Participant(s) Technology Multi_Details Submission_Name Type challenge_cat FP.al FP.gt METRIC.F1_Score METRIC.Precision METRIC.Recall QUERY.FP QUERY.TP TRUTH.FN TRUTH.TP The Genomics Team in Google Health ILLUMINA NA DeepTrio Illumina INDEL All Benchmark Regions 337 716 0.996079 0.997359997 0.994800999 1395 527126 2642 505487 The Genomics Team in Google Health ILLUMINA NA DeepTrio Illumina INDEL Difficult-to-Map Regions 47 104 0.945030848 0.978266991 0.913980319 339 15282 1418 15071 The Genomics Team in Google Health ILLUMINA NA DeepTrio Illumina INDEL MHC 19 9 0.972508853 0.980170011 0.964982926 34 1707 58 1633 The Genomics Team in Google Health ILLUMINA NA DeepTrio Illumina SNP All Benchmark Regions 681 1707 0.995794998 0.997969999 0.993629486 6759 3323858 21292 3322222 The Genomics Team in Google Health ILLUMINA NA DeepTrio Illumina SNP Difficult-to-Map Regions 403 1531 0.94963321 0.978754498 0.922195026 5232 241041 20328 240976 The Genomics Team in Google Health ILLUMINA NA DeepTrio Illumina SNP MHC 153 60 0.980033364 0.981534738 0.978553589 364 19695 422 19721 The Genomics Team in Google Health ILLUMINA NA DeepTrio Illumina SNVandINDEL All Benchmark Regions 1019 2423 0.995831138 0.997886531 0.993784204 8154 3850988 23934 3827711 The Genomics Team in Google Health ILLUMINA NA DeepTrio Illumina SNVandINDEL Difficult-to-Map Regions 450 1636 0.949360685 0.97872538 0.921707147 5572 256323 21746 256047 The Genomics Team in Google Health ILLUMINA NA DeepTrio Illumina SNVandINDEL MHC 173 70 0.979451712 0.981425531 0.977502244 398 21402 481 21354 The Genomics Team in Google Health PACBIO NA DeepTrio PacBio INDEL All Benchmark Regions 1052 1241 0.99491849 0.995142998 0.994692973 2572 527069 2694 505433 The Genomics Team in Google Health PACBIO NA DeepTrio PacBio INDEL Difficult-to-Map Regions 17 17 0.984227376 0.990119389 0.97840572 162 16291 355 16134 The Genomics Team in Google Health PACBIO NA DeepTrio PacBio INDEL MHC 11 5 0.977185474 0.989661238 0.96503941 18 1719 57 1633 The Genomics Team in Google Health PACBIO NA DeepTrio PacBio SNP All Benchmark Regions 297 642 0.9985175 0.999403499 0.997632499 1986 3338473 7915 3335605 The Genomics Team in Google Health PACBIO NA DeepTrio PacBio SNP Difficult-to-Map Regions 58 262 0.985593849 0.996720379 0.974712816 829 254888 6606 254699 The Genomics Team in Google Health PACBIO NA DeepTrio PacBio SNP MHC 10 21 0.985884745 0.998146414 0.973949468 35 19609 475 19629 The Genomics Team in Google Health PACBIO NA DeepTrio PacBio SNVandINDEL All Benchmark Regions 1349 1885 0.998031911 0.998820586 0.997244483 4563 3865544 10609 3841039 The Genomics Team in Google Health PACBIO NA DeepTrio PacBio SNVandINDEL Difficult-to-Map Regions 75 279 0.985510185 0.996321047 0.974931424 991 271179 6961 270833 The Genomics Team in Google Health PACBIO NA DeepTrio PacBio SNVandINDEL MHC 23 27 0.985195329 0.997456748 0.973259277 53 21328 532 21261 The Genomics Team in Google Health MULTI ILLUMINAPACBIO DeepVariant Hybrid PacBio-Illumina INDEL All Benchmark Regions 974 641 0.996950999 0.996488 0.997413495 1863 528765 1313 506815 The Genomics Team in Google Health MULTI ILLUMINAPACBIO DeepVariant Hybrid PacBio-Illumina INDEL Difficult-to-Map Regions 36 29 0.989601372 0.987971698 0.991236473 201 16553 144 16345 The Genomics Team in Google Health MULTI ILLUMINAPACBIO DeepVariant Hybrid PacBio-Illumina INDEL MHC 15 14 0.979263493 0.982917416 0.975642943 30 1751 39 1651 The Genomics Team in Google Health MULTI ILLUMINAPACBIO DeepVariant Hybrid PacBio-Illumina SNP All Benchmark Regions 550 609 0.9991895 0.998961999 0.999417 3470 3343869 1950 3341571 The Genomics Team in Google Health MULTI ILLUMINAPACBIO DeepVariant Hybrid PacBio-Illumina SNP Difficult-to-Map Regions 128 294 0.993762869 0.993101722 0.994425961 1795 259956 1455 259850 The Genomics Team in Google Health MULTI ILLUMINAPACBIO DeepVariant Hybrid PacBio-Illumina SNP MHC 24 21 0.994946361 0.997455 0.992453514 51 19988 134 20002 The Genomics Team in Google Health MULTI ILLUMINAPACBIO DeepVariant Hybrid PacBio-Illumina SNVandINDEL All Benchmark Regions 1525 1251 0.998888104 0.998623873 0.999152476 5334 3872637 3264 3848388 The Genomics Team in Google Health MULTI ILLUMINAPACBIO DeepVariant Hybrid PacBio-Illumina SNVandINDEL Difficult-to-Map Regions 164 323 0.993514011 0.99279285 0.994236276 1996 276510 1599 276196 The Genomics Team in Google Health MULTI ILLUMINAPACBIO DeepVariant Hybrid PacBio-Illumina SNVandINDEL MHC 39 35 0.993701854 0.996269382 0.99115097 81 21738 173 21652 The Genomics Team in Google Health ILLUMINA NA DeepVariant Illumina INDEL All Benchmark Regions 263 717 0.995949497 0.997436 0.994466987 1354 526937 2810 505318 The Genomics Team in Google Health ILLUMINA NA DeepVariant Illumina INDEL Difficult-to-Map Regions 42 106 0.943395445 0.97556221 0.913282622 382 15270 1430 15060 The Genomics Team in Google Health ILLUMINA NA DeepVariant Illumina INDEL MHC 11 15 0.971728673 0.983747232 0.96004225 28 1695 64 1624 The Genomics Team in Google Health ILLUMINA NA DeepVariant Illumina SNP All Benchmark Regions 569 1804 0.995632497 0.997735999 0.993537981 7539 3323526 21596 3321916 The Genomics Team in Google Health ILLUMINA NA DeepVariant Illumina SNP Difficult-to-Map Regions 421 1627 0.947394661 0.975122979 0.921200938 6142 240780 20586 240716 The Genomics Team in Google Health ILLUMINA NA DeepVariant Illumina SNP MHC 36 38 0.987170784 0.994250378 0.98019952 114 19736 386 19755 The Genomics Team in Google Health ILLUMINA NA DeepVariant Illumina SNVandINDEL All Benchmark Regions 833 2522 0.995673757 0.997695046 0.993660657 8894 3850466 24406 3827235 The Genomics Team in Google Health ILLUMINA NA DeepVariant Illumina SNVandINDEL Difficult-to-Map Regions 463 1734 0.947158301 0.975148971 0.920730623 6525 256051 22016 255776 The Genomics Team in Google Health ILLUMINA NA DeepVariant Illumina SNVandINDEL MHC 47 53 0.985964348 0.993410868 0.978638064 142 21432 450 21379 The Genomics Team in Google Health ILLUMINA NA DeepVariant Illumina (filtered for precision) INDEL All Benchmark Regions 201 497 0.995582 0.998238498 0.992939493 928 526006 3587 504542 The Genomics Team in Google Health ILLUMINA NA DeepVariant Illumina (filtered for precision) INDEL Difficult-to-Map Regions 26 66 0.942043116 0.98562386 0.902154783 220 15083 1613 14876 The Genomics Team in Google Health ILLUMINA NA DeepVariant Illumina (filtered for precision) INDEL MHC 13 10 0.970900625 0.984848414 0.957371519 26 1689 70 1620 The Genomics Team in Google Health ILLUMINA NA DeepVariant Illumina (filtered for precision) SNP All Benchmark Regions 355 990 0.995580496 0.998688999 0.992491977 4357 3319991 25094 3318417 The Genomics Team in Google Health ILLUMINA NA DeepVariant Illumina (filtered for precision) SNP Difficult-to-Map Regions 224 873 0.946178519 0.9863185 0.909179341 3296 237639 23727 237575 The Genomics Team in Google Health ILLUMINA NA DeepVariant Illumina (filtered for precision) SNP MHC 29 34 0.98657217 0.995021468 0.978274187 98 19699 422 19716 The Genomics Team in Google Health ILLUMINA NA DeepVariant Illumina (filtered for precision) SNVandINDEL All Benchmark Regions 556 1487 0.995579716 0.998627195 0.992550795 5285 3846000 28681 3822961 The Genomics Team in Google Health ILLUMINA NA DeepVariant Illumina (filtered for precision) SNVandINDEL Difficult-to-Map Regions 250 939 0.94593392 0.986276831 0.908762518 3516 252723 25340 252452 The Genomics Team in Google Health ILLUMINA NA DeepVariant Illumina (filtered for precision) SNVandINDEL MHC 43 44 0.985349231 0.994210438 0.97665457 124 21389 492 21336 The Genomics Team in Google Health PACBIO NA DeepVariant PacBio INDEL All Benchmark Regions 884 1782 0.993614973 0.993776989 0.993452452 3292 525845 3323 504802 The Genomics Team in Google Health PACBIO NA DeepVariant PacBio INDEL Difficult-to-Map Regions 20 25 0.989142788 0.987570348 0.990719718 207 16489 153 16337 The Genomics Team in Google Health PACBIO NA DeepVariant PacBio INDEL MHC 13 15 0.972634647 0.981919328 0.963530046 31 1706 60 1630 The Genomics Team in Google Health PACBIO NA DeepVariant PacBio SNP All Benchmark Regions 373 630 0.999049999 0.999034497 0.9990655 3220 3343303 3125 3340396 The Genomics Team in Google Health PACBIO NA DeepVariant PacBio SNP Difficult-to-Map Regions 124 311 0.991785238 0.992254085 0.991317855 2010 259232 2264 259038 The Genomics Team in Google Health PACBIO NA DeepVariant PacBio SNP MHC 14 25 0.992834449 0.997716493 0.988003022 45 19895 234 19912 The Genomics Team in Google Health PACBIO NA DeepVariant PacBio SNVandINDEL All Benchmark Regions 1258 2414 0.998320583 0.99831637 0.998324799 6522 3869151 6450 3845200 The Genomics Team in Google Health PACBIO NA DeepVariant PacBio SNVandINDEL Difficult-to-Map Regions 144 336 0.991627257 0.991972764 0.991282018 2217 275722 2417 275375 The Genomics Team in Google Health PACBIO NA DeepVariant PacBio SNVandINDEL MHC 27 41 0.991250529 0.996450825 0.986106891 77 21602 294 21542 The Genomics Team in Google Health PACBIO NA DeepVariant PacBio (filtered for precision) INDEL All Benchmark Regions 597 1312 0.993157462 0.995617496 0.990708893 2306 524048 4715 503408 The Genomics Team in Google Health PACBIO NA DeepVariant PacBio (filtered for precision) INDEL Difficult-to-Map Regions 18 20 0.989486213 0.990042816 0.988930087 165 16459 182 16307 The Genomics Team in Google Health PACBIO NA DeepVariant PacBio (filtered for precision) INDEL MHC 12 13 0.972230895 0.983850938 0.960893199 28 1702 64 1626 The Genomics Team in Google Health PACBIO NA DeepVariant PacBio (filtered for precision) SNP All Benchmark Regions 362 493 0.999005 0.999208998 0.998801 2636 3342311 4009 3339511 The Genomics Team in Google Health PACBIO NA DeepVariant PacBio (filtered for precision) SNP Difficult-to-Map Regions 108 270 0.991442277 0.993406713 0.989486333 1706 258753 2743 258559 The Genomics Team in Google Health PACBIO NA DeepVariant PacBio (filtered for precision) SNP MHC 14 23 0.992772781 0.997842499 0.987757577 43 19890 238 19907 The Genomics Team in Google Health PACBIO NA DeepVariant PacBio (filtered for precision) SNVandINDEL All Benchmark Regions 959 1808 0.998226582 0.998720544 0.997733112 4950 3866360 8726 3842921 The Genomics Team in Google Health PACBIO NA DeepVariant PacBio (filtered for precision) SNVandINDEL Difficult-to-Map Regions 126 290 0.991325435 0.993204995 0.989452981 1871 275212 2925 274867 The Genomics Team in Google Health PACBIO NA DeepVariant PacBio (filtered for precision) SNVandINDEL MHC 26 37 0.991168935 0.996726096 0.985676382 71 21592 303 21533 0GOOR PACBIO NA 0GOOR INDEL All Benchmark Regions 4139 18992 0.930478249 0.920077266 0.941117685 42088 484683 29908 478209 0GOOR PACBIO NA 0GOOR INDEL Difficult-to-Map Regions 139 165 0.952550761 0.926184782 0.980471323 1309 16468 322 16168 0GOOR PACBIO NA 0GOOR INDEL MHC 70 19 0.949005847 0.919047305 0.981035948 154 1772 32 1660 0GOOR PACBIO NA 0GOOR SNP All Benchmark Regions 2602 3242 0.995945489 0.993606961 0.998295 21460 3338642 5699 3337822 0GOOR PACBIO NA 0GOOR SNP Difficult-to-Map Regions 1158 563 0.971897894 0.951638288 0.993043432 13161 259552 1815 259489 0GOOR PACBIO NA 0GOOR SNP MHC 436 38 0.972591366 0.949681361 0.996634678 1061 20030 56 20086 0GOOR PACBIO NA 0GOOR SNVandINDEL All Benchmark Regions 6748 22235 0.987183743 0.983641387 0.990751729 63549 3823326 35609 3816031 0GOOR PACBIO NA 0GOOR SNVandINDEL Difficult-to-Map Regions 1298 728 0.97072829 0.950080812 0.992296858 14470 276021 2137 275657 0GOOR PACBIO NA 0GOOR SNVandINDEL MHC 506 61 0.9706631 0.947102589 0.995426642 1218 21802 91 21746 BARQS ILLUMINA NA BARQS INDEL All Benchmark Regions 1919 6054 0.974985842 0.981356577 0.968698075 9138 491634 15612 492225 BARQS ILLUMINA NA BARQS INDEL Difficult-to-Map Regions 130 253 0.859684307 0.938448748 0.793131862 849 12986 3411 13080 BARQS ILLUMINA NA BARQS INDEL MHC 52 22 0.941063069 0.939762618 0.942377052 102 1644 91 1594 BARQS ILLUMINA NA BARQS SNP All Benchmark Regions 6987 3980 0.986938115 0.99037993 0.983519956 31618 3293444 55091 3288421 BARQS ILLUMINA NA BARQS SNP Difficult-to-Map Regions 1155 2474 0.875641372 0.947185448 0.814146461 11876 212990 48563 212742 BARQS ILLUMINA NA BARQS SNP MHC 429 101 0.956848296 0.955493947 0.958209434 897 19319 834 19311 BARQS ILLUMINA NA BARQS SNVandINDEL All Benchmark Regions 8917 10035 0.9853665 0.989197789 0.981564905 40769 3785079 70891 3780648 BARQS ILLUMINA NA BARQS SNVandINDEL Difficult-to-Map Regions 1285 2728 0.874701781 0.94667718 0.812897764 12728 225977 51975 225822 BARQS ILLUMINA NA BARQS SNVandINDEL MHC 481 123 0.955600692 0.954219944 0.956987402 1001 20963 927 20906 Wasai Technology ILLUMINA NA Wasai Technology INDEL All Benchmark Regions 318 2546 0.981986997 0.991615998 0.972543497 4356 515228 13951 494178 Wasai Technology ILLUMINA NA Wasai Technology INDEL Difficult-to-Map Regions 149 267 0.882067148 0.912522491 0.853580018 1369 14286 2414 14075 Wasai Technology ILLUMINA NA Wasai Technology INDEL MHC 3 17 0.013890766 0.367665505 0.007092695 22 13 1679 12 Wasai Technology ILLUMINA NA Wasai Technology SNP All Benchmark Regions 2515 6603 0.979766496 0.990072492 0.969673499 32515 3243063 101397 3242124 Wasai Technology ILLUMINA NA Wasai Technology SNP Difficult-to-Map Regions 1897 4274 0.886173305 0.906253234 0.866963871 23431 226553 34760 226543 Wasai Technology ILLUMINA NA Wasai Technology SNP MHC 44 140 0.023043199 0.52909996 0.011793909 210 238 19906 238 Wasai Technology ILLUMINA NA Wasai Technology SNVandINDEL All Benchmark Regions 2835 9149 0.980063646 0.990283929 0.970052168 36872 3758293 115349 3736304 Wasai Technology ILLUMINA NA Wasai Technology SNVandINDEL Difficult-to-Map Regions 2048 4542 0.885934278 0.906622044 0.866169579 24801 240839 37174 240619 Wasai Technology ILLUMINA NA Wasai Technology SNVandINDEL MHC 48 157 0.022340487 0.517250424 0.011432581 233 251 21586 250 TryHard ILLUMINA NA bwamem-deepvariant INDEL All Benchmark Regions 252 2600 0.990076471 0.993911997 0.986271418 3200 522518 6973 501153 TryHard ILLUMINA NA bwamem-deepvariant INDEL Difficult-to-Map Regions 48 137 0.934560791 0.970115 0.901520732 464 15078 1624 14866 TryHard ILLUMINA NA bwamem-deepvariant INDEL MHC 9 11 0.956403451 0.985898965 0.928785137 23 1643 112 1571 TryHard ILLUMINA NA bwamem-deepvariant SNP All Benchmark Regions 625 2875 0.994568986 0.9974075 0.991745934 8622 3317522 27571 3315924 TryHard ILLUMINA NA bwamem-deepvariant SNP Difficult-to-Map Regions 475 1951 0.939364543 0.971602 0.909198341 6946 237641 23722 237580 TryHard ILLUMINA NA bwamem-deepvariant SNP MHC 42 91 0.955350256 0.991310854 0.922127593 161 18564 1437 18584 TryHard ILLUMINA NA bwamem-deepvariant SNVandINDEL All Benchmark Regions 877 5475 0.993968238 0.996930426 0.991023638 11823 3840043 34544 3817079 TryHard ILLUMINA NA bwamem-deepvariant SNVandINDEL Difficult-to-Map Regions 524 2088 0.939079624 0.971513071 0.908742535 7410 252720 25346 252446 TryHard ILLUMINA NA bwamem-deepvariant SNVandINDEL MHC 51 103 0.95542593 0.990869185 0.922645916 185 20207 1549 20156 TryHard MULTI ILLUMINAPACBIO Winnowmap-bwamem-deepvariant INDEL All Benchmark Regions 4236 2707 0.987305463 0.985610985 0.98900543 7735 529881 5583 502543 TryHard MULTI ILLUMINAPACBIO Winnowmap-bwamem-deepvariant INDEL Difficult-to-Map Regions 252 147 0.961192947 0.956393437 0.966041457 749 16438 560 15930 TryHard MULTI ILLUMINAPACBIO Winnowmap-bwamem-deepvariant INDEL MHC 87 12 0.93987412 0.942576975 0.937354115 102 1682 96 1586 TryHard MULTI ILLUMINAPACBIO Winnowmap-bwamem-deepvariant SNP All Benchmark Regions 2984 861 0.997680999 0.996861999 0.998500994 10508 3338299 5000 3338509 TryHard MULTI ILLUMINAPACBIO Winnowmap-bwamem-deepvariant SNP Difficult-to-Map Regions 671 362 0.981496369 0.97530344 0.987768768 6535 258117 3191 258111 TryHard MULTI ILLUMINAPACBIO Winnowmap-bwamem-deepvariant SNP MHC 78 41 0.972161062 0.991296922 0.953869277 167 19197 805 19224 TryHard MULTI ILLUMINAPACBIO Winnowmap-bwamem-deepvariant SNVandINDEL All Benchmark Regions 7220 3568 0.996275786 0.995305473 0.997247998 18245 3868182 10585 3841053 TryHard MULTI ILLUMINAPACBIO Winnowmap-bwamem-deepvariant SNVandINDEL Difficult-to-Map Regions 923 509 0.980276099 0.974150329 0.986479423 7285 274556 3752 274042 TryHard MULTI ILLUMINAPACBIO Winnowmap-bwamem-deepvariant SNVandINDEL MHC 165 53 0.969515717 0.987185661 0.952589746 270 20880 902 20810 TryHard PACBIO NA winnowmap-deepvariant INDEL All Benchmark Regions 2618 4226 0.98585626 0.98628884 0.985423164 7354 529433 7395 500722 TryHard PACBIO NA winnowmap-deepvariant INDEL Difficult-to-Map Regions 74 43 0.987297998 0.987816995 0.986779478 208 16864 218 16272 TryHard PACBIO NA winnowmap-deepvariant INDEL MHC 23 12 0.958867699 0.97888255 0.939705791 36 1713 97 1590 TryHard PACBIO NA winnowmap-deepvariant SNP All Benchmark Regions 712 966 0.998501999 0.998875 0.998129495 3759 3336911 6244 3337268 TryHard PACBIO NA winnowmap-deepvariant SNP Difficult-to-Map Regions 102 330 0.989881435 0.993457498 0.986330697 1697 257731 3566 257736 TryHard PACBIO NA winnowmap-deepvariant SNP MHC 26 37 0.972450224 0.99526279 0.950746681 88 19112 906 19161 TryHard PACBIO NA winnowmap-deepvariant SNVandINDEL All Benchmark Regions 3330 5192 0.99679252 0.997132045 0.99645323 11117 3866345 13640 3837991 TryHard PACBIO NA winnowmap-deepvariant SNVandINDEL Difficult-to-Map Regions 176 373 0.989722037 0.99310949 0.986357777 1905 274596 3784 274009 TryHard PACBIO NA winnowmap-deepvariant SNVandINDEL MHC 49 51 0.971350993 0.993893842 0.94989249 124 20825 1004 20751 H9OJ3 ILLUMINA NA H9OJ3 INDEL All Benchmark Regions 253 31817 0.810871683 0.918869966 0.725590828 32530 368432 139433 368694 H9OJ3 ILLUMINA NA H9OJ3 INDEL Difficult-to-Map Regions 77 534 0.690885762 0.902001418 0.559851776 1002 9222 7258 9232 H9OJ3 ILLUMINA NA H9OJ3 INDEL MHC 4 61 0.758573227 0.939317516 0.636224578 69 1076 615 1076 H9OJ3 ILLUMINA NA H9OJ3 SNP All Benchmark Regions 1092 22935 0.942478394 0.990123971 0.899208291 29988 3007200 336992 3006523 H9OJ3 ILLUMINA NA H9OJ3 SNP Difficult-to-Map Regions 817 3381 0.750472768 0.944142575 0.622733234 9627 162740 98581 162724 H9OJ3 ILLUMINA NA H9OJ3 SNP MHC 37 294 0.798710756 0.973122662 0.677334997 375 13655 6498 13651 H9OJ3 ILLUMINA NA H9OJ3 SNVandINDEL All Benchmark Regions 1345 54759 0.926063141 0.981813955 0.876303667 62523 3375633 476425 3375217 H9OJ3 ILLUMINA NA H9OJ3 SNVandINDEL Difficult-to-Map Regions 895 3915 0.747014135 0.941782841 0.618999904 10629 171962 105840 171956 H9OJ3 ILLUMINA NA H9OJ3 SNVandINDEL MHC 42 356 0.795634168 0.970569754 0.674150522 445 14731 7113 14727 Genomics Division at ITER ILLUMINA NA ITER (v1) - Illumina INDEL All Benchmark Regions 499 2527 0.978953215 0.9923125 0.965949367 3965 511826 17285 490827 Genomics Division at ITER ILLUMINA NA ITER (v1) - Illumina INDEL Difficult-to-Map Regions 78 147 0.84626672 0.953439806 0.760753904 622 12751 3945 12545 Genomics Division at ITER ILLUMINA NA ITER (v1) - Illumina INDEL MHC 3 17 0.010370073 0.3011696 0.005285769 21 9 1682 9 Genomics Division at ITER ILLUMINA NA ITER (v1) - Illumina SNP All Benchmark Regions 1535 1522 0.972782348 0.995780437 0.950823026 13427 3180030 164357 3179098 Genomics Division at ITER ILLUMINA NA ITER (v1) - Illumina SNP Difficult-to-Map Regions 467 413 0.770171732 0.968868308 0.639237694 5319 167047 94085 167037 Genomics Division at ITER ILLUMINA NA ITER (v1) - Illumina SNP MHC 3 40 0.008052021 0.620455962 0.004054873 45 82 20070 82 Genomics Division at ITER ILLUMINA NA ITER (v1) - Illumina SNVandINDEL All Benchmark Regions 2036 4049 0.973595129 0.995298522 0.952818784 17401 3691859 181644 3669927 Genomics Division at ITER ILLUMINA NA ITER (v1) - Illumina SNVandINDEL Difficult-to-Map Regions 551 563 0.775051926 0.96774271 0.6464715 5954 179803 98032 179588 Genomics Division at ITER ILLUMINA NA ITER (v1) - Illumina SNVandINDEL MHC 6 57 0.008271426 0.564239949 0.004169365 67 91 21751 91 Genomics Division at ITER ILLUMINA NA ITER (v2) - Illumina filtered INDEL All Benchmark Regions 222 2292 0.975079254 0.994258498 0.956626654 2928 507070 22029 486090 Genomics Division at ITER ILLUMINA NA ITER (v2) - Illumina filtered INDEL Difficult-to-Map Regions 25 35 0.722909472 0.981590752 0.572133951 179 9628 7055 9434 Genomics Division at ITER ILLUMINA NA ITER (v2) - Illumina filtered INDEL MHC 0 0 0.004078527 0.603022388 0.002047393 0 3 1689 3 Genomics Division at ITER ILLUMINA NA ITER (v2) - Illumina filtered SNP All Benchmark Regions 612 1342 0.970000999 0.997755499 0.943749494 7099 3156376 188076 3155445 Genomics Division at ITER ILLUMINA NA ITER (v2) - Illumina filtered SNP Difficult-to-Map Regions 232 295 0.712104099 0.978492604 0.559727847 3212 146269 115041 146260 Genomics Division at ITER ILLUMINA NA ITER (v2) - Illumina filtered SNP MHC 2 27 0.006560098 0.642416142 0.00329927 31 66 20085 66 Genomics Division at ITER ILLUMINA NA ITER (v2) - Illumina filtered SNVandINDEL All Benchmark Regions 835 3634 0.970668143 0.997270164 0.945448479 10028 3663452 210111 3641539 Genomics Division at ITER ILLUMINA NA ITER (v2) - Illumina filtered SNVandINDEL Difficult-to-Map Regions 258 331 0.712751691 0.978680882 0.560465608 3394 155898 122096 155696 Genomics Division at ITER ILLUMINA NA ITER (v2) - Illumina filtered SNVandINDEL MHC 2 28 0.006369691 0.640125448 0.003202668 32 70 21774 70 Genomics Division at ITER MULTI ILLUMINAPACBIOONT ITER (v3) - Illumina + PacBio + ONT INDEL All Benchmark Regions 1042 2515 0.978237707 0.991283 0.965531863 4496 511299 17497 490616 Genomics Division at ITER MULTI ILLUMINAPACBIOONT ITER (v3) - Illumina + PacBio + ONT INDEL Difficult-to-Map Regions 124 144 0.845532797 0.950224701 0.761620053 665 12708 3933 12566 Genomics Division at ITER MULTI ILLUMINAPACBIOONT ITER (v3) - Illumina + PacBio + ONT INDEL MHC 3 17 0.010370073 0.3011696 0.005285769 21 9 1682 9 Genomics Division at ITER MULTI ILLUMINAPACBIOONT ITER (v3) - Illumina + PacBio + ONT SNP All Benchmark Regions 26837 5625 0.981110972 0.981098229 0.981124465 63175 3281592 63106 3280409 Genomics Division at ITER MULTI ILLUMINAPACBIOONT ITER (v3) - Illumina + PacBio + ONT SNP Difficult-to-Map Regions 1835 3222 0.927499984 0.934276766 0.92082215 16930 240708 20688 240617 Genomics Division at ITER MULTI ILLUMINAPACBIOONT ITER (v3) - Illumina + PacBio + ONT SNP MHC 25 507 0.079107701 0.592812312 0.042381617 578 854 19295 854 Genomics Division at ITER MULTI ILLUMINAPACBIOONT ITER (v3) - Illumina + PacBio + ONT SNVandINDEL All Benchmark Regions 27880 8140 0.980760402 0.982459298 0.97906765 67674 3792896 80608 3771029 Genomics Division at ITER MULTI ILLUMINAPACBIOONT ITER (v3) - Illumina + PacBio + ONT SNVandINDEL Difficult-to-Map Regions 1961 3366 0.923061865 0.935062751 0.911366137 17597 253416 24621 253183 Genomics Division at ITER MULTI ILLUMINAPACBIOONT ITER (v3) - Illumina + PacBio + ONT SNVandINDEL MHC 29 524 0.074191282 0.586868565 0.039598673 600 865 20977 865 Genomics Division at ITER MULTI ILLUMINAPACBIOONT ITER (v4) - Illumina + PacBio + ONT filtered INDEL All Benchmark Regions 1020 2514 0.978258203 0.9913275 0.96552936 4473 511323 17499 490615 Genomics Division at ITER MULTI ILLUMINAPACBIOONT ITER (v4) - Illumina + PacBio + ONT filtered INDEL Difficult-to-Map Regions 123 145 0.845497298 0.950262299 0.761538975 664 12709 3933 12562 Genomics Division at ITER MULTI ILLUMINAPACBIOONT ITER (v4) - Illumina + PacBio + ONT filtered INDEL MHC 3 17 0.010370073 0.3011696 0.005285769 21 9 1682 9 Genomics Division at ITER MULTI ILLUMINAPACBIOONT ITER (v4) - Illumina + PacBio + ONT filtered SNP All Benchmark Regions 15276 4809 0.9832765 0.989532478 0.977097977 34563 3268090 76570 3266948 Genomics Division at ITER MULTI ILLUMINAPACBIOONT ITER (v4) - Illumina + PacBio + ONT filtered SNP Difficult-to-Map Regions 1194 2898 0.930263324 0.954190498 0.907506907 11389 237226 24167 237138 Genomics Division at ITER MULTI ILLUMINAPACBIOONT ITER (v4) - Illumina + PacBio + ONT filtered SNP MHC 5 237 0.043536955 0.647701925 0.022525411 247 454 19700 454 Genomics Division at ITER MULTI ILLUMINAPACBIOONT ITER (v4) - Illumina + PacBio + ONT filtered SNVandINDEL All Benchmark Regions 16296 7324 0.982622517 0.98977508 0.975572595 39037 3779420 94086 3757567 Genomics Division at ITER MULTI ILLUMINAPACBIOONT ITER (v4) - Illumina + PacBio + ONT filtered SNVandINDEL Difficult-to-Map Regions 1319 3043 0.925593051 0.95398949 0.898838433 12054 249935 28102 249700 Genomics Division at ITER MULTI ILLUMINAPACBIOONT ITER (v4) - Illumina + PacBio + ONT filtered SNVandINDEL MHC 8 255 0.041132627 0.632685001 0.021257405 269 464 21381 464 Sentieon MULTI ILLUMINAPACBIO Combination of Illumina and PacBio HIFI submission INDEL All Benchmark Regions 298 827 0.997514 0.997390498 0.997636999 1383 528737 1201 506928 Sentieon MULTI ILLUMINAPACBIO Combination of Illumina and PacBio HIFI submission INDEL Difficult-to-Map Regions 24 85 0.988107652 0.988984115 0.987232687 183 16523 210 16279 Sentieon MULTI ILLUMINAPACBIO Combination of Illumina and PacBio HIFI submission INDEL MHC 12 10 0.984985008 0.9873077 0.982683803 24 1870 28 1663 Sentieon MULTI ILLUMINAPACBIO Combination of Illumina and PacBio HIFI submission SNP All Benchmark Regions 246 749 0.999205999 0.999192999 0.9992195 2694 3341715 2608 3340912 Sentieon MULTI ILLUMINAPACBIO Combination of Illumina and PacBio HIFI submission SNP Difficult-to-Map Regions 142 630 0.991676849 0.99226591 0.99108827 2015 258972 2322 258978 Sentieon MULTI ILLUMINAPACBIO Combination of Illumina and PacBio HIFI submission SNP MHC 9 20 0.995787193 0.998094932 0.993492643 37 19839 112 20022 Sentieon MULTI ILLUMINAPACBIO Combination of Illumina and PacBio HIFI submission SNVandINDEL All Benchmark Regions 544 1577 0.998978575 0.99894639 0.999010763 4078 3870455 3810 3847842 Sentieon MULTI ILLUMINAPACBIO Combination of Illumina and PacBio HIFI submission SNVandINDEL Difficult-to-Map Regions 166 715 0.991463577 0.992068336 0.990859569 2199 275495 2532 275258 Sentieon MULTI ILLUMINAPACBIO Combination of Illumina and PacBio HIFI submission SNVandINDEL MHC 22 31 0.99489905 0.997156432 0.992654648 62 21708 140 21685 Sentieon MULTI ILLUMINAPACBIO Combination of Illumina and PacBio HIFI submission Model2 INDEL All Benchmark Regions 270 793 0.997556 0.997530496 0.9975815 1308 528708 1229 506900 Sentieon MULTI ILLUMINAPACBIO Combination of Illumina and PacBio HIFI submission Model2 INDEL Difficult-to-Map Regions 23 81 0.987345469 0.989377235 0.985322158 176 16491 242 16248 Sentieon MULTI ILLUMINAPACBIO Combination of Illumina and PacBio HIFI submission Model2 INDEL MHC 11 12 0.984505338 0.987254662 0.981779671 24 1862 30 1661 Sentieon MULTI ILLUMINAPACBIO Combination of Illumina and PacBio HIFI submission Model2 SNP All Benchmark Regions 233 720 0.999065 0.999213999 0.9989155 2623 3340703 3625 3339896 Sentieon MULTI ILLUMINAPACBIO Combination of Illumina and PacBio HIFI submission Model2 SNP Difficult-to-Map Regions 120 606 0.990097852 0.992762394 0.987447803 1877 258020 3276 258027 Sentieon MULTI ILLUMINAPACBIO Combination of Illumina and PacBio HIFI submission Model2 SNP MHC 8 19 0.994153937 0.998236975 0.990108342 35 19774 180 19954 Sentieon MULTI ILLUMINAPACBIO Combination of Illumina and PacBio HIFI submission Model2 SNVandINDEL All Benchmark Regions 504 1514 0.998861728 0.998983748 0.998739739 3931 3869413 4854 3846798 Sentieon MULTI ILLUMINAPACBIO Combination of Illumina and PacBio HIFI submission Model2 SNVandINDEL Difficult-to-Map Regions 144 687 0.989932859 0.992557954 0.987321618 2053 274512 3518 274275 Sentieon MULTI ILLUMINAPACBIO Combination of Illumina and PacBio HIFI submission Model2 SNVandINDEL MHC 20 31 0.99335526 0.997282463 0.989463243 59 21637 210 21615 Sentieon MULTI ILLUMINAPACBIOONT "Combination of Illumina, PacBio HIFI, and Oxford Nanopore submission" INDEL All Benchmark Regions 294 821 0.997536 0.997407999 0.997663 1373 528555 1187 506942 Sentieon MULTI ILLUMINAPACBIOONT "Combination of Illumina, PacBio HIFI, and Oxford Nanopore submission" INDEL Difficult-to-Map Regions 23 85 0.988102178 0.989003144 0.987202211 183 16507 211 16279 Sentieon MULTI ILLUMINAPACBIOONT "Combination of Illumina, PacBio HIFI, and Oxford Nanopore submission" INDEL MHC 8 4 0.991062807 0.991505143 0.990622453 14 1687 15 1676 Sentieon MULTI ILLUMINAPACBIOONT "Combination of Illumina, PacBio HIFI, and Oxford Nanopore submission" SNP All Benchmark Regions 250 742 0.999222499 0.999194999 0.999249999 2688 3342088 2506 3341012 Sentieon MULTI ILLUMINAPACBIOONT "Combination of Illumina, PacBio HIFI, and Oxford Nanopore submission" SNP Difficult-to-Map Regions 142 630 0.991685351 0.992277905 0.991094785 2012 258993 2321 258980 Sentieon MULTI ILLUMINAPACBIOONT "Combination of Illumina, PacBio HIFI, and Oxford Nanopore submission" SNP MHC 11 13 0.998441789 0.998453881 0.998429171 30 20211 27 20122 Sentieon MULTI ILLUMINAPACBIOONT "Combination of Illumina, PacBio HIFI, and Oxford Nanopore submission" SNVandINDEL All Benchmark Regions 544 1563 0.998995435 0.998950574 0.9990403 4062 3870646 3695 3847956 Sentieon MULTI ILLUMINAPACBIOONT "Combination of Illumina, PacBio HIFI, and Oxford Nanopore submission" SNVandINDEL Difficult-to-Map Regions 165 716 0.99147176 0.992080897 0.99086338 2195 275500 2531 275259 Sentieon MULTI ILLUMINAPACBIOONT "Combination of Illumina, PacBio HIFI, and Oxford Nanopore submission" SNVandINDEL MHC 21 17 0.997869585 0.99791522 0.997824008 44 21898 42 21798 Sentieon MULTI ILLUMINAPACBIOONT "Combination of Illumina, PacBio HIFI, and Oxford Nanopore submission Model2" INDEL All Benchmark Regions 268 786 0.9975795 0.997547997 0.997611 1299 528533 1214 506915 Sentieon MULTI ILLUMINAPACBIOONT "Combination of Illumina, PacBio HIFI, and Oxford Nanopore submission Model2" INDEL Difficult-to-Map Regions 21 82 0.98737003 0.989456346 0.985292183 175 16475 242 16247 Sentieon MULTI ILLUMINAPACBIOONT "Combination of Illumina, PacBio HIFI, and Oxford Nanopore submission Model2" INDEL MHC 8 4 0.991062807 0.991505143 0.990622453 14 1687 15 1676 Sentieon MULTI ILLUMINAPACBIOONT "Combination of Illumina, PacBio HIFI, and Oxford Nanopore submission Model2" SNP All Benchmark Regions 238 714 0.999090499 0.999215499 0.998966499 2619 3341141 3454 3340065 Sentieon MULTI ILLUMINAPACBIOONT "Combination of Illumina, PacBio HIFI, and Oxford Nanopore submission Model2" SNP Difficult-to-Map Regions 120 606 0.990111855 0.992768391 0.987469314 1876 258045 3271 258032 Sentieon MULTI ILLUMINAPACBIOONT "Combination of Illumina, PacBio HIFI, and Oxford Nanopore submission Model2" SNP MHC 11 13 0.998441789 0.998453881 0.998429171 30 20211 27 20122 Sentieon MULTI ILLUMINAPACBIOONT "Combination of Illumina, PacBio HIFI, and Oxford Nanopore submission Model2" SNVandINDEL All Benchmark Regions 506 1500 0.998887296 0.998987179 0.998787433 3918 3869676 4669 3846982 Sentieon MULTI ILLUMINAPACBIOONT "Combination of Illumina, PacBio HIFI, and Oxford Nanopore submission Model2" SNVandINDEL Difficult-to-Map Regions 142 688 0.98994747 0.992568961 0.987339793 2050 274520 3513 274280 Sentieon MULTI ILLUMINAPACBIOONT "Combination of Illumina, PacBio HIFI, and Oxford Nanopore submission Model2" SNVandINDEL MHC 21 17 0.997869585 0.99791522 0.997824008 44 21898 42 21798 Sentieon ILLUMINA NA Illumina short-read-data-only submission INDEL All Benchmark Regions 195 1071 0.995750998 0.996969 0.99453549 1602 526973 2776 505353 Sentieon ILLUMINA NA Illumina short-read-data-only submission INDEL Difficult-to-Map Regions 35 126 0.945674879 0.976463325 0.916769509 370 15351 1372 15117 Sentieon ILLUMINA NA Illumina short-read-data-only submission INDEL MHC 12 7 0.982261092 0.987477407 0.977116071 23 1854 36 1653 Sentieon ILLUMINA NA Illumina short-read-data-only submission SNP All Benchmark Regions 579 1525 0.995924998 0.998283999 0.993575985 5708 3322859 21469 3322044 Sentieon ILLUMINA NA Illumina short-read-data-only submission SNP Difficult-to-Map Regions 445 1385 0.949949265 0.980527959 0.921220767 4780 240721 20582 240721 Sentieon ILLUMINA NA Illumina short-read-data-only submission SNP MHC 28 63 0.986758986 0.994418061 0.979220732 108 19561 415 19735 Sentieon ILLUMINA NA Illumina short-read-data-only submission SNVandINDEL All Benchmark Regions 774 2596 0.995898712 0.998104134 0.993703027 7310 3849834 24245 3827399 Sentieon ILLUMINA NA Illumina short-read-data-only submission SNVandINDEL Difficult-to-Map Regions 481 1512 0.949693644 0.980283105 0.920956381 5150 256073 21954 255839 Sentieon ILLUMINA NA Illumina short-read-data-only submission SNVandINDEL MHC 40 71 0.986377851 0.993813363 0.979057127 132 21415 452 21388 Sentieon PACBIO NA PacBio HIFI only submission INDEL All Benchmark Regions 1565 4721 0.98063347 0.984819499 0.976482407 7963 516576 11948 496179 Sentieon PACBIO NA PacBio HIFI only submission INDEL Difficult-to-Map Regions 22 47 0.989120888 0.992120946 0.986139827 130 16503 228 16261 Sentieon PACBIO NA PacBio HIFI only submission INDEL MHC 12 10 0.984985008 0.9873077 0.982683803 24 1870 28 1663 Sentieon PACBIO NA PacBio HIFI only submission SNP All Benchmark Regions 257 580 0.999214 0.999300999 0.999127 2332 3341349 2919 3340602 Sentieon PACBIO NA PacBio HIFI only submission SNP Difficult-to-Map Regions 113 335 0.993155333 0.994608907 0.991705739 1400 259132 2159 259139 Sentieon PACBIO NA PacBio HIFI only submission SNP MHC 9 20 0.995787193 0.998094932 0.993492643 37 19839 112 20022 Sentieon PACBIO NA PacBio HIFI only submission SNVandINDEL All Benchmark Regions 1822 5302 0.996738037 0.997337324 0.996139473 10299 3857927 14867 3836783 Sentieon PACBIO NA PacBio HIFI only submission SNVandINDEL Difficult-to-Map Regions 136 383 0.992915047 0.994459435 0.991375469 1530 275636 2387 275401 Sentieon PACBIO NA PacBio HIFI only submission SNVandINDEL MHC 22 31 0.99489905 0.997156432 0.992654648 62 21708 140 21685 Sentieon PACBIO NA PacBio HIFI only submission Model2 INDEL All Benchmark Regions 1551 4686 0.980702477 0.984964999 0.976477426 7885 516568 11951 496177 Sentieon PACBIO NA PacBio HIFI only submission Model2 INDEL Difficult-to-Map Regions 19 42 0.988636278 0.993330414 0.98398663 109 16468 263 16226 Sentieon PACBIO NA PacBio HIFI only submission Model2 INDEL MHC 11 12 0.984505338 0.987254662 0.981779671 24 1862 30 1661 Sentieon PACBIO NA PacBio HIFI only submission Model2 SNP All Benchmark Regions 215 538 0.9990445 0.999406499 0.9986815 1979 3339864 4408 3339113 Sentieon PACBIO NA PacBio HIFI only submission Model2 SNP Difficult-to-Map Regions 72 304 0.990983872 0.995779447 0.986234268 1089 257703 3593 257710 Sentieon PACBIO NA PacBio HIFI only submission Model2 SNP MHC 8 19 0.994153937 0.998236975 0.990108342 35 19774 180 19954 Sentieon PACBIO NA PacBio HIFI only submission Model2 SNVandINDEL All Benchmark Regions 1766 5224 0.996599286 0.997447766 0.995752251 9867 3856434 16359 3835292 Sentieon PACBIO NA PacBio HIFI only submission Model2 SNVandINDEL Difficult-to-Map Regions 92 347 0.990843161 0.995631616 0.986100575 1199 274171 3856 273936 Sentieon PACBIO NA PacBio HIFI only submission Model2 SNVandINDEL MHC 20 31 0.99335526 0.997282463 0.989463243 59 21637 210 21615 ISKOS ILLUMINA NA ISKOS INDEL All Benchmark Regions 203 1189 0.950943442 0.994947998 0.91066683 2405 473599 45392 462736 ISKOS ILLUMINA NA ISKOS INDEL Difficult-to-Map Regions 79 150 0.879938336 0.934017674 0.831779012 976 13822 2774 13716 ISKOS ILLUMINA NA ISKOS INDEL MHC 51 13 0.890381177 0.923707299 0.859381995 122 1485 238 1454 ISKOS ILLUMINA NA ISKOS SNP All Benchmark Regions 1568 2252 0.991084495 0.995171 0.987030486 16012 3300118 43360 3300158 ISKOS ILLUMINA NA ISKOS SNP Difficult-to-Map Regions 835 1536 0.903855042 0.95183676 0.860479048 11376 224847 36454 224849 ISKOS ILLUMINA NA ISKOS SNP MHC 576 119 0.946154321 0.936990048 0.955499513 1292 19228 894 19257 ISKOS ILLUMINA NA ISKOS SNVandINDEL All Benchmark Regions 1772 3443 0.985965864 0.995143261 0.976956203 18417 3773718 88752 3762896 ISKOS ILLUMINA NA ISKOS SNVandINDEL Difficult-to-Map Regions 915 1687 0.902441249 0.950786279 0.858775146 12352 238670 39228 238565 ISKOS ILLUMINA NA ISKOS SNVandINDEL MHC 628 132 0.94200137 0.936025035 0.948054511 1414 20713 1133 20711 The UCSC CGL and Google Health PACBIO NA Margin-PEPPER-DeepVariant (PacBIO) INDEL All Benchmark Regions 1430 4670 0.983675948 0.986673467 0.980695926 6990 517650 9807 498320 The UCSC CGL and Google Health PACBIO NA Margin-PEPPER-DeepVariant (PacBIO) INDEL Difficult-to-Map Regions 20 42 0.972309059 0.97878535 0.965920189 345 16058 562 15928 The UCSC CGL and Google Health PACBIO NA Margin-PEPPER-DeepVariant (PacBIO) INDEL MHC 15 12 0.973224419 0.980500844 0.966069773 32 1718 57 1635 The UCSC CGL and Google Health PACBIO NA Margin-PEPPER-DeepVariant (PacBIO) SNP All Benchmark Regions 692 347 0.997543493 0.998542951 0.996546498 4751 3334762 11544 3331974 The UCSC CGL and Google Health PACBIO NA Margin-PEPPER-DeepVariant (PacBIO) SNP Difficult-to-Map Regions 282 147 0.974845682 0.985782786 0.964158539 3429 252138 9359 251941 The UCSC CGL and Google Health PACBIO NA Margin-PEPPER-DeepVariant (PacBIO) SNP MHC 49 18 0.989277716 0.992735282 0.985844142 145 19850 285 19868 The UCSC CGL and Google Health PACBIO NA Margin-PEPPER-DeepVariant (PacBIO) SNVandINDEL All Benchmark Regions 2125 5018 0.995691856 0.996931559 0.994455257 11796 3852413 21356 3830296 The UCSC CGL and Google Health PACBIO NA Margin-PEPPER-DeepVariant (PacBIO) SNVandINDEL Difficult-to-Map Regions 303 189 0.974691714 0.98535549 0.96426374 3812 268196 9921 267870 The UCSC CGL and Google Health PACBIO NA Margin-PEPPER-DeepVariant (PacBIO) SNVandINDEL MHC 64 32 0.988015541 0.991747295 0.984311819 178 21568 342 21503 The UCSC CGL and Google Health ONT NA PEPPER-DeepVariant (ONT_9to6) INDEL All Benchmark Regions 20512 19296 0.728498349 0.863327264 0.630098709 52012 328621 187924 320172 The UCSC CGL and Google Health ONT NA PEPPER-DeepVariant (ONT_9to6) INDEL Difficult-to-Map Regions 215 215 0.892170901 0.954081668 0.837807935 670 13932 2673 13815 The UCSC CGL and Google Health ONT NA PEPPER-DeepVariant (ONT_9to6) INDEL MHC 60 30 0.863966531 0.936336012 0.802003104 95 1404 334 1357 The UCSC CGL and Google Health ONT NA PEPPER-DeepVariant (ONT_9to6) SNP All Benchmark Regions 4440 1481 0.996450455 0.99731847 0.995583936 8915 3329291 14716 3328757 The UCSC CGL and Google Health ONT NA PEPPER-DeepVariant (ONT_9to6) SNP Difficult-to-Map Regions 241 482 0.987859057 0.990451873 0.985280708 2466 257540 3841 257460 The UCSC CGL and Google Health ONT NA PEPPER-DeepVariant (ONT_9to6) SNP MHC 30 17 0.973493351 0.997345958 0.950793749 51 19145 957 19162 The UCSC CGL and Google Health ONT NA PEPPER-DeepVariant (ONT_9to6) SNVandINDEL All Benchmark Regions 24952 20778 0.965146708 0.98360495 0.947368549 60971 3657918 202706 3648934 The UCSC CGL and Google Health ONT NA PEPPER-DeepVariant (ONT_9to6) SNVandINDEL Difficult-to-Map Regions 456 697 0.98248787 0.98851945 0.976529507 3141 271473 6519 271277 The UCSC CGL and Google Health ONT NA PEPPER-DeepVariant (ONT_9to6) SNVandINDEL MHC 90 47 0.965333896 0.992928155 0.939269308 145 20550 1295 20519 The UCSC CGL and Google Health ONT NA PEPPER-DeepVariant (ONT) INDEL All Benchmark Regions 22479 20981 0.725414114 0.855058796 0.629912498 55717 328735 188017 320077 The UCSC CGL and Google Health ONT NA PEPPER-DeepVariant (ONT) INDEL Difficult-to-Map Regions 225 233 0.891077881 0.95217231 0.837352933 699 13927 2681 13808 The UCSC CGL and Google Health ONT NA PEPPER-DeepVariant (ONT) INDEL MHC 63 32 0.861912261 0.933143698 0.80080522 100 1402 336 1355 The UCSC CGL and Google Health ONT NA PEPPER-DeepVariant (ONT) SNP All Benchmark Regions 4535 1616 0.996415454 0.997249969 0.995582437 9143 3329275 14722 3328751 The UCSC CGL and Google Health ONT NA PEPPER-DeepVariant (ONT) SNP Difficult-to-Map Regions 249 486 0.987837545 0.990405864 0.985282195 2477 257540 3840 257461 The UCSC CGL and Google Health ONT NA PEPPER-DeepVariant (ONT) SNP MHC 33 17 0.973352813 0.997188491 0.950668406 54 19142 961 19159 The UCSC CGL and Google Health ONT NA PEPPER-DeepVariant (ONT) SNVandINDEL All Benchmark Regions 27015 22598 0.964633487 0.982567488 0.947342519 64899 3658016 202806 3648834 The UCSC CGL and Google Health ONT NA PEPPER-DeepVariant (ONT) SNVandINDEL Difficult-to-Map Regions 474 719 0.982402083 0.988371694 0.976504203 3182 271468 6525 271270 The UCSC CGL and Google Health ONT NA PEPPER-DeepVariant (ONT) SNVandINDEL MHC 96 50 0.965040359 0.992539978 0.939061037 154 20544 1301 20514 The UCSC CGL and Google Health PACBIO NA PEPPER-DeepVariant (PacBIO) INDEL All Benchmark Regions 1445 4915 0.984640988 0.98644899 0.982839486 7124 518618 8719 499409 The UCSC CGL and Google Health PACBIO NA PEPPER-DeepVariant (PacBIO) INDEL Difficult-to-Map Regions 25 50 0.984531931 0.985259979 0.983806249 240 16350 267 16223 The UCSC CGL and Google Health PACBIO NA PEPPER-DeepVariant (PacBIO) INDEL MHC 9 11 0.977391731 0.986807015 0.968158553 23 1724 54 1638 The UCSC CGL and Google Health PACBIO NA PEPPER-DeepVariant (PacBIO) SNP All Benchmark Regions 542 630 0.9986225 0.999154497 0.998090997 2815 3339914 6377 3337139 The UCSC CGL and Google Health PACBIO NA PEPPER-DeepVariant (PacBIO) SNP Difficult-to-Map Regions 147 404 0.990104987 0.993186812 0.98704307 1763 258121 3377 257921 The UCSC CGL and Google Health PACBIO NA PEPPER-DeepVariant (PacBIO) SNP MHC 18 16 0.992795917 0.997800698 0.987841551 41 19888 243 19909 The UCSC CGL and Google Health PACBIO NA PEPPER-DeepVariant (PacBIO) SNVandINDEL All Benchmark Regions 1987 5546 0.996752932 0.997427684 0.996079097 9945 3858535 15101 3836550 The UCSC CGL and Google Health PACBIO NA PEPPER-DeepVariant (PacBIO) SNVandINDEL Difficult-to-Map Regions 173 454 0.989771314 0.992709441 0.986850961 2013 274471 3644 274144 The UCSC CGL and Google Health PACBIO NA PEPPER-DeepVariant (PacBIO) SNVandINDEL MHC 28 28 0.991587312 0.996914895 0.98631638 64 21612 298 21547 The UCSC CGL and Google Health MULTI PACBIOONT PEPPER-DeepVariant (PacBIO+ONT) INDEL All Benchmark Regions 1442 4855 0.984820961 0.986617465 0.983030957 7035 518784 8621 499507 The UCSC CGL and Google Health MULTI PACBIOONT PEPPER-DeepVariant (PacBIO+ONT) INDEL Difficult-to-Map Regions 25 51 0.984065833 0.986426767 0.981715999 224 16319 301 16188 The UCSC CGL and Google Health MULTI PACBIOONT PEPPER-DeepVariant (PacBIO+ONT) INDEL MHC 10 9 0.977048544 0.988252918 0.966095813 20 1719 57 1635 The UCSC CGL and Google Health MULTI PACBIOONT PEPPER-DeepVariant (PacBIO+ONT) SNP All Benchmark Regions 512 619 0.998709 0.999195998 0.998222999 2682 3340344 5940 3337579 The UCSC CGL and Google Health MULTI PACBIOONT PEPPER-DeepVariant (PacBIO+ONT) SNP Difficult-to-Map Regions 92 399 0.99071831 0.995860951 0.98562958 1068 257746 3748 257551 The UCSC CGL and Google Health MULTI PACBIOONT PEPPER-DeepVariant (PacBIO+ONT) SNP MHC 12 15 0.992231434 0.998156413 0.986375952 36 19858 274 19879 The UCSC CGL and Google Health MULTI PACBIOONT PEPPER-DeepVariant (PacBIO+ONT) SNVandINDEL All Benchmark Regions 1955 5477 0.996852048 0.997486333 0.996218571 9719 3859130 14565 3837088 The UCSC CGL and Google Health MULTI PACBIOONT PEPPER-DeepVariant (PacBIO+ONT) SNVandINDEL Difficult-to-Map Regions 117 450 0.990320722 0.99529368 0.985397272 1292 274066 4050 273740 The UCSC CGL and Google Health MULTI PACBIOONT PEPPER-DeepVariant (PacBIO+ONT) SNVandINDEL MHC 22 25 0.991043003 0.997360688 0.98480486 57 21577 332 21514 GENeTres ILLUMINA NA GENeTres AUTh Illumina ABD INDEL All Benchmark Regions 242 2657 0.989529458 0.99381999 0.985275406 3245 521948 7479 500647 GENeTres ILLUMINA NA GENeTres AUTh Illumina ABD INDEL Difficult-to-Map Regions 45 133 0.934372317 0.970869497 0.900520419 452 15064 1640 14850 GENeTres ILLUMINA NA GENeTres AUTh Illumina ABD INDEL MHC 7 13 0.952550294 0.986410928 0.921100409 22 1633 126 1558 GENeTres ILLUMINA NA GENeTres AUTh Illumina ABD SNP All Benchmark Regions 611 2908 0.994468485 0.997403 0.991551433 8636 3316873 28222 3315273 GENeTres ILLUMINA NA GENeTres AUTh Illumina ABD SNP Difficult-to-Map Regions 459 1935 0.938703428 0.971696997 0.907877563 6912 237293 24067 237234 GENeTres ILLUMINA NA GENeTres AUTh Illumina ABD SNP MHC 36 116 0.948314348 0.990286775 0.909974183 179 18313 1704 18339 GENeTres ILLUMINA NA GENeTres AUTh Illumina ABD SNVandINDEL All Benchmark Regions 854 5567 0.993809021 0.996914085 0.990723276 11883 3838823 35701 3815922 GENeTres ILLUMINA NA GENeTres AUTh Illumina ABD SNVandINDEL Difficult-to-Map Regions 505 2068 0.938446659 0.97164778 0.907440348 7364 252358 25707 252085 GENeTres ILLUMINA NA GENeTres AUTh Illumina ABD SNVandINDEL MHC 43 130 0.948640045 0.989968569 0.910838069 202 19947 1830 19898 GENeTres ILLUMINA NA GENeTres AUTh Illumina ABMD INDEL All Benchmark Regions 247 2478 0.990009968 0.994093495 0.985959419 3103 522342 7132 500995 GENeTres ILLUMINA NA GENeTres AUTh Illumina ABMD INDEL Difficult-to-Map Regions 45 142 0.933532255 0.968604304 0.900911964 488 15070 1634 14856 GENeTres ILLUMINA NA GENeTres AUTh Illumina ABMD INDEL MHC 9 12 0.953298033 0.984969863 0.92376199 25 1638 122 1563 GENeTres ILLUMINA NA GENeTres AUTh Illumina ABMD SNP All Benchmark Regions 640 3690 0.994286492 0.996966998 0.991620947 10090 3317103 27995 3315506 GENeTres ILLUMINA NA GENeTres AUTh Illumina ABMD SNP Difficult-to-Map Regions 482 2025 0.938093648 0.969178484 0.908941446 7555 237569 23790 237512 GENeTres ILLUMINA NA GENeTres AUTh Illumina ABMD SNP MHC 36 119 0.949102249 0.989859998 0.911776328 188 18350 1677 18376 GENeTres ILLUMINA NA GENeTres AUTh Illumina ABMD SNVandINDEL All Benchmark Regions 887 6170 0.993716196 0.99657481 0.99087397 13195 3839448 35126 3816502 GENeTres ILLUMINA NA GENeTres AUTh Illumina ABMD SNVandINDEL Difficult-to-Map Regions 528 2167 0.93782379 0.969144474 0.908465025 8043 252640 25423 252369 GENeTres ILLUMINA NA GENeTres AUTh Illumina ABMD SNVandINDEL MHC 45 132 0.949422905 0.989457413 0.912706153 213 19988 1798 19939 GENeTres ILLUMINA NA GENeTres AUTh Illumina BBDBM INDEL All Benchmark Regions 257 2462 0.990426479 0.994107999 0.986771433 3099 522810 6719 501403 GENeTres ILLUMINA NA GENeTres AUTh Illumina BBDBM INDEL Difficult-to-Map Regions 46 145 0.933172669 0.968426402 0.900395844 491 15059 1642 14847 GENeTres ILLUMINA NA GENeTres AUTh Illumina BBDBM INDEL MHC 7 12 0.953359338 0.986126866 0.922873383 23 1634 123 1561 GENeTres ILLUMINA NA GENeTres AUTh Illumina BBDBM SNP All Benchmark Regions 625 3690 0.994277991 0.996961498 0.991608947 10107 3317059 28035 3315458 GENeTres ILLUMINA NA GENeTres AUTh Illumina BBDBM SNP Difficult-to-Map Regions 476 2027 0.937983687 0.96909948 0.908805069 7574 237537 23826 237477 GENeTres ILLUMINA NA GENeTres AUTh Illumina BBDBM SNP MHC 38 122 0.948790161 0.98956499 0.911452595 193 18346 1683 18369 GENeTres ILLUMINA NA GENeTres AUTh Illumina BBDBM SNVandINDEL All Benchmark Regions 883 6153 0.993763442 0.996572069 0.990970637 13207 3839872 34754 3816862 GENeTres ILLUMINA NA GENeTres AUTh Illumina BBDBM SNVandINDEL Difficult-to-Map Regions 522 2173 0.937699122 0.969059202 0.908305922 8065 252597 25468 252325 GENeTres ILLUMINA NA GENeTres AUTh Illumina BBDBM SNVandINDEL MHC 46 134 0.949141966 0.989282712 0.912338643 216 19981 1806 19931 GENeTres ILLUMINA NA GENeTres AUTh Illumina BBTBD INDEL All Benchmark Regions 259 2580 0.990133468 0.993924994 0.986371424 3193 522578 6922 501199 GENeTres ILLUMINA NA GENeTres AUTh Illumina BBTBD INDEL Difficult-to-Map Regions 46 138 0.934126231 0.97005898 0.900759769 465 15065 1636 14853 GENeTres ILLUMINA NA GENeTres AUTh Illumina BBTBD INDEL MHC 8 13 0.952127436 0.985513364 0.921101417 24 1632 126 1558 GENeTres ILLUMINA NA GENeTres AUTh Illumina BBTBD SNP All Benchmark Regions 615 3273 0.994394988 0.997179999 0.991625938 9380 3317104 27974 3315515 GENeTres ILLUMINA NA GENeTres AUTh Illumina BBTBD SNP Difficult-to-Map Regions 464 1980 0.938359566 0.970277 0.908474882 7274 237451 23911 237391 GENeTres ILLUMINA NA GENeTres AUTh Illumina BBTBD SNP MHC 37 119 0.948657866 0.989925873 0.910901179 186 18335 1691 18358 GENeTres ILLUMINA NA GENeTres AUTh Illumina BBTBD SNVandINDEL All Benchmark Regions 875 5854 0.993825678 0.996735635 0.990932698 12575 3839685 34897 3816716 GENeTres ILLUMINA NA GENeTres AUTh Illumina BBTBD SNVandINDEL Difficult-to-Map Regions 511 2119 0.93810881 0.970264479 0.908016883 7739 252516 25548 252244 GENeTres ILLUMINA NA GENeTres AUTh Illumina BBTBD SNVandINDEL MHC 45 133 0.948922382 0.989564332 0.911693306 210 19967 1817 19917 Genetalks ILLUMINA NA Illumina-bwaalt-deepvariant(Genetalks) INDEL All Benchmark Regions 323 1227 0.994503 0.996131494 0.992880497 2042 526130 3617 504507 Genetalks ILLUMINA NA Illumina-bwaalt-deepvariant(Genetalks) INDEL Difficult-to-Map Regions 53 155 0.932707194 0.965540486 0.902033103 538 15088 1615 14874 Genetalks ILLUMINA NA Illumina-bwaalt-deepvariant(Genetalks) INDEL MHC 7 15 0.948850424 0.984247855 0.916078787 26 1624 135 1550 Genetalks ILLUMINA NA Illumina-bwaalt-deepvariant(Genetalks) SNP All Benchmark Regions 714 4070 0.994116995 0.996620995 0.991625458 11241 3317119 27983 3315514 Genetalks ILLUMINA NA Illumina-bwaalt-deepvariant(Genetalks) SNP Difficult-to-Map Regions 553 2178 0.937259843 0.966663461 0.909592624 8198 237743 23621 237683 Genetalks ILLUMINA NA Illumina-bwaalt-deepvariant(Genetalks) SNP MHC 39 123 0.946069699 0.989292995 0.906695994 197 18250 1772 18273 Genetalks ILLUMINA NA Illumina-bwaalt-deepvariant(Genetalks) SNVandINDEL All Benchmark Regions 1037 5297 0.994167045 0.996554342 0.991791192 13283 3843252 31601 3820023 Genetalks ILLUMINA NA Illumina-bwaalt-deepvariant(Genetalks) SNVandINDEL Difficult-to-Map Regions 607 2333 0.936990223 0.966596785 0.909144033 8737 252832 25237 252557 Genetalks ILLUMINA NA Illumina-bwaalt-deepvariant(Genetalks) SNVandINDEL MHC 46 139 0.946280342 0.988879799 0.907425306 223 19874 1908 19823 Genetalks MULTI ILLUMINAPACBIO Illumina-Pacbio-asmMHC v1(Genetalks) INDEL All Benchmark Regions 537 1136 0.9938505 0.996095495 0.991615999 2059 525348 4260 503869 Genetalks MULTI ILLUMINAPACBIO Illumina-Pacbio-asmMHC v1(Genetalks) INDEL Difficult-to-Map Regions 88 115 0.937927833 0.974461991 0.904034262 395 15091 1582 14907 Genetalks MULTI ILLUMINAPACBIO Illumina-Pacbio-asmMHC v1(Genetalks) INDEL MHC 26 10 0.979180115 0.970129771 0.988401619 53 1723 19 1672 Genetalks MULTI ILLUMINAPACBIO Illumina-Pacbio-asmMHC v1(Genetalks) SNP All Benchmark Regions 841 1241 0.998185498 0.998673997 0.997697998 4426 3337439 7694 3335823 Genetalks MULTI ILLUMINAPACBIO Illumina-Pacbio-asmMHC v1(Genetalks) SNP Difficult-to-Map Regions 161 379 0.987732194 0.993200417 0.982323838 1755 256788 4609 256688 Genetalks MULTI ILLUMINAPACBIO Illumina-Pacbio-asmMHC v1(Genetalks) SNP MHC 162 24 0.989532208 0.982314865 0.996856543 360 20092 49 20090 Genetalks MULTI ILLUMINAPACBIO Illumina-Pacbio-asmMHC v1(Genetalks) SNVandINDEL All Benchmark Regions 1377 2377 0.997608272 0.998322259 0.996895306 6485 3862790 11957 3839694 Genetalks MULTI ILLUMINAPACBIO Illumina-Pacbio-asmMHC v1(Genetalks) SNVandINDEL Difficult-to-Map Regions 249 494 0.984856537 0.992141487 0.977677894 2151 271880 6194 271596 Genetalks MULTI ILLUMINAPACBIO Illumina-Pacbio-asmMHC v1(Genetalks) SNVandINDEL MHC 189 34 0.988715658 0.981341141 0.996201863 413 21816 70 21763 Genetalks MULTI ILLUMINAPACBIO Illumina-Pacbio-asmMHC v2(Genetalks) INDEL All Benchmark Regions 785 1167 0.9941075 0.9955715 0.992648 2338 525709 3736 504393 Genetalks MULTI ILLUMINAPACBIO Illumina-Pacbio-asmMHC v2(Genetalks) INDEL Difficult-to-Map Regions 101 115 0.937480278 0.973495493 0.904034338 410 15077 1582 14907 Genetalks MULTI ILLUMINAPACBIO Illumina-Pacbio-asmMHC v2(Genetalks) INDEL MHC 26 10 0.979180115 0.970129771 0.988401619 53 1723 19 1672 Genetalks MULTI ILLUMINAPACBIO Illumina-Pacbio-asmMHC v2(Genetalks) SNP All Benchmark Regions 831 1253 0.998177997 0.998672497 0.997683497 4428 3337504 7741 3335776 Genetalks MULTI ILLUMINAPACBIO Illumina-Pacbio-asmMHC v2(Genetalks) SNP Difficult-to-Map Regions 158 381 0.987720188 0.993204412 0.982295836 1754 256803 4616 256680 Genetalks MULTI ILLUMINAPACBIO Illumina-Pacbio-asmMHC v2(Genetalks) SNP MHC 162 24 0.989532208 0.982314865 0.996856543 360 20092 49 20090 Genetalks MULTI ILLUMINAPACBIO Illumina-Pacbio-asmMHC v2(Genetalks) SNVandINDEL All Benchmark Regions 1617 2420 0.997634041 0.998249593 0.997019248 6769 3863215 11479 3840172 Genetalks MULTI ILLUMINAPACBIO Illumina-Pacbio-asmMHC v2(Genetalks) SNVandINDEL Difficult-to-Map Regions 259 496 0.984817864 0.992090857 0.97765084 2165 271881 6202 271588 Genetalks MULTI ILLUMINAPACBIO Illumina-Pacbio-asmMHC v2(Genetalks) SNVandINDEL MHC 189 34 0.988715658 0.981341141 0.996201863 413 21816 70 21763 Genetalks ILLUMINA NA Ilumina-bwa-dvnm(Genetalks) INDEL All Benchmark Regions 304 1139 0.994806999 0.996569499 0.99304999 1811 526134 3531 504598 Genetalks ILLUMINA NA Ilumina-bwa-dvnm(Genetalks) INDEL Difficult-to-Map Regions 48 115 0.939112333 0.977093498 0.903973837 354 15121 1583 14906 Genetalks ILLUMINA NA Ilumina-bwa-dvnm(Genetalks) INDEL MHC 6 17 0.953248883 0.983795481 0.924648983 26 1640 120 1564 Genetalks ILLUMINA NA Ilumina-bwa-dvnm(Genetalks) SNP All Benchmark Regions 621 2097 0.995132489 0.997903 0.992377449 6976 3319620 25464 3318035 Genetalks ILLUMINA NA Ilumina-bwa-dvnm(Genetalks) SNP Difficult-to-Map Regions 422 1767 0.943387663 0.977883492 0.911243459 5386 238167 23190 238114 Genetalks ILLUMINA NA Ilumina-bwa-dvnm(Genetalks) SNP MHC 31 120 0.958866986 0.991029803 0.928905701 168 18689 1314 18721 Genetalks ILLUMINA NA Ilumina-bwa-dvnm(Genetalks) SNVandINDEL All Benchmark Regions 925 3237 0.995086239 0.997720131 0.992466244 8787 3845757 28995 3822635 Genetalks ILLUMINA NA Ilumina-bwa-dvnm(Genetalks) SNVandINDEL Difficult-to-Map Regions 471 1883 0.943134275 0.977836186 0.910811401 5741 253289 24773 253021 Genetalks ILLUMINA NA Ilumina-bwa-dvnm(Genetalks) SNVandINDEL MHC 39 138 0.958419957 0.990441211 0.928576974 194 20330 1434 20285 Genetalks ILLUMINA NA Ilumina-bwaalt-dvnm-gatkMHC(Genetalks) INDEL All Benchmark Regions 414 1140 0.9946625 0.996141997 0.993186498 2038 526320 3462 504667 Genetalks ILLUMINA NA Ilumina-bwaalt-dvnm-gatkMHC(Genetalks) INDEL Difficult-to-Map Regions 63 118 0.938274798 0.975281498 0.903973837 383 15131 1583 14906 Genetalks ILLUMINA NA Ilumina-bwaalt-dvnm-gatkMHC(Genetalks) INDEL MHC 117 19 0.919594486 0.877882946 0.965478799 254 1827 58 1634 Genetalks ILLUMINA NA Ilumina-bwaalt-dvnm-gatkMHC(Genetalks) SNP All Benchmark Regions 1681 2128 0.994950999 0.997267999 0.992644491 9095 3320387 24589 3318929 Genetalks ILLUMINA NA Ilumina-bwaalt-dvnm-gatkMHC(Genetalks) SNP Difficult-to-Map Regions 608 1786 0.942880688 0.976510989 0.911489066 5730 238219 23126 238178 Genetalks ILLUMINA NA Ilumina-bwaalt-dvnm-gatkMHC(Genetalks) SNP MHC 1091 139 0.932255361 0.894699988 0.973101772 2288 19453 539 19612 Genetalks ILLUMINA NA Ilumina-bwaalt-dvnm-gatkMHC(Genetalks) SNVandINDEL All Benchmark Regions 2095 3269 0.994910093 0.997113775 0.992716137 11133 3846710 28051 3823597 Genetalks ILLUMINA NA Ilumina-bwaalt-dvnm-gatkMHC(Genetalks) SNVandINDEL Difficult-to-Map Regions 671 1904 0.942607397 0.976437825 0.911043055 6113 253350 24709 253085 Genetalks ILLUMINA NA Ilumina-bwaalt-dvnm-gatkMHC(Genetalks) SNVandINDEL MHC 1208 158 0.93118623 0.893230412 0.97251126 2542 21280 598 21245 Genetalks ILLUMINA NA Ilumina-bwaalt-gatk(Genetalks) INDEL All Benchmark Regions 479 2102 0.990564994 0.990906994 0.990223494 4812 524412 4967 503162 Genetalks ILLUMINA NA Ilumina-bwaalt-gatk(Genetalks) INDEL Difficult-to-Map Regions 188 229 0.895817149 0.892775888 0.898879339 1808 15057 1667 14822 Genetalks ILLUMINA NA Ilumina-bwaalt-gatk(Genetalks) INDEL MHC 97 27 0.914815413 0.880963037 0.951386837 241 1787 82 1610 Genetalks ILLUMINA NA Ilumina-bwaalt-gatk(Genetalks) SNP All Benchmark Regions 3424 4065 0.990764484 0.989636473 0.991895492 34731 3317224 27095 3316423 Genetalks ILLUMINA NA Ilumina-bwaalt-gatk(Genetalks) SNP Difficult-to-Map Regions 2150 3241 0.902357976 0.89968877 0.905042838 26360 236488 24811 236494 Genetalks ILLUMINA NA Ilumina-bwaalt-gatk(Genetalks) SNP MHC 894 172 0.926570329 0.900518956 0.954188841 2106 19089 922 19230 Genetalks ILLUMINA NA Ilumina-bwaalt-gatk(Genetalks) SNVandINDEL All Benchmark Regions 3904 6167 0.990741255 0.989809372 0.991674898 39543 3841639 32062 3819587 Genetalks ILLUMINA NA Ilumina-bwaalt-gatk(Genetalks) SNVandINDEL Difficult-to-Map Regions 2340 3470 0.901966058 0.899271491 0.904677154 28169 251546 26479 251317 Genetalks ILLUMINA NA Ilumina-bwaalt-gatk(Genetalks) SNVandINDEL MHC 991 199 0.925563469 0.898811467 0.953971266 2348 20877 1003 20840 Genetalks PACBIO NA Pacbio-bwaalt-deepvariant(Genetalks) INDEL All Benchmark Regions 1371 4037 0.986464792 0.988132898 0.984803649 6259 521521 7710 500407 Genetalks PACBIO NA Pacbio-bwaalt-deepvariant(Genetalks) INDEL Difficult-to-Map Regions 39 36 0.975457066 0.966548736 0.984531874 568 16414 254 16235 Genetalks PACBIO NA Pacbio-bwaalt-deepvariant(Genetalks) INDEL MHC 19 14 0.941825656 0.978940999 0.907480703 35 1627 154 1535 Genetalks PACBIO NA Pacbio-bwaalt-deepvariant(Genetalks) SNP All Benchmark Regions 835 998 0.997368499 0.996951999 0.997784491 10206 3338902 7393 3336114 Genetalks PACBIO NA Pacbio-bwaalt-deepvariant(Genetalks) SNP Difficult-to-Map Regions 520 414 0.976862194 0.968424733 0.985448151 8399 257675 3796 257504 Genetalks PACBIO NA Pacbio-bwaalt-deepvariant(Genetalks) SNP MHC 27 95 0.947522204 0.992194525 0.906825941 142 18247 1815 18276 Genetalks PACBIO NA Pacbio-bwaalt-deepvariant(Genetalks) SNVandINDEL All Benchmark Regions 2206 5034 0.995911568 0.995751362 0.996071836 16471 3860424 15103 3836522 Genetalks PACBIO NA Pacbio-bwaalt-deepvariant(Genetalks) SNVandINDEL Difficult-to-Map Regions 559 450 0.976777919 0.968311665 0.985393529 8967 274089 4050 273739 Genetalks PACBIO NA Pacbio-bwaalt-deepvariant(Genetalks) SNVandINDEL MHC 46 110 0.947054732 0.991096321 0.906881247 178 19874 1969 19811 Genetalks PACBIO NA Pacbio-bwaalt-dvMHC(Genetalks) INDEL All Benchmark Regions 1396 4043 0.986466822 0.988003409 0.984934706 6329 521600 7645 500474 Genetalks PACBIO NA Pacbio-bwaalt-dvMHC(Genetalks) INDEL Difficult-to-Map Regions 40 37 0.975400304 0.966378917 0.984592183 571 16415 253 16236 Genetalks PACBIO NA Pacbio-bwaalt-dvMHC(Genetalks) INDEL MHC 44 21 0.944252143 0.94184247 0.946675353 104 1706 90 1602 Genetalks PACBIO NA Pacbio-bwaalt-dvMHC(Genetalks) SNP All Benchmark Regions 1151 980 0.997436496 0.996739493 0.998133498 10918 3340072 6238 3337280 Genetalks PACBIO NA Pacbio-bwaalt-dvMHC(Genetalks) SNP Difficult-to-Map Regions 525 423 0.976876144 0.968329674 0.985574112 8426 257711 3763 257537 Genetalks PACBIO NA Pacbio-bwaalt-dvMHC(Genetalks) SNP MHC 339 61 0.960832316 0.957309953 0.964382278 832 19411 695 19436 Genetalks PACBIO NA Pacbio-bwaalt-dvMHC(Genetalks) SNVandINDEL All Benchmark Regions 2548 5026 0.995971067 0.995550577 0.996391915 17258 3861673 13896 3837755 Genetalks PACBIO NA Pacbio-bwaalt-dvMHC(Genetalks) SNVandINDEL Difficult-to-Map Regions 566 460 0.976787276 0.968212374 0.985515422 8997 274126 4016 273773 Genetalks PACBIO NA Pacbio-bwaalt-dvMHC(Genetalks) SNVandINDEL MHC 383 86 0.959512512 0.956041803 0.963010589 937 21117 786 21038 Genetalks PACBIO NA Pacbio-mm2-deepvariant(Genetalks) INDEL All Benchmark Regions 2543 4080 0.986199267 0.986931863 0.985467645 7058 533458 7372 500745 Genetalks PACBIO NA Pacbio-mm2-deepvariant(Genetalks) INDEL Difficult-to-Map Regions 75 36 0.986428157 0.988086104 0.984776706 204 16965 251 16239 Genetalks PACBIO NA Pacbio-mm2-deepvariant(Genetalks) INDEL MHC 24 12 0.961813764 0.977995454 0.946207439 38 1731 86 1601 Genetalks PACBIO NA Pacbio-mm2-deepvariant(Genetalks) SNP All Benchmark Regions 656 1177 0.9983865 0.998851999 0.997921498 3830 3335707 6945 3336572 Genetalks PACBIO NA Pacbio-mm2-deepvariant(Genetalks) SNP Difficult-to-Map Regions 84 325 0.988565769 0.993879455 0.983308443 1580 256926 4353 256946 Genetalks PACBIO NA Pacbio-mm2-deepvariant(Genetalks) SNP MHC 24 39 0.973888322 0.995507759 0.953277732 85 19165 853 19212 Genetalks PACBIO NA Pacbio-mm2-deepvariant(Genetalks) SNVandINDEL All Benchmark Regions 3200 5259 0.996734515 0.997191039 0.996278414 10898 3869166 14318 3837318 Genetalks PACBIO NA Pacbio-mm2-deepvariant(Genetalks) SNVandINDEL Difficult-to-Map Regions 159 361 0.988431199 0.993518357 0.983395996 1784 273891 4604 273185 Genetalks PACBIO NA Pacbio-mm2-deepvariant(Genetalks) SNVandINDEL MHC 49 53 0.972898418 0.99403188 0.952730334 124 20896 939 20813 Genetalks PACBIO NA Pacbio-mm2dv-asmmhc(Genetalks) INDEL All Benchmark Regions 2545 4078 0.986257297 0.986905873 0.985609204 7072 533451 7302 500817 Genetalks PACBIO NA Pacbio-mm2dv-asmmhc(Genetalks) INDEL Difficult-to-Map Regions 77 37 0.986283051 0.987703523 0.984867077 210 16953 249 16240 Genetalks PACBIO NA Pacbio-mm2dv-asmmhc(Genetalks) INDEL MHC 26 10 0.979180115 0.970129771 0.988401619 53 1723 19 1672 Genetalks PACBIO NA Pacbio-mm2dv-asmmhc(Genetalks) SNP All Benchmark Regions 795 1164 0.998477498 0.998769998 0.998185498 4103 3336637 6064 3337454 Genetalks PACBIO NA Pacbio-mm2dv-asmmhc(Genetalks) SNP Difficult-to-Map Regions 146 328 0.988413178 0.993456411 0.983420309 1689 256961 4321 256975 Genetalks PACBIO NA Pacbio-mm2dv-asmmhc(Genetalks) SNP MHC 162 24 0.989532208 0.982314865 0.996856543 360 20092 49 20090 Genetalks PACBIO NA Pacbio-mm2dv-asmmhc(Genetalks) SNVandINDEL All Benchmark Regions 3341 5246 0.996821681 0.997117534 0.996526003 11187 3870090 13379 3838272 Genetalks PACBIO NA Pacbio-mm2dv-asmmhc(Genetalks) SNVandINDEL Difficult-to-Map Regions 223 365 0.988278864 0.993098052 0.983506344 1899 273914 4571 273216 Genetalks PACBIO NA Pacbio-mm2dv-asmmhc(Genetalks) SNVandINDEL MHC 189 34 0.988715658 0.981341141 0.996201863 413 21816 70 21763 Genetalks PACBIO NA Pacbio-mm2SNP-bwaINDEL-asmMHC(Genetalks) INDEL All Benchmark Regions 1774 5167 0.982955351 0.985187928 0.980732747 7807 519434 9783 498339 Genetalks PACBIO NA Pacbio-mm2SNP-bwaINDEL-asmMHC(Genetalks) INDEL Difficult-to-Map Regions 73 50 0.972521194 0.963617932 0.981590406 618 16370 303 16186 Genetalks PACBIO NA Pacbio-mm2SNP-bwaINDEL-asmMHC(Genetalks) INDEL MHC 26 10 0.979180115 0.970129771 0.988401619 53 1723 19 1672 Genetalks PACBIO NA Pacbio-mm2SNP-bwaINDEL-asmMHC(Genetalks) SNP All Benchmark Regions 596 1182 0.998220999 0.998801499 0.997640499 4001 3336700 7888 3335632 Genetalks PACBIO NA Pacbio-mm2SNP-bwaINDEL-asmMHC(Genetalks) SNP Difficult-to-Map Regions 137 379 0.987786184 0.993290908 0.982341332 1731 256806 4604 256692 Genetalks PACBIO NA Pacbio-mm2SNP-bwaINDEL-asmMHC(Genetalks) SNP MHC 162 24 0.989532208 0.982314865 0.996856543 360 20092 49 20090 Genetalks PACBIO NA Pacbio-mm2SNP-bwaINDEL-asmMHC(Genetalks) SNVandINDEL All Benchmark Regions 2371 6350 0.996177183 0.996945768 0.995409782 11813 3856135 17678 3833972 Genetalks PACBIO NA Pacbio-mm2SNP-bwaINDEL-asmMHC(Genetalks) SNVandINDEL Difficult-to-Map Regions 210 429 0.98685755 0.991461105 0.982296668 2349 273176 4907 272879 Genetalks PACBIO NA Pacbio-mm2SNP-bwaINDEL-asmMHC(Genetalks) SNVandINDEL MHC 189 34 0.988715658 0.981341141 0.996201863 413 21816 70 21763 Wang Genomics Lab ONT NA ONT NanoCaller Clair Medaka Ensemble INDEL All Benchmark Regions 53001 19137 0.551069881 0.668061956 0.468960009 120575 243279 269772 238292 Wang Genomics Lab ONT NA ONT NanoCaller Clair Medaka Ensemble INDEL Difficult-to-Map Regions 952 319 0.726877996 0.755970042 0.700017963 3732 11571 4945 11544 Wang Genomics Lab ONT NA ONT NanoCaller Clair Medaka Ensemble INDEL MHC 189 63 0.716365559 0.777774015 0.66395519 328 1151 568 1123 Wang Genomics Lab ONT NA ONT NanoCaller Clair Medaka Ensemble SNP All Benchmark Regions 5765 2045 0.992057976 0.992998486 0.991119464 23360 3314169 29679 3313829 Wang Genomics Lab ONT NA ONT NanoCaller Clair Medaka Ensemble SNP Difficult-to-Map Regions 778 589 0.97530646 0.959726845 0.991400976 10864 259165 2246 259060 Wang Genomics Lab ONT NA ONT NanoCaller Clair Medaka Ensemble SNP MHC 68 33 0.991833175 0.994395915 0.989283784 112 19928 215 19938 Wang Genomics Lab ONT NA ONT NanoCaller Clair Medaka Ensemble SNVandINDEL All Benchmark Regions 58766 21183 0.941236494 0.961033316 0.922239106 144022 3557476 299482 3552144 Wang Genomics Lab ONT NA ONT NanoCaller Clair Medaka Ensemble SNVandINDEL Difficult-to-Map Regions 1732 908 0.961279887 0.948785882 0.974109073 14597 270737 7192 270605 Wang Genomics Lab ONT NA ONT NanoCaller Clair Medaka Ensemble SNVandINDEL MHC 258 96 0.971731423 0.979497902 0.964087147 440 21079 784 21061 Wang Genomics Lab PACBIO NA PacBio NanoCaller INDEL All Benchmark Regions 26856 86561 0.416079499 0.503862674 0.354346987 179283 182077 328075 180054 Wang Genomics Lab PACBIO NA PacBio NanoCaller INDEL Difficult-to-Map Regions 533 2605 0.466208048 0.537244965 0.411764689 5811 6747 9700 6790 Wang Genomics Lab PACBIO NA PacBio NanoCaller INDEL MHC 175 327 0.450703048 0.510632909 0.403401659 658 692 1007 683 Wang Genomics Lab PACBIO NA PacBio NanoCaller SNP All Benchmark Regions 2705 1756 0.996780994 0.996831485 0.996730499 10579 3333086 10931 3332589 Wang Genomics Lab PACBIO NA PacBio NanoCaller SNP Difficult-to-Map Regions 538 385 0.983347434 0.978487254 0.988256 5677 258362 3069 258238 Wang Genomics Lab PACBIO NA PacBio NanoCaller SNP MHC 68 33 0.983762377 0.994378933 0.97337528 111 19612 527 19617 Wang Genomics Lab PACBIO NA PacBio NanoCaller SNVandINDEL All Benchmark Regions 29567 88317 0.930003906 0.948750694 0.911983656 189880 3515164 339007 3512644 Wang Genomics Lab PACBIO NA PacBio NanoCaller SNVandINDEL Difficult-to-Map Regions 1074 2991 0.956238727 0.958451855 0.954035872 11492 265110 12769 265029 Wang Genomics Lab PACBIO NA PacBio NanoCaller SNVandINDEL MHC 244 361 0.946027037 0.963354877 0.929319008 770 20307 1543 20302 Roche Sequencing Solutions ILLUMINA NA RN-Illumina INDEL All Benchmark Regions 832 1576 0.991137493 0.994748999 0.987551481 2761 523073 6324 501804 Roche Sequencing Solutions ILLUMINA NA RN-Illumina INDEL Difficult-to-Map Regions 85 146 0.931044665 0.974428379 0.89136007 390 14861 1791 14698 Roche Sequencing Solutions ILLUMINA NA RN-Illumina INDEL MHC 21 18 0.954154762 0.97453947 0.934619027 42 1642 109 1581 Roche Sequencing Solutions ILLUMINA NA RN-Illumina SNP All Benchmark Regions 755 1831 0.995188996 0.998236999 0.992159478 5859 3318352 26205 3317307 Roche Sequencing Solutions ILLUMINA NA RN-Illumina SNP Difficult-to-Map Regions 460 1571 0.943462209 0.981045498 0.908652382 4589 237542 23866 237437 Roche Sequencing Solutions ILLUMINA NA RN-Illumina SNP MHC 19 57 0.976972662 0.99549736 0.959133859 87 19310 813 19330 Roche Sequencing Solutions ILLUMINA NA RN-Illumina SNVandINDEL All Benchmark Regions 1587 3407 0.994646496 0.99776061 0.991551773 8621 3841427 32530 3819113 Roche Sequencing Solutions ILLUMINA NA RN-Illumina SNVandINDEL Difficult-to-Map Regions 545 1717 0.942727364 0.98065321 0.907626401 4979 252403 25658 252136 Roche Sequencing Solutions ILLUMINA NA RN-Illumina SNVandINDEL MHC 41 75 0.975180748 0.99382179 0.95723502 129 20952 922 20911 Roche Sequencing Solutions MULTI ILLUMINAPACBIO RN-Illumina-PacBio INDEL All Benchmark Regions 641 775 0.996380985 0.996142475 0.996618492 2042 528139 1717 506411 Roche Sequencing Solutions MULTI ILLUMINAPACBIO RN-Illumina-PacBio INDEL Difficult-to-Map Regions 45 40 0.985008962 0.985208407 0.984809493 247 16450 250 16239 Roche Sequencing Solutions MULTI ILLUMINAPACBIO RN-Illumina-PacBio INDEL MHC 30 12 0.968849809 0.97546676 0.962328271 44 1747 63 1628 Roche Sequencing Solutions MULTI ILLUMINAPACBIO RN-Illumina-PacBio SNP All Benchmark Regions 208 343 0.9992925 0.999556 0.9990285 1483 3341274 3249 3340272 Roche Sequencing Solutions MULTI ILLUMINAPACBIO RN-Illumina-PacBio SNP Difficult-to-Map Regions 70 282 0.993735927 0.996483932 0.991003423 909 259003 2349 258956 Roche Sequencing Solutions MULTI ILLUMINAPACBIO RN-Illumina-PacBio SNP MHC 14 17 0.989082807 0.998280462 0.980055532 33 19683 394 19752 Roche Sequencing Solutions MULTI ILLUMINAPACBIO RN-Illumina-PacBio SNVandINDEL All Benchmark Regions 849 1118 0.998899416 0.999088618 0.998710286 3529 3869416 4966 3846685 Roche Sequencing Solutions MULTI ILLUMINAPACBIO RN-Illumina-PacBio SNVandINDEL Difficult-to-Map Regions 116 323 0.993212993 0.995803574 0.990635857 1157 275453 2599 275196 Roche Sequencing Solutions MULTI ILLUMINAPACBIO RN-Illumina-PacBio SNVandINDEL MHC 45 29 0.987450347 0.996380856 0.978681901 77 21430 457 21380 Roche Sequencing Solutions MULTI ILLUMINAPACBIOONT RN-Illumina-PacBio-ONT INDEL All Benchmark Regions 641 839 0.996116981 0.995958966 0.996274491 2138 527938 1892 506236 Roche Sequencing Solutions MULTI ILLUMINAPACBIOONT RN-Illumina-PacBio-ONT INDEL Difficult-to-Map Regions 51 34 0.983972 0.983924963 0.984019969 268 16433 263 16226 Roche Sequencing Solutions MULTI ILLUMINAPACBIOONT RN-Illumina-PacBio-ONT INDEL MHC 31 11 0.967700018 0.974625317 0.960875012 44 1743 65 1626 Roche Sequencing Solutions MULTI ILLUMINAPACBIOONT RN-Illumina-PacBio-ONT SNP All Benchmark Regions 188 301 0.999348496 0.999626499 0.999070991 1236 3341409 3075 3340415 Roche Sequencing Solutions MULTI ILLUMINAPACBIOONT RN-Illumina-PacBio-ONT SNP Difficult-to-Map Regions 51 232 0.99511589 0.997225831 0.993014436 706 259534 1823 259481 Roche Sequencing Solutions MULTI ILLUMINAPACBIOONT RN-Illumina-PacBio-ONT SNP MHC 14 19 0.990807961 0.998234976 0.983492703 35 19748 326 19821 Roche Sequencing Solutions MULTI ILLUMINAPACBIOONT RN-Illumina-PacBio-ONT SNVandINDEL All Benchmark Regions 830 1141 0.998913005 0.999124229 0.998701872 3391 3869350 4986 3846652 Roche Sequencing Solutions MULTI ILLUMINAPACBIOONT RN-Illumina-PacBio-ONT SNVandINDEL Difficult-to-Map Regions 102 266 0.994448603 0.996424272 0.992480761 979 275967 2087 275708 Roche Sequencing Solutions MULTI ILLUMINAPACBIOONT RN-Illumina-PacBio-ONT SNVandINDEL MHC 45 30 0.988956001 0.996280488 0.981740665 79 21492 391 21447 Roche Sequencing Solutions PACBIO NA RN-PacBio INDEL All Benchmark Regions 5106 7819 0.969751755 0.96839032 0.971117179 16767 513769 14671 493453 Roche Sequencing Solutions PACBIO NA RN-PacBio INDEL Difficult-to-Map Regions 115 59 0.978540958 0.980100912 0.976985987 331 16302 379 16110 Roche Sequencing Solutions PACBIO NA RN-PacBio INDEL MHC 43 19 0.945246518 0.96308529 0.928064346 63 1642 121 1570 Roche Sequencing Solutions PACBIO NA RN-PacBio SNP All Benchmark Regions 730 756 0.99878 0.999105 0.998455 2991 3339521 5165 3338356 Roche Sequencing Solutions PACBIO NA RN-PacBio SNP Difficult-to-Map Regions 143 326 0.992335854 0.995113909 0.989573286 1265 258661 2719 258582 Roche Sequencing Solutions PACBIO NA RN-PacBio SNP MHC 16 51 0.984112653 0.996361494 0.97216429 71 19567 556 19593 Roche Sequencing Solutions PACBIO NA RN-PacBio SNVandINDEL All Benchmark Regions 5836 8575 0.994872954 0.99489746 0.99484845 19759 3853291 19836 3831810 Roche Sequencing Solutions PACBIO NA RN-PacBio SNVandINDEL Difficult-to-Map Regions 259 385 0.991511623 0.994211357 0.988826525 1597 274963 3099 274693 Roche Sequencing Solutions PACBIO NA RN-PacBio SNVandINDEL MHC 59 70 0.981065294 0.993703536 0.9687479 134 21209 677 21163 YUI27 ILLUMINA NA YUI27 INDEL All Benchmark Regions 421 4581 0.986144 0.986586 0.985703 7135 524767 7312 504138 YUI27 ILLUMINA NA YUI27 INDEL Difficult-to-Map Regions 176 253 0.895043 0.894709 0.895377 1771 15049 1729 14797 YUI27 ILLUMINA NA YUI27 INDEL MHC 127 15 0.919891 0.87896 0.964821 256 1859 61 1673 YUI27 ILLUMINA NA YUI27 SNP All Benchmark Regions 4007 5003 0.989879 0.988111 0.991652 40046 3328339 28011 3327586 YUI27 ILLUMINA NA YUI27 SNP Difficult-to-Map Regions 2383 3456 0.899321 0.894536 0.904158 28121 238519 25284 238525 YUI27 ILLUMINA NA YUI27 SNP MHC 1081 89 0.937792 0.903467 0.974827 2127 19907 518 20060 YUI27 ILLUMINA NA YUI27 SNVandINDEL All Benchmark Regions 4428 9584 0.989382201 0.987903198 0.99086564 47181 3853106 35323 3831724 YUI27 ILLUMINA NA YUI27 SNVandINDEL Difficult-to-Map Regions 2559 3709 0.89907013 0.894545968 0.903640288 29892 253568 27013 253322 YUI27 ILLUMINA NA YUI27 SNVandINDEL MHC 1208 104 0.936275151 0.901320966 0.974049839 2383 21766 579 21733 Canadian Center for Computational Genomics PACBIO NA McGill - (C3G) submission v1 INDEL All Benchmark Regions 5650 4475 0.940173928 0.927938942 0.952738386 37551 483966 24014 484114 Canadian Center for Computational Genomics PACBIO NA McGill - (C3G) submission v1 INDEL Difficult-to-Map Regions 211 60 0.955079071 0.938897069 0.971831488 1038 15970 464 16025 Canadian Center for Computational Genomics PACBIO NA McGill - (C3G) submission v1 INDEL MHC 90 17 0.919176278 0.918230283 0.920217174 137 1583 135 1557 Canadian Center for Computational Genomics PACBIO NA McGill - (C3G) submission v1 SNP All Benchmark Regions 2508 690 0.9974415 0.996592998 0.9982905 11411 3338761 5715 3337806 Canadian Center for Computational Genomics PACBIO NA McGill - (C3G) submission v1 SNP Difficult-to-Map Regions 698 390 0.979883797 0.969506407 0.990486473 8134 258924 2485 258821 Canadian Center for Computational Genomics PACBIO NA McGill - (C3G) submission v1 SNP MHC 116 23 0.983566186 0.980228307 0.986993911 216 19872 262 19892 Canadian Center for Computational Genomics PACBIO NA McGill - (C3G) submission v1 SNVandINDEL All Benchmark Regions 8158 5165 0.989806102 0.987343624 0.992280937 48964 3822728 29730 3821921 Canadian Center for Computational Genomics PACBIO NA McGill - (C3G) submission v1 SNVandINDEL Difficult-to-Map Regions 909 450 0.978405734 0.967673966 0.989379025 9173 274894 2950 274847 Canadian Center for Computational Genomics PACBIO NA McGill - (C3G) submission v1 SNVandINDEL MHC 223 41 0.978550642 0.97536878 0.98182191 394 21455 397 21449 Seven Bridges Genomics ILLUMINA NA Seven Bridges GRAF - Illumina INDEL All Benchmark Regions 234 1153 0.994425996 0.996397 0.992462489 1894 523856 3829 504299 Seven Bridges Genomics ILLUMINA NA Seven Bridges GRAF - Illumina INDEL Difficult-to-Map Regions 44 162 0.938095009 0.961568933 0.915741469 605 15150 1389 15101 Seven Bridges Genomics ILLUMINA NA Seven Bridges GRAF - Illumina INDEL MHC 9 2 0.98939899 0.991746339 0.987062478 14 1734 21 1670 Seven Bridges Genomics ILLUMINA NA Seven Bridges GRAF - Illumina SNP All Benchmark Regions 428 2415 0.995243498 0.997834 0.99266599 7212 3322242 24517 3319000 Seven Bridges Genomics ILLUMINA NA Seven Bridges GRAF - Illumina SNP Difficult-to-Map Regions 306 2108 0.941739818 0.9751235 0.910566873 6076 238159 23368 237937 Seven Bridges Genomics ILLUMINA NA Seven Bridges GRAF - Illumina SNP MHC 23 33 0.992497502 0.996428937 0.988597668 71 19910 227 19924 Seven Bridges Genomics ILLUMINA NA Seven Bridges GRAF - Illumina SNVandINDEL All Benchmark Regions 663 3567 0.995132179 0.997637694 0.992639224 9107 3846101 28346 3823301 Seven Bridges Genomics ILLUMINA NA Seven Bridges GRAF - Illumina SNVandINDEL Difficult-to-Map Regions 352 2270 0.94152103 0.974301814 0.910874633 6681 253310 24757 253039 Seven Bridges Genomics ILLUMINA NA Seven Bridges GRAF - Illumina SNVandINDEL MHC 32 35 0.992250838 0.996052287 0.988478677 85 21643 249 21594 HB8P3 ILLUMINA NA HB8P3 INDEL All Benchmark Regions 361 1889 0.992873991 0.993745992 0.99200399 3308 525726 4062 504066 HB8P3 ILLUMINA NA HB8P3 INDEL Difficult-to-Map Regions 121 161 0.922079858 0.937209957 0.907430755 1018 15201 1526 14963 HB8P3 ILLUMINA NA HB8P3 INDEL MHC 34 18 0.940567602 0.958202798 0.923570432 75 1717 129 1563 HB8P3 ILLUMINA NA HB8P3 SNP All Benchmark Regions 1010 2682 0.993559492 0.996301999 0.99083148 12297 3313724 30648 3312866 HB8P3 ILLUMINA NA HB8P3 SNP Difficult-to-Map Regions 719 2212 0.927414242 0.958849818 0.897974379 10069 234644 26656 234647 HB8P3 ILLUMINA NA HB8P3 SNP MHC 183 130 0.937661993 0.974898166 0.903165281 465 18081 1951 18202 HB8P3 ILLUMINA NA HB8P3 SNVandINDEL All Benchmark Regions 1372 4571 0.993462694 0.995951564 0.990986236 15605 3839453 34710 3816934 HB8P3 ILLUMINA NA HB8P3 SNVandINDEL Difficult-to-Map Regions 842 2373 0.927083198 0.957504774 0.898535517 11087 249845 28182 249610 HB8P3 ILLUMINA NA HB8P3 SNVandINDEL MHC 217 148 0.937830642 0.973427015 0.904745901 540 19798 2080 19765 4GKR1 MULTI ILLUMINAPACBIO 4GKR1 INDEL All Benchmark Regions 610 1901 0.993247998 0.994400997 0.992096999 2960 525755 4016 504113 4GKR1 MULTI ILLUMINAPACBIO 4GKR1 INDEL Difficult-to-Map Regions 66 161 0.964045977 0.970385867 0.957787846 489 16041 696 15794 4GKR1 MULTI ILLUMINAPACBIO 4GKR1 INDEL MHC 17 16 0.929309117 0.976372619 0.886576671 39 1643 192 1500 4GKR1 MULTI ILLUMINAPACBIO 4GKR1 SNP All Benchmark Regions 593 2774 0.99683 0.997718 0.9959445 7619 3330858 13560 3329961 4GKR1 MULTI ILLUMINAPACBIO 4GKR1 SNP Difficult-to-Map Regions 343 2278 0.968864499 0.977303475 0.960569994 5829 251001 10303 251003 4GKR1 MULTI ILLUMINAPACBIO 4GKR1 SNP MHC 55 149 0.93505172 0.986552873 0.888661437 239 17796 2244 17910 4GKR1 MULTI ILLUMINAPACBIO 4GKR1 SNVandINDEL All Benchmark Regions 1206 4676 0.996349663 0.99726419 0.995436812 10579 3856616 17575 3834077 4GKR1 MULTI ILLUMINAPACBIO 4GKR1 SNVandINDEL Difficult-to-Map Regions 411 2439 0.968574558 0.976884908 0.960404441 6319 267042 10999 266797 4GKR1 MULTI ILLUMINAPACBIO 4GKR1 SNVandINDEL MHC 72 165 0.934571221 0.985682786 0.888499952 278 19439 2436 19410 MECML MULTI ILLUMINAPACBIO MECML INDEL All Benchmark Regions 584 1896 0.994121999 0.994455998 0.993788 2936 526651 3156 504973 MECML MULTI ILLUMINAPACBIO MECML INDEL Difficult-to-Map Regions 75 161 0.966126523 0.969853282 0.962428169 501 16119 619 15870 MECML MULTI ILLUMINAPACBIO MECML INDEL MHC 14 18 0.931209924 0.977352486 0.88923034 38 1654 187 1505 MECML MULTI ILLUMINAPACBIO MECML SNP All Benchmark Regions 682 2765 0.9968885 0.9976915 0.996087 7708 3331302 13083 3330438 MECML MULTI ILLUMINAPACBIO MECML SNP Difficult-to-Map Regions 416 2277 0.968822999 0.977011471 0.960770991 5907 251052 10251 251056 MECML MULTI ILLUMINAPACBIO MECML SNP MHC 57 148 0.937101991 0.986607206 0.892332324 239 17866 2169 17984 MECML MULTI ILLUMINAPACBIO MECML SNVandINDEL All Benchmark Regions 1269 4661 0.996515508 0.997248386 0.995783706 10644 3857956 16240 3835413 MECML MULTI ILLUMINAPACBIO MECML SNVandINDEL Difficult-to-Map Regions 494 2438 0.968658836 0.976576329 0.960868728 6408 267171 10870 266926 MECML MULTI ILLUMINAPACBIO MECML SNVandINDEL MHC 71 166 0.936612525 0.985815578 0.892091344 277 19519 2357 19488 DRAGEN ILLUMINA NA DRAGEN Experimental Extension into Difficult Regions Ð Illumina reads INDEL All Benchmark Regions 242 703 0.997079497 0.997287499 0.996870493 1437 528477 1589 506539 DRAGEN ILLUMINA NA DRAGEN Experimental Extension into Difficult Regions Ð Illumina reads INDEL Difficult-to-Map Regions 36 133 0.968817851 0.974478898 0.963222645 420 16128 606 15883 DRAGEN ILLUMINA NA DRAGEN Experimental Extension into Difficult Regions Ð Illumina reads INDEL MHC 17 8 0.978161195 0.983467321 0.972912516 30 1834 45 1646 DRAGEN ILLUMINA NA DRAGEN Experimental Extension into Difficult Regions Ð Illumina reads SNP All Benchmark Regions 375 2825 0.997073496 0.997730998 0.996416994 7576 3332359 11973 3331542 DRAGEN ILLUMINA NA DRAGEN Experimental Extension into Difficult Regions Ð Illumina reads SNP Difficult-to-Map Regions 229 2155 0.969369987 0.978114902 0.960780563 5610 251050 10245 251058 DRAGEN ILLUMINA NA DRAGEN Experimental Extension into Difficult Regions Ð Illumina reads SNP MHC 43 48 0.982933779 0.993555659 0.972537021 119 19440 553 19600 DRAGEN ILLUMINA NA DRAGEN Experimental Extension into Difficult Regions Ð Illumina reads SNVandINDEL All Benchmark Regions 619 3528 0.997073322 0.997670306 0.996477053 9013 3860838 13562 3838083 DRAGEN ILLUMINA NA DRAGEN Experimental Extension into Difficult Regions Ð Illumina reads SNVandINDEL Difficult-to-Map Regions 265 2288 0.96933616 0.97789516 0.960925693 6031 267178 10851 266942 DRAGEN ILLUMINA NA DRAGEN Experimental Extension into Difficult Regions Ð Illumina reads SNVandINDEL MHC 60 56 0.982518784 0.992678342 0.972565387 148 21274 599 21246 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v1 INDEL All Benchmark Regions 66448 128382 0.379067458 0.367043481 0.391907504 350073 203003 308988 199140 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v1 INDEL Difficult-to-Map Regions 1271 3365 0.394750944 0.402486554 0.387326215 9475 6382 10103 6387 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v1 INDEL MHC 345 425 0.349282263 0.354771647 0.343968987 1085 596 1110 582 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v1 SNP All Benchmark Regions 4788 2062 0.995550488 0.993217955 0.9978935 22768 3337721 7042 3336479 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v1 SNP Difficult-to-Map Regions 1144 595 0.967677214 0.944763706 0.991732987 15140 259243 2160 259146 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v1 SNP MHC 54 40 0.98966314 0.99451047 0.98486346 109 19852 304 19849 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v1 SNVandINDEL All Benchmark Regions 71239 130445 0.911289088 0.904725621 0.917948514 372865 3540725 316031 3535619 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v1 SNVandINDEL Difficult-to-Map Regions 2418 3960 0.935045633 0.915123679 0.955855131 24633 265626 12263 265534 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v1 SNVandINDEL MHC 401 472 0.940002314 0.944819466 0.935234061 1194 20448 1415 20431 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v2 INDEL All Benchmark Regions 72621 127938 0.38487795 0.369221512 0.40192338 355743 208232 303899 204229 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v2 INDEL Difficult-to-Map Regions 7555 3316 0.538772939 0.430084602 0.720984395 15939 12028 4601 11889 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v2 INDEL MHC 2 0 0.150503678 0.974066618 0.081551898 3 147 1554 138 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v2 SNP All Benchmark Regions 4190 3453 0.990432451 0.994851454 0.986051447 17037 3298068 46624 3296885 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v2 SNP Difficult-to-Map Regions 598 2028 0.934587727 0.961423055 0.90920942 9506 237626 23720 237583 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v2 SNP MHC 12 20 0.185221193 0.977110962 0.102313819 47 2058 18090 2062 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v2 SNVandINDEL All Benchmark Regions 76812 131391 0.906434203 0.903892714 0.908990116 372811 3506300 350529 3501114 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v2 SNVandINDEL Difficult-to-Map Regions 8153 5344 0.902695154 0.907402255 0.898036638 25472 249655 28321 249472 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v2 SNVandINDEL MHC 14 20 0.182585774 0.976878787 0.100709864 51 2205 19644 2200 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v3 INDEL All Benchmark Regions 74057 127201 0.387148461 0.370176563 0.405754098 357718 210248 301953 206175 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v3 INDEL Difficult-to-Map Regions 8974 2587 0.576442968 0.439299196 0.838081693 17906 14029 2670 13820 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v3 INDEL MHC 17 0 0.159636278 0.884274125 0.08774246 20 157 1544 148 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v3 SNP All Benchmark Regions 5281 2074 0.992073968 0.991460434 0.99268849 28573 3320252 24441 3319076 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v3 SNP Difficult-to-Map Regions 1689 649 0.958316848 0.925004473 0.99412099 21047 259807 1536 259770 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v3 SNP MHC 15 9 0.200169262 0.980219159 0.111472405 43 2242 17905 2247 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v3 SNVandINDEL All Benchmark Regions 79340 129275 0.90826006 0.901369509 0.915256808 386317 3530500 326396 3525251 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v3 SNVandINDEL Difficult-to-Map Regions 10664 3237 0.926914194 0.875411091 0.984857843 38967 273837 4206 273591 Lab of Systems and Network Biology MULTI ILLUMINAPACBIO Deepvariant_Clair_v3 SNVandINDEL MHC 32 9 0.197068762 0.973137134 0.109640146 63 2400 19449 2395 0O7FL MULTI ILLUMINAPACBIOONT 0O7FL INDEL All Benchmark Regions 2387 316 0.989122 0.993398 0.984881499 3468 521820 7682 500447 0O7FL MULTI ILLUMINAPACBIOONT 0O7FL INDEL Difficult-to-Map Regions 81 21 0.965560494 0.971831795 0.959370418 463 15992 670 15820 0O7FL MULTI ILLUMINAPACBIOONT 0O7FL INDEL MHC 11 0 0.229807433 0.939904709 0.130907864 14 226 1470 221 0O7FL MULTI ILLUMINAPACBIOONT 0O7FL SNP All Benchmark Regions 1372 162 0.995186993 0.997640496 0.992745491 7845 3320443 24251 3319266 0O7FL MULTI ILLUMINAPACBIOONT 0O7FL SNP Difficult-to-Map Regions 351 119 0.977395972 0.9790505 0.97574638 5458 255065 6336 254969 0O7FL MULTI ILLUMINAPACBIOONT 0O7FL SNP MHC 74 11 0.442788118 0.965405234 0.287555561 189 5795 14334 5795 0O7FL MULTI ILLUMINAPACBIOONT 0O7FL SNVandINDEL All Benchmark Regions 3759 479 0.994378108 0.997062566 0.991708066 11316 3842265 31934 3819715 0O7FL MULTI ILLUMINAPACBIOONT 0O7FL SNVandINDEL Difficult-to-Map Regions 432 140 0.97669415 0.978621374 0.974774573 5921 271057 7006 270789 0O7FL MULTI ILLUMINAPACBIOONT 0O7FL SNVandINDEL MHC 87 12 0.428237104 0.964401276 0.275464132 204 6022 15805 6018 61YRJ MULTI ILLUMINAPACBIOONT 61YRJ INDEL All Benchmark Regions 2067 310 0.987866999 0.9934375 0.982357496 3438 520449 8964 499165 61YRJ MULTI ILLUMINAPACBIOONT 61YRJ INDEL Difficult-to-Map Regions 134 19 0.937546488 0.951865289 0.923652665 778 15394 1258 15231 61YRJ MULTI ILLUMINAPACBIOONT 61YRJ INDEL MHC 28 8 0.474672765 0.905634254 0.321738782 56 561 1147 544 61YRJ MULTI ILLUMINAPACBIOONT 61YRJ SNP All Benchmark Regions 1516 205 0.99511249 0.997494999 0.992741971 8338 3320465 24253 3319254 61YRJ MULTI ILLUMINAPACBIOONT 61YRJ SNP Difficult-to-Map Regions 388 128 0.975981954 0.978586991 0.973390889 5568 254458 6952 254354 61YRJ MULTI ILLUMINAPACBIOONT 61YRJ SNP MHC 268 44 0.474850193 0.89796443 0.323670936 719 6522 13561 6523 61YRJ MULTI ILLUMINAPACBIOONT 61YRJ SNVandINDEL All Benchmark Regions 3585 517 0.994149908 0.996943331 0.991372105 11776 3840916 33221 3818421 61YRJ MULTI ILLUMINAPACBIOONT 61YRJ SNVandINDEL Difficult-to-Map Regions 524 147 0.973719766 0.977022399 0.970439424 6346 269853 8210 269585 61YRJ MULTI ILLUMINAPACBIOONT 61YRJ SNVandINDEL MHC 297 53 0.474975971 0.898590196 0.32362026 775 7086 14710 7070