PrecisionFDA
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Explore HG002 comparison results
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| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
45601-45650 / 86044 show all | |||||||||||||||
| gduggal-snapvard | INDEL | I1_5 | map_l125_m1_e0 | het | 88.6113 | 98.7654 | 80.3504 | 90.3081 | 480 | 6 | 642 | 157 | 63 | 40.1274 | |
| ckim-vqsr | INDEL | D16_PLUS | HG002compoundhet | het | 88.8043 | 99.2593 | 80.3419 | 59.7015 | 402 | 3 | 282 | 69 | 67 | 97.1014 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 86.2677 | 93.1373 | 80.3419 | 74.6753 | 95 | 7 | 94 | 23 | 22 | 95.6522 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 73.4644 | 67.6763 | 80.3352 | 54.3953 | 2659 | 1270 | 2684 | 657 | 598 | 91.0198 | |
| anovak-vg | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 85.1154 | 90.5013 | 80.3346 | 69.7300 | 30079 | 3157 | 33518 | 8205 | 5776 | 70.3961 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 86.7610 | 94.3089 | 80.3318 | 79.6037 | 348 | 21 | 339 | 83 | 46 | 55.4217 | |
| gduggal-snapvard | SNP | * | map_l125_m0_e0 | het | 87.4804 | 96.0281 | 80.3301 | 84.3236 | 12161 | 503 | 12023 | 2944 | 184 | 6.2500 | |
| gduggal-bwavard | INDEL | D6_15 | map_l125_m2_e1 | * | 78.8076 | 77.3438 | 80.3279 | 92.3845 | 99 | 29 | 98 | 24 | 17 | 70.8333 | |
| gduggal-bwavard | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 75.1438 | 70.5882 | 80.3279 | 96.6630 | 48 | 20 | 49 | 12 | 11 | 91.6667 | |
| anovak-vg | SNP | ti | map_siren | het | 85.3428 | 91.0279 | 80.3260 | 62.0963 | 56785 | 5597 | 56323 | 13795 | 3334 | 24.1682 | |
| ciseli-custom | INDEL | D1_5 | map_l150_m1_e0 | * | 74.0933 | 68.7587 | 80.3252 | 92.6268 | 493 | 224 | 494 | 121 | 55 | 45.4545 | |
| ghariani-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 88.8489 | 99.4083 | 80.3175 | 86.3311 | 504 | 3 | 506 | 124 | 83 | 66.9355 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 43.8171 | 30.1266 | 80.3150 | 57.0116 | 714 | 1656 | 714 | 175 | 158 | 90.2857 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 81.1322 | 81.9681 | 80.3133 | 62.9774 | 2982 | 656 | 2974 | 729 | 725 | 99.4513 | |
| ciseli-custom | INDEL | D1_5 | map_l150_m2_e0 | * | 74.1130 | 68.8073 | 80.3053 | 92.8974 | 525 | 238 | 526 | 129 | 61 | 47.2868 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 40.3286 | 26.9258 | 80.2982 | 58.7796 | 755 | 2049 | 754 | 185 | 171 | 92.4324 | |
| anovak-vg | INDEL | D1_5 | map_l150_m2_e0 | * | 82.1745 | 84.1415 | 80.2974 | 90.0210 | 642 | 121 | 648 | 159 | 63 | 39.6226 | |
| anovak-vg | INDEL | I1_5 | func_cds | homalt | 87.3563 | 95.7983 | 80.2817 | 31.0680 | 114 | 5 | 114 | 28 | 26 | 92.8571 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 29.2460 | 17.8797 | 80.2817 | 70.2306 | 113 | 519 | 114 | 28 | 24 | 85.7143 | |
| eyeh-varpipe | INDEL | I6_15 | map_l100_m1_e0 | homalt | 77.9540 | 75.7576 | 80.2817 | 77.2436 | 25 | 8 | 57 | 14 | 14 | 100.0000 | |
| gduggal-snapvard | INDEL | I1_5 | map_l125_m2_e1 | het | 88.5797 | 98.8189 | 80.2632 | 90.8843 | 502 | 6 | 671 | 165 | 69 | 41.8182 | |
| eyeh-varpipe | INDEL | D16_PLUS | map_siren | het | 77.8836 | 75.6410 | 80.2632 | 78.7709 | 59 | 19 | 61 | 15 | 15 | 100.0000 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 51.6683 | 38.0989 | 80.2508 | 24.4970 | 501 | 814 | 512 | 126 | 126 | 100.0000 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 78.0369 | 75.9494 | 80.2425 | 77.9111 | 4620 | 1463 | 4699 | 1157 | 1067 | 92.2213 | |
| anovak-vg | INDEL | D6_15 | map_siren | * | 73.2509 | 67.3870 | 80.2326 | 79.8971 | 343 | 166 | 345 | 85 | 60 | 70.5882 | |
| asubramanian-gatk | INDEL | D16_PLUS | HG002compoundhet | het | 87.8383 | 97.0370 | 80.2326 | 59.6717 | 393 | 12 | 276 | 68 | 64 | 94.1176 | |
| ciseli-custom | SNP | * | map_l150_m2_e1 | het | 73.3676 | 67.5883 | 80.2276 | 84.7439 | 13763 | 6600 | 13747 | 3388 | 114 | 3.3648 | |
| astatham-gatk | INDEL | D16_PLUS | HG002compoundhet | het | 88.8320 | 99.5062 | 80.2260 | 58.8850 | 403 | 2 | 284 | 70 | 68 | 97.1429 | |
| gduggal-bwafb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 88.3710 | 98.3627 | 80.2220 | 89.1848 | 781 | 13 | 795 | 196 | 29 | 14.7959 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 64.6148 | 54.0919 | 80.2207 | 60.1084 | 1236 | 1049 | 1890 | 466 | 171 | 36.6953 | |
| gduggal-snapfb | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 88.4727 | 98.6270 | 80.2142 | 81.5986 | 1724 | 24 | 1723 | 425 | 22 | 5.1765 | |
| jpowers-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 87.8581 | 97.1203 | 80.2087 | 86.4645 | 8870 | 263 | 8916 | 2200 | 30 | 1.3636 | |
| jpowers-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 87.8581 | 97.1203 | 80.2087 | 86.4645 | 8870 | 263 | 8916 | 2200 | 30 | 1.3636 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 87.0098 | 95.0798 | 80.2025 | 58.7471 | 715 | 37 | 713 | 176 | 170 | 96.5909 | |
| gduggal-snapvard | SNP | tv | map_l150_m0_e0 | * | 87.3397 | 95.8793 | 80.1968 | 85.6633 | 4002 | 172 | 3993 | 986 | 44 | 4.4625 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 79.3931 | 78.6070 | 80.1951 | 58.1462 | 790 | 215 | 822 | 203 | 195 | 96.0591 | |
| anovak-vg | INDEL | D1_5 | map_l150_m2_e1 | * | 82.1438 | 84.1902 | 80.1944 | 89.9891 | 655 | 123 | 660 | 163 | 64 | 39.2638 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 77.4344 | 74.8652 | 80.1862 | 50.9245 | 1805 | 606 | 1809 | 447 | 421 | 94.1834 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 83.6015 | 87.3211 | 80.1860 | 72.6837 | 13602 | 1975 | 12246 | 3026 | 728 | 24.0582 | |
| ciseli-custom | SNP | * | map_l150_m2_e0 | het | 73.2869 | 67.4862 | 80.1784 | 84.7273 | 13587 | 6546 | 13571 | 3355 | 112 | 3.3383 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 84.8128 | 90.0176 | 80.1769 | 69.3559 | 1533 | 170 | 1541 | 381 | 365 | 95.8005 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 87.8594 | 97.1731 | 80.1749 | 65.9384 | 275 | 8 | 275 | 68 | 62 | 91.1765 | |
| anovak-vg | SNP | * | map_l100_m2_e1 | * | 84.3316 | 88.9439 | 80.1741 | 71.0026 | 66474 | 8263 | 65661 | 16237 | 3582 | 22.0607 | |
| gduggal-snapvard | INDEL | I1_5 | map_l125_m2_e0 | het | 88.5120 | 98.7928 | 80.1693 | 90.7999 | 491 | 6 | 663 | 164 | 68 | 41.4634 | |
| qzeng-custom | INDEL | I16_PLUS | * | homalt | 86.1427 | 93.0814 | 80.1667 | 65.0757 | 1453 | 108 | 1443 | 357 | 186 | 52.1008 | |
| qzeng-custom | INDEL | D16_PLUS | HG002complexvar | * | 86.2026 | 93.2441 | 80.1500 | 61.6049 | 1532 | 111 | 1603 | 397 | 75 | 18.8917 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 65.3595 | 55.1783 | 80.1480 | 73.4881 | 650 | 528 | 650 | 161 | 115 | 71.4286 | |
| gduggal-bwavard | INDEL | D1_5 | map_l125_m0_e0 | het | 88.6305 | 99.1304 | 80.1418 | 91.5077 | 342 | 3 | 339 | 84 | 8 | 9.5238 | |
| gduggal-snapplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 85.3269 | 91.2425 | 80.1316 | 82.4013 | 1219 | 117 | 1218 | 302 | 5 | 1.6556 | |
| hfeng-pmm1 | INDEL | D16_PLUS | HG002compoundhet | het | 84.9405 | 90.3704 | 80.1262 | 57.0461 | 366 | 39 | 254 | 63 | 59 | 93.6508 | |