PrecisionFDA
Truth Challenge
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
39451-39500 / 86044 show all | |||||||||||||||
| gduggal-snapplat | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 81.2213 | 71.4171 | 94.1457 | 64.2321 | 5322 | 2130 | 5339 | 332 | 30 | 9.0361 | |
| gduggal-snapplat | INDEL | D1_5 | map_l250_m2_e1 | * | 81.2198 | 75.6757 | 87.6404 | 97.8476 | 140 | 45 | 156 | 22 | 5 | 22.7273 | |
| qzeng-custom | INDEL | * | map_l150_m2_e0 | het | 81.2179 | 72.2958 | 92.6521 | 95.0610 | 655 | 251 | 807 | 64 | 30 | 46.8750 | |
| qzeng-custom | INDEL | * | map_l150_m2_e1 | het | 81.2150 | 72.2944 | 92.6471 | 95.0678 | 668 | 256 | 819 | 65 | 30 | 46.1538 | |
| gduggal-bwaplat | SNP | tv | map_l100_m2_e0 | * | 81.2147 | 68.6414 | 99.4272 | 84.5184 | 17183 | 7850 | 17184 | 99 | 19 | 19.1919 | |
| gduggal-snapplat | INDEL | I1_5 | map_l150_m0_e0 | * | 81.2121 | 76.1364 | 87.0130 | 96.7157 | 134 | 42 | 134 | 20 | 1 | 5.0000 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 81.2115 | 77.3016 | 85.5379 | 66.6471 | 487 | 143 | 485 | 82 | 76 | 92.6829 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 81.2103 | 79.4781 | 83.0196 | 65.6096 | 14438 | 3728 | 14423 | 2950 | 2467 | 83.6271 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 81.2103 | 79.4781 | 83.0196 | 65.6096 | 14438 | 3728 | 14423 | 2950 | 2467 | 83.6271 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 81.2086 | 91.0256 | 73.3029 | 53.9573 | 4047 | 399 | 4017 | 1463 | 1454 | 99.3848 | |
| anovak-vg | SNP | * | map_l100_m0_e0 | * | 81.2078 | 85.4511 | 77.3660 | 74.7301 | 28063 | 4778 | 27745 | 8117 | 2172 | 26.7587 | |
| ndellapenna-hhga | INDEL | * | map_l100_m0_e0 | hetalt | 81.2065 | 75.7576 | 87.5000 | 92.6380 | 25 | 8 | 21 | 3 | 0 | 0.0000 | |
| anovak-vg | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 81.2064 | 88.9071 | 74.7333 | 41.7707 | 5971 | 745 | 6655 | 2250 | 1626 | 72.2667 | |
| ckim-vqsr | SNP | * | map_l125_m2_e0 | het | 81.2064 | 69.0122 | 98.6348 | 89.1411 | 20233 | 9085 | 20230 | 280 | 4 | 1.4286 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 81.2017 | 96.8037 | 69.9308 | 71.0611 | 636 | 21 | 1314 | 565 | 439 | 77.6991 | |
| eyeh-varpipe | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 81.2006 | 94.8980 | 70.9586 | 87.8472 | 1674 | 90 | 1251 | 512 | 45 | 8.7891 | |
| ckim-gatk | SNP | ti | map_l150_m2_e0 | * | 81.1968 | 69.3155 | 97.9938 | 88.2579 | 14218 | 6294 | 14214 | 291 | 35 | 12.0275 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 81.1947 | 74.8148 | 88.7640 | 73.9003 | 101 | 34 | 79 | 10 | 8 | 80.0000 | |
| ciseli-custom | SNP | * | map_l125_m2_e1 | * | 81.1911 | 76.9289 | 85.9532 | 77.6472 | 36312 | 10890 | 36237 | 5922 | 1525 | 25.7514 | |
| gduggal-snapplat | INDEL | D1_5 | map_l250_m2_e1 | het | 81.1906 | 79.5082 | 82.9457 | 97.9666 | 97 | 25 | 107 | 22 | 5 | 22.7273 | |
| mlin-fermikit | INDEL | D6_15 | map_siren | * | 81.1872 | 77.0138 | 85.8388 | 82.0071 | 392 | 117 | 394 | 65 | 53 | 81.5385 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 81.1856 | 91.0405 | 73.2558 | 68.6589 | 315 | 31 | 315 | 115 | 55 | 47.8261 | |
| anovak-vg | INDEL | D1_5 | map_l150_m2_e0 | het | 81.1800 | 88.1323 | 75.2443 | 90.1933 | 453 | 61 | 462 | 152 | 57 | 37.5000 | |
| ciseli-custom | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 81.1779 | 95.3254 | 70.6870 | 69.0825 | 4629 | 227 | 4671 | 1937 | 164 | 8.4667 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 81.1769 | 94.8227 | 70.9646 | 59.4330 | 1337 | 73 | 1442 | 590 | 557 | 94.4068 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 81.1730 | 89.2820 | 74.4143 | 49.8151 | 858 | 103 | 2827 | 972 | 485 | 49.8971 | |
| eyeh-varpipe | INDEL | I6_15 | segdup | * | 81.1709 | 76.0000 | 87.0968 | 88.6197 | 133 | 42 | 135 | 20 | 20 | 100.0000 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 81.1651 | 84.7285 | 77.8894 | 53.1421 | 8067 | 1454 | 8067 | 2290 | 2086 | 91.0917 | |
| ciseli-custom | SNP | * | map_l100_m0_e0 | * | 81.1632 | 76.8673 | 85.9677 | 74.4366 | 25244 | 7597 | 25198 | 4113 | 1141 | 27.7413 | |
| jpowers-varprowl | SNP | tv | lowcmp_SimpleRepeat_quadTR_51to200 | * | 81.1610 | 90.4762 | 73.5849 | 91.1519 | 38 | 4 | 39 | 14 | 2 | 14.2857 | |
| qzeng-custom | SNP | * | map_l100_m1_e0 | hetalt | 81.1594 | 68.2927 | 100.0000 | 88.6179 | 28 | 13 | 28 | 0 | 0 | ||
| qzeng-custom | SNP | tv | map_l100_m1_e0 | hetalt | 81.1594 | 68.2927 | 100.0000 | 88.6179 | 28 | 13 | 28 | 0 | 0 | ||
| qzeng-custom | INDEL | * | map_l150_m2_e0 | * | 81.1578 | 71.3778 | 94.0432 | 94.0095 | 1005 | 403 | 1263 | 80 | 39 | 48.7500 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 81.1561 | 92.0082 | 72.5938 | 67.9226 | 449 | 39 | 445 | 168 | 63 | 37.5000 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 81.1540 | 77.3058 | 85.4054 | 60.1508 | 637 | 187 | 632 | 108 | 59 | 54.6296 | |
| anovak-vg | SNP | ti | map_l100_m0_e0 | * | 81.1499 | 85.0168 | 77.6195 | 74.1271 | 18509 | 3262 | 18364 | 5295 | 1408 | 26.5911 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 81.1499 | 74.3504 | 89.3182 | 33.8346 | 3548 | 1224 | 393 | 47 | 47 | 100.0000 | |
| jmaeng-gatk | SNP | ti | map_l150_m2_e0 | * | 81.1449 | 69.3009 | 97.8719 | 88.3988 | 14215 | 6297 | 14211 | 309 | 34 | 11.0032 | |
| anovak-vg | INDEL | D1_5 | map_l150_m2_e1 | het | 81.1378 | 88.3142 | 75.0400 | 90.1683 | 461 | 61 | 469 | 156 | 58 | 37.1795 | |
| anovak-vg | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 81.1375 | 80.9173 | 81.3588 | 37.8886 | 3299 | 778 | 3365 | 771 | 561 | 72.7626 | |
| ghariani-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 81.1357 | 96.1059 | 70.2007 | 87.2590 | 2542 | 103 | 2589 | 1099 | 4 | 0.3640 | |
| 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 | SNP | ti | map_siren | hetalt | 81.1321 | 75.4386 | 87.7551 | 63.1579 | 43 | 14 | 43 | 6 | 6 | 100.0000 | |
| gduggal-bwavard | SNP | tv | HG002compoundhet | * | 81.1305 | 78.3481 | 84.1178 | 52.1015 | 6991 | 1932 | 7113 | 1343 | 1177 | 87.6396 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | * | 81.1268 | 69.5652 | 97.2973 | 43.0769 | 32 | 14 | 36 | 1 | 1 | 100.0000 | |
| gduggal-bwaplat | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | het | 81.1243 | 68.8494 | 98.7257 | 59.8978 | 1472 | 666 | 1472 | 19 | 4 | 21.0526 | |
| ciseli-custom | SNP | * | map_l125_m2_e0 | * | 81.1188 | 76.8380 | 85.9047 | 77.6345 | 35901 | 10822 | 35830 | 5879 | 1516 | 25.7867 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 81.1184 | 79.6209 | 82.6733 | 50.0000 | 168 | 43 | 167 | 35 | 34 | 97.1429 | |
| gduggal-bwavard | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 81.1166 | 86.3636 | 76.4706 | 96.8460 | 38 | 6 | 39 | 12 | 11 | 91.6667 | |
| hfeng-pmm3 | INDEL | I6_15 | HG002compoundhet | het | 81.1158 | 79.8077 | 82.4675 | 86.8038 | 166 | 42 | 127 | 27 | 25 | 92.5926 | |