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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
11201-11250 / 86044 show all | |||||||||||||||
| gduggal-bwaplat | INDEL | D1_5 | HG002compoundhet | hetalt | 84.6945 | 73.7471 | 99.4587 | 70.0372 | 7534 | 2682 | 7533 | 41 | 39 | 95.1220 | |
| ndellapenna-hhga | INDEL | D1_5 | HG002complexvar | hetalt | 79.8795 | 68.7130 | 95.3795 | 77.9155 | 929 | 423 | 867 | 42 | 39 | 92.8571 | |
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 75.5641 | 66.4251 | 87.6190 | 72.9614 | 275 | 139 | 276 | 39 | 39 | 100.0000 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 90.2393 | 98.2456 | 83.4395 | 66.8543 | 392 | 7 | 393 | 78 | 39 | 50.0000 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 78.9414 | 87.4016 | 71.9745 | 49.1909 | 111 | 16 | 113 | 44 | 39 | 88.6364 | |
| qzeng-custom | SNP | ti | segdup | homalt | 99.3042 | 99.2005 | 99.4081 | 87.0359 | 7445 | 60 | 7390 | 44 | 39 | 88.6364 | |
| qzeng-custom | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.9643 | 99.4833 | 98.4507 | 67.9503 | 27535 | 143 | 27515 | 433 | 39 | 9.0069 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 97.6068 | 96.9183 | 98.3051 | 69.3951 | 3428 | 109 | 3422 | 59 | 39 | 66.1017 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 94.5098 | 93.8352 | 95.1942 | 74.3325 | 1446 | 95 | 1446 | 73 | 39 | 53.4247 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 94.5857 | 90.9615 | 98.5106 | 44.8835 | 2838 | 282 | 2844 | 43 | 39 | 90.6977 | |
| ndellapenna-hhga | SNP | ti | map_siren | het | 99.3687 | 98.9067 | 99.8350 | 52.2716 | 61700 | 682 | 61701 | 102 | 39 | 38.2353 | |
| ndellapenna-hhga | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5343 | 99.4751 | 99.5935 | 60.5291 | 10044 | 53 | 10045 | 41 | 39 | 95.1220 | |
| qzeng-custom | INDEL | * | map_l150_m2_e0 | * | 81.1578 | 71.3778 | 94.0432 | 94.0095 | 1005 | 403 | 1263 | 80 | 39 | 48.7500 | |
| qzeng-custom | INDEL | * | map_l150_m2_e1 | * | 81.2984 | 71.5775 | 94.0746 | 94.0057 | 1030 | 409 | 1286 | 81 | 39 | 48.1481 | |
| mlin-fermikit | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 83.2118 | 71.5131 | 99.4866 | 35.3667 | 7491 | 2984 | 7558 | 39 | 39 | 100.0000 | |
| mlin-fermikit | INDEL | D1_5 | map_l125_m0_e0 | homalt | 67.8201 | 66.2162 | 69.5035 | 79.0490 | 98 | 50 | 98 | 43 | 39 | 90.6977 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 98.3080 | 97.2255 | 99.4149 | 40.8780 | 6623 | 189 | 6627 | 39 | 39 | 100.0000 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 97.6454 | 95.9224 | 99.4314 | 31.5401 | 6822 | 290 | 6820 | 39 | 39 | 100.0000 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.9176 | 98.2314 | 99.6135 | 43.6336 | 10886 | 196 | 10826 | 42 | 39 | 92.8571 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 97.6517 | 95.9297 | 99.4366 | 32.4551 | 6882 | 292 | 6883 | 39 | 39 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.9726 | 98.5812 | 99.3672 | 71.8268 | 15356 | 221 | 15545 | 99 | 39 | 39.3939 | |
| jmaeng-gatk | INDEL | D1_5 | HG002compoundhet | hetalt | 96.4037 | 93.4123 | 99.5930 | 58.4493 | 9543 | 673 | 9543 | 39 | 39 | 100.0000 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.3724 | 94.0724 | 98.7877 | 56.0658 | 3666 | 231 | 3667 | 45 | 39 | 86.6667 | |
| jmaeng-gatk | SNP | * | HG002complexvar | homalt | 99.3008 | 98.6263 | 99.9845 | 20.0307 | 284610 | 3964 | 284586 | 44 | 39 | 88.6364 | |
| jmaeng-gatk | SNP | * | HG002compoundhet | * | 99.3502 | 98.8847 | 99.8202 | 41.8705 | 25534 | 288 | 25531 | 46 | 39 | 84.7826 | |
| jmaeng-gatk | SNP | * | map_l150_m1_e0 | het | 84.2606 | 74.8343 | 96.4038 | 89.9614 | 14455 | 4861 | 14449 | 539 | 39 | 7.2356 | |
| jmaeng-gatk | SNP | * | map_l150_m2_e0 | het | 84.8178 | 75.7016 | 96.4302 | 90.4936 | 15241 | 4892 | 15235 | 564 | 39 | 6.9149 | |
| jmaeng-gatk | SNP | ti | map_l125_m1_e0 | het | 88.5520 | 81.2876 | 97.2421 | 86.2223 | 14848 | 3418 | 14844 | 421 | 39 | 9.2637 | |
| jmaeng-gatk | SNP | ti | map_l125_m2_e0 | het | 88.8720 | 81.8288 | 97.2418 | 86.9822 | 15446 | 3430 | 15442 | 438 | 39 | 8.9041 | |
| jmaeng-gatk | SNP | ti | map_l125_m2_e1 | het | 88.9909 | 82.0139 | 97.2654 | 86.9813 | 15654 | 3433 | 15650 | 440 | 39 | 8.8636 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.4583 | 97.2091 | 99.7401 | 57.5217 | 17659 | 507 | 17653 | 46 | 39 | 84.7826 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.4583 | 97.2091 | 99.7401 | 57.5217 | 17659 | 507 | 17653 | 46 | 39 | 84.7826 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 79.5890 | 75.9398 | 83.6066 | 81.9793 | 202 | 64 | 204 | 40 | 39 | 97.5000 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 80.1689 | 87.7049 | 73.8255 | 66.0592 | 107 | 15 | 110 | 39 | 39 | 100.0000 | |
| jpowers-varprowl | SNP | tv | map_l100_m1_e0 | homalt | 99.1519 | 98.9052 | 99.3999 | 66.3513 | 8944 | 99 | 8944 | 54 | 39 | 72.2222 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.1940 | 95.0822 | 99.4017 | 40.6176 | 6477 | 335 | 6480 | 39 | 39 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.1709 | 93.1280 | 99.4195 | 32.5705 | 6681 | 493 | 6679 | 39 | 39 | 100.0000 | |
| jli-custom | SNP | * | map_l125_m0_e0 | het | 98.5516 | 98.0575 | 99.0508 | 71.6081 | 12418 | 246 | 12418 | 119 | 39 | 32.7731 | |
| jli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.0535 | 95.4837 | 98.6758 | 53.2615 | 3721 | 176 | 3726 | 50 | 39 | 78.0000 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 95.4252 | 92.3274 | 98.7380 | 54.1740 | 3598 | 299 | 3599 | 46 | 39 | 84.7826 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.3679 | 99.4491 | 99.2868 | 52.6423 | 6679 | 37 | 6682 | 48 | 39 | 81.2500 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.1408 | 94.9941 | 99.3867 | 29.3238 | 6471 | 341 | 6482 | 40 | 39 | 97.5000 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 77.5982 | 99.4083 | 63.6364 | 84.3528 | 168 | 1 | 70 | 40 | 39 | 97.5000 | |
| astatham-gatk | INDEL | D1_5 | HG002compoundhet | hetalt | 97.2654 | 95.0470 | 99.5898 | 58.5927 | 9710 | 506 | 9711 | 40 | 39 | 97.5000 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.7394 | 96.9504 | 96.5293 | 75.1304 | 1367 | 43 | 1335 | 48 | 39 | 81.2500 | |
| astatham-gatk | INDEL | D6_15 | * | hetalt | 97.1014 | 94.8251 | 99.4898 | 33.5762 | 7751 | 423 | 7800 | 40 | 39 | 97.5000 | |
| astatham-gatk | INDEL | I1_5 | HG002complexvar | * | 99.6397 | 99.4275 | 99.8527 | 57.1222 | 33172 | 191 | 33219 | 49 | 39 | 79.5918 | |
| astatham-gatk | INDEL | I6_15 | HG002complexvar | * | 98.5836 | 98.0175 | 99.1563 | 57.7225 | 4697 | 95 | 4701 | 40 | 39 | 97.5000 | |
| astatham-gatk | SNP | * | map_l150_m1_e0 | * | 91.4460 | 84.4686 | 99.6799 | 78.7872 | 25855 | 4754 | 25849 | 83 | 39 | 46.9880 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.1461 | 96.8750 | 97.4186 | 69.7659 | 1736 | 56 | 1736 | 46 | 39 | 84.7826 | |