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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
74801-74850 / 86044 show all | |||||||||||||||
| 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 | |
| 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 | * | 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 21.6505 | 12.3145 | 89.5161 | 61.9632 | 448 | 3190 | 333 | 39 | 39 | 100.0000 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 69.3384 | 66.5414 | 72.3810 | 85.5372 | 177 | 89 | 152 | 58 | 39 | 67.2414 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 42.2961 | 66.6667 | 30.9735 | 85.3532 | 34 | 17 | 70 | 156 | 39 | 25.0000 | |
| gduggal-snapvard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 62.1311 | 88.2872 | 47.9310 | 90.8828 | 701 | 93 | 695 | 755 | 39 | 5.1656 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 69.8922 | 57.3374 | 89.4866 | 50.3641 | 1516 | 1128 | 366 | 43 | 39 | 90.6977 | |
| gduggal-snapplat | INDEL | * | map_l100_m2_e0 | * | 80.0736 | 72.4343 | 89.5141 | 91.6820 | 2675 | 1018 | 2911 | 341 | 39 | 11.4370 | |
| gduggal-snapplat | INDEL | * | map_l100_m2_e1 | * | 79.8823 | 72.1512 | 89.4689 | 91.7596 | 2710 | 1046 | 2948 | 347 | 39 | 11.2392 | |
| gduggal-snapplat | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 86.9295 | 80.9834 | 93.8179 | 77.6360 | 1367 | 321 | 1381 | 91 | 39 | 42.8571 | |
| gduggal-snapplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 66.2377 | 71.5690 | 61.6456 | 93.1383 | 1893 | 752 | 1903 | 1184 | 39 | 3.2939 | |
| gduggal-snapvard | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 0.0000 | 0.0000 | 36.8627 | 88.3108 | 0 | 0 | 188 | 322 | 39 | 12.1118 | |
| gduggal-snapvard | INDEL | C6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 0.0000 | 0.0000 | 34.0000 | 87.9130 | 0 | 0 | 102 | 198 | 39 | 19.6970 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 4.6119 | 2.5026 | 29.3478 | 74.2297 | 24 | 935 | 27 | 65 | 39 | 60.0000 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 5.8388 | 3.2419 | 29.3478 | 73.4870 | 13 | 388 | 27 | 65 | 39 | 60.0000 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 63.3512 | 58.0645 | 69.6970 | 83.6836 | 90 | 65 | 92 | 40 | 39 | 97.5000 | |
| ghariani-varprowl | SNP | * | map_l125_m1_e0 | homalt | 99.0868 | 98.5271 | 99.6530 | 67.5166 | 16656 | 249 | 16656 | 58 | 39 | 67.2414 | |
| ghariani-varprowl | SNP | * | map_l125_m2_e0 | homalt | 99.1058 | 98.5554 | 99.6624 | 70.0500 | 17124 | 251 | 17124 | 58 | 39 | 67.2414 | |
| ghariani-varprowl | SNP | * | map_l125_m2_e1 | homalt | 99.1110 | 98.5626 | 99.6655 | 70.0625 | 17280 | 252 | 17280 | 58 | 39 | 67.2414 | |
| ghariani-varprowl | SNP | tv | map_l100_m2_e0 | homalt | 99.1079 | 98.8713 | 99.3457 | 66.7718 | 9110 | 104 | 9110 | 60 | 39 | 65.0000 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 88.8708 | 82.4960 | 96.3134 | 28.0265 | 5632 | 1195 | 1672 | 64 | 39 | 60.9375 | |
| gduggal-snapfb | INDEL | I1_5 | map_siren | * | 95.6890 | 96.4725 | 94.9180 | 82.9590 | 2899 | 106 | 2895 | 155 | 39 | 25.1613 | |
| gduggal-snapplat | INDEL | D6_15 | HG002complexvar | hetalt | 48.9308 | 33.8598 | 88.1797 | 67.9303 | 343 | 670 | 373 | 50 | 39 | 78.0000 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 81.0304 | 79.3233 | 82.8125 | 82.8188 | 211 | 55 | 212 | 44 | 39 | 88.6364 | |
| 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 | |
| cchapple-custom | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.6632 | 99.5223 | 99.8044 | 57.7539 | 28125 | 135 | 28578 | 56 | 39 | 69.6429 | |
| asubramanian-gatk | SNP | * | * | homalt | 98.8858 | 97.8294 | 99.9654 | 17.5292 | 1154544 | 25617 | 1154521 | 400 | 39 | 9.7500 | |
| astatham-gatk | SNP | * | map_l150_m1_e0 | * | 91.4460 | 84.4686 | 99.6799 | 78.7872 | 25855 | 4754 | 25849 | 83 | 39 | 46.9880 | |