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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
54151-54200 / 86044 show all | |||||||||||||||
| gduggal-bwafb | INDEL | I16_PLUS | map_l125_m1_e0 | * | 42.1053 | 26.6667 | 100.0000 | 87.0968 | 4 | 11 | 4 | 0 | 0 | ||
| hfeng-pmm1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 94.5883 | 90.0626 | 99.5930 | 87.0976 | 2447 | 270 | 2447 | 10 | 4 | 40.0000 | |
| jli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.8825 | 98.9969 | 98.7683 | 87.0977 | 1283 | 13 | 1283 | 16 | 6 | 37.5000 | |
| gduggal-snapfb | INDEL | I1_5 | map_l125_m1_e0 | * | 96.2822 | 96.8675 | 95.7041 | 87.0978 | 804 | 26 | 802 | 36 | 7 | 19.4444 | |
| ckim-gatk | INDEL | I1_5 | map_l100_m1_e0 | * | 97.9664 | 98.7304 | 97.2141 | 87.0980 | 1322 | 17 | 1326 | 38 | 5 | 13.1579 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 96.7604 | 97.5124 | 96.0199 | 87.0988 | 196 | 5 | 193 | 8 | 1 | 12.5000 | |
| gduggal-snapvard | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 0.0000 | 0.0000 | 21.0702 | 87.1009 | 0 | 0 | 63 | 236 | 11 | 4.6610 | |
| asubramanian-gatk | INDEL | I1_5 | map_l100_m1_e0 | * | 91.2060 | 85.1382 | 98.2051 | 87.1018 | 1140 | 199 | 1149 | 21 | 4 | 19.0476 | |
| egarrison-hhga | INDEL | D6_15 | map_l100_m2_e0 | het | 94.4089 | 98.4733 | 90.6667 | 87.1023 | 129 | 2 | 136 | 14 | 9 | 64.2857 | |
| jmaeng-gatk | INDEL | I1_5 | map_l150_m1_e0 | homalt | 98.7406 | 98.9899 | 98.4925 | 87.1030 | 196 | 2 | 196 | 3 | 2 | 66.6667 | |
| ckim-dragen | INDEL | I1_5 | map_l100_m2_e0 | het | 96.2025 | 95.8386 | 96.5693 | 87.1089 | 760 | 33 | 760 | 27 | 3 | 11.1111 | |
| ckim-dragen | INDEL | * | map_l100_m2_e0 | * | 96.9907 | 97.3734 | 96.6111 | 87.1158 | 3596 | 97 | 3592 | 126 | 19 | 15.0794 | |
| gduggal-snapfb | INDEL | I1_5 | map_l100_m2_e0 | homalt | 98.6891 | 99.2467 | 98.1378 | 87.1161 | 527 | 4 | 527 | 10 | 4 | 40.0000 | |
| jmaeng-gatk | INDEL | D1_5 | map_l125_m0_e0 | homalt | 98.3051 | 97.9730 | 98.6395 | 87.1166 | 145 | 3 | 145 | 2 | 2 | 100.0000 | |
| ndellapenna-hhga | INDEL | I1_5 | map_l125_m2_e0 | het | 98.4833 | 97.9879 | 98.9837 | 87.1170 | 487 | 10 | 487 | 5 | 0 | 0.0000 | |
| qzeng-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 96.9150 | 98.5617 | 95.3224 | 87.1181 | 6784 | 99 | 6888 | 338 | 49 | 14.4970 | |
| dgrover-gatk | INDEL | I16_PLUS | map_siren | hetalt | 100.0000 | 100.0000 | 100.0000 | 87.1212 | 16 | 0 | 17 | 0 | 0 | ||
| cchapple-custom | INDEL | I6_15 | map_l100_m1_e0 | * | 92.7767 | 92.1053 | 93.4579 | 87.1239 | 105 | 9 | 100 | 7 | 2 | 28.5714 | |
| asubramanian-gatk | INDEL | I1_5 | map_l125_m0_e0 | homalt | 96.8326 | 93.8596 | 100.0000 | 87.1239 | 107 | 7 | 107 | 0 | 0 | ||
| jpowers-varprowl | INDEL | * | map_l150_m2_e1 | homalt | 95.1579 | 91.8699 | 98.6900 | 87.1240 | 452 | 40 | 452 | 6 | 4 | 66.6667 | |
| gduggal-bwaplat | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 39.1304 | 25.0000 | 90.0000 | 87.1245 | 27 | 81 | 27 | 3 | 3 | 100.0000 | |
| gduggal-snapfb | INDEL | I6_15 | segdup | * | 85.8304 | 80.5714 | 91.8239 | 87.1255 | 141 | 34 | 146 | 13 | 13 | 100.0000 | |
| anovak-vg | INDEL | * | map_l100_m0_e0 | * | 72.6539 | 73.0006 | 72.3105 | 87.1262 | 1141 | 422 | 1183 | 453 | 264 | 58.2781 | |
| hfeng-pmm3 | INDEL | D1_5 | map_l150_m2_e0 | het | 98.5517 | 99.0272 | 98.0806 | 87.1263 | 509 | 5 | 511 | 10 | 2 | 20.0000 | |
| dgrover-gatk | INDEL | * | map_siren | hetalt | 97.0971 | 94.7368 | 99.5781 | 87.1266 | 234 | 13 | 236 | 1 | 0 | 0.0000 | |
| gduggal-snapfb | INDEL | I1_5 | map_l125_m0_e0 | het | 92.5065 | 93.2292 | 91.7949 | 87.1287 | 179 | 13 | 179 | 16 | 2 | 12.5000 | |
| anovak-vg | INDEL | C6_15 | HG002complexvar | * | 55.5556 | 100.0000 | 38.4615 | 87.1287 | 4 | 0 | 10 | 16 | 4 | 25.0000 | |
| bgallagher-sentieon | INDEL | D6_15 | map_l100_m2_e1 | homalt | 98.4848 | 97.0149 | 100.0000 | 87.1287 | 65 | 2 | 65 | 0 | 0 | ||
| ciseli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 14.2857 | 100.0000 | 7.6923 | 87.1287 | 1 | 0 | 1 | 12 | 10 | 83.3333 | |
| hfeng-pmm1 | INDEL | * | map_l100_m1_e0 | hetalt | 94.9153 | 90.3226 | 100.0000 | 87.1298 | 112 | 12 | 113 | 0 | 0 | ||
| gduggal-snapvard | SNP | tv | map_l150_m0_e0 | het | 83.5823 | 96.6936 | 73.6022 | 87.1311 | 2749 | 94 | 2738 | 982 | 41 | 4.1752 | |
| anovak-vg | SNP | ti | segdup | homalt | 98.8024 | 98.6009 | 99.0047 | 87.1313 | 7400 | 105 | 7361 | 74 | 73 | 98.6486 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 79.3103 | 100.0000 | 65.7143 | 87.1324 | 23 | 0 | 23 | 12 | 11 | 91.6667 | |
| bgallagher-sentieon | INDEL | D1_5 | map_l125_m0_e0 | homalt | 98.9899 | 99.3243 | 98.6577 | 87.1330 | 147 | 1 | 147 | 2 | 2 | 100.0000 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 71.8766 | 64.7541 | 80.7595 | 87.1336 | 316 | 172 | 319 | 76 | 1 | 1.3158 | |
| jli-custom | INDEL | * | map_siren | hetalt | 93.3352 | 87.8543 | 99.5455 | 87.1345 | 217 | 30 | 219 | 1 | 0 | 0.0000 | |
| qzeng-custom | SNP | tv | map_l150_m2_e1 | * | 83.1087 | 72.8830 | 96.6721 | 87.1352 | 8383 | 3119 | 8366 | 288 | 243 | 84.3750 | |
| bgallagher-sentieon | INDEL | I1_5 | map_l125_m2_e1 | * | 98.7952 | 98.8506 | 98.7400 | 87.1353 | 860 | 10 | 862 | 11 | 2 | 18.1818 | |
| jli-custom | INDEL | I6_15 | map_l100_m2_e0 | homalt | 96.8750 | 93.9394 | 100.0000 | 87.1369 | 31 | 2 | 31 | 0 | 0 | ||
| jpowers-varprowl | INDEL | * | map_l150_m2_e0 | homalt | 95.3714 | 92.0998 | 98.8839 | 87.1375 | 443 | 38 | 443 | 5 | 3 | 60.0000 | |
| raldana-dualsentieon | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 93.8925 | 88.9660 | 99.3966 | 87.1383 | 1153 | 143 | 1153 | 7 | 4 | 57.1429 | |
| ckim-vqsr | INDEL | * | map_siren | het | 97.3739 | 96.6060 | 98.1540 | 87.1388 | 4355 | 153 | 4360 | 82 | 11 | 13.4146 | |
| hfeng-pmm3 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 93.8877 | 88.8889 | 99.4823 | 87.1394 | 1152 | 144 | 1153 | 6 | 1 | 16.6667 | |
| ckim-isaac | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 88.3117 | 82.9268 | 94.4444 | 87.1429 | 34 | 7 | 34 | 2 | 1 | 50.0000 | |
| gduggal-snapvard | INDEL | C6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 0.0000 | 0.0000 | 11.1111 | 87.1429 | 0 | 0 | 4 | 32 | 2 | 6.2500 | |
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 94.5603 | 90.2098 | 99.3517 | 87.1432 | 2451 | 266 | 2452 | 16 | 4 | 25.0000 | |
| jpowers-varprowl | INDEL | D6_15 | map_l100_m2_e0 | het | 74.6835 | 90.0763 | 63.7838 | 87.1438 | 118 | 13 | 118 | 67 | 64 | 95.5224 | |
| eyeh-varpipe | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 90.0673 | 98.7902 | 82.7599 | 87.1462 | 2613 | 32 | 2285 | 476 | 24 | 5.0420 | |
| anovak-vg | SNP | ti | map_l250_m1_e0 | homalt | 84.7951 | 73.9266 | 99.4103 | 87.1481 | 1188 | 419 | 1180 | 7 | 5 | 71.4286 | |
| gduggal-bwaplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 85.7476 | 75.5007 | 99.2126 | 87.1486 | 1131 | 367 | 1134 | 9 | 8 | 88.8889 | |