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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
16551-16600 / 86044 show all | |||||||||||||||
| bgallagher-sentieon | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.3799 | 99.5525 | 99.2079 | 75.4457 | 48055 | 216 | 47847 | 382 | 297 | 77.7487 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 92.5242 | 92.9345 | 92.1175 | 55.9701 | 12785 | 972 | 12446 | 1065 | 828 | 77.7465 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 92.5242 | 92.9345 | 92.1175 | 55.9701 | 12785 | 972 | 12446 | 1065 | 828 | 77.7465 | |
| ciseli-custom | SNP | tv | map_l125_m1_e0 | homalt | 87.0129 | 84.8123 | 89.3307 | 67.3979 | 4970 | 890 | 4965 | 593 | 461 | 77.7403 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 58.8295 | 52.0303 | 67.6729 | 41.0135 | 2473 | 2280 | 2623 | 1253 | 974 | 77.7334 | |
| anovak-vg | INDEL | I1_5 | map_siren | * | 58.1927 | 58.9351 | 57.4687 | 78.9889 | 1771 | 1234 | 1789 | 1324 | 1029 | 77.7190 | |
| hfeng-pmm2 | INDEL | * | HG002complexvar | * | 99.1003 | 98.4520 | 99.7572 | 57.3339 | 75747 | 1191 | 75614 | 184 | 143 | 77.7174 | |
| qzeng-custom | SNP | ti | map_l100_m2_e1 | het | 87.6458 | 79.3605 | 97.8627 | 80.9215 | 24570 | 6390 | 24451 | 534 | 415 | 77.7154 | |
| 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 | |
| ciseli-custom | SNP | tv | map_l125_m2_e1 | homalt | 87.1141 | 84.9193 | 89.4252 | 70.0769 | 5158 | 916 | 5150 | 609 | 473 | 77.6683 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 56.4171 | 52.9438 | 60.3781 | 34.2544 | 9667 | 8592 | 10315 | 6769 | 5257 | 77.6629 | |
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 69.5027 | 72.7855 | 66.5031 | 38.8732 | 11471 | 4289 | 21148 | 10652 | 8272 | 77.6568 | |
| anovak-vg | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 53.3229 | 48.2739 | 59.5513 | 59.8591 | 7761 | 8316 | 10724 | 7284 | 5656 | 77.6496 | |
| anovak-vg | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 53.3229 | 48.2739 | 59.5513 | 59.8591 | 7761 | 8316 | 10724 | 7284 | 5656 | 77.6496 | |
| egarrison-hhga | INDEL | I1_5 | HG002compoundhet | * | 96.1134 | 95.0631 | 97.1871 | 62.4825 | 11746 | 610 | 11747 | 340 | 264 | 77.6471 | |
| jli-custom | SNP | * | * | homalt | 99.9850 | 99.9771 | 99.9928 | 17.2570 | 1179891 | 270 | 1179875 | 85 | 66 | 77.6471 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 66.4676 | 77.4068 | 58.2374 | 31.9666 | 5170 | 1509 | 7692 | 5516 | 4283 | 77.6468 | |
| cchapple-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.8427 | 98.3427 | 99.3479 | 69.0114 | 47471 | 800 | 76325 | 501 | 389 | 77.6447 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 28.7100 | 20.4082 | 48.3974 | 46.2069 | 150 | 585 | 151 | 161 | 125 | 77.6398 | |
| anovak-vg | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 23.7087 | 15.9091 | 46.5116 | 54.5317 | 133 | 703 | 140 | 161 | 125 | 77.6398 | |
| anovak-vg | SNP | ti | HG002complexvar | het | 97.2372 | 96.4650 | 98.0220 | 17.7484 | 303639 | 11127 | 299610 | 6046 | 4694 | 77.6381 | |
| jli-custom | INDEL | D1_5 | HG002complexvar | * | 99.5191 | 99.2725 | 99.7668 | 57.5505 | 32477 | 238 | 32518 | 76 | 59 | 77.6316 | |
| astatham-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.3786 | 99.4717 | 99.2856 | 75.6401 | 48016 | 255 | 47805 | 344 | 267 | 77.6163 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.1287 | 97.8680 | 98.3908 | 64.4221 | 8217 | 179 | 8193 | 134 | 104 | 77.6119 | |
| gduggal-snapplat | INDEL | D6_15 | HG002compoundhet | hetalt | 51.7417 | 35.1859 | 97.7226 | 44.3646 | 2868 | 5283 | 2875 | 67 | 52 | 77.6119 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 64.5845 | 75.5146 | 56.4183 | 33.5145 | 5576 | 1808 | 8421 | 6505 | 5048 | 77.6018 | |
| ciseli-custom | INDEL | I1_5 | map_siren | homalt | 62.7683 | 50.4950 | 82.9235 | 77.4631 | 612 | 600 | 607 | 125 | 97 | 77.6000 | |
| eyeh-varpipe | INDEL | * | map_l100_m2_e1 | * | 94.4339 | 93.4771 | 95.4104 | 92.6391 | 3511 | 245 | 5010 | 241 | 187 | 77.5934 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.6427 | 99.5150 | 99.7707 | 54.4892 | 25236 | 123 | 25236 | 58 | 45 | 77.5862 | |
| mlin-fermikit | INDEL | D16_PLUS | HG002complexvar | het | 90.4295 | 87.7145 | 93.3180 | 67.0463 | 971 | 136 | 810 | 58 | 45 | 77.5862 | |
| gduggal-snapvard | INDEL | I1_5 | * | * | 88.2138 | 87.9937 | 88.4349 | 55.6066 | 132574 | 18089 | 133297 | 17432 | 13523 | 77.5757 | |
| ciseli-custom | SNP | tv | map_l150_m1_e0 | homalt | 85.3488 | 82.6913 | 88.1828 | 71.9082 | 3263 | 683 | 3261 | 437 | 339 | 77.5744 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 55.4070 | 49.8753 | 62.3188 | 47.9245 | 200 | 201 | 258 | 156 | 121 | 77.5641 | |
| gduggal-snapvard | INDEL | D6_15 | segdup | * | 67.8956 | 65.9686 | 69.9387 | 92.8194 | 126 | 65 | 114 | 49 | 38 | 77.5510 | |
| dgrover-gatk | INDEL | I1_5 | HG002complexvar | * | 99.7285 | 99.6044 | 99.8530 | 57.2674 | 33231 | 132 | 33279 | 49 | 38 | 77.5510 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 54.3121 | 49.8996 | 59.5807 | 47.5940 | 21624 | 21711 | 28700 | 19470 | 15099 | 77.5501 | |
| qzeng-custom | INDEL | I6_15 | HG002compoundhet | * | 75.9258 | 69.2571 | 84.0157 | 36.6439 | 6078 | 2698 | 5992 | 1140 | 884 | 77.5439 | |
| qzeng-custom | SNP | * | map_l100_m2_e0 | het | 87.9050 | 79.8638 | 97.7467 | 81.4691 | 37056 | 9343 | 36699 | 846 | 656 | 77.5414 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.9984 | 98.8832 | 99.1137 | 59.5275 | 15584 | 176 | 15433 | 138 | 107 | 77.5362 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.9803 | 95.8192 | 98.1699 | 71.2843 | 4790 | 209 | 4774 | 89 | 69 | 77.5281 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.9803 | 95.8192 | 98.1699 | 71.2843 | 4790 | 209 | 4774 | 89 | 69 | 77.5281 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 56.5143 | 51.2341 | 63.0078 | 48.1760 | 4878 | 4643 | 6033 | 3542 | 2746 | 77.5268 | |
| ciseli-custom | SNP | tv | map_l150_m2_e1 | homalt | 85.5896 | 82.9463 | 88.4069 | 74.3629 | 3429 | 705 | 3424 | 449 | 348 | 77.5056 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 51.2305 | 44.8305 | 59.7622 | 50.2699 | 7922 | 9749 | 8093 | 5449 | 4223 | 77.5005 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 51.2305 | 44.8305 | 59.7622 | 50.2699 | 7922 | 9749 | 8093 | 5449 | 4223 | 77.5005 | |
| qzeng-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 90.9981 | 84.0955 | 99.1351 | 58.5016 | 12965 | 2452 | 4585 | 40 | 31 | 77.5000 | |
| eyeh-varpipe | INDEL | C6_15 | HG002complexvar | homalt | 0.0000 | 0.0000 | 70.3704 | 81.7321 | 0 | 0 | 95 | 40 | 31 | 77.5000 | |
| mlin-fermikit | INDEL | * | map_l100_m2_e0 | * | 75.2930 | 65.9626 | 87.6978 | 80.5947 | 2436 | 1257 | 2438 | 342 | 265 | 77.4854 | |
| hfeng-pmm3 | INDEL | D6_15 | HG002complexvar | * | 97.0065 | 94.7378 | 99.3864 | 56.7243 | 5023 | 279 | 5021 | 31 | 24 | 77.4194 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.4824 | 96.4286 | 96.5363 | 69.2228 | 1728 | 64 | 1728 | 62 | 48 | 77.4194 | |