# 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.v1.1.0.deepvariant.glnexus.vcf.gz # # Definition of sets: # ID [2]id [3]tab-separated file names ID 0 CoLoRSdb.CHM13.v1.1.0.deepvariant.glnexus.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: 64859662 SN 0 number of no-ALTs: 0 SN 0 number of SNPs: 51625590 SN 0 number of MNPs: 0 SN 0 number of indels: 13233676 SN 0 number of others: 396 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 31002913 20622677 1.50 31002913 20622677 1.50 # ICS, Indel context summary: # ICS [2]id [3]repeat-consistent [4]repeat-inconsistent [5]not applicable [6]c/(c+i) ratio ICS 0 4084106 896609 8252961 0.8200 # 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 885765 134343 1251104 183271 0.8706 ICL 0 3 195984 45982 118285 51158 0.7639 ICL 0 4 286430 93270 292726 118512 0.7322 ICL 0 5 392056 88067 580747 81521 0.8515 ICL 0 6 20406 15170 17218 21775 0.5046 ICL 0 7 7789 8803 3778 10309 0.3770 ICL 0 8 7502 6798 4189 9066 0.4243 ICL 0 9 5010 5542 2878 7279 0.3809 ICL 0 10 9178 6683 3061 9060 0.4374 # 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 34967412 21007555 13959857 8329166 2560696 657448 5111022 AF 0 0.010000 3771515 2204069 1567446 1260872 415685 74938 770249 AF 0 0.020000 1642277 949356 692921 603377 204922 32977 365478 AF 0 0.030000 1018523 588531 429992 379755 130888 19947 228920 AF 0 0.040000 740132 428740 311392 271194 93916 13975 163303 AF 0 0.050000 584964 340168 244796 208852 72732 10609 125511 AF 0 0.060000 492066 288151 203915 168803 58493 8345 101965 AF 0 0.070000 423910 250217 173693 142445 48705 6889 86851 AF 0 0.080000 374321 222414 151907 122581 41308 5594 75679 AF 0 0.090000 326238 194448 131790 104122 34393 4895 64834 AF 0 0.100000 309277 185787 123490 96403 31144 4384 60875 AF 0 0.110000 285308 171750 113558 86631 27692 3868 55071 AF 0 0.120000 260540 156902 103638 78462 24569 3449 50444 AF 0 0.130000 242384 146579 95805 71642 22235 3017 46390 AF 0 0.140000 230165 140068 90097 66369 20068 2801 43500 AF 0 0.150000 215801 131335 84466 61285 18344 2562 40379 AF 0 0.160000 205040 125148 79892 56994 16516 2272 38206 AF 0 0.170000 193116 118274 74842 53002 15279 2145 35578 AF 0 0.180000 179132 109554 69578 49320 13861 2055 33404 AF 0 0.190000 167359 102517 64842 44635 12421 1763 30451 AF 0 0.200000 164620 101136 63484 43580 12094 1723 29763 AF 0 0.210000 155752 95436 60316 41132 11200 1567 28365 AF 0 0.220000 148778 91706 57072 38515 10423 1463 26629 AF 0 0.230000 142431 87950 54481 36596 9617 1328 25651 AF 0 0.240000 138557 85587 52970 34948 9228 1220 24500 AF 0 0.250000 133452 82671 50781 32960 8448 1181 23331 AF 0 0.260000 130033 80441 49592 31524 8051 1152 22321 AF 0 0.270000 123895 77043 46852 30218 7616 1096 21506 AF 0 0.280000 120249 74613 45636 28766 7143 1045 20578 AF 0 0.290000 112524 69703 42821 26345 6425 921 18999 AF 0 0.300000 113615 70622 42993 26484 6376 885 19223 AF 0 0.310000 109622 68081 41541 25175 5912 848 18415 AF 0 0.320000 107477 66770 40707 23890 5725 804 17361 AF 0 0.330000 103537 64323 39214 22958 5420 782 16756 AF 0 0.340000 100230 62575 37655 22303 5160 702 16441 AF 0 0.350000 97564 60874 36690 21148 5086 697 15365 AF 0 0.360000 94529 59273 35256 20465 4581 713 15171 AF 0 0.370000 90567 56671 33896 19518 4429 643 14446 AF 0 0.380000 88491 55184 33307 18605 4234 638 13733 AF 0 0.390000 84146 52585 31561 17515 3854 506 13155 AF 0 0.400000 84404 52746 31658 17319 3825 578 12916 AF 0 0.410000 84672 53109 31563 16744 3607 542 12595 AF 0 0.420000 80736 50675 30061 15788 3448 478 11862 AF 0 0.430000 75784 47598 28186 15131 3233 501 11397 AF 0 0.440000 73520 46044 27476 14348 2977 421 10950 AF 0 0.450000 72799 45531 27268 14122 2944 432 10746 AF 0 0.460000 71662 45059 26603 13485 2855 420 10210 AF 0 0.470000 70120 44243 25877 13184 2763 406 10015 AF 0 0.480000 68157 42822 25335 12656 2569 400 9687 AF 0 0.490000 65449 41504 23945 11952 2467 366 9119 AF 0 0.500000 64646 40576 24070 11805 2293 367 9145 AF 0 0.510000 61573 38588 22985 11244 2280 373 8591 AF 0 0.520000 61367 38386 22981 10809 2177 306 8326 AF 0 0.530000 60359 37962 22397 10385 2145 315 7925 AF 0 0.540000 60385 37968 22417 10309 2016 315 7978 AF 0 0.550000 57808 36491 21317 10026 1945 292 7789 AF 0 0.560000 57748 36486 21262 9749 1833 288 7628 AF 0 0.570000 56334 35591 20743 9323 1742 276 7305 AF 0 0.580000 56544 35764 20780 9187 1721 276 7190 AF 0 0.590000 52701 33395 19306 8294 1561 265 6468 AF 0 0.600000 52516 33308 19208 8427 1619 226 6582 AF 0 0.610000 50416 32339 18077 8039 1400 272 6367 AF 0 0.620000 50740 32375 18365 7852 1432 233 6187 AF 0 0.630000 49480 31644 17836 7420 1351 208 5861 AF 0 0.640000 47874 30410 17464 7171 1297 222 5652 AF 0 0.650000 46790 29689 17101 6900 1189 212 5499 AF 0 0.660000 44549 28365 16184 6631 1179 208 5244 AF 0 0.670000 44420 28025 16395 6398 1121 192 5085 AF 0 0.680000 44930 28668 16262 6368 1146 194 5028 AF 0 0.690000 41234 26364 14870 5698 1006 185 4507 AF 0 0.700000 41860 26694 15166 5660 1014 170 4476 AF 0 0.710000 40296 25808 14488 5617 987 173 4457 AF 0 0.720000 39499 25181 14318 5548 931 169 4448 AF 0 0.730000 39002 25100 13902 5302 939 154 4209 AF 0 0.740000 38292 24494 13798 5149 859 123 4167 AF 0 0.750000 37056 23826 13230 4895 811 142 3942 AF 0 0.760000 36412 23318 13094 4831 837 143 3851 AF 0 0.770000 35461 22841 12620 4499 740 114 3645 AF 0 0.780000 33883 21709 12174 4165 672 121 3372 AF 0 0.790000 32359 20810 11549 4174 688 113 3373 AF 0 0.800000 31921 20641 11280 3954 676 126 3152 AF 0 0.810000 31568 20300 11268 3849 599 113 3137 AF 0 0.820000 29969 19273 10696 3527 585 118 2824 AF 0 0.830000 29224 18983 10241 3371 518 95 2758 AF 0 0.840000 28347 18458 9889 3250 506 136 2608 AF 0 0.850000 26241 17112 9129 3114 503 93 2518 AF 0 0.860000 24923 16195 8728 2881 485 81 2315 AF 0 0.870000 24299 15857 8442 2796 401 109 2286 AF 0 0.880000 24020 15669 8351 2670 420 83 2167 AF 0 0.890000 22685 14781 7904 2391 379 76 1936 AF 0 0.900000 22650 14887 7763 2322 354 77 1891 AF 0 0.910000 19728 12895 6833 2178 352 71 1755 AF 0 0.920000 18332 12139 6193 1906 280 59 1567 AF 0 0.930000 17848 11748 6100 1791 289 54 1448 AF 0 0.940000 17186 11379 5807 1839 284 54 1501 AF 0 0.950000 17231 11515 5716 1673 269 47 1357 AF 0 0.960000 18329 12453 5876 1730 234 65 1431 AF 0 0.970000 21961 14861 7100 1709 245 55 1409 AF 0 0.980000 24855 16914 7941 1535 216 58 1261 AF 0 0.990000 887 540 347 31 3 1 27 # 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 . 51625590 31002913 20622677 13233676 # IDD, InDel distribution: # IDD [2]id [3]length (deletions negative) [4]number of sites [5]number of genotypes [6]mean VAF IDD 0 -60 25819 0 . IDD 0 -59 763 0 . IDD 0 -58 1594 0 . IDD 0 -57 1024 0 . IDD 0 -56 2279 0 . IDD 0 -55 2016 0 . IDD 0 -54 2477 0 . IDD 0 -53 1232 0 . IDD 0 -52 3225 0 . IDD 0 -51 1855 0 . IDD 0 -50 4932 0 . IDD 0 -49 4448 0 . IDD 0 -48 4988 0 . IDD 0 -47 1915 0 . IDD 0 -46 3492 0 . IDD 0 -45 4274 0 . IDD 0 -44 4943 0 . IDD 0 -43 2312 0 . IDD 0 -42 6235 0 . IDD 0 -41 2774 0 . IDD 0 -40 11181 0 . IDD 0 -39 3634 0 . IDD 0 -38 6019 0 . IDD 0 -37 3860 0 . IDD 0 -36 10552 0 . IDD 0 -35 8155 0 . IDD 0 -34 8843 0 . IDD 0 -33 5274 0 . IDD 0 -32 14328 0 . IDD 0 -31 5722 0 . IDD 0 -30 21362 0 . IDD 0 -29 6776 0 . IDD 0 -28 21014 0 . IDD 0 -27 9291 0 . IDD 0 -26 23212 0 . IDD 0 -25 20131 0 . IDD 0 -24 33520 0 . IDD 0 -23 16557 0 . IDD 0 -22 26339 0 . IDD 0 -21 15340 0 . IDD 0 -20 75749 0 . IDD 0 -19 16225 0 . IDD 0 -18 43641 0 . IDD 0 -17 19143 0 . IDD 0 -16 68050 0 . IDD 0 -15 92309 0 . IDD 0 -14 66371 0 . IDD 0 -13 37732 0 . IDD 0 -12 123938 0 . IDD 0 -11 49580 0 . IDD 0 -10 235908 0 . IDD 0 -9 71503 0 . IDD 0 -8 183270 0 . IDD 0 -7 93450 0 . IDD 0 -6 215558 0 . IDD 0 -5 405084 0 . IDD 0 -4 606669 0 . IDD 0 -3 469840 0 . IDD 0 -2 952523 0 . IDD 0 -1 1967363 0 . IDD 0 1 2019208 0 . IDD 0 2 1027270 0 . IDD 0 3 418050 0 . IDD 0 4 519549 0 . IDD 0 5 452769 0 . IDD 0 6 253104 0 . IDD 0 7 89245 0 . IDD 0 8 225751 0 . IDD 0 9 77095 0 . IDD 0 10 268119 0 . IDD 0 11 47998 0 . IDD 0 12 149444 0 . IDD 0 13 39280 0 . IDD 0 14 85417 0 . IDD 0 15 107139 0 . IDD 0 16 90006 0 . IDD 0 17 22285 0 . IDD 0 18 64766 0 . IDD 0 19 21405 0 . IDD 0 20 112396 0 . IDD 0 21 22035 0 . IDD 0 22 43295 0 . IDD 0 23 19907 0 . IDD 0 24 54732 0 . IDD 0 25 36871 0 . IDD 0 26 36686 0 . IDD 0 27 14930 0 . IDD 0 28 38437 0 . IDD 0 29 11642 0 . IDD 0 30 42239 0 . IDD 0 31 9970 0 . IDD 0 32 28400 0 . IDD 0 33 9197 0 . IDD 0 34 18732 0 . IDD 0 35 15838 0 . IDD 0 36 21810 0 . IDD 0 37 6362 0 . IDD 0 38 13360 0 . IDD 0 39 6140 0 . IDD 0 40 21742 0 . IDD 0 41 4629 0 . IDD 0 42 13048 0 . IDD 0 43 3898 0 . IDD 0 44 10821 0 . IDD 0 45 9367 0 . IDD 0 46 7538 0 . IDD 0 47 3110 0 . IDD 0 48 10061 0 . IDD 0 49 5457 0 . IDD 0 50 11712 0 . IDD 0 51 3368 0 . IDD 0 52 7800 0 . IDD 0 53 2639 0 . IDD 0 54 6884 0 . IDD 0 55 6337 0 . IDD 0 56 6553 0 . IDD 0 57 2750 0 . IDD 0 58 4806 0 . IDD 0 59 2307 0 . IDD 0 60 400357 0 . # ST, Substitution types: # ST [2]id [3]type [4]count ST 0 A>C 2194038 ST 0 A>G 6424945 ST 0 A>T 2591993 ST 0 C>A 2859599 ST 0 C>G 2734995 ST 0 C>T 9072557 ST 0 G>A 8974453 ST 0 G>C 2683402 ST 0 G>T 2816775 ST 0 T>A 2603054 ST 0 T>C 6530958 ST 0 T>G 2138821 # DP, Depth distribution # DP [2]id [3]bin [4]number of genotypes [5]fraction of genotypes (%) [6]number of sites [7]fraction of sites (%)