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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
67351-67400 / 86044 show all | |||||||||||||||
| ckim-vqsr | INDEL | * | map_l100_m2_e0 | homalt | 99.2070 | 99.2070 | 99.2070 | 85.1821 | 1251 | 10 | 1251 | 10 | 5 | 50.0000 | |
| gduggal-snapplat | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 93.2439 | 87.5263 | 99.7608 | 37.2372 | 1249 | 178 | 1251 | 3 | 0 | 0.0000 | |
| eyeh-varpipe | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 81.2006 | 94.8980 | 70.9586 | 87.8472 | 1674 | 90 | 1251 | 512 | 45 | 8.7891 | |
| gduggal-bwafb | INDEL | D6_15 | * | hetalt | 90.9853 | 84.6464 | 98.3504 | 52.1249 | 6919 | 1255 | 1252 | 21 | 21 | 100.0000 | |
| hfeng-pmm3 | INDEL | * | map_l100_m2_e0 | homalt | 99.2469 | 99.2863 | 99.2076 | 82.1525 | 1252 | 9 | 1252 | 10 | 4 | 40.0000 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 97.0579 | 95.3612 | 98.8161 | 48.1800 | 1254 | 61 | 1252 | 15 | 10 | 66.6667 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.2278 | 94.9810 | 97.5078 | 52.7941 | 1249 | 66 | 1252 | 32 | 24 | 75.0000 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 56.8293 | 53.5459 | 60.5416 | 56.3805 | 974 | 845 | 1252 | 816 | 596 | 73.0392 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 56.8293 | 53.5459 | 60.5416 | 56.3805 | 974 | 845 | 1252 | 816 | 596 | 73.0392 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.4597 | 95.3612 | 97.5838 | 52.4639 | 1254 | 61 | 1252 | 31 | 26 | 83.8710 | |
| ltrigg-rtg1 | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 97.6901 | 96.3664 | 99.0506 | 57.6833 | 1273 | 48 | 1252 | 12 | 6 | 50.0000 | |
| jmaeng-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.3262 | 99.0514 | 99.6025 | 88.3465 | 1253 | 12 | 1253 | 5 | 5 | 100.0000 | |
| jli-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.1690 | 99.0514 | 99.2868 | 87.9764 | 1253 | 12 | 1253 | 9 | 4 | 44.4444 | |
| asubramanian-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.1886 | 98.1028 | 98.2745 | 88.1406 | 1241 | 24 | 1253 | 22 | 8 | 36.3636 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 96.3560 | 93.3144 | 99.6025 | 30.4588 | 656 | 47 | 1253 | 5 | 4 | 80.0000 | |
| hfeng-pmm2 | INDEL | * | map_l100_m2_e0 | homalt | 99.1690 | 99.3656 | 98.9731 | 82.9472 | 1253 | 8 | 1253 | 13 | 6 | 46.1538 | |
| hfeng-pmm1 | INDEL | * | map_l100_m2_e0 | homalt | 99.2082 | 99.3656 | 99.0514 | 82.7233 | 1253 | 8 | 1253 | 12 | 5 | 41.6667 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 78.4352 | 68.5826 | 91.5936 | 64.7059 | 1229 | 563 | 1253 | 115 | 90 | 78.2609 | |
| ltrigg-rtg2 | INDEL | * | map_l100_m2_e1 | homalt | 98.6597 | 97.6581 | 99.6820 | 78.7966 | 1251 | 30 | 1254 | 4 | 2 | 50.0000 | |
| jli-custom | INDEL | D1_5 | map_l100_m2_e1 | het | 98.6620 | 98.8170 | 98.5075 | 82.6685 | 1253 | 15 | 1254 | 19 | 5 | 26.3158 | |
| jmaeng-gatk | SNP | * | map_l250_m2_e0 | homalt | 63.6387 | 46.6865 | 99.9203 | 93.0743 | 1254 | 1432 | 1254 | 1 | 1 | 100.0000 | |
| bgallagher-sentieon | INDEL | * | map_l100_m2_e0 | homalt | 99.1696 | 99.4449 | 98.8959 | 84.6359 | 1254 | 7 | 1254 | 14 | 6 | 42.8571 | |
| astatham-gatk | INDEL | * | map_l100_m2_e0 | homalt | 99.2874 | 99.4449 | 99.1304 | 84.8358 | 1254 | 7 | 1254 | 11 | 6 | 54.5455 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 81.0388 | 91.2786 | 72.8646 | 69.9021 | 1235 | 118 | 1254 | 467 | 416 | 89.0792 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 55.0422 | 49.2827 | 62.3260 | 55.4966 | 1168 | 1202 | 1254 | 758 | 535 | 70.5805 | |
| gduggal-snapfb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 41.5632 | 96.5217 | 26.4836 | 86.5727 | 1221 | 44 | 1254 | 3481 | 67 | 1.9247 | |
| gduggal-snapvard | SNP | tv | map_l150_m0_e0 | homalt | 96.9441 | 94.3524 | 99.6823 | 78.3751 | 1253 | 75 | 1255 | 4 | 3 | 75.0000 | |
| jmaeng-gatk | INDEL | D1_5 | map_l100_m2_e1 | het | 96.1672 | 98.7382 | 93.7267 | 89.6330 | 1252 | 16 | 1255 | 84 | 6 | 7.1429 | |
| gduggal-bwafb | INDEL | * | map_l100_m2_e1 | homalt | 98.4321 | 98.0484 | 98.8189 | 84.9917 | 1256 | 25 | 1255 | 15 | 13 | 86.6667 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 79.6904 | 73.7069 | 86.7312 | 40.6237 | 342 | 122 | 1255 | 192 | 190 | 98.9583 | |
| ciseli-custom | INDEL | I1_5 | HG002compoundhet | * | 12.1122 | 9.5913 | 16.4310 | 70.5188 | 1185 | 11170 | 1255 | 6383 | 5985 | 93.7647 | |
| ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.3666 | 99.2095 | 99.5242 | 88.1418 | 1255 | 10 | 1255 | 6 | 6 | 100.0000 | |
| astatham-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.2387 | 96.8364 | 99.6823 | 87.5285 | 1255 | 41 | 1255 | 4 | 4 | 100.0000 | |
| ckim-dragen | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.4458 | 99.2885 | 99.6035 | 87.7940 | 1256 | 9 | 1256 | 5 | 5 | 100.0000 | |
| ckim-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.4064 | 99.2885 | 99.5246 | 88.1335 | 1256 | 9 | 1256 | 6 | 6 | 100.0000 | |
| ghariani-varprowl | INDEL | D1_5 | map_l100_m2_e1 | het | 91.5448 | 98.9748 | 85.1525 | 89.0375 | 1255 | 13 | 1256 | 219 | 64 | 29.2237 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 96.3029 | 95.1201 | 97.5155 | 59.3306 | 1267 | 65 | 1256 | 32 | 19 | 59.3750 | |
| ckim-gatk | SNP | * | map_l250_m2_e0 | homalt | 63.7586 | 46.7982 | 100.0000 | 93.4789 | 1257 | 1429 | 1257 | 0 | 0 | ||
| bgallagher-sentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.4462 | 99.3676 | 99.5249 | 88.0409 | 1257 | 8 | 1257 | 6 | 6 | 100.0000 | |
| rpoplin-dv42 | INDEL | D1_5 | HG002complexvar | hetalt | 94.1845 | 91.9379 | 96.5438 | 71.6833 | 1243 | 109 | 1257 | 45 | 44 | 97.7778 | |
| gduggal-snapfb | INDEL | * | map_l125_m1_e0 | het | 93.2290 | 92.6592 | 93.8060 | 83.9790 | 1237 | 98 | 1257 | 83 | 14 | 16.8675 | |
| dgrover-gatk | INDEL | D1_5 | map_l100_m2_e1 | het | 98.7031 | 98.8959 | 98.5110 | 85.7047 | 1254 | 14 | 1257 | 19 | 3 | 15.7895 | |
| dgrover-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.4856 | 99.3676 | 99.6038 | 88.3504 | 1257 | 8 | 1257 | 5 | 5 | 100.0000 | |
| ndellapenna-hhga | INDEL | * | map_l100_m2_e1 | homalt | 98.4736 | 98.2045 | 98.7441 | 83.1392 | 1258 | 23 | 1258 | 16 | 11 | 68.7500 | |
| jli-custom | INDEL | D1_5 | HG002complexvar | hetalt | 93.0817 | 89.7929 | 96.6206 | 73.4123 | 1214 | 138 | 1258 | 44 | 43 | 97.7273 | |
| jli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 97.0712 | 95.8175 | 98.3581 | 49.4267 | 1260 | 55 | 1258 | 21 | 13 | 61.9048 | |
| gduggal-bwaplat | INDEL | I16_PLUS | * | homalt | 87.5361 | 80.5253 | 95.8841 | 57.8947 | 1257 | 304 | 1258 | 54 | 51 | 94.4444 | |
| gduggal-snapvard | SNP | ti | map_l250_m0_e0 | * | 79.9224 | 92.7007 | 70.2401 | 94.4256 | 1270 | 100 | 1258 | 533 | 20 | 3.7524 | |
| jlack-gatk | INDEL | D1_5 | map_l100_m2_e1 | het | 93.6001 | 98.9748 | 88.7791 | 88.5873 | 1255 | 13 | 1258 | 159 | 10 | 6.2893 | |
| hfeng-pmm3 | INDEL | D1_5 | map_l100_m2_e1 | het | 99.0158 | 99.0536 | 98.9780 | 81.3490 | 1256 | 12 | 1259 | 13 | 2 | 15.3846 | |