# This file was produced by bcftools stats (1.19+htslib-1.19) and can be plotted using plot-vcfstats. # The command line was: bcftools stats -f PASS -s - /data/jobs/showcase-hg002-30x/out/HG002.30x.vcf.gz # # Definition of sets: # ID [2]id [3]tab-separated file names ID 0 /data/jobs/showcase-hg002-30x/out/HG002.30x.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: 1 SN 0 number of records: 4801758 SN 0 number of no-ALTs: 0 SN 0 number of SNPs: 3895143 SN 0 number of MNPs: 0 SN 0 number of indels: 912757 SN 0 number of others: 762 SN 0 number of multiallelic sites: 90838 SN 0 number of multiallelic SNP sites: 2331 # 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 2592728 1304752 1.99 2590370 1301339 1.99 # 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 2290208 1536782 753426 663180 0 0 663180 # 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 2291331 1537317 754014 670386 0 0 670386 AF 0 0.990000 1606149 1055411 550738 325876 0 0 325876 # 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 3.0 131 87 44 73 QUAL 0 3.1 1373 761 612 435 QUAL 0 3.2 1751 935 816 514 QUAL 0 3.3 1789 939 850 520 QUAL 0 3.4 1880 988 892 523 QUAL 0 3.5 1891 1031 860 518 QUAL 0 3.6 1912 1003 909 537 QUAL 0 3.7 1986 1056 930 564 QUAL 0 3.8 1954 1051 903 541 QUAL 0 3.9 1916 1060 856 546 QUAL 0 4.0 1926 1032 894 593 QUAL 0 4.1 1867 1019 848 536 QUAL 0 4.2 1899 1024 875 553 QUAL 0 4.3 1853 981 872 555 QUAL 0 4.4 1859 1056 803 518 QUAL 0 4.5 1894 1056 838 512 QUAL 0 4.6 1864 1005 859 582 QUAL 0 4.7 1851 990 861 551 QUAL 0 4.8 1810 999 811 578 QUAL 0 4.9 1748 987 761 600 QUAL 0 5.0 1753 960 793 556 QUAL 0 5.1 1663 935 728 553 QUAL 0 5.2 1657 912 745 528 QUAL 0 5.3 1634 881 753 538 QUAL 0 5.4 1679 926 753 527 QUAL 0 5.5 1723 948 775 555 QUAL 0 5.6 1642 918 724 534 QUAL 0 5.7 1575 883 692 525 QUAL 0 5.8 1591 877 714 563 QUAL 0 5.9 1528 862 666 507 QUAL 0 6.0 1506 800 706 530 QUAL 0 6.1 1503 814 689 535 QUAL 0 6.2 1458 784 674 523 QUAL 0 6.3 1444 827 617 503 QUAL 0 6.4 1447 795 652 558 QUAL 0 6.5 1508 800 708 561 QUAL 0 6.6 1479 801 678 485 QUAL 0 6.7 1424 814 610 545 QUAL 0 6.8 1367 776 591 530 QUAL 0 6.9 1445 787 658 540 QUAL 0 7.0 1407 748 659 520 QUAL 0 7.1 1421 769 652 512 QUAL 0 7.2 1290 704 586 546 QUAL 0 7.3 1327 723 604 555 QUAL 0 7.4 1376 765 611 560 QUAL 0 7.5 1275 689 586 536 QUAL 0 7.6 1240 663 577 494 QUAL 0 7.7 1278 687 591 557 QUAL 0 7.8 1235 645 590 505 QUAL 0 7.9 1257 708 549 593 QUAL 0 8.0 1262 690 572 501 QUAL 0 8.1 1289 697 592 529 QUAL 0 8.2 1229 677 552 504 QUAL 0 8.3 1291 696 595 496 QUAL 0 8.4 1334 750 584 517 QUAL 0 8.5 1262 667 595 521 QUAL 0 8.6 1233 673 560 544 QUAL 0 8.7 1168 644 524 563 QUAL 0 8.8 1222 666 556 516 QUAL 0 8.9 1226 651 575 534 QUAL 0 9.0 1212 665 547 523 QUAL 0 9.1 1168 650 518 588 QUAL 0 9.2 1169 654 515 518 QUAL 0 9.3 1210 678 532 574 QUAL 0 9.4 1169 647 522 548 QUAL 0 9.5 1176 629 547 531 QUAL 0 9.6 1166 649 517 577 QUAL 0 9.7 1197 646 551 532 QUAL 0 9.8 1108 637 471 551 QUAL 0 9.9 1148 620 528 569 QUAL 0 10.0 1127 618 509 561 QUAL 0 10.1 1134 614 520 581 QUAL 0 10.2 1106 626 480 509 QUAL 0 10.3 1155 677 478 566 QUAL 0 10.4 1150 629 521 529 QUAL 0 10.5 1093 610 483 542 QUAL 0 10.6 1138 637 501 568 QUAL 0 10.7 1085 610 475 524 QUAL 0 10.8 1149 649 500 587 QUAL 0 10.9 1100 627 473 549 QUAL 0 11.0 1098 601 497 525 QUAL 0 11.1 1110 627 483 523 QUAL 0 11.2 1093 630 463 601 QUAL 0 11.3 1094 587 507 605 QUAL 0 11.4 1165 655 510 578 QUAL 0 11.5 1096 608 488 619 QUAL 0 11.6 1114 651 463 567 QUAL 0 11.7 1120 618 502 564 QUAL 0 11.8 1065 588 477 602 QUAL 0 11.9 1127 607 520 561 QUAL 0 12.0 1109 624 485 629 QUAL 0 12.1 1068 607 461 589 QUAL 0 12.2 1049 593 456 573 QUAL 0 12.3 1090 621 469 609 QUAL 0 12.4 1121 620 501 604 QUAL 0 12.5 1144 627 517 573 QUAL 0 12.6 1113 614 499 638 QUAL 0 12.7 1076 608 468 638 QUAL 0 12.8 1106 612 494 566 QUAL 0 12.9 1062 610 452 612 QUAL 0 13.0 1174 631 543 630 QUAL 0 13.1 1124 614 510 627 QUAL 0 13.2 1050 599 451 627 QUAL 0 13.3 1084 593 491 622 QUAL 0 13.4 1054 597 457 658 QUAL 0 13.5 1092 620 472 631 QUAL 0 13.6 1131 632 499 631 QUAL 0 13.7 1110 621 489 683 QUAL 0 13.8 1074 611 463 639 QUAL 0 13.9 1064 614 450 639 QUAL 0 14.0 1073 650 423 615 QUAL 0 14.1 1105 614 491 593 QUAL 0 14.2 1046 598 448 643 QUAL 0 14.3 1078 609 469 648 QUAL 0 14.4 1102 618 484 629 QUAL 0 14.5 1052 545 507 628 QUAL 0 14.6 1125 615 510 679 QUAL 0 14.7 1053 585 468 654 QUAL 0 14.8 1171 648 523 689 QUAL 0 14.9 1066 615 451 735 QUAL 0 15.0 1066 630 436 626 QUAL 0 15.1 1074 600 474 690 QUAL 0 15.2 1132 655 477 641 QUAL 0 15.3 1177 683 494 693 QUAL 0 15.4 1085 615 470 642 QUAL 0 15.5 1154 655 499 733 QUAL 0 15.6 1124 613 511 710 QUAL 0 15.7 1205 681 524 721 QUAL 0 15.8 1139 635 504 706 QUAL 0 15.9 1137 650 487 736 QUAL 0 16.0 1094 580 514 736 QUAL 0 16.1 1089 602 487 696 QUAL 0 16.2 1113 631 482 714 QUAL 0 16.3 1091 654 437 737 QUAL 0 16.4 1119 618 501 814 QUAL 0 16.5 1172 654 518 740 QUAL 0 16.6 1125 660 465 734 QUAL 0 16.7 1154 663 491 788 QUAL 0 16.8 1159 676 483 713 QUAL 0 16.9 1133 656 477 793 QUAL 0 17.0 1111 616 495 766 QUAL 0 17.1 1195 693 502 803 QUAL 0 17.2 1195 691 504 812 QUAL 0 17.3 1137 641 496 855 QUAL 0 17.4 1170 659 511 788 QUAL 0 17.5 1176 638 538 831 QUAL 0 17.6 1251 744 507 856 QUAL 0 17.7 1194 673 521 858 QUAL 0 17.8 1183 648 535 869 QUAL 0 17.9 1224 700 524 892 QUAL 0 18.0 1242 698 544 947 QUAL 0 18.1 1214 687 527 912 QUAL 0 18.2 1291 747 544 881 QUAL 0 18.3 1171 659 512 928 QUAL 0 18.4 1224 729 495 919 QUAL 0 18.5 1276 748 528 976 QUAL 0 18.6 1289 754 535 925 QUAL 0 18.7 1348 766 582 1027 QUAL 0 18.8 1394 769 625 983 QUAL 0 18.9 1301 773 528 999 QUAL 0 19.0 1393 826 567 1001 QUAL 0 19.1 1354 757 597 1043 QUAL 0 19.2 1387 783 604 1050 QUAL 0 19.3 1390 798 592 1020 QUAL 0 19.4 1398 799 599 1089 QUAL 0 19.5 1417 814 603 1067 QUAL 0 19.6 1395 811 584 1061 QUAL 0 19.7 1508 863 645 1143 QUAL 0 19.8 1512 845 667 1101 QUAL 0 19.9 1491 820 671 1181 QUAL 0 20.0 1467 820 647 1112 QUAL 0 20.1 1539 856 683 1206 QUAL 0 20.2 1596 891 705 1134 QUAL 0 20.3 1614 936 678 1294 QUAL 0 20.4 1679 937 742 1269 QUAL 0 20.5 1750 988 762 1327 QUAL 0 20.6 1668 931 737 1362 QUAL 0 20.7 1769 1007 762 1330 QUAL 0 20.8 1760 978 782 1398 QUAL 0 20.9 1803 1048 755 1450 QUAL 0 21.0 1853 1028 825 1446 QUAL 0 21.1 1873 1104 769 1466 QUAL 0 21.2 2000 1172 828 1563 QUAL 0 21.3 1955 1098 857 1623 QUAL 0 21.4 2079 1199 880 1706 QUAL 0 21.5 2062 1213 849 1745 QUAL 0 21.6 2262 1295 967 1761 QUAL 0 21.7 2282 1366 916 1807 QUAL 0 21.8 2396 1391 1005 1913 QUAL 0 21.9 2358 1397 961 2033 QUAL 0 22.0 2419 1418 1001 2013 QUAL 0 22.1 2664 1551 1113 2101 QUAL 0 22.2 2754 1566 1188 2181 QUAL 0 22.3 2755 1590 1165 2372 QUAL 0 22.4 2870 1705 1165 2349 QUAL 0 22.5 2961 1725 1236 2444 QUAL 0 22.6 3278 1951 1327 2673 QUAL 0 22.7 3406 2028 1378 2817 QUAL 0 22.8 3441 2022 1419 3058 QUAL 0 22.9 3728 2198 1530 3249 QUAL 0 23.0 4064 2460 1604 3345 QUAL 0 23.1 4366 2568 1798 3737 QUAL 0 23.2 4566 2774 1792 3882 QUAL 0 23.3 5069 3031 2038 4102 QUAL 0 23.4 5583 3353 2230 4627 QUAL 0 23.5 6191 3694 2497 5037 QUAL 0 23.6 6860 4117 2743 5493 QUAL 0 23.7 7792 4765 3027 6286 QUAL 0 23.8 9071 5536 3535 6972 QUAL 0 23.9 10717 6614 4103 7996 QUAL 0 24.0 12904 7976 4928 9382 QUAL 0 24.1 16473 10166 6307 11301 QUAL 0 24.2 22241 13792 8449 14238 QUAL 0 24.3 32899 20724 12175 18614 QUAL 0 24.4 56817 36595 20222 26551 QUAL 0 24.5 131205 86200 45005 42259 QUAL 0 24.6 437468 293163 144305 78777 QUAL 0 24.7 1402576 949637 452939 165849 QUAL 0 24.8 1192910 812482 380428 202554 QUAL 0 24.9 196174 133805 62369 74006 QUAL 0 25.0 27997 18817 9180 24191 QUAL 0 25.1 5983 3993 1990 11132 QUAL 0 25.2 1654 1094 560 5421 QUAL 0 25.3 725 480 245 2523 QUAL 0 25.4 405 255 150 1332 QUAL 0 25.5 233 140 93 882 QUAL 0 25.6 160 93 67 644 QUAL 0 25.7 120 72 48 538 QUAL 0 25.8 74 55 19 516 QUAL 0 25.9 52 28 24 438 QUAL 0 26.0 41 20 21 374 QUAL 0 26.1 37 25 12 343 QUAL 0 26.2 22 9 13 335 QUAL 0 26.3 23 9 14 317 QUAL 0 26.4 18 7 11 274 QUAL 0 26.5 20 8 12 256 QUAL 0 26.6 9 3 6 267 QUAL 0 26.7 11 4 7 257 QUAL 0 26.8 12 3 9 224 QUAL 0 26.9 12 7 5 234 QUAL 0 27.0 13 8 5 202 QUAL 0 27.1 15 7 8 209 QUAL 0 27.2 11 6 5 184 QUAL 0 27.3 7 1 6 205 QUAL 0 27.4 8 2 6 164 QUAL 0 27.5 11 1 10 157 QUAL 0 27.6 7 3 4 122 QUAL 0 27.7 9 2 7 122 QUAL 0 27.8 8 3 5 101 QUAL 0 27.9 3 1 2 78 QUAL 0 28.0 5 0 5 62 QUAL 0 28.1 4 0 4 41 QUAL 0 28.2 4 3 1 30 QUAL 0 28.3 4 2 2 15 QUAL 0 28.4 2 0 2 6 QUAL 0 28.5 5 1 4 21 QUAL 0 28.6 2 1 1 3 QUAL 0 28.7 3 1 2 6 QUAL 0 28.8 3 0 3 5 QUAL 0 28.9 2 1 1 2 QUAL 0 29.0 0 0 0 2 QUAL 0 29.1 2 2 0 3 QUAL 0 29.2 0 0 0 4 QUAL 0 29.3 1 1 0 1 QUAL 0 29.4 1 0 1 2 QUAL 0 29.5 0 0 0 2 QUAL 0 29.6 0 0 0 1 QUAL 0 30.2 0 0 0 1 QUAL 0 30.3 0 0 0 1 QUAL 0 31.2 1 0 1 0 # IDD, InDel distribution: # IDD [2]id [3]length (deletions negative) [4]number of sites [5]number of genotypes [6]mean VAF IDD 0 -60 79 76 0.70 IDD 0 -59 6 6 0.73 IDD 0 -58 17 17 0.71 IDD 0 -57 13 13 0.71 IDD 0 -56 30 30 0.65 IDD 0 -55 21 20 0.69 IDD 0 -54 36 35 0.65 IDD 0 -53 33 33 0.61 IDD 0 -52 63 63 0.70 IDD 0 -51 37 37 0.69 IDD 0 -50 86 85 0.64 IDD 0 -49 66 65 0.70 IDD 0 -48 108 107 0.64 IDD 0 -47 54 54 0.67 IDD 0 -46 115 114 0.66 IDD 0 -45 66 64 0.66 IDD 0 -44 137 137 0.64 IDD 0 -43 71 70 0.62 IDD 0 -42 148 147 0.64 IDD 0 -41 87 87 0.67 IDD 0 -40 229 229 0.60 IDD 0 -39 117 117 0.66 IDD 0 -38 222 220 0.61 IDD 0 -37 129 129 0.62 IDD 0 -36 334 329 0.61 IDD 0 -35 148 146 0.57 IDD 0 -34 296 296 0.61 IDD 0 -33 176 173 0.63 IDD 0 -32 475 471 0.58 IDD 0 -31 233 231 0.62 IDD 0 -30 589 582 0.61 IDD 0 -29 278 276 0.61 IDD 0 -28 772 764 0.60 IDD 0 -27 359 356 0.60 IDD 0 -26 735 726 0.59 IDD 0 -25 534 527 0.59 IDD 0 -24 1343 1334 0.58 IDD 0 -23 496 492 0.57 IDD 0 -22 1165 1151 0.58 IDD 0 -21 667 662 0.56 IDD 0 -20 2319 2297 0.55 IDD 0 -19 878 868 0.56 IDD 0 -18 2085 2062 0.57 IDD 0 -17 1082 1068 0.55 IDD 0 -16 3611 3582 0.58 IDD 0 -15 2140 2114 0.56 IDD 0 -14 3518 3480 0.57 IDD 0 -13 1991 1976 0.57 IDD 0 -12 7555 7482 0.57 IDD 0 -11 2556 2525 0.56 IDD 0 -10 7374 7283 0.56 IDD 0 -9 4110 4055 0.57 IDD 0 -8 13328 13172 0.58 IDD 0 -7 5318 5248 0.57 IDD 0 -6 15906 15722 0.58 IDD 0 -5 14280 14145 0.60 IDD 0 -4 49659 49296 0.61 IDD 0 -3 33434 33135 0.59 IDD 0 -2 90557 89833 0.60 IDD 0 -1 229604 228570 0.63 IDD 0 1 236142 4130926 0.69 IDD 0 2 91128 89720 0.57 IDD 0 3 32209 31490 0.56 IDD 0 4 47797 47090 0.58 IDD 0 5 13145 12826 0.55 IDD 0 6 15392 14996 0.50 IDD 0 7 4640 4488 0.47 IDD 0 8 12863 12565 0.48 IDD 0 9 3632 3529 0.47 IDD 0 10 6583 6399 0.45 IDD 0 11 2141 2066 0.45 IDD 0 12 6845 6661 0.44 IDD 0 13 1496 1441 0.44 IDD 0 14 2882 2785 0.41 IDD 0 15 1740 1693 0.43 IDD 0 16 3157 3048 0.42 IDD 0 17 723 716 0.46 IDD 0 18 1653 1601 0.39 IDD 0 19 552 539 0.46 IDD 0 20 1895 1840 0.39 IDD 0 21 528 519 0.45 IDD 0 22 785 757 0.39 IDD 0 23 367 359 0.44 IDD 0 24 1128 1089 0.38 IDD 0 25 390 381 0.42 IDD 0 26 509 495 0.37 IDD 0 27 261 259 0.45 IDD 0 28 522 493 0.37 IDD 0 29 183 180 0.40 IDD 0 30 368 358 0.36 IDD 0 31 144 145 0.40 IDD 0 32 308 299 0.35 IDD 0 33 116 115 0.39 IDD 0 34 177 175 0.36 IDD 0 35 113 113 0.37 IDD 0 36 197 193 0.33 IDD 0 37 90 89 0.40 IDD 0 38 121 121 0.34 IDD 0 39 64 64 0.37 IDD 0 40 129 126 0.34 IDD 0 41 73 72 0.36 IDD 0 42 90 89 0.33 IDD 0 43 54 53 0.32 IDD 0 44 60 59 0.35 IDD 0 45 38 38 0.34 IDD 0 46 55 55 0.32 IDD 0 47 44 44 0.31 IDD 0 48 57 56 0.30 IDD 0 49 29 29 0.30 IDD 0 50 54 53 0.30 IDD 0 51 30 30 0.33 IDD 0 52 46 44 0.32 IDD 0 53 28 28 0.30 IDD 0 54 34 34 0.29 IDD 0 55 27 27 0.26 IDD 0 56 32 32 0.29 IDD 0 57 23 23 0.29 IDD 0 58 21 21 0.29 IDD 0 59 29 29 0.26 IDD 0 60 448 441 0.21 # ST, Substitution types: # ST [2]id [3]type [4]count ST 0 A>C 164827 ST 0 A>G 633650 ST 0 A>T 146453 ST 0 C>A 168461 ST 0 C>G 171340 ST 0 C>T 662680 ST 0 G>A 661928 ST 0 G>C 171833 ST 0 G>T 169748 ST 0 T>A 146536 ST 0 T>C 634470 ST 0 T>G 165554 # 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 2 11476 0.238996 0 0.000000 DP 0 3 10266 0.213797 0 0.000000 DP 0 4 9524 0.198344 0 0.000000 DP 0 5 9117 0.189868 0 0.000000 DP 0 6 9128 0.190097 0 0.000000 DP 0 7 9241 0.192450 0 0.000000 DP 0 8 9906 0.206299 0 0.000000 DP 0 9 11076 0.230666 0 0.000000 DP 0 10 12452 0.259322 0 0.000000 DP 0 11 14310 0.298016 0 0.000000 DP 0 12 16135 0.336023 0 0.000000 DP 0 13 18164 0.378278 0 0.000000 DP 0 14 20370 0.424220 0 0.000000 DP 0 15 22456 0.467662 0 0.000000 DP 0 16 25296 0.526807 0 0.000000 DP 0 17 28312 0.589617 0 0.000000 DP 0 18 32579 0.678481 0 0.000000 DP 0 19 39173 0.815805 0 0.000000 DP 0 20 47629 0.991908 0 0.000000 DP 0 21 59415 1.237359 0 0.000000 DP 0 22 73431 1.529252 0 0.000000 DP 0 23 91312 1.901637 0 0.000000 DP 0 24 111783 2.327960 0 0.000000 DP 0 25 134553 2.802161 0 0.000000 DP 0 26 158154 3.293669 0 0.000000 DP 0 27 182219 3.794839 0 0.000000 DP 0 28 205938 4.288804 0 0.000000 DP 0 29 225455 4.695260 0 0.000000 DP 0 30 243690 5.075016 0 0.000000 DP 0 31 253710 5.283690 0 0.000000 DP 0 32 260820 5.431761 0 0.000000 DP 0 33 262874 5.474537 0 0.000000 DP 0 34 257130 5.354914 0 0.000000 DP 0 35 248577 5.176792 0 0.000000 DP 0 36 233804 4.869133 0 0.000000 DP 0 37 216868 4.516429 0 0.000000 DP 0 38 196040 4.082671 0 0.000000 DP 0 39 174865 3.641687 0 0.000000 DP 0 40 152536 3.176670 0 0.000000 DP 0 41 130900 2.726085 0 0.000000 DP 0 42 110604 2.303406 0 0.000000 DP 0 43 91197 1.899242 0 0.000000 DP 0 44 75265 1.567447 0 0.000000 DP 0 45 60302 1.255832 0 0.000000 DP 0 46 47697 0.993324 0 0.000000 DP 0 47 37407 0.779027 0 0.000000 DP 0 48 29049 0.604966 0 0.000000 DP 0 49 22435 0.467225 0 0.000000 DP 0 50 16919 0.352350 0 0.000000 DP 0 51 12802 0.266611 0 0.000000 DP 0 52 9598 0.199885 0 0.000000 DP 0 53 7204 0.150028 0 0.000000 DP 0 54 5358 0.111584 0 0.000000 DP 0 55 4126 0.085927 0 0.000000 DP 0 56 3217 0.066996 0 0.000000 DP 0 57 2517 0.052418 0 0.000000 DP 0 58 2106 0.043859 0 0.000000 DP 0 59 1741 0.036258 0 0.000000 DP 0 60 1485 0.030926 0 0.000000 DP 0 61 1270 0.026449 0 0.000000 DP 0 62 1193 0.024845 0 0.000000 DP 0 63 1022 0.021284 0 0.000000 DP 0 64 954 0.019868 0 0.000000 DP 0 65 870 0.018118 0 0.000000 DP 0 66 858 0.017868 0 0.000000 DP 0 67 769 0.016015 0 0.000000 DP 0 68 780 0.016244 0 0.000000 DP 0 69 674 0.014037 0 0.000000 DP 0 70 656 0.013662 0 0.000000 DP 0 71 616 0.012829 0 0.000000 DP 0 72 617 0.012849 0 0.000000 DP 0 73 554 0.011537 0 0.000000 DP 0 74 486 0.010121 0 0.000000 DP 0 75 490 0.010205 0 0.000000 DP 0 76 455 0.009476 0 0.000000 DP 0 77 445 0.009267 0 0.000000 DP 0 78 406 0.008455 0 0.000000 DP 0 79 415 0.008643 0 0.000000 DP 0 80 386 0.008039 0 0.000000 DP 0 81 324 0.006748 0 0.000000 DP 0 82 343 0.007143 0 0.000000 DP 0 83 314 0.006539 0 0.000000 DP 0 84 271 0.005644 0 0.000000 DP 0 85 259 0.005394 0 0.000000 DP 0 86 245 0.005102 0 0.000000 DP 0 87 258 0.005373 0 0.000000 DP 0 88 270 0.005623 0 0.000000 DP 0 89 242 0.005040 0 0.000000 DP 0 90 239 0.004977 0 0.000000 DP 0 91 244 0.005081 0 0.000000 DP 0 92 212 0.004415 0 0.000000 DP 0 93 246 0.005123 0 0.000000 DP 0 94 189 0.003936 0 0.000000 DP 0 95 229 0.004769 0 0.000000 DP 0 96 195 0.004061 0 0.000000 DP 0 97 191 0.003978 0 0.000000 DP 0 98 175 0.003644 0 0.000000 DP 0 99 165 0.003436 0 0.000000 DP 0 100 186 0.003874 0 0.000000 DP 0 101 186 0.003874 0 0.000000 DP 0 102 169 0.003520 0 0.000000 DP 0 103 137 0.002853 0 0.000000 DP 0 104 147 0.003061 0 0.000000 DP 0 105 175 0.003644 0 0.000000 DP 0 106 156 0.003249 0 0.000000 DP 0 107 153 0.003186 0 0.000000 DP 0 108 174 0.003624 0 0.000000 DP 0 109 147 0.003061 0 0.000000 DP 0 110 133 0.002770 0 0.000000 DP 0 111 148 0.003082 0 0.000000 DP 0 112 156 0.003249 0 0.000000 DP 0 113 133 0.002770 0 0.000000 DP 0 114 141 0.002936 0 0.000000 DP 0 115 144 0.002999 0 0.000000 DP 0 116 139 0.002895 0 0.000000 DP 0 117 135 0.002811 0 0.000000 DP 0 118 138 0.002874 0 0.000000 DP 0 119 124 0.002582 0 0.000000 DP 0 120 90 0.001874 0 0.000000 DP 0 121 127 0.002645 0 0.000000 DP 0 122 110 0.002291 0 0.000000 DP 0 123 124 0.002582 0 0.000000 DP 0 124 126 0.002624 0 0.000000 DP 0 125 112 0.002332 0 0.000000 DP 0 126 112 0.002332 0 0.000000 DP 0 127 91 0.001895 0 0.000000 DP 0 128 90 0.001874 0 0.000000 DP 0 129 109 0.002270 0 0.000000 DP 0 130 104 0.002166 0 0.000000 DP 0 131 96 0.001999 0 0.000000 DP 0 132 81 0.001687 0 0.000000 DP 0 133 84 0.001749 0 0.000000 DP 0 134 94 0.001958 0 0.000000 DP 0 135 94 0.001958 0 0.000000 DP 0 136 74 0.001541 0 0.000000 DP 0 137 74 0.001541 0 0.000000 DP 0 138 57 0.001187 0 0.000000 DP 0 139 84 0.001749 0 0.000000 DP 0 140 76 0.001583 0 0.000000 DP 0 141 69 0.001437 0 0.000000 DP 0 142 72 0.001499 0 0.000000 DP 0 143 70 0.001458 0 0.000000 DP 0 144 72 0.001499 0 0.000000 DP 0 145 83 0.001729 0 0.000000 DP 0 146 55 0.001145 0 0.000000 DP 0 147 57 0.001187 0 0.000000 DP 0 148 62 0.001291 0 0.000000 DP 0 149 61 0.001270 0 0.000000 DP 0 150 62 0.001291 0 0.000000 DP 0 151 63 0.001312 0 0.000000 DP 0 152 52 0.001083 0 0.000000 DP 0 153 67 0.001395 0 0.000000 DP 0 154 72 0.001499 0 0.000000 DP 0 155 59 0.001229 0 0.000000 DP 0 156 69 0.001437 0 0.000000 DP 0 157 63 0.001312 0 0.000000 DP 0 158 55 0.001145 0 0.000000 DP 0 159 53 0.001104 0 0.000000 DP 0 160 72 0.001499 0 0.000000 DP 0 161 45 0.000937 0 0.000000 DP 0 162 60 0.001250 0 0.000000 DP 0 163 48 0.001000 0 0.000000 DP 0 164 56 0.001166 0 0.000000 DP 0 165 56 0.001166 0 0.000000 DP 0 166 63 0.001312 0 0.000000 DP 0 167 61 0.001270 0 0.000000 DP 0 168 48 0.001000 0 0.000000 DP 0 169 49 0.001020 0 0.000000 DP 0 170 39 0.000812 0 0.000000 DP 0 171 55 0.001145 0 0.000000 DP 0 172 60 0.001250 0 0.000000 DP 0 173 66 0.001374 0 0.000000 DP 0 174 43 0.000896 0 0.000000 DP 0 175 47 0.000979 0 0.000000 DP 0 176 45 0.000937 0 0.000000 DP 0 177 50 0.001041 0 0.000000 DP 0 178 51 0.001062 0 0.000000 DP 0 179 49 0.001020 0 0.000000 DP 0 180 46 0.000958 0 0.000000 DP 0 181 44 0.000916 0 0.000000 DP 0 182 50 0.001041 0 0.000000 DP 0 183 43 0.000896 0 0.000000 DP 0 184 48 0.001000 0 0.000000 DP 0 185 50 0.001041 0 0.000000 DP 0 186 47 0.000979 0 0.000000 DP 0 187 42 0.000875 0 0.000000 DP 0 188 34 0.000708 0 0.000000 DP 0 189 53 0.001104 0 0.000000 DP 0 190 42 0.000875 0 0.000000 DP 0 191 39 0.000812 0 0.000000 DP 0 192 43 0.000896 0 0.000000 DP 0 193 43 0.000896 0 0.000000 DP 0 194 36 0.000750 0 0.000000 DP 0 195 38 0.000791 0 0.000000 DP 0 196 47 0.000979 0 0.000000 DP 0 197 40 0.000833 0 0.000000 DP 0 198 42 0.000875 0 0.000000 DP 0 199 40 0.000833 0 0.000000 DP 0 200 42 0.000875 0 0.000000 DP 0 201 46 0.000958 0 0.000000 DP 0 202 35 0.000729 0 0.000000 DP 0 203 27 0.000562 0 0.000000 DP 0 204 41 0.000854 0 0.000000 DP 0 205 37 0.000771 0 0.000000 DP 0 206 39 0.000812 0 0.000000 DP 0 207 34 0.000708 0 0.000000 DP 0 208 22 0.000458 0 0.000000 DP 0 209 26 0.000541 0 0.000000 DP 0 210 39 0.000812 0 0.000000 DP 0 211 30 0.000625 0 0.000000 DP 0 212 22 0.000458 0 0.000000 DP 0 213 25 0.000521 0 0.000000 DP 0 214 28 0.000583 0 0.000000 DP 0 215 32 0.000666 0 0.000000 DP 0 216 35 0.000729 0 0.000000 DP 0 217 30 0.000625 0 0.000000 DP 0 218 32 0.000666 0 0.000000 DP 0 219 30 0.000625 0 0.000000 DP 0 220 23 0.000479 0 0.000000 DP 0 221 25 0.000521 0 0.000000 DP 0 222 35 0.000729 0 0.000000 DP 0 223 20 0.000417 0 0.000000 DP 0 224 30 0.000625 0 0.000000 DP 0 225 22 0.000458 0 0.000000 DP 0 226 17 0.000354 0 0.000000 DP 0 227 23 0.000479 0 0.000000 DP 0 228 27 0.000562 0 0.000000 DP 0 229 22 0.000458 0 0.000000 DP 0 230 22 0.000458 0 0.000000 DP 0 231 20 0.000417 0 0.000000 DP 0 232 25 0.000521 0 0.000000 DP 0 233 25 0.000521 0 0.000000 DP 0 234 15 0.000312 0 0.000000 DP 0 235 26 0.000541 0 0.000000 DP 0 236 27 0.000562 0 0.000000 DP 0 237 22 0.000458 0 0.000000 DP 0 238 21 0.000437 0 0.000000 DP 0 239 25 0.000521 0 0.000000 DP 0 240 15 0.000312 0 0.000000 DP 0 241 15 0.000312 0 0.000000 DP 0 242 24 0.000500 0 0.000000 DP 0 243 28 0.000583 0 0.000000 DP 0 244 14 0.000292 0 0.000000 DP 0 245 14 0.000292 0 0.000000 DP 0 246 10 0.000208 0 0.000000 DP 0 247 19 0.000396 0 0.000000 DP 0 248 13 0.000271 0 0.000000 DP 0 249 19 0.000396 0 0.000000 DP 0 250 24 0.000500 0 0.000000 DP 0 251 20 0.000417 0 0.000000 DP 0 252 12 0.000250 0 0.000000 DP 0 253 17 0.000354 0 0.000000 DP 0 254 13 0.000271 0 0.000000 DP 0 255 13 0.000271 0 0.000000 DP 0 256 19 0.000396 0 0.000000 DP 0 257 15 0.000312 0 0.000000 DP 0 258 19 0.000396 0 0.000000 DP 0 259 14 0.000292 0 0.000000 DP 0 260 12 0.000250 0 0.000000 DP 0 261 11 0.000229 0 0.000000 DP 0 262 13 0.000271 0 0.000000 DP 0 263 13 0.000271 0 0.000000 DP 0 264 13 0.000271 0 0.000000 DP 0 265 20 0.000417 0 0.000000 DP 0 266 10 0.000208 0 0.000000 DP 0 267 20 0.000417 0 0.000000 DP 0 268 13 0.000271 0 0.000000 DP 0 269 14 0.000292 0 0.000000 DP 0 270 12 0.000250 0 0.000000 DP 0 271 13 0.000271 0 0.000000 DP 0 272 20 0.000417 0 0.000000 DP 0 273 10 0.000208 0 0.000000 DP 0 274 15 0.000312 0 0.000000 DP 0 275 14 0.000292 0 0.000000 DP 0 276 20 0.000417 0 0.000000 DP 0 277 15 0.000312 0 0.000000 DP 0 278 9 0.000187 0 0.000000 DP 0 279 16 0.000333 0 0.000000 DP 0 280 17 0.000354 0 0.000000 DP 0 281 13 0.000271 0 0.000000 DP 0 282 12 0.000250 0 0.000000 DP 0 283 9 0.000187 0 0.000000 DP 0 284 18 0.000375 0 0.000000 DP 0 285 19 0.000396 0 0.000000 DP 0 286 8 0.000167 0 0.000000 DP 0 287 11 0.000229 0 0.000000 DP 0 288 12 0.000250 0 0.000000 DP 0 289 12 0.000250 0 0.000000 DP 0 290 9 0.000187 0 0.000000 DP 0 291 6 0.000125 0 0.000000 DP 0 292 13 0.000271 0 0.000000 DP 0 293 13 0.000271 0 0.000000 DP 0 294 8 0.000167 0 0.000000 DP 0 295 10 0.000208 0 0.000000 DP 0 296 9 0.000187 0 0.000000 DP 0 297 10 0.000208 0 0.000000 DP 0 298 6 0.000125 0 0.000000 DP 0 299 6 0.000125 0 0.000000 DP 0 300 12 0.000250 0 0.000000 DP 0 301 4 0.000083 0 0.000000 DP 0 302 9 0.000187 0 0.000000 DP 0 303 8 0.000167 0 0.000000 DP 0 304 9 0.000187 0 0.000000 DP 0 305 6 0.000125 0 0.000000 DP 0 306 5 0.000104 0 0.000000 DP 0 307 7 0.000146 0 0.000000 DP 0 308 9 0.000187 0 0.000000 DP 0 309 13 0.000271 0 0.000000 DP 0 310 11 0.000229 0 0.000000 DP 0 311 6 0.000125 0 0.000000 DP 0 312 5 0.000104 0 0.000000 DP 0 313 8 0.000167 0 0.000000 DP 0 314 11 0.000229 0 0.000000 DP 0 315 8 0.000167 0 0.000000 DP 0 316 8 0.000167 0 0.000000 DP 0 317 8 0.000167 0 0.000000 DP 0 318 9 0.000187 0 0.000000 DP 0 319 9 0.000187 0 0.000000 DP 0 320 7 0.000146 0 0.000000 DP 0 321 5 0.000104 0 0.000000 DP 0 322 9 0.000187 0 0.000000 DP 0 323 9 0.000187 0 0.000000 DP 0 324 7 0.000146 0 0.000000 DP 0 325 6 0.000125 0 0.000000 DP 0 326 6 0.000125 0 0.000000 DP 0 327 8 0.000167 0 0.000000 DP 0 328 6 0.000125 0 0.000000 DP 0 329 4 0.000083 0 0.000000 DP 0 330 7 0.000146 0 0.000000 DP 0 331 7 0.000146 0 0.000000 DP 0 332 10 0.000208 0 0.000000 DP 0 333 8 0.000167 0 0.000000 DP 0 334 5 0.000104 0 0.000000 DP 0 335 5 0.000104 0 0.000000 DP 0 336 7 0.000146 0 0.000000 DP 0 337 6 0.000125 0 0.000000 DP 0 338 9 0.000187 0 0.000000 DP 0 339 4 0.000083 0 0.000000 DP 0 340 9 0.000187 0 0.000000 DP 0 341 4 0.000083 0 0.000000 DP 0 342 8 0.000167 0 0.000000 DP 0 343 2 0.000042 0 0.000000 DP 0 344 8 0.000167 0 0.000000 DP 0 345 9 0.000187 0 0.000000 DP 0 346 4 0.000083 0 0.000000 DP 0 347 6 0.000125 0 0.000000 DP 0 348 7 0.000146 0 0.000000 DP 0 349 7 0.000146 0 0.000000 DP 0 350 6 0.000125 0 0.000000 DP 0 351 8 0.000167 0 0.000000 DP 0 352 6 0.000125 0 0.000000 DP 0 353 6 0.000125 0 0.000000 DP 0 354 8 0.000167 0 0.000000 DP 0 355 4 0.000083 0 0.000000 DP 0 356 6 0.000125 0 0.000000 DP 0 357 9 0.000187 0 0.000000 DP 0 358 12 0.000250 0 0.000000 DP 0 359 6 0.000125 0 0.000000 DP 0 360 5 0.000104 0 0.000000 DP 0 361 4 0.000083 0 0.000000 DP 0 362 7 0.000146 0 0.000000 DP 0 363 5 0.000104 0 0.000000 DP 0 364 6 0.000125 0 0.000000 DP 0 365 3 0.000062 0 0.000000 DP 0 366 3 0.000062 0 0.000000 DP 0 367 5 0.000104 0 0.000000 DP 0 368 7 0.000146 0 0.000000 DP 0 369 7 0.000146 0 0.000000 DP 0 370 6 0.000125 0 0.000000 DP 0 371 1 0.000021 0 0.000000 DP 0 372 5 0.000104 0 0.000000 DP 0 373 8 0.000167 0 0.000000 DP 0 374 3 0.000062 0 0.000000 DP 0 375 3 0.000062 0 0.000000 DP 0 376 9 0.000187 0 0.000000 DP 0 377 4 0.000083 0 0.000000 DP 0 378 9 0.000187 0 0.000000 DP 0 379 6 0.000125 0 0.000000 DP 0 380 5 0.000104 0 0.000000 DP 0 381 12 0.000250 0 0.000000 DP 0 382 8 0.000167 0 0.000000 DP 0 383 3 0.000062 0 0.000000 DP 0 384 2 0.000042 0 0.000000 DP 0 385 5 0.000104 0 0.000000 DP 0 386 3 0.000062 0 0.000000 DP 0 387 4 0.000083 0 0.000000 DP 0 388 3 0.000062 0 0.000000 DP 0 389 6 0.000125 0 0.000000 DP 0 390 4 0.000083 0 0.000000 DP 0 391 5 0.000104 0 0.000000 DP 0 392 4 0.000083 0 0.000000 DP 0 393 7 0.000146 0 0.000000 DP 0 394 7 0.000146 0 0.000000 DP 0 395 5 0.000104 0 0.000000 DP 0 396 7 0.000146 0 0.000000 DP 0 397 2 0.000042 0 0.000000 DP 0 398 7 0.000146 0 0.000000 DP 0 399 2 0.000042 0 0.000000 DP 0 400 8 0.000167 0 0.000000 DP 0 401 2 0.000042 0 0.000000 DP 0 402 12 0.000250 0 0.000000 DP 0 403 2 0.000042 0 0.000000 DP 0 404 7 0.000146 0 0.000000 DP 0 405 9 0.000187 0 0.000000 DP 0 406 1 0.000021 0 0.000000 DP 0 407 4 0.000083 0 0.000000 DP 0 408 5 0.000104 0 0.000000 DP 0 409 3 0.000062 0 0.000000 DP 0 410 3 0.000062 0 0.000000 DP 0 411 4 0.000083 0 0.000000 DP 0 412 5 0.000104 0 0.000000 DP 0 413 5 0.000104 0 0.000000 DP 0 414 5 0.000104 0 0.000000 DP 0 415 4 0.000083 0 0.000000 DP 0 416 6 0.000125 0 0.000000 DP 0 417 3 0.000062 0 0.000000 DP 0 418 8 0.000167 0 0.000000 DP 0 419 4 0.000083 0 0.000000 DP 0 420 3 0.000062 0 0.000000 DP 0 421 3 0.000062 0 0.000000 DP 0 422 3 0.000062 0 0.000000 DP 0 423 1 0.000021 0 0.000000 DP 0 424 2 0.000042 0 0.000000 DP 0 425 5 0.000104 0 0.000000 DP 0 426 3 0.000062 0 0.000000 DP 0 427 1 0.000021 0 0.000000 DP 0 428 4 0.000083 0 0.000000 DP 0 429 4 0.000083 0 0.000000 DP 0 430 3 0.000062 0 0.000000 DP 0 431 3 0.000062 0 0.000000 DP 0 432 6 0.000125 0 0.000000 DP 0 434 2 0.000042 0 0.000000 DP 0 435 4 0.000083 0 0.000000 DP 0 436 3 0.000062 0 0.000000 DP 0 437 2 0.000042 0 0.000000 DP 0 438 5 0.000104 0 0.000000 DP 0 439 3 0.000062 0 0.000000 DP 0 440 7 0.000146 0 0.000000 DP 0 441 2 0.000042 0 0.000000 DP 0 442 4 0.000083 0 0.000000 DP 0 443 2 0.000042 0 0.000000 DP 0 444 3 0.000062 0 0.000000 DP 0 445 3 0.000062 0 0.000000 DP 0 446 6 0.000125 0 0.000000 DP 0 447 4 0.000083 0 0.000000 DP 0 448 2 0.000042 0 0.000000 DP 0 449 8 0.000167 0 0.000000 DP 0 450 3 0.000062 0 0.000000 DP 0 451 3 0.000062 0 0.000000 DP 0 452 5 0.000104 0 0.000000 DP 0 453 1 0.000021 0 0.000000 DP 0 454 5 0.000104 0 0.000000 DP 0 455 1 0.000021 0 0.000000 DP 0 456 4 0.000083 0 0.000000 DP 0 457 1 0.000021 0 0.000000 DP 0 458 2 0.000042 0 0.000000 DP 0 459 3 0.000062 0 0.000000 DP 0 460 1 0.000021 0 0.000000 DP 0 461 2 0.000042 0 0.000000 DP 0 462 3 0.000062 0 0.000000 DP 0 463 1 0.000021 0 0.000000 DP 0 464 2 0.000042 0 0.000000 DP 0 465 2 0.000042 0 0.000000 DP 0 466 3 0.000062 0 0.000000 DP 0 467 4 0.000083 0 0.000000 DP 0 468 2 0.000042 0 0.000000 DP 0 469 2 0.000042 0 0.000000 DP 0 470 3 0.000062 0 0.000000 DP 0 471 1 0.000021 0 0.000000 DP 0 472 4 0.000083 0 0.000000 DP 0 473 2 0.000042 0 0.000000 DP 0 474 4 0.000083 0 0.000000 DP 0 475 2 0.000042 0 0.000000 DP 0 476 7 0.000146 0 0.000000 DP 0 477 2 0.000042 0 0.000000 DP 0 478 4 0.000083 0 0.000000 DP 0 479 2 0.000042 0 0.000000 DP 0 480 2 0.000042 0 0.000000 DP 0 481 6 0.000125 0 0.000000 DP 0 482 1 0.000021 0 0.000000 DP 0 483 1 0.000021 0 0.000000 DP 0 485 6 0.000125 0 0.000000 DP 0 486 3 0.000062 0 0.000000 DP 0 487 1 0.000021 0 0.000000 DP 0 488 4 0.000083 0 0.000000 DP 0 489 4 0.000083 0 0.000000 DP 0 490 3 0.000062 0 0.000000 DP 0 491 3 0.000062 0 0.000000 DP 0 492 3 0.000062 0 0.000000 DP 0 493 3 0.000062 0 0.000000 DP 0 494 4 0.000083 0 0.000000 DP 0 495 3 0.000062 0 0.000000 DP 0 497 2 0.000042 0 0.000000 DP 0 498 2 0.000042 0 0.000000 DP 0 499 3 0.000062 0 0.000000 DP 0 500 4 0.000083 0 0.000000 DP 0 >500 395 0.008226 0 0.000000 # PSC, Per-sample counts. Note that the ref/het/hom counts include only SNPs, for indels see PSI. The rest include both SNPs and indels. # PSC [2]id [3]sample [4]nRefHom [5]nNonRefHom [6]nHets [7]nTransitions [8]nTransversions [9]nIndels [10]average depth [11]nSingletons [12]nHapRef [13]nHapAlt [14]nMissing PSC 0 HG002 461 1606149 2287986 2592193 1304164 911968 32.7 4801297 0 0 0 # PSI, Per-Sample Indels. Note that alt-het genotypes with both ins and del allele are counted twice, in both nInsHets and nDelHets. # PSI [2]id [3]sample [4]in-frame [5]out-frame [6]not applicable [7]out/(in+out) ratio [8]nInsHets [9]nDelHets [10]nInsAltHoms [11]nDelAltHoms PSI 0 HG002 0 0 0 0.00 300603 308641 161697 164179 # HWE # HWE [2]id [3]1st ALT allele frequency [4]Number of observations [5]25th percentile [6]median [7]75th percentile HWE 0 0.000000 2869714 0.990000 0.990000 0.990000 HWE 0 0.990000 1932044 0.000000 0.000000 0.000000 # VAF, Variant Allele Frequency determined as fraction of alternate reads in FORMAT/AD # VAF [2]id [3]sample [4]SNV VAF distribution [5]indel VAF distribution VAF 0 HG002 0,0,1248,9472,16033,29903,73673,140817,303924,410811,478296,392918,274873,121898,55915,21659,12777,12172,23760,189065,1326768 0,4286,21008,21936,25268,29834,42798,50391,76054,83352,94336,86569,74597,42442,29507,19004,18613,23057,41721,89453,112182