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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
58001-58050 / 86044 show all | |||||||||||||||
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.0563 | 99.8206 | 98.3037 | 63.5993 | 8345 | 15 | 8345 | 144 | 142 | 98.6111 | |
| astatham-gatk | INDEL | D6_15 | HG002compoundhet | het | 89.8182 | 98.2477 | 82.7210 | 68.4623 | 841 | 15 | 833 | 174 | 172 | 98.8506 | |
| astatham-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.4245 | 96.5596 | 98.3051 | 85.6945 | 421 | 15 | 406 | 7 | 5 | 71.4286 | |
| astatham-gatk | INDEL | I6_15 | map_siren | het | 93.7729 | 89.5105 | 98.4615 | 87.4396 | 128 | 15 | 128 | 2 | 1 | 50.0000 | |
| asubramanian-gatk | SNP | tv | map_l150_m1_e0 | hetalt | 40.0000 | 25.0000 | 100.0000 | 94.6237 | 5 | 15 | 5 | 0 | 0 | ||
| asubramanian-gatk | SNP | tv | map_l150_m2_e0 | hetalt | 40.0000 | 25.0000 | 100.0000 | 95.6140 | 5 | 15 | 5 | 0 | 0 | ||
| asubramanian-gatk | SNP | tv | map_l150_m2_e1 | hetalt | 40.0000 | 25.0000 | 100.0000 | 95.6140 | 5 | 15 | 5 | 0 | 0 | ||
| bgallagher-sentieon | INDEL | * | map_l150_m2_e1 | het | 97.5914 | 98.3766 | 96.8187 | 91.2287 | 909 | 15 | 913 | 30 | 4 | 13.3333 | |
| bgallagher-sentieon | INDEL | D16_PLUS | HG002complexvar | het | 98.0634 | 98.6450 | 97.4886 | 68.5684 | 1092 | 15 | 854 | 22 | 12 | 54.5455 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 92.5887 | 97.7444 | 87.9496 | 86.9299 | 650 | 15 | 489 | 67 | 56 | 83.5821 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 95.7830 | 98.8722 | 92.8811 | 83.4809 | 1315 | 15 | 1109 | 85 | 72 | 84.7059 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.6951 | 99.7767 | 99.6136 | 53.1211 | 6701 | 15 | 6703 | 26 | 9 | 34.6154 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 98.0971 | 98.0315 | 98.1627 | 67.6020 | 747 | 15 | 748 | 14 | 7 | 50.0000 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.7177 | 99.6321 | 99.8035 | 42.5670 | 4062 | 15 | 4064 | 8 | 5 | 62.5000 | |
| rpoplin-dv42 | INDEL | D1_5 | map_l125_m1_e0 | het | 98.0040 | 97.9339 | 98.0743 | 85.2983 | 711 | 15 | 713 | 14 | 3 | 21.4286 | |
| rpoplin-dv42 | INDEL | D1_5 | map_l125_m2_e0 | het | 98.1032 | 98.0366 | 98.1699 | 85.9427 | 749 | 15 | 751 | 14 | 3 | 21.4286 | |
| rpoplin-dv42 | INDEL | D1_5 | map_l125_m2_e1 | het | 98.1180 | 98.0519 | 98.1842 | 86.0452 | 755 | 15 | 757 | 14 | 3 | 21.4286 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.2764 | 99.1329 | 99.4203 | 34.7086 | 1715 | 15 | 1715 | 10 | 10 | 100.0000 | |
| rpoplin-dv42 | INDEL | D6_15 | map_l100_m2_e1 | * | 94.8905 | 94.5455 | 95.2381 | 86.0143 | 260 | 15 | 260 | 13 | 7 | 53.8462 | |
| rpoplin-dv42 | INDEL | I1_5 | map_l125_m1_e0 | het | 98.1263 | 96.9136 | 99.3697 | 85.6928 | 471 | 15 | 473 | 3 | 2 | 66.6667 | |
| rpoplin-dv42 | INDEL | I1_5 | segdup | * | 98.8177 | 98.5836 | 99.0530 | 94.2377 | 1044 | 15 | 1046 | 10 | 9 | 90.0000 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 85.9813 | 75.4098 | 100.0000 | 55.3398 | 46 | 15 | 46 | 0 | 0 | ||
| rpoplin-dv42 | INDEL | I6_15 | map_siren | het | 92.4188 | 89.5105 | 95.5224 | 83.4568 | 128 | 15 | 128 | 6 | 6 | 100.0000 | |
| rpoplin-dv42 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 99.0365 | 99.1497 | 98.9235 | 87.9760 | 1749 | 15 | 1746 | 19 | 14 | 73.6842 | |
| raldana-dualsentieon | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.8403 | 99.7607 | 99.9201 | 44.0150 | 6253 | 15 | 6253 | 5 | 3 | 60.0000 | |
| raldana-dualsentieon | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.7436 | 99.6160 | 99.8716 | 27.5888 | 3891 | 15 | 3890 | 5 | 1 | 20.0000 | |
| raldana-dualsentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5619 | 99.3100 | 99.8151 | 62.4675 | 2159 | 15 | 2159 | 4 | 0 | 0.0000 | |
| raldana-dualsentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.3123 | 98.9185 | 99.7093 | 62.6392 | 1372 | 15 | 1372 | 4 | 0 | 0.0000 | |
| rpoplin-dv42 | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.8805 | 99.8672 | 99.8937 | 56.0776 | 11281 | 15 | 11280 | 12 | 12 | 100.0000 | |
| rpoplin-dv42 | INDEL | * | map_l100_m2_e1 | hetalt | 92.8571 | 88.6364 | 97.5000 | 88.9807 | 117 | 15 | 117 | 3 | 0 | 0.0000 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 97.3655 | 95.4268 | 99.3846 | 34.3434 | 313 | 15 | 323 | 2 | 2 | 100.0000 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.3817 | 99.0272 | 99.7387 | 76.7007 | 1527 | 15 | 1527 | 4 | 3 | 75.0000 | |
| raldana-dualsentieon | INDEL | D6_15 | map_l100_m2_e0 | * | 96.1390 | 94.3182 | 98.0315 | 84.0452 | 249 | 15 | 249 | 5 | 2 | 40.0000 | |
| raldana-dualsentieon | INDEL | I16_PLUS | HG002complexvar | het | 98.7816 | 97.7444 | 99.8410 | 62.2675 | 650 | 15 | 628 | 1 | 1 | 100.0000 | |
| raldana-dualsentieon | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 88.3436 | 82.7586 | 94.7368 | 83.5498 | 72 | 15 | 72 | 4 | 2 | 50.0000 | |
| raldana-dualsentieon | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 92.7659 | 88.7218 | 97.1963 | 86.4213 | 118 | 15 | 104 | 3 | 1 | 33.3333 | |
| raldana-dualsentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 90.1961 | 82.1429 | 100.0000 | 59.6491 | 69 | 15 | 69 | 0 | 0 | ||
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.1406 | 96.7672 | 99.5536 | 69.6682 | 449 | 15 | 446 | 2 | 1 | 50.0000 | |
| raldana-dualsentieon | SNP | * | HG002compoundhet | homalt | 99.8887 | 99.8609 | 99.9165 | 34.8192 | 10767 | 15 | 10768 | 9 | 8 | 88.8889 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.7953 | 99.6169 | 99.9744 | 76.0807 | 3900 | 15 | 3900 | 1 | 1 | 100.0000 | |
| dgrover-gatk | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.9125 | 99.8688 | 97.9744 | 43.3648 | 11418 | 15 | 11415 | 236 | 2 | 0.8475 | |
| dgrover-gatk | SNP | tv | HG002compoundhet | het | 99.6470 | 99.6790 | 99.6151 | 55.4242 | 4658 | 15 | 4658 | 18 | 10 | 55.5556 | |
| dgrover-gatk | SNP | tv | map_l250_m1_e0 | homalt | 98.8830 | 98.2477 | 99.5266 | 85.6901 | 841 | 15 | 841 | 4 | 3 | 75.0000 | |
| egarrison-hhga | INDEL | * | map_l150_m0_e0 | het | 95.7536 | 95.6012 | 95.9064 | 92.1703 | 326 | 15 | 328 | 14 | 4 | 28.5714 | |
| ckim-isaac | INDEL | D16_PLUS | map_l150_m2_e1 | * | 27.2727 | 16.6667 | 75.0000 | 97.3856 | 3 | 15 | 3 | 1 | 0 | 0.0000 | |
| ckim-isaac | INDEL | D1_5 | map_l100_m1_e0 | hetalt | 77.8589 | 68.0851 | 90.9091 | 88.5813 | 32 | 15 | 30 | 3 | 3 | 100.0000 | |
| ckim-isaac | INDEL | D6_15 | map_l150_m1_e0 | homalt | 59.4595 | 42.3077 | 100.0000 | 77.5510 | 11 | 15 | 11 | 0 | 0 | ||
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 80.9173 | 71.6981 | 92.8571 | 63.4783 | 38 | 15 | 39 | 3 | 0 | 0.0000 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 77.6371 | 75.4098 | 80.0000 | 77.2727 | 46 | 15 | 48 | 12 | 9 | 75.0000 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 77.9874 | 66.6667 | 93.9394 | 73.1707 | 30 | 15 | 31 | 2 | 2 | 100.0000 | |