# 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 variants.vcf # # Definition of sets: # ID [2]id [3]tab-separated file names ID 0 variants.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: 37046 SN 0 number of no-ALTs: 0 SN 0 number of SNPs: 36828 SN 0 number of MNPs: 0 SN 0 number of indels: 218 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 26708 10120 2.64 26708 10120 2.64 # 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 36828 26708 10120 218 0 0 218 # 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 43 0 0 0 1 QUAL 0 46 0 0 0 2 QUAL 0 48 0 0 0 1 QUAL 0 53 0 0 0 1 QUAL 0 57 0 0 0 1 QUAL 0 58 0 0 0 1 QUAL 0 61 0 0 0 1 QUAL 0 63 0 0 0 1 QUAL 0 64 0 0 0 2 QUAL 0 65 0 0 0 1 QUAL 0 68 0 0 0 1 QUAL 0 73 0 0 0 3 QUAL 0 74 0 0 0 2 QUAL 0 76 0 0 0 2 QUAL 0 77 0 0 0 2 QUAL 0 78 0 0 0 6 QUAL 0 79 0 0 0 1 QUAL 0 81 0 0 0 2 QUAL 0 82 0 0 0 1 QUAL 0 83 0 0 0 1 QUAL 0 84 0 0 0 3 QUAL 0 85 0 0 0 1 QUAL 0 86 0 0 0 1 QUAL 0 87 0 0 0 2 QUAL 0 89 0 0 0 2 QUAL 0 90 0 0 0 1 QUAL 0 91 0 0 0 4 QUAL 0 93 0 0 0 2 QUAL 0 94 0 0 0 1 QUAL 0 95 0 0 0 1 QUAL 0 98 0 0 0 1 QUAL 0 99 0 0 0 2 QUAL 0 100 0 0 0 1 QUAL 0 101 0 0 0 1 QUAL 0 102 0 0 0 2 QUAL 0 105 0 0 0 1 QUAL 0 107 0 0 0 1 QUAL 0 108 0 0 0 1 QUAL 0 109 0 0 0 2 QUAL 0 110 1 1 0 2 QUAL 0 112 0 0 0 1 QUAL 0 113 1 1 0 1 QUAL 0 114 0 0 0 1 QUAL 0 116 0 0 0 2 QUAL 0 117 1 1 0 2 QUAL 0 118 0 0 0 1 QUAL 0 119 1 1 0 2 QUAL 0 120 0 0 0 1 QUAL 0 123 0 0 0 1 QUAL 0 124 0 0 0 1 QUAL 0 126 0 0 0 1 QUAL 0 129 1 1 0 0 QUAL 0 130 0 0 0 3 QUAL 0 131 1 1 0 4 QUAL 0 132 2 2 0 1 QUAL 0 133 0 0 0 1 QUAL 0 134 3 2 1 1 QUAL 0 135 3 3 0 2 QUAL 0 136 1 0 1 1 QUAL 0 137 1 1 0 1 QUAL 0 138 2 1 1 1 QUAL 0 139 1 0 1 0 QUAL 0 140 1 1 0 1 QUAL 0 141 5 4 1 3 QUAL 0 142 1 1 0 0 QUAL 0 143 3 1 2 0 QUAL 0 144 4 2 2 1 QUAL 0 145 3 1 2 0 QUAL 0 146 2 2 0 1 QUAL 0 147 2 2 0 1 QUAL 0 148 4 4 0 0 QUAL 0 149 4 3 1 1 QUAL 0 150 7 6 1 2 QUAL 0 151 4 4 0 1 QUAL 0 152 3 2 1 1 QUAL 0 153 5 4 1 0 QUAL 0 154 2 2 0 0 QUAL 0 155 7 6 1 0 QUAL 0 156 6 6 0 1 QUAL 0 157 8 8 0 0 QUAL 0 158 7 4 3 0 QUAL 0 159 4 2 2 1 QUAL 0 160 6 5 1 1 QUAL 0 161 5 3 2 0 QUAL 0 162 7 7 0 1 QUAL 0 163 7 3 4 1 QUAL 0 164 9 7 2 0 QUAL 0 165 12 9 3 1 QUAL 0 166 5 5 0 0 QUAL 0 167 7 6 1 2 QUAL 0 168 6 3 3 0 QUAL 0 169 7 5 2 1 QUAL 0 170 7 5 2 0 QUAL 0 171 14 9 5 3 QUAL 0 172 6 2 4 0 QUAL 0 173 7 5 2 0 QUAL 0 174 12 9 3 1 QUAL 0 175 17 11 6 0 QUAL 0 176 14 12 2 0 QUAL 0 177 12 9 3 0 QUAL 0 178 15 11 4 1 QUAL 0 179 18 14 4 0 QUAL 0 180 11 4 7 0 QUAL 0 181 11 8 3 0 QUAL 0 182 13 10 3 1 QUAL 0 183 12 8 4 0 QUAL 0 184 13 10 3 1 QUAL 0 185 21 19 2 0 QUAL 0 186 20 15 5 0 QUAL 0 187 14 10 4 2 QUAL 0 188 13 10 3 1 QUAL 0 189 19 13 6 0 QUAL 0 190 16 11 5 1 QUAL 0 191 21 11 10 0 QUAL 0 192 13 11 2 0 QUAL 0 193 21 19 2 0 QUAL 0 194 23 19 4 0 QUAL 0 195 26 13 13 0 QUAL 0 196 20 12 8 1 QUAL 0 197 17 12 5 1 QUAL 0 198 15 12 3 0 QUAL 0 199 17 15 2 0 QUAL 0 200 17 11 6 0 QUAL 0 201 23 14 9 1 QUAL 0 202 18 13 5 0 QUAL 0 203 17 13 4 0 QUAL 0 204 30 21 9 0 QUAL 0 205 28 18 10 0 QUAL 0 206 23 16 7 0 QUAL 0 207 23 15 8 0 QUAL 0 208 30 22 8 0 QUAL 0 209 35 19 16 0 QUAL 0 210 34 22 12 1 QUAL 0 211 43 33 10 2 QUAL 0 212 36 26 10 0 QUAL 0 213 25 20 5 1 QUAL 0 214 44 33 11 0 QUAL 0 215 27 15 12 0 QUAL 0 216 34 18 16 1 QUAL 0 217 43 31 12 0 QUAL 0 218 44 32 12 0 QUAL 0 219 42 27 15 0 QUAL 0 220 47 36 11 0 QUAL 0 221 52 33 19 0 QUAL 0 222 51 39 12 3 QUAL 0 223 44 29 15 0 QUAL 0 224 59 32 27 0 QUAL 0 225 33717 25048 8669 17 QUAL 0 226 4 2 2 1 QUAL 0 227 3 1 2 0 QUAL 0 228 1605 607 998 63 # IDD, InDel distribution: # IDD [2]id [3]length (deletions negative) [4]count IDD 0 -15 1 IDD 0 -13 1 IDD 0 -7 1 IDD 0 -5 2 IDD 0 -3 7 IDD 0 -2 6 IDD 0 -1 78 IDD 0 1 100 IDD 0 2 10 IDD 0 3 7 IDD 0 4 2 IDD 0 5 1 IDD 0 6 2 # ST, Substitution types: # ST [2]id [3]type [4]count ST 0 A>C 2106 ST 0 A>G 6649 ST 0 A>T 862 ST 0 C>A 1097 ST 0 C>G 936 ST 0 C>T 6879 ST 0 G>A 6665 ST 0 G>C 947 ST 0 G>T 1144 ST 0 T>A 860 ST 0 T>C 6515 ST 0 T>G 2168 # 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 0 0.000000 691 1.865249 DP 0 11 0 0.000000 642 1.732981 DP 0 12 0 0.000000 725 1.957026 DP 0 13 0 0.000000 681 1.838255 DP 0 14 0 0.000000 689 1.859850 DP 0 15 0 0.000000 711 1.919236 DP 0 16 0 0.000000 667 1.800464 DP 0 17 0 0.000000 652 1.759974 DP 0 18 0 0.000000 662 1.786968 DP 0 19 0 0.000000 719 1.940830 DP 0 20 0 0.000000 630 1.700588 DP 0 21 0 0.000000 686 1.851752 DP 0 22 0 0.000000 684 1.846353 DP 0 23 0 0.000000 655 1.768072 DP 0 24 0 0.000000 635 1.714085 DP 0 25 0 0.000000 664 1.792366 DP 0 26 0 0.000000 652 1.759974 DP 0 27 0 0.000000 650 1.754575 DP 0 28 0 0.000000 601 1.622307 DP 0 29 0 0.000000 642 1.732981 DP 0 30 0 0.000000 582 1.571020 DP 0 31 0 0.000000 596 1.608811 DP 0 32 0 0.000000 599 1.616909 DP 0 33 0 0.000000 619 1.670896 DP 0 34 0 0.000000 549 1.481941 DP 0 35 0 0.000000 581 1.568320 DP 0 36 0 0.000000 566 1.527830 DP 0 37 0 0.000000 551 1.487340 DP 0 38 0 0.000000 544 1.468445 DP 0 39 0 0.000000 516 1.392863 DP 0 40 0 0.000000 531 1.433353 DP 0 41 0 0.000000 474 1.279490 DP 0 42 0 0.000000 506 1.365869 DP 0 43 0 0.000000 484 1.306484 DP 0 44 0 0.000000 445 1.201209 DP 0 45 0 0.000000 536 1.446850 DP 0 46 0 0.000000 439 1.185013 DP 0 47 0 0.000000 477 1.287588 DP 0 48 0 0.000000 439 1.185013 DP 0 49 0 0.000000 460 1.241700 DP 0 50 0 0.000000 484 1.306484 DP 0 51 0 0.000000 410 1.106732 DP 0 52 0 0.000000 410 1.106732 DP 0 53 0 0.000000 420 1.133726 DP 0 54 0 0.000000 448 1.209307 DP 0 55 0 0.000000 426 1.149922 DP 0 56 0 0.000000 422 1.139124 DP 0 57 0 0.000000 385 1.039249 DP 0 58 0 0.000000 414 1.117530 DP 0 59 0 0.000000 389 1.050046 DP 0 60 0 0.000000 416 1.122928 DP 0 61 0 0.000000 378 1.020353 DP 0 62 0 0.000000 384 1.036549 DP 0 63 0 0.000000 396 1.068941 DP 0 64 0 0.000000 359 0.969065 DP 0 65 0 0.000000 383 1.033850 DP 0 66 0 0.000000 346 0.933974 DP 0 67 0 0.000000 390 1.052745 DP 0 68 0 0.000000 337 0.909680 DP 0 69 0 0.000000 346 0.933974 DP 0 70 0 0.000000 354 0.955569 DP 0 71 0 0.000000 299 0.807105 DP 0 72 0 0.000000 319 0.861092 DP 0 73 0 0.000000 283 0.763915 DP 0 74 0 0.000000 292 0.788209 DP 0 75 0 0.000000 285 0.769314 DP 0 76 0 0.000000 296 0.799007 DP 0 77 0 0.000000 271 0.731523 DP 0 78 0 0.000000 255 0.688333 DP 0 79 0 0.000000 223 0.601954 DP 0 80 0 0.000000 230 0.620850 DP 0 81 0 0.000000 196 0.529072 DP 0 82 0 0.000000 188 0.507477 DP 0 83 0 0.000000 172 0.464288 DP 0 84 0 0.000000 145 0.391405 DP 0 85 0 0.000000 156 0.421098 DP 0 86 0 0.000000 142 0.383307 DP 0 87 0 0.000000 118 0.318523 DP 0 88 0 0.000000 122 0.329320 DP 0 89 0 0.000000 108 0.291529 DP 0 90 0 0.000000 105 0.283431 DP 0 91 0 0.000000 84 0.226745 DP 0 92 0 0.000000 77 0.207850 DP 0 93 0 0.000000 92 0.248340 DP 0 94 0 0.000000 42 0.113373 DP 0 95 0 0.000000 48 0.129569 DP 0 96 0 0.000000 51 0.137667 DP 0 97 0 0.000000 42 0.113373 DP 0 98 0 0.000000 41 0.110673 DP 0 99 0 0.000000 29 0.078281 DP 0 100 0 0.000000 37 0.099876 DP 0 101 0 0.000000 24 0.064784 DP 0 102 0 0.000000 18 0.048588 DP 0 103 0 0.000000 20 0.053987 DP 0 104 0 0.000000 11 0.029693 DP 0 105 0 0.000000 10 0.026993 DP 0 106 0 0.000000 12 0.032392 DP 0 107 0 0.000000 12 0.032392 DP 0 108 0 0.000000 10 0.026993 DP 0 109 0 0.000000 10 0.026993 DP 0 110 0 0.000000 5 0.013497 DP 0 111 0 0.000000 3 0.008098 DP 0 112 0 0.000000 8 0.021595 DP 0 113 0 0.000000 3 0.008098 DP 0 114 0 0.000000 6 0.016196 DP 0 115 0 0.000000 2 0.005399 DP 0 116 0 0.000000 2 0.005399 DP 0 117 0 0.000000 1 0.002699 DP 0 121 0 0.000000 1 0.002699 DP 0 122 0 0.000000 2 0.005399 DP 0 125 0 0.000000 2 0.005399 DP 0 126 0 0.000000 1 0.002699 DP 0 127 0 0.000000 2 0.005399 DP 0 129 0 0.000000 1 0.002699 DP 0 133 0 0.000000 1 0.002699 DP 0 220 0 0.000000 1 0.002699 DP 0 223 0 0.000000 1 0.002699