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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
28101-28150 / 86044 show all | |||||||||||||||
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 94.6479 | 90.3226 | 99.4083 | 69.9288 | 168 | 18 | 168 | 1 | 1 | 100.0000 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 94.6479 | 90.3226 | 99.4083 | 67.9924 | 168 | 18 | 168 | 1 | 1 | 100.0000 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 94.6465 | 93.3333 | 95.9971 | 67.9047 | 1316 | 94 | 1319 | 55 | 15 | 27.2727 | |
| bgallagher-sentieon | INDEL | D1_5 | map_l100_m2_e0 | hetalt | 94.6463 | 91.6667 | 97.8261 | 89.7092 | 44 | 4 | 45 | 1 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | D1_5 | map_l100_m2_e0 | hetalt | 94.6463 | 91.6667 | 97.8261 | 90.8367 | 44 | 4 | 45 | 1 | 0 | 0.0000 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 94.6459 | 92.4171 | 96.9849 | 47.4934 | 195 | 16 | 193 | 6 | 0 | 0.0000 | |
| gduggal-bwavard | INDEL | I1_5 | map_l125_m1_e0 | * | 94.6449 | 95.3012 | 93.9976 | 87.8589 | 791 | 39 | 783 | 50 | 20 | 40.0000 | |
| gduggal-snapvard | INDEL | D1_5 | map_l150_m1_e0 | homalt | 94.6446 | 90.7895 | 98.8417 | 83.6490 | 207 | 21 | 256 | 3 | 3 | 100.0000 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 94.6440 | 90.0688 | 99.7088 | 29.5734 | 6149 | 678 | 1712 | 5 | 5 | 100.0000 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 94.6431 | 90.7255 | 98.9142 | 65.3727 | 3639 | 372 | 3644 | 40 | 7 | 17.5000 | |
| gduggal-bwavard | INDEL | * | map_l250_m2_e0 | homalt | 94.6429 | 92.1739 | 97.2477 | 93.3211 | 106 | 9 | 106 | 3 | 2 | 66.6667 | |
| jli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 94.6429 | 100.0000 | 89.8305 | 67.3582 | 211 | 0 | 212 | 24 | 24 | 100.0000 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 94.6429 | 92.9825 | 96.3636 | 99.4786 | 53 | 4 | 53 | 2 | 0 | 0.0000 | |
| qzeng-custom | INDEL | C6_15 | HG002complexvar | * | 94.6429 | 100.0000 | 89.8305 | 90.1503 | 4 | 0 | 53 | 6 | 1 | 16.6667 | |
| gduggal-bwafb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 94.6420 | 95.6229 | 93.6811 | 78.6041 | 18722 | 857 | 18784 | 1267 | 139 | 10.9708 | |
| gduggal-bwafb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 94.6420 | 95.6229 | 93.6811 | 78.6041 | 18722 | 857 | 18784 | 1267 | 139 | 10.9708 | |
| ltrigg-rtg1 | INDEL | D1_5 | HG002complexvar | hetalt | 94.6417 | 92.8994 | 96.4505 | 77.3885 | 1256 | 96 | 1413 | 52 | 51 | 98.0769 | |
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 94.6404 | 92.1400 | 97.2803 | 85.0563 | 1395 | 119 | 1395 | 39 | 17 | 43.5897 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.6399 | 91.5309 | 97.9675 | 67.1249 | 1686 | 156 | 1687 | 35 | 30 | 85.7143 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 94.6398 | 99.5152 | 90.2198 | 70.6072 | 821 | 4 | 821 | 89 | 86 | 96.6292 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 94.6398 | 99.5152 | 90.2198 | 70.6072 | 821 | 4 | 821 | 89 | 86 | 96.6292 | |
| ltrigg-rtg1 | INDEL | I6_15 | HG002compoundhet | het | 94.6384 | 94.2308 | 95.0495 | 73.6292 | 196 | 12 | 192 | 10 | 6 | 60.0000 | |
| gduggal-snapvard | INDEL | I1_5 | map_l100_m1_e0 | homalt | 94.6381 | 90.5405 | 99.1241 | 73.0527 | 469 | 49 | 679 | 6 | 3 | 50.0000 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 94.6365 | 93.5989 | 95.6973 | 34.7531 | 658 | 45 | 645 | 29 | 24 | 82.7586 | |
| ltrigg-rtg1 | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 94.6357 | 90.3010 | 99.4076 | 53.2928 | 810 | 87 | 839 | 5 | 5 | 100.0000 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 94.6355 | 97.3799 | 92.0415 | 69.2422 | 1338 | 36 | 1330 | 115 | 100 | 86.9565 | |
| anovak-vg | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 94.6346 | 95.8110 | 93.4868 | 75.2785 | 3751 | 164 | 3818 | 266 | 220 | 82.7068 | |
| gduggal-snapvard | INDEL | I1_5 | map_l125_m0_e0 | homalt | 94.6345 | 91.2281 | 98.3051 | 82.6130 | 104 | 10 | 174 | 3 | 1 | 33.3333 | |
| gduggal-bwavard | SNP | ti | map_l125_m2_e0 | het | 94.6336 | 97.6319 | 91.8139 | 83.0438 | 18429 | 447 | 18293 | 1631 | 107 | 6.5604 | |
| gduggal-snapplat | SNP | tv | map_l100_m1_e0 | het | 94.6299 | 94.5320 | 94.7279 | 81.7875 | 14574 | 843 | 14572 | 811 | 394 | 48.5820 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 94.6297 | 90.2717 | 99.4297 | 29.8103 | 7275 | 784 | 7323 | 42 | 36 | 85.7143 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 94.6297 | 90.2717 | 99.4297 | 29.8103 | 7275 | 784 | 7323 | 42 | 36 | 85.7143 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 94.6263 | 91.4498 | 98.0315 | 68.7192 | 246 | 23 | 249 | 5 | 2 | 40.0000 | |
| qzeng-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 94.6261 | 95.9485 | 93.3397 | 58.3275 | 17430 | 736 | 20671 | 1475 | 1218 | 82.5763 | |
| qzeng-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 94.6261 | 95.9485 | 93.3397 | 58.3275 | 17430 | 736 | 20671 | 1475 | 1218 | 82.5763 | |
| asubramanian-gatk | INDEL | * | map_l100_m2_e0 | hetalt | 94.6259 | 91.2000 | 98.3193 | 88.0762 | 114 | 11 | 117 | 2 | 1 | 50.0000 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 94.6258 | 94.3116 | 94.9422 | 66.8176 | 6350 | 383 | 6401 | 341 | 317 | 92.9619 | |
| ltrigg-rtg1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 94.6243 | 90.3481 | 99.3255 | 49.4027 | 571 | 61 | 589 | 4 | 4 | 100.0000 | |
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 94.6238 | 92.9702 | 96.3373 | 84.5241 | 2526 | 191 | 2525 | 96 | 61 | 63.5417 | |
| rpoplin-dv42 | INDEL | D6_15 | map_l100_m2_e1 | het | 94.6237 | 97.7778 | 91.6667 | 88.4430 | 132 | 3 | 132 | 12 | 7 | 58.3333 | |
| rpoplin-dv42 | INDEL | D6_15 | segdup | hetalt | 94.6237 | 89.7959 | 100.0000 | 90.1786 | 44 | 5 | 44 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 94.6237 | 89.7959 | 100.0000 | 27.8689 | 44 | 5 | 44 | 0 | 0 | ||
| jmaeng-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 94.6237 | 89.7959 | 100.0000 | 25.4237 | 44 | 5 | 44 | 0 | 0 | ||
| dgrover-gatk | INDEL | D6_15 | segdup | hetalt | 94.6237 | 89.7959 | 100.0000 | 90.4555 | 44 | 5 | 44 | 0 | 0 | ||
| ckim-vqsr | INDEL | D6_15 | segdup | hetalt | 94.6237 | 89.7959 | 100.0000 | 90.4968 | 44 | 5 | 44 | 0 | 0 | ||
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 94.6237 | 89.7959 | 100.0000 | 27.8689 | 44 | 5 | 44 | 0 | 0 | ||
| astatham-gatk | INDEL | D6_15 | segdup | hetalt | 94.6237 | 89.7959 | 100.0000 | 90.3720 | 44 | 5 | 44 | 0 | 0 | ||
| cchapple-custom | INDEL | D1_5 | map_l250_m0_e0 | * | 94.6237 | 95.6522 | 93.6170 | 97.1567 | 44 | 2 | 44 | 3 | 0 | 0.0000 | |
| ckim-gatk | INDEL | D6_15 | segdup | hetalt | 94.6237 | 89.7959 | 100.0000 | 90.4968 | 44 | 5 | 44 | 0 | 0 | ||
| ckim-gatk | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 94.6237 | 92.3077 | 97.0588 | 92.7312 | 132 | 11 | 132 | 4 | 3 | 75.0000 | |