# This file was produced by bcftools stats (1.17+htslib-1.17) and can be plotted using plot-vcfstats. # The command line was: bcftools stats --threads 3 --fasta-ref ../colorsdb_resources/CHM13/human_chm13v2.0_maskedY_rCRS.fasta CoLoRSdb.CHM13.v1.0.0.pbsv.jasmine.vcf.gz # # Definition of sets: # ID [2]id [3]tab-separated file names ID 0 CoLoRSdb.CHM13.v1.0.0.pbsv.jasmine.vcf.gz # 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: 0 SN 0 number of records: 842591 SN 0 number of no-ALTs: 0 SN 0 number of SNPs: 0 SN 0 number of MNPs: 0 SN 0 number of indels: 841754 SN 0 number of others: 837 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 0 0 0.00 0 0 0.00 # ICS, Indel context summary: # ICS [2]id [3]repeat-consistent [4]repeat-inconsistent [5]not applicable [6]c/(c+i) ratio ICS 0 188132 72301 581321 0.7224 # ICL, Indel context by length: # ICL [2]id [3]length of repeat element [4]repeat-consistent deletions) [5]repeat-inconsistent deletions [6]consistent insertions [7]inconsistent insertions [8]c/(c+i) ratio ICL 0 2 37460 12247 42204 12163 0.7655 ICL 0 3 5350 8123 5050 5865 0.4264 ICL 0 4 10967 4003 12055 4774 0.7240 ICL 0 5 37640 11605 34447 7025 0.7946 ICL 0 6 541 969 759 1107 0.3851 ICL 0 7 144 480 200 557 0.2491 ICL 0 8 151 492 212 549 0.2585 ICL 0 9 138 515 135 440 0.2223 ICL 0 10 344 807 335 580 0.3287 # 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 0.000000 0 0 0 593411 117149 49038 427224 AF 0 0.010000 0 0 0 67815 17517 5669 44629 AF 0 0.020000 0 0 0 29611 7914 2535 19162 AF 0 0.030000 0 0 0 17764 5095 1636 11033 AF 0 0.040000 0 0 0 12547 3622 1165 7760 AF 0 0.050000 0 0 0 9571 2827 884 5860 AF 0 0.060000 0 0 0 7932 2345 785 4802 AF 0 0.070000 0 0 0 6554 1976 629 3949 AF 0 0.080000 0 0 0 5687 1717 548 3422 AF 0 0.090000 0 0 0 4799 1482 483 2834 AF 0 0.100000 0 0 0 4491 1328 469 2694 AF 0 0.110000 0 0 0 4124 1263 414 2447 AF 0 0.120000 0 0 0 3711 1180 355 2176 AF 0 0.130000 0 0 0 3496 1114 351 2031 AF 0 0.140000 0 0 0 3124 943 332 1849 AF 0 0.150000 0 0 0 2965 906 320 1739 AF 0 0.160000 0 0 0 2708 824 274 1610 AF 0 0.170000 0 0 0 2672 845 277 1550 AF 0 0.180000 0 0 0 2376 766 239 1371 AF 0 0.190000 0 0 0 2157 664 207 1286 AF 0 0.200000 0 0 0 2087 665 267 1155 AF 0 0.210000 0 0 0 2065 667 206 1192 AF 0 0.220000 0 0 0 1956 631 221 1104 AF 0 0.230000 0 0 0 1887 665 178 1044 AF 0 0.240000 0 0 0 1758 571 196 991 AF 0 0.250000 0 0 0 1699 533 173 993 AF 0 0.260000 0 0 0 1707 566 176 965 AF 0 0.270000 0 0 0 1530 500 162 868 AF 0 0.280000 0 0 0 1485 512 153 820 AF 0 0.290000 0 0 0 1402 446 142 814 AF 0 0.300000 0 0 0 1357 424 161 772 AF 0 0.310000 0 0 0 1327 403 122 802 AF 0 0.320000 0 0 0 1253 405 124 724 AF 0 0.330000 0 0 0 1226 408 132 686 AF 0 0.340000 0 0 0 1203 355 134 714 AF 0 0.350000 0 0 0 1161 351 112 698 AF 0 0.360000 0 0 0 1144 359 118 667 AF 0 0.370000 0 0 0 1051 346 118 587 AF 0 0.380000 0 0 0 1042 315 106 621 AF 0 0.390000 0 0 0 1012 284 108 620 AF 0 0.400000 0 0 0 1009 299 99 611 AF 0 0.410000 0 0 0 961 316 104 541 AF 0 0.420000 0 0 0 942 299 95 548 AF 0 0.430000 0 0 0 841 272 94 475 AF 0 0.440000 0 0 0 816 273 78 465 AF 0 0.450000 0 0 0 823 260 84 479 AF 0 0.460000 0 0 0 793 236 83 474 AF 0 0.470000 0 0 0 802 237 101 464 AF 0 0.480000 0 0 0 801 228 89 484 AF 0 0.490000 0 0 0 719 205 72 442 AF 0 0.500000 0 0 0 719 238 77 404 AF 0 0.510000 0 0 0 718 231 77 410 AF 0 0.520000 0 0 0 670 214 73 383 AF 0 0.530000 0 0 0 616 179 77 360 AF 0 0.540000 0 0 0 652 220 62 370 AF 0 0.550000 0 0 0 588 164 68 356 AF 0 0.560000 0 0 0 615 179 53 383 AF 0 0.570000 0 0 0 587 170 72 345 AF 0 0.580000 0 0 0 551 159 56 336 AF 0 0.590000 0 0 0 511 147 57 307 AF 0 0.600000 0 0 0 537 161 67 309 AF 0 0.610000 0 0 0 491 137 57 297 AF 0 0.620000 0 0 0 488 141 58 289 AF 0 0.630000 0 0 0 480 156 53 271 AF 0 0.640000 0 0 0 452 139 34 279 AF 0 0.650000 0 0 0 446 126 57 263 AF 0 0.660000 0 0 0 421 117 36 268 AF 0 0.670000 0 0 0 413 128 42 243 AF 0 0.680000 0 0 0 398 112 46 240 AF 0 0.690000 0 0 0 387 118 41 228 AF 0 0.700000 0 0 0 345 98 34 213 AF 0 0.710000 0 0 0 355 103 35 217 AF 0 0.720000 0 0 0 328 94 31 203 AF 0 0.730000 0 0 0 342 107 30 205 AF 0 0.740000 0 0 0 287 77 23 187 AF 0 0.750000 0 0 0 295 87 26 182 AF 0 0.760000 0 0 0 259 67 25 167 AF 0 0.770000 0 0 0 278 78 27 173 AF 0 0.780000 0 0 0 258 66 22 170 AF 0 0.790000 0 0 0 232 52 27 153 AF 0 0.800000 0 0 0 259 64 27 168 AF 0 0.810000 0 0 0 218 52 20 146 AF 0 0.820000 0 0 0 189 44 17 128 AF 0 0.830000 0 0 0 197 39 23 135 AF 0 0.840000 0 0 0 189 46 15 128 AF 0 0.850000 0 0 0 160 43 12 105 AF 0 0.860000 0 0 0 139 28 15 96 AF 0 0.870000 0 0 0 157 30 15 112 AF 0 0.880000 0 0 0 134 25 13 96 AF 0 0.890000 0 0 0 125 28 13 84 AF 0 0.900000 0 0 0 108 24 8 76 AF 0 0.910000 0 0 0 130 32 13 85 AF 0 0.920000 0 0 0 104 20 9 75 AF 0 0.930000 0 0 0 120 23 12 85 AF 0 0.940000 0 0 0 102 22 5 75 AF 0 0.950000 0 0 0 83 13 3 67 AF 0 0.960000 0 0 0 78 11 7 60 AF 0 0.970000 0 0 0 95 10 9 76 AF 0 0.980000 0 0 0 74 5 4 65 # 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 0 841754 # IDD, InDel distribution: # IDD [2]id [3]length (deletions negative) [4]number of sites [5]number of genotypes [6]mean VAF IDD 0 -60 260425 0 . IDD 0 -59 1065 0 . IDD 0 -58 813 0 . IDD 0 -57 676 0 . IDD 0 -56 898 0 . IDD 0 -55 2616 0 . IDD 0 -54 1147 0 . IDD 0 -53 751 0 . IDD 0 -52 1384 0 . IDD 0 -51 976 0 . IDD 0 -50 3611 0 . IDD 0 -49 4614 0 . IDD 0 -48 1825 0 . IDD 0 -47 989 0 . IDD 0 -46 1480 0 . IDD 0 -45 3325 0 . IDD 0 -44 1512 0 . IDD 0 -43 1102 0 . IDD 0 -42 6495 0 . IDD 0 -41 1623 0 . IDD 0 -40 5541 0 . IDD 0 -39 1687 0 . IDD 0 -38 1806 0 . IDD 0 -37 1881 0 . IDD 0 -36 2646 0 . IDD 0 -35 4810 0 . IDD 0 -34 2773 0 . IDD 0 -33 2033 0 . IDD 0 -32 3653 0 . IDD 0 -31 2256 0 . IDD 0 -30 9088 0 . IDD 0 -29 2928 0 . IDD 0 -28 5606 0 . IDD 0 -27 3734 0 . IDD 0 -26 11393 0 . IDD 0 -25 12084 0 . IDD 0 -24 11376 0 . IDD 0 -23 12271 0 . IDD 0 -22 10160 0 . IDD 0 -21 7963 0 . IDD 0 -20 38848 0 . IDD 0 20 61606 0 . IDD 0 21 13108 0 . IDD 0 22 14445 0 . IDD 0 23 9574 0 . IDD 0 24 12946 0 . IDD 0 25 12168 0 . IDD 0 26 8902 0 . IDD 0 27 4043 0 . IDD 0 28 6352 0 . IDD 0 29 3194 0 . IDD 0 30 9441 0 . IDD 0 31 2590 0 . IDD 0 32 4347 0 . IDD 0 33 2109 0 . IDD 0 34 3283 0 . IDD 0 35 4513 0 . IDD 0 36 3230 0 . IDD 0 37 1917 0 . IDD 0 38 2067 0 . IDD 0 39 1477 0 . IDD 0 40 4425 0 . IDD 0 41 1278 0 . IDD 0 42 4622 0 . IDD 0 43 981 0 . IDD 0 44 1425 0 . IDD 0 45 2506 0 . IDD 0 46 1179 0 . IDD 0 47 923 0 . IDD 0 48 1450 0 . IDD 0 49 2118 0 . IDD 0 50 2722 0 . IDD 0 51 786 0 . IDD 0 52 1176 0 . IDD 0 53 567 0 . IDD 0 54 1020 0 . IDD 0 55 1930 0 . IDD 0 56 845 0 . IDD 0 57 580 0 . IDD 0 58 628 0 . IDD 0 59 827 0 . IDD 0 60 176590 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 0 ST 0 G>C 0 ST 0 G>T 0 ST 0 T>A 0 ST 0 T>C 0 ST 0 T>G 0 # DP, Depth distribution # DP [2]id [3]bin [4]number of genotypes [5]fraction of genotypes (%) [6]number of sites [7]fraction of sites (%)