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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
22151-22200 / 86044 show all | |||||||||||||||
| ckim-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.0364 | 98.8318 | 99.2419 | 76.8770 | 6345 | 75 | 6284 | 48 | 25 | 52.0833 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 88.3047 | 90.1065 | 86.5734 | 76.6949 | 592 | 65 | 619 | 96 | 50 | 52.0833 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 87.7499 | 80.8367 | 95.9562 | 58.8989 | 599 | 142 | 1139 | 48 | 25 | 52.0833 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 78.1375 | 85.3261 | 72.0660 | 79.7424 | 942 | 162 | 1179 | 457 | 238 | 52.0788 | |
| ndellapenna-hhga | SNP | ti | map_l100_m1_e0 | * | 99.3542 | 98.8671 | 99.8462 | 61.3943 | 47388 | 543 | 47390 | 73 | 38 | 52.0548 | |
| gduggal-snapfb | SNP | ti | map_l250_m2_e0 | * | 94.5805 | 94.0895 | 95.0767 | 89.6969 | 4712 | 296 | 4712 | 244 | 127 | 52.0492 | |
| rpoplin-dv42 | SNP | * | * | * | 99.9587 | 99.9447 | 99.9728 | 19.0681 | 3052930 | 1689 | 3052766 | 832 | 433 | 52.0433 | |
| gduggal-snapplat | SNP | tv | map_l125_m2_e0 | * | 93.3644 | 91.2184 | 95.6138 | 83.0664 | 15041 | 1448 | 15041 | 690 | 359 | 52.0290 | |
| gduggal-snapvard | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.0218 | 96.6030 | 99.4830 | 58.8566 | 9754 | 343 | 9622 | 50 | 26 | 52.0000 | |
| egarrison-hhga | INDEL | * | map_siren | * | 97.8660 | 97.7598 | 97.9724 | 96.4159 | 7244 | 166 | 7248 | 150 | 78 | 52.0000 | |
| ndellapenna-hhga | INDEL | * | map_siren | * | 97.7903 | 97.6113 | 97.9700 | 96.5183 | 7233 | 177 | 7239 | 150 | 78 | 52.0000 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 94.3155 | 95.0867 | 93.5567 | 70.3591 | 329 | 17 | 363 | 25 | 13 | 52.0000 | |
| gduggal-bwaplat | INDEL | I16_PLUS | * | het | 55.5939 | 38.8521 | 97.6895 | 77.4865 | 1056 | 1662 | 1057 | 25 | 13 | 52.0000 | |
| gduggal-snapplat | SNP | ti | map_l250_m2_e0 | het | 88.7434 | 85.9865 | 91.6830 | 94.7245 | 2798 | 456 | 2800 | 254 | 132 | 51.9685 | |
| anovak-vg | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 96.3676 | 96.1079 | 96.6286 | 54.1432 | 24372 | 987 | 24047 | 839 | 436 | 51.9666 | |
| ndellapenna-hhga | SNP | * | map_l150_m1_e0 | * | 99.0061 | 98.2783 | 99.7447 | 72.1099 | 30082 | 527 | 30082 | 77 | 40 | 51.9481 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 17.1893 | 11.5659 | 33.4554 | 78.2586 | 243 | 1858 | 274 | 545 | 283 | 51.9266 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 94.1085 | 91.0009 | 97.4359 | 68.1633 | 1982 | 196 | 1976 | 52 | 27 | 51.9231 | |
| jpowers-varprowl | INDEL | D1_5 | map_l125_m2_e0 | * | 94.6208 | 93.8758 | 95.3778 | 87.2043 | 1073 | 70 | 1073 | 52 | 27 | 51.9231 | |
| gduggal-snapplat | SNP | ti | map_l100_m2_e1 | * | 95.8022 | 94.4145 | 97.2313 | 76.1409 | 46721 | 2764 | 46742 | 1331 | 691 | 51.9159 | |
| jpowers-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 94.4849 | 99.6935 | 89.7936 | 83.3014 | 3903 | 12 | 3915 | 445 | 231 | 51.9101 | |
| gduggal-snapplat | SNP | ti | map_l250_m1_e0 | het | 88.1746 | 85.1415 | 91.4317 | 94.5451 | 2527 | 441 | 2529 | 237 | 123 | 51.8987 | |
| gduggal-snapplat | SNP | tv | map_l125_m2_e1 | * | 93.3986 | 91.2649 | 95.6344 | 83.1005 | 15202 | 1455 | 15203 | 694 | 360 | 51.8732 | |
| dgrover-gatk | INDEL | D1_5 | * | het | 99.7614 | 99.7979 | 99.7250 | 59.4296 | 87397 | 177 | 87406 | 241 | 125 | 51.8672 | |
| gduggal-snapplat | SNP | ti | map_l100_m1_e0 | * | 95.7091 | 94.2918 | 97.1698 | 74.6083 | 45195 | 2736 | 45216 | 1317 | 683 | 51.8603 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 96.1044 | 93.8977 | 98.4174 | 74.4802 | 1708 | 111 | 1679 | 27 | 14 | 51.8519 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 96.1044 | 93.8977 | 98.4174 | 74.4802 | 1708 | 111 | 1679 | 27 | 14 | 51.8519 | |
| jpowers-varprowl | INDEL | D1_5 | map_l125_m2_e1 | * | 94.5581 | 93.8634 | 95.2632 | 87.2725 | 1086 | 71 | 1086 | 54 | 28 | 51.8519 | |
| ltrigg-rtg1 | INDEL | I1_5 | HG002complexvar | het | 99.2372 | 98.7905 | 99.6881 | 51.9353 | 17969 | 220 | 17257 | 54 | 28 | 51.8519 | |
| ndellapenna-hhga | INDEL | I16_PLUS | HG002complexvar | * | 92.7599 | 90.0688 | 95.6169 | 66.4762 | 1179 | 130 | 1178 | 54 | 28 | 51.8519 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.3687 | 96.7718 | 97.9730 | 70.6802 | 1319 | 44 | 1305 | 27 | 14 | 51.8519 | |
| qzeng-custom | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.3772 | 99.5369 | 99.2181 | 66.4594 | 3439 | 16 | 3426 | 27 | 14 | 51.8519 | |
| gduggal-snapplat | SNP | tv | map_l125_m1_e0 | * | 93.2502 | 91.0465 | 95.5633 | 81.8317 | 14582 | 1434 | 14582 | 677 | 351 | 51.8464 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 78.3192 | 73.5341 | 83.7704 | 54.2583 | 31866 | 11469 | 36291 | 7031 | 3645 | 51.8418 | |
| gduggal-snapplat | SNP | ti | map_l100_m2_e0 | * | 95.7724 | 94.3751 | 97.2116 | 76.1299 | 46207 | 2754 | 46228 | 1326 | 687 | 51.8100 | |
| rpoplin-dv42 | SNP | tv | map_l125_m0_e0 | het | 98.3333 | 98.5458 | 98.1217 | 74.3380 | 4337 | 64 | 4336 | 83 | 43 | 51.8072 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 75.3156 | 74.9046 | 75.7313 | 50.0285 | 2943 | 986 | 3314 | 1062 | 550 | 51.7891 | |
| gduggal-snapfb | SNP | ti | map_l150_m1_e0 | * | 96.2042 | 95.8452 | 96.5660 | 76.1103 | 18893 | 819 | 18897 | 672 | 348 | 51.7857 | |
| ghariani-varprowl | SNP | tv | segdup | homalt | 99.0657 | 99.8456 | 98.2979 | 91.0501 | 3233 | 5 | 3234 | 56 | 29 | 51.7857 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 95.6374 | 95.8769 | 95.3990 | 63.4546 | 17417 | 749 | 17417 | 840 | 435 | 51.7857 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 95.6374 | 95.8769 | 95.3990 | 63.4546 | 17417 | 749 | 17417 | 840 | 435 | 51.7857 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 90.4376 | 83.7686 | 98.2603 | 35.1614 | 1636 | 317 | 1638 | 29 | 15 | 51.7241 | |
| ciseli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 20.7836 | 13.0081 | 51.6667 | 91.2281 | 32 | 214 | 31 | 29 | 15 | 51.7241 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.3931 | 96.1967 | 98.6197 | 73.1673 | 2074 | 82 | 2072 | 29 | 15 | 51.7241 | |
| anovak-vg | INDEL | * | segdup | het | 72.6201 | 63.5061 | 84.7882 | 95.6374 | 931 | 535 | 981 | 176 | 91 | 51.7045 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 87.2372 | 87.9811 | 86.5058 | 47.3544 | 13008 | 1777 | 14193 | 2214 | 1144 | 51.6712 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 46.1795 | 45.3564 | 47.0329 | 65.4087 | 1807 | 2177 | 1815 | 2044 | 1056 | 51.6634 | |
| gduggal-snapfb | SNP | ti | map_l250_m2_e1 | het | 94.1247 | 95.4229 | 92.8614 | 87.6593 | 3148 | 151 | 3148 | 242 | 125 | 51.6529 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 57.2983 | 42.6638 | 87.2144 | 64.2116 | 4728 | 6354 | 4543 | 666 | 344 | 51.6517 | |
| gduggal-snapplat | SNP | tv | map_l125_m2_e0 | het | 93.2998 | 93.1527 | 93.4473 | 85.9522 | 9727 | 715 | 9726 | 682 | 352 | 51.6129 | |