0 273 0 0.000000 2 0.008535 DP 0 277 0 0.000000 2 0.008535 DP 0 278 0 0.000000 1 0.004268