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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
4851-4900 / 86044 show all | |||||||||||||||
| hfeng-pmm2 | INDEL | I1_5 | * | * | 99.4998 | 99.2726 | 99.7280 | 57.5644 | 149568 | 1096 | 149613 | 408 | 306 | 75.0000 | |
| hfeng-pmm2 | SNP | * | HG002compoundhet | het | 95.9129 | 92.2768 | 99.8474 | 42.7742 | 13083 | 1095 | 13083 | 20 | 3 | 15.0000 | |
| jlack-gatk | INDEL | I1_5 | HG002compoundhet | * | 93.1060 | 91.1379 | 95.1609 | 67.4017 | 11261 | 1095 | 11268 | 573 | 557 | 97.2077 | |
| gduggal-snapvard | SNP | ti | map_l100_m2_e1 | het | 93.6568 | 96.4632 | 91.0091 | 78.1383 | 29865 | 1095 | 29608 | 2925 | 251 | 8.5812 | |
| ckim-vqsr | SNP | tv | map_l150_m0_e0 | homalt | 29.9616 | 17.6205 | 100.0000 | 94.7814 | 234 | 1094 | 234 | 0 | 0 | ||
| ckim-isaac | INDEL | * | map_l100_m1_e0 | * | 81.4370 | 69.4925 | 98.3399 | 83.2871 | 2492 | 1094 | 2488 | 42 | 20 | 47.6190 | |
| gduggal-bwavard | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 60.8979 | 43.9836 | 98.9498 | 39.8596 | 859 | 1094 | 848 | 9 | 7 | 77.7778 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 9.0082 | 7.4513 | 11.3874 | 43.3234 | 88 | 1093 | 87 | 677 | 676 | 99.8523 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 94.1021 | 89.2612 | 99.4983 | 58.0297 | 9085 | 1093 | 9122 | 46 | 12 | 26.0870 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 25.7297 | 17.3354 | 49.8866 | 62.4361 | 229 | 1092 | 220 | 221 | 16 | 7.2398 | |
| gduggal-snapvard | SNP | ti | map_l100_m2_e0 | het | 93.6224 | 96.4339 | 90.9701 | 78.1195 | 29530 | 1092 | 29276 | 2906 | 248 | 8.5341 | |
| gduggal-bwavard | SNP | * | map_l125_m2_e1 | * | 95.7732 | 97.6865 | 93.9333 | 79.9451 | 46110 | 1092 | 45506 | 2939 | 183 | 6.2266 | |
| ciseli-custom | SNP | ti | map_l150_m2_e0 | homalt | 87.0824 | 85.6618 | 88.5509 | 72.6120 | 6524 | 1092 | 6520 | 843 | 689 | 81.7319 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.4536 | 93.4690 | 99.6351 | 39.9267 | 15614 | 1091 | 15838 | 58 | 57 | 98.2759 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.4536 | 93.4690 | 99.6351 | 39.9267 | 15614 | 1091 | 15838 | 58 | 57 | 98.2759 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 91.3158 | 84.0193 | 100.0000 | 93.1818 | 5736 | 1091 | 3 | 0 | 0 | ||
| jpowers-varprowl | SNP | ti | map_l100_m1_e0 | * | 98.2270 | 97.7259 | 98.7332 | 68.5176 | 46841 | 1090 | 46843 | 601 | 190 | 31.6140 | |
| gduggal-bwaplat | INDEL | I6_15 | HG002complexvar | * | 86.2963 | 77.2538 | 97.7362 | 64.0519 | 3702 | 1090 | 3713 | 86 | 50 | 58.1395 | |
| gduggal-bwaplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 88.6934 | 79.9189 | 99.6323 | 81.5479 | 4334 | 1089 | 4335 | 16 | 15 | 93.7500 | |
| gduggal-bwaplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 88.6934 | 79.9189 | 99.6323 | 81.5479 | 4334 | 1089 | 4335 | 16 | 15 | 93.7500 | |
| ndellapenna-hhga | INDEL | D16_PLUS | HG002compoundhet | * | 63.8133 | 53.4814 | 79.0931 | 40.7537 | 1252 | 1089 | 1343 | 355 | 284 | 80.0000 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 26.6407 | 17.5625 | 55.1471 | 66.3088 | 232 | 1089 | 225 | 183 | 170 | 92.8962 | |
| qzeng-custom | INDEL | I16_PLUS | * | * | 83.4199 | 82.9387 | 83.9068 | 61.2425 | 5289 | 1088 | 5292 | 1015 | 362 | 35.6650 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 58.8469 | 92.5566 | 43.1364 | 52.0545 | 13529 | 1088 | 13550 | 17862 | 17494 | 97.9398 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 91.1545 | 88.4965 | 93.9771 | 38.2912 | 8370 | 1088 | 8301 | 532 | 447 | 84.0226 | |
| gduggal-snapplat | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 0.0000 | 0.0000 | 0.0000 | 0 | 1088 | 0 | 0 | 0 | |||
| gduggal-snapfb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 0.0000 | 0.0000 | 0.0000 | 0 | 1088 | 0 | 0 | 0 | |||
| ckim-isaac | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 92.7405 | 88.7846 | 97.0653 | 58.2458 | 8605 | 1087 | 8798 | 266 | 144 | 54.1353 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 48.8684 | 40.9881 | 60.5000 | 69.8341 | 755 | 1087 | 726 | 474 | 272 | 57.3840 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 72.4268 | 57.1879 | 98.7375 | 38.9205 | 1452 | 1087 | 1486 | 19 | 19 | 100.0000 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 95.8065 | 92.2605 | 99.6360 | 30.7769 | 12946 | 1086 | 13139 | 48 | 48 | 100.0000 | |
| ckim-isaac | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 97.1734 | 94.6284 | 99.8591 | 48.1340 | 19114 | 1085 | 19138 | 27 | 18 | 66.6667 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 16.5740 | 9.2050 | 83.0918 | 78.3246 | 110 | 1085 | 172 | 35 | 24 | 68.5714 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 0.7326 | 0.3676 | 100.0000 | 86.4865 | 4 | 1084 | 5 | 0 | 0 | ||
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 41.1620 | 27.4615 | 82.1429 | 68.1214 | 410 | 1083 | 414 | 90 | 76 | 84.4444 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 89.9396 | 84.3248 | 96.3555 | 40.6305 | 5826 | 1083 | 5843 | 221 | 166 | 75.1131 | |
| jpowers-varprowl | SNP | * | HG002compoundhet | het | 94.4520 | 92.3614 | 96.6395 | 53.1760 | 13095 | 1083 | 13286 | 462 | 40 | 8.6580 | |
| gduggal-bwavard | SNP | * | map_l125_m2_e0 | * | 95.7523 | 97.6821 | 93.8973 | 79.8955 | 45640 | 1083 | 45051 | 2928 | 182 | 6.2159 | |
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 43.4388 | 29.2157 | 84.6482 | 63.0999 | 447 | 1083 | 397 | 72 | 71 | 98.6111 | |
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 43.4388 | 29.2157 | 84.6482 | 63.0999 | 447 | 1083 | 397 | 72 | 71 | 98.6111 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 0.0000 | 4.3324 | 0.0000 | 0.0000 | 49 | 1082 | 0 | 0 | 0 | ||
| anovak-vg | SNP | ti | map_l125_m0_e0 | homalt | 86.0648 | 75.9296 | 99.3223 | 69.5933 | 3410 | 1081 | 3371 | 23 | 21 | 91.3043 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.0742 | 96.5582 | 99.6386 | 56.1134 | 30327 | 1081 | 30328 | 110 | 94 | 85.4545 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.0742 | 96.5582 | 99.6386 | 56.1134 | 30327 | 1081 | 30328 | 110 | 94 | 85.4545 | |
| raldana-dualsentieon | SNP | * | HG002compoundhet | het | 95.9874 | 92.3755 | 99.8932 | 43.8424 | 13097 | 1081 | 13096 | 14 | 7 | 50.0000 | |
| gduggal-snapplat | SNP | ti | map_l150_m0_e0 | * | 90.2459 | 86.2613 | 94.6165 | 87.8341 | 6781 | 1080 | 6784 | 386 | 225 | 58.2902 | |
| ckim-isaac | INDEL | I16_PLUS | * | hetalt | 65.0682 | 48.5224 | 98.7366 | 42.1910 | 1018 | 1080 | 1016 | 13 | 11 | 84.6154 | |
| gduggal-bwafb | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 95.7841 | 93.1472 | 98.5746 | 46.7673 | 14680 | 1080 | 25103 | 363 | 284 | 78.2369 | |
| anovak-vg | SNP | tv | map_l125_m0_e0 | * | 78.9708 | 83.7129 | 74.7373 | 81.6028 | 5551 | 1080 | 5547 | 1875 | 540 | 28.8000 | |
| anovak-vg | SNP | * | map_l150_m0_e0 | het | 75.3571 | 86.4106 | 66.8109 | 87.0439 | 6861 | 1079 | 6796 | 3376 | 934 | 27.6659 | |