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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
34201-34250 / 86044 show all | |||||||||||||||
| jlack-gatk | INDEL | D1_5 | map_l150_m0_e0 | * | 89.7284 | 97.9239 | 82.7988 | 93.2798 | 283 | 6 | 284 | 59 | 1 | 1.6949 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 89.7219 | 95.2762 | 84.7795 | 79.3418 | 1190 | 59 | 1192 | 214 | 189 | 88.3178 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 89.7219 | 95.2762 | 84.7795 | 79.3418 | 1190 | 59 | 1192 | 214 | 189 | 88.3178 | |
| gduggal-snapvard | SNP | ti | map_l150_m1_e0 | het | 89.7218 | 96.4268 | 83.8886 | 83.9806 | 11928 | 442 | 11835 | 2273 | 169 | 7.4351 | |
| gduggal-snapvard | INDEL | I1_5 | map_l150_m2_e0 | * | 89.7214 | 94.9904 | 85.0062 | 90.8896 | 493 | 26 | 686 | 121 | 44 | 36.3636 | |
| jli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 89.7196 | 81.3559 | 100.0000 | 72.0430 | 48 | 11 | 52 | 0 | 0 | ||
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 89.7154 | 88.6381 | 90.8193 | 44.6755 | 5968 | 765 | 9932 | 1004 | 991 | 98.7052 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 89.7127 | 90.8139 | 88.6378 | 45.2529 | 10064 | 1018 | 10984 | 1408 | 719 | 51.0653 | |
| rpoplin-dv42 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 89.7118 | 87.9829 | 91.5099 | 73.1427 | 5352 | 731 | 5303 | 492 | 469 | 95.3252 | |
| anovak-vg | SNP | * | map_l125_m2_e1 | homalt | 89.7095 | 81.8047 | 99.3055 | 67.9368 | 14342 | 3190 | 14156 | 99 | 83 | 83.8384 | |
| hfeng-pmm3 | INDEL | D16_PLUS | map_l100_m2_e0 | het | 89.7079 | 93.7500 | 86.0000 | 94.7917 | 45 | 3 | 43 | 7 | 2 | 28.5714 | |
| jlack-gatk | INDEL | D6_15 | map_l100_m1_e0 | het | 89.7059 | 96.8254 | 83.5616 | 91.2365 | 122 | 4 | 122 | 24 | 3 | 12.5000 | |
| jlack-gatk | INDEL | D6_15 | map_l125_m1_e0 | het | 89.7059 | 95.3125 | 84.7222 | 93.7984 | 61 | 3 | 61 | 11 | 1 | 9.0909 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 89.7059 | 100.0000 | 81.3333 | 90.5779 | 61 | 0 | 61 | 14 | 13 | 92.8571 | |
| ckim-gatk | INDEL | D1_5 | map_l250_m2_e1 | het | 89.7059 | 100.0000 | 81.3333 | 97.2355 | 122 | 0 | 122 | 28 | 1 | 3.5714 | |
| gduggal-bwaplat | SNP | ti | HG002complexvar | hetalt | 89.7041 | 82.1256 | 98.8235 | 43.1438 | 170 | 37 | 168 | 2 | 2 | 100.0000 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 89.7025 | 92.8910 | 86.7257 | 67.8063 | 196 | 15 | 196 | 30 | 26 | 86.6667 | |
| qzeng-custom | INDEL | D1_5 | map_l100_m1_e0 | het | 89.6970 | 83.6228 | 96.7227 | 89.7617 | 1011 | 198 | 1151 | 39 | 27 | 69.2308 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 89.6970 | 85.0575 | 94.8718 | 84.4000 | 74 | 13 | 74 | 4 | 2 | 50.0000 | |
| ciseli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 89.6962 | 98.4278 | 82.3875 | 81.4243 | 2379 | 38 | 2381 | 509 | 127 | 24.9509 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 89.6938 | 81.4584 | 99.7817 | 61.4370 | 4837 | 1101 | 2742 | 6 | 5 | 83.3333 | |
| astatham-gatk | SNP | * | map_siren | het | 89.6918 | 81.4059 | 99.8557 | 63.3177 | 74072 | 16919 | 74058 | 107 | 41 | 38.3178 | |
| gduggal-bwavard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 89.6918 | 90.6694 | 88.7352 | 58.9619 | 447 | 46 | 449 | 57 | 36 | 63.1579 | |
| jlack-gatk | INDEL | I16_PLUS | HG002compoundhet | * | 89.6882 | 87.2608 | 92.2546 | 52.5070 | 1870 | 273 | 1870 | 157 | 144 | 91.7197 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 89.6870 | 88.2788 | 91.1408 | 63.5606 | 5370 | 713 | 5257 | 511 | 485 | 94.9119 | |
| gduggal-snapvard | INDEL | I1_5 | map_l150_m1_e0 | * | 89.6858 | 94.8617 | 85.0455 | 90.4043 | 480 | 26 | 654 | 115 | 40 | 34.7826 | |
| gduggal-snapvard | SNP | * | map_l150_m2_e1 | het | 89.6801 | 96.8079 | 83.5299 | 85.0251 | 19713 | 650 | 19475 | 3840 | 262 | 6.8229 | |
| jlack-gatk | INDEL | D6_15 | map_l100_m2_e0 | het | 89.6797 | 96.1832 | 84.0000 | 91.6574 | 126 | 5 | 126 | 24 | 3 | 12.5000 | |
| asubramanian-gatk | INDEL | I1_5 | map_l150_m1_e0 | * | 89.6780 | 83.2016 | 97.2477 | 92.2073 | 421 | 85 | 424 | 12 | 1 | 8.3333 | |
| ndellapenna-hhga | INDEL | I16_PLUS | * | hetalt | 89.6769 | 82.4118 | 98.3466 | 51.6538 | 1729 | 369 | 1725 | 29 | 24 | 82.7586 | |
| anovak-vg | SNP | tv | tech_badpromoters | * | 89.6729 | 84.7222 | 95.2381 | 42.7273 | 61 | 11 | 60 | 3 | 3 | 100.0000 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 89.6701 | 85.6906 | 94.0373 | 58.9423 | 2066 | 345 | 2066 | 131 | 124 | 94.6565 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 89.6694 | 81.2734 | 100.0000 | 41.5512 | 217 | 50 | 211 | 0 | 0 | ||
| asubramanian-gatk | INDEL | I1_5 | map_l150_m2_e1 | * | 89.6631 | 83.2392 | 97.1616 | 92.9647 | 442 | 89 | 445 | 13 | 1 | 7.6923 | |
| asubramanian-gatk | INDEL | * | map_l125_m0_e0 | het | 89.6574 | 87.7342 | 91.6667 | 93.1495 | 515 | 72 | 517 | 47 | 2 | 4.2553 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 89.6574 | 81.4353 | 99.7264 | 37.3608 | 522 | 119 | 729 | 2 | 2 | 100.0000 | |
| qzeng-custom | INDEL | D6_15 | func_cds | homalt | 89.6552 | 100.0000 | 81.2500 | 50.0000 | 12 | 0 | 13 | 3 | 1 | 33.3333 | |
| rpoplin-dv42 | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | hetalt | 89.6552 | 81.2500 | 100.0000 | 99.8895 | 13 | 3 | 13 | 0 | 0 | ||
| rpoplin-dv42 | INDEL | I16_PLUS | map_siren | hetalt | 89.6552 | 81.2500 | 100.0000 | 79.4118 | 13 | 3 | 14 | 0 | 0 | ||
| raldana-dualsentieon | INDEL | D16_PLUS | map_l150_m1_e0 | het | 89.6552 | 92.8571 | 86.6667 | 93.4211 | 13 | 1 | 13 | 2 | 0 | 0.0000 | |
| raldana-dualsentieon | INDEL | I16_PLUS | map_l125_m2_e0 | * | 89.6552 | 86.6667 | 92.8571 | 94.6970 | 13 | 2 | 13 | 1 | 0 | 0.0000 | |
| raldana-dualsentieon | INDEL | I16_PLUS | map_l125_m2_e1 | * | 89.6552 | 86.6667 | 92.8571 | 94.7170 | 13 | 2 | 13 | 1 | 0 | 0.0000 | |
| raldana-dualsentieon | SNP | ti | lowcmp_SimpleRepeat_diTR_51to200 | * | 89.6552 | 81.2500 | 100.0000 | 97.7816 | 13 | 3 | 13 | 0 | 0 | ||
| astatham-gatk | INDEL | I6_15 | map_l150_m1_e0 | het | 89.6552 | 86.6667 | 92.8571 | 95.4248 | 13 | 2 | 13 | 1 | 1 | 100.0000 | |
| astatham-gatk | INDEL | I6_15 | map_l150_m2_e0 | het | 89.6552 | 86.6667 | 92.8571 | 95.8333 | 13 | 2 | 13 | 1 | 1 | 100.0000 | |
| bgallagher-sentieon | INDEL | I6_15 | map_l150_m1_e0 | het | 89.6552 | 86.6667 | 92.8571 | 95.2703 | 13 | 2 | 13 | 1 | 1 | 100.0000 | |
| bgallagher-sentieon | INDEL | I6_15 | map_l150_m2_e0 | het | 89.6552 | 86.6667 | 92.8571 | 95.7187 | 13 | 2 | 13 | 1 | 1 | 100.0000 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | het | 89.6552 | 81.2500 | 100.0000 | 83.5052 | 13 | 3 | 16 | 0 | 0 | ||
| gduggal-snapfb | INDEL | I1_5 | map_l250_m1_e0 | het | 89.6552 | 86.6667 | 92.8571 | 95.7831 | 52 | 8 | 52 | 4 | 1 | 25.0000 | |
| ltrigg-rtg2 | INDEL | I1_5 | map_l250_m0_e0 | het | 89.6552 | 86.6667 | 92.8571 | 94.4444 | 13 | 2 | 13 | 1 | 0 | 0.0000 | |