# 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/GRCh38/human_GRCh38_no_alt_analysis_set.fasta CoLoRSdb.GRCh38.v1.1.0.deepvariant.glnexus.vcf.gz # # Definition of sets: # ID [2]id [3]tab-separated file names ID 0 CoLoRSdb.GRCh38.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: 49550902 SN 0 number of no-ALTs: 0 SN 0 number of SNPs: 38385578 SN 0 number of MNPs: 0 SN 0 number of indels: 11165006 SN 0 number of others: 318 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 25096885 13288693 1.89 25096885 13288693 1.89 # ICS, Indel context summary: # ICS [2]id [3]repeat-consistent [4]repeat-inconsistent [5]not applicable [6]c/(c+i) ratio ICS 0 3028953 697190 7438863 0.8129 # 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 813007 115480 1199887 168313 0.8764 ICL 0 3 170675 37691 106023 45425 0.7690 ICL 0 4 264195 86508 281957 117030 0.7285 ICL 0 5 62655 22123 64678 29170 0.7128 ICL 0 6 17987 11772 16181 16416 0.5480 ICL 0 7 5889 6267 3525 9203 0.3783 ICL 0 8 6469 5245 3912 7998 0.4394 ICL 0 9 3787 3455 2163 5616 0.3961 ICL 0 10 4053 3408 1910 6070 0.3862 # 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 25315690 16676465 8639225 6841635 1850006 502907 4488722 AF 0 0.010000 2569595 1659724 909871 1039570 297840 56965 684765 AF 0 0.020000 1113874 712933 400941 502509 149407 25285 327817 AF 0 0.030000 699345 446242 253103 318855 96951 15196 206708 AF 0 0.040000 522942 333644 189298 231325 71106 10979 149240 AF 0 0.050000 424962 272153 152809 179244 54996 8386 115862 AF 0 0.060000 359696 229966 129730 146405 44949 6658 94798 AF 0 0.070000 317033 203876 113157 124558 37877 5555 81126 AF 0 0.080000 284848 183200 101648 108061 32333 4625 71103 AF 0 0.090000 250547 160786 89761 91874 26988 3989 60897 AF 0 0.100000 241622 155770 85852 85821 24904 3679 57238 AF 0 0.110000 221869 143115 78754 76955 21868 3309 51778 AF 0 0.120000 206865 133244 73621 70546 19840 2982 47724 AF 0 0.130000 195886 127013 68873 64786 17966 2642 44178 AF 0 0.140000 185737 119753 65984 60009 16507 2432 41070 AF 0 0.150000 176299 113958 62341 56181 15209 2216 38756 AF 0 0.160000 167575 108710 58865 51903 13777 1950 36176 AF 0 0.170000 157636 102176 55460 48518 12675 1932 33911 AF 0 0.180000 149829 97060 52769 45421 11744 1762 31915 AF 0 0.190000 137144 88860 48284 41358 10589 1586 29183 AF 0 0.200000 138176 89680 48496 40242 10136 1481 28625 AF 0 0.210000 134038 86716 47322 38526 9631 1392 27503 AF 0 0.220000 126997 82414 44583 36340 9127 1378 25835 AF 0 0.230000 122194 79174 43020 34272 8239 1239 24794 AF 0 0.240000 119861 77908 41953 32800 8011 1123 23666 AF 0 0.250000 114987 74746 40241 31001 7475 1091 22435 AF 0 0.260000 111889 72704 39185 29722 6982 1051 21689 AF 0 0.270000 106536 69113 37423 27876 6588 989 20299 AF 0 0.280000 104488 67871 36617 27243 6239 955 20049 AF 0 0.290000 99226 64321 34905 25165 5726 893 18546 AF 0 0.300000 99930 64935 34995 24888 5654 851 18383 AF 0 0.310000 95617 62070 33547 23620 5232 850 17538 AF 0 0.320000 92153 59763 32390 22640 4987 796 16857 AF 0 0.330000 91437 59572 31865 21830 4866 664 16300 AF 0 0.340000 88353 57454 30899 21125 4606 725 15794 AF 0 0.350000 86081 56033 30048 20287 4382 627 15278 AF 0 0.360000 81578 53126 28452 19017 4032 620 14365 AF 0 0.370000 81313 52844 28469 18622 3954 573 14095 AF 0 0.380000 78438 50714 27724 17645 3689 542 13414 AF 0 0.390000 74136 48030 26106 16869 3436 531 12902 AF 0 0.400000 75424 48889 26535 16761 3451 520 12790 AF 0 0.410000 72976 47328 25648 16019 3275 486 12258 AF 0 0.420000 71320 46349 24971 15327 3090 435 11802 AF 0 0.430000 69288 44879 24409 14708 2957 451 11300 AF 0 0.440000 67101 43570 23531 13891 2792 404 10695 AF 0 0.450000 65100 41792 23308 13607 2755 417 10435 AF 0 0.460000 64985 42081 22904 13306 2696 370 10240 AF 0 0.470000 65824 42626 23198 13260 2604 388 10268 AF 0 0.480000 73568 47673 25895 13887 2515 455 10917 AF 0 0.490000 60770 39219 21551 11703 2228 381 9094 AF 0 0.500000 57225 37100 20125 11504 2181 362 8961 AF 0 0.510000 56069 36288 19781 10862 2054 328 8480 AF 0 0.520000 54988 35519 19469 10588 1977 325 8286 AF 0 0.530000 53051 34381 18670 10227 2050 288 7889 AF 0 0.540000 52230 33792 18438 10022 1854 324 7844 AF 0 0.550000 50655 32786 17869 9496 1790 276 7430 AF 0 0.560000 51112 33075 18037 9550 1711 271 7568 AF 0 0.570000 49465 32154 17311 9115 1705 284 7126 AF 0 0.580000 47370 30542 16828 8960 1598 261 7101 AF 0 0.590000 46921 30336 16585 8291 1482 281 6528 AF 0 0.600000 46350 30012 16338 8290 1529 235 6526 AF 0 0.610000 44937 28983 15954 7909 1405 259 6245 AF 0 0.620000 46279 30096 16183 7851 1370 233 6248 AF 0 0.630000 44881 28973 15908 7511 1296 203 6012 AF 0 0.640000 42658 27604 15054 7306 1233 210 5863 AF 0 0.650000 42339 27391 14948 7117 1204 210 5703 AF 0 0.660000 40940 26363 14577 6744 1209 216 5319 AF 0 0.670000 40955 26380 14575 6614 1159 194 5261 AF 0 0.680000 40816 26376 14440 6493 1086 220 5187 AF 0 0.690000 38232 24705 13527 6109 991 192 4926 AF 0 0.700000 38366 24976 13390 5919 953 191 4775 AF 0 0.710000 38223 24716 13507 5896 963 169 4764 AF 0 0.720000 37180 23930 13250 5822 933 172 4717 AF 0 0.730000 37189 23964 13225 5700 933 169 4598 AF 0 0.740000 36475 23483 12992 5578 896 158 4524 AF 0 0.750000 35633 22868 12765 5364 777 177 4410 AF 0 0.760000 37133 23856 13277 5260 854 152 4254 AF 0 0.770000 37698 24123 13575 5354 831 138 4385 AF 0 0.780000 42949 27849 15100 5664 862 164 4638 AF 0 0.790000 49950 32293 17657 6846 817 218 5811 AF 0 0.800000 27667 17713 9954 4061 614 117 3330 AF 0 0.810000 27730 17649 10081 3921 570 110 3241 AF 0 0.820000 27741 17608 10133 3856 590 100 3166 AF 0 0.830000 26081 16599 9482 3697 566 113 3018 AF 0 0.840000 26081 16563 9518 3509 540 116 2853 AF 0 0.850000 26113 16556 9557 3645 516 100 3029 AF 0 0.860000 24837 15660 9177 3459 500 102 2857 AF 0 0.870000 24924 15695 9229 3356 499 82 2775 AF 0 0.880000 24348 15198 9150 3242 432 112 2698 AF 0 0.890000 23375 14618 8757 3063 447 98 2518 AF 0 0.900000 23555 14796 8759 3036 410 91 2535 AF 0 0.910000 23274 14447 8827 3073 410 90 2573 AF 0 0.920000 23726 14704 9022 3076 419 92 2565 AF 0 0.930000 24539 15307 9232 3140 462 97 2581 AF 0 0.940000 25999 16219 9780 3367 424 99 2844 AF 0 0.950000 30941 19644 11297 3705 537 96 3072 AF 0 0.960000 39160 25101 14059 4477 636 131 3710 AF 0 0.970000 60907 39827 21080 6069 791 175 5103 AF 0 0.980000 99892 63990 35902 13005 991 636 11378 AF 0 0.990000 3641 1835 1806 554 9 40 505 # 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 . 38385578 25096885 13288693 11165006 # IDD, InDel distribution: # IDD [2]id [3]length (deletions negative) [4]number of sites [5]number of genotypes [6]mean VAF IDD 0 -60 18751 0 . IDD 0 -59 624 0 . IDD 0 -58 1340 0 . IDD 0 -57 869 0 . IDD 0 -56 1874 0 . IDD 0 -55 878 0 . IDD 0 -54 2106 0 . IDD 0 -53 1016 0 . IDD 0 -52 2487 0 . IDD 0 -51 1435 0 . IDD 0 -50 2882 0 . IDD 0 -49 2766 0 . IDD 0 -48 3909 0 . IDD 0 -47 1514 0 . IDD 0 -46 3023 0 . IDD 0 -45 2100 0 . IDD 0 -44 4197 0 . IDD 0 -43 1906 0 . IDD 0 -42 4376 0 . IDD 0 -41 2271 0 . IDD 0 -40 7662 0 . IDD 0 -39 2913 0 . IDD 0 -38 5437 0 . IDD 0 -37 3134 0 . IDD 0 -36 9215 0 . IDD 0 -35 3902 0 . IDD 0 -34 7738 0 . IDD 0 -33 4257 0 . IDD 0 -32 12829 0 . IDD 0 -31 4702 0 . IDD 0 -30 13598 0 . IDD 0 -29 5487 0 . IDD 0 -28 18861 0 . IDD 0 -27 7744 0 . IDD 0 -26 16897 0 . IDD 0 -25 9784 0 . IDD 0 -24 30169 0 . IDD 0 -23 9706 0 . IDD 0 -22 24076 0 . IDD 0 -21 13273 0 . IDD 0 -20 45596 0 . IDD 0 -19 14228 0 . IDD 0 -18 39834 0 . IDD 0 -17 16682 0 . IDD 0 -16 62284 0 . IDD 0 -15 33521 0 . IDD 0 -14 60731 0 . IDD 0 -13 33447 0 . IDD 0 -12 114763 0 . IDD 0 -11 45231 0 . IDD 0 -10 109602 0 . IDD 0 -9 62340 0 . IDD 0 -8 168027 0 . IDD 0 -7 82907 0 . IDD 0 -6 197647 0 . IDD 0 -5 176325 0 . IDD 0 -4 537861 0 . IDD 0 -3 403501 0 . IDD 0 -2 852686 0 . IDD 0 -1 1772268 0 . IDD 0 1 1868390 0 . IDD 0 2 947349 0 . IDD 0 3 372245 0 . IDD 0 4 476024 0 . IDD 0 5 160797 0 . IDD 0 6 236685 0 . IDD 0 7 81640 0 . IDD 0 8 210391 0 . IDD 0 9 68658 0 . IDD 0 10 135211 0 . IDD 0 11 45340 0 . IDD 0 12 141577 0 . IDD 0 13 35080 0 . IDD 0 14 80271 0 . IDD 0 15 41181 0 . IDD 0 16 85624 0 . IDD 0 17 20958 0 . IDD 0 18 61944 0 . IDD 0 19 20008 0 . IDD 0 20 72876 0 . IDD 0 21 20813 0 . IDD 0 22 41976 0 . IDD 0 23 15719 0 . IDD 0 24 52852 0 . IDD 0 25 17377 0 . IDD 0 26 32166 0 . IDD 0 27 13962 0 . IDD 0 28 37103 0 . IDD 0 29 10712 0 . IDD 0 30 29244 0 . IDD 0 31 9218 0 . IDD 0 32 27202 0 . IDD 0 33 8545 0 . IDD 0 34 17528 0 . IDD 0 35 8540 0 . IDD 0 36 20613 0 . IDD 0 37 5647 0 . IDD 0 38 12382 0 . IDD 0 39 5615 0 . IDD 0 40 15784 0 . IDD 0 41 4072 0 . IDD 0 42 10018 0 . IDD 0 43 3518 0 . IDD 0 44 10237 0 . IDD 0 45 4676 0 . IDD 0 46 6983 0 . IDD 0 47 3092 0 . IDD 0 48 9628 0 . IDD 0 49 3555 0 . IDD 0 50 7137 0 . IDD 0 51 3199 0 . IDD 0 52 7144 0 . IDD 0 53 2402 0 . IDD 0 54 6253 0 . IDD 0 55 2666 0 . IDD 0 56 6417 0 . IDD 0 57 2523 0 . IDD 0 58 4602 0 . IDD 0 59 1870 0 . IDD 0 60 398578 0 . # ST, Substitution types: # ST [2]id [3]type [4]count ST 0 A>C 1490262 ST 0 A>G 5148672 ST 0 A>T 1505962 ST 0 C>A 1841082 ST 0 C>G 1763362 ST 0 C>T 7380322 ST 0 G>A 7369573 ST 0 G>C 1766431 ST 0 G>T 1864161 ST 0 T>A 1541234 ST 0 T>C 5198318 ST 0 T>G 1516199 # DP, Depth distribution # DP [2]id [3]bin [4]number of genotypes [5]fraction of genotypes (%) [6]number of sites [7]fraction of sites (%)