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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
16101-16150 / 86044 show all | |||||||||||||||
| ghariani-varprowl | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 44.2731 | 30.1494 | 83.2915 | 76.5745 | 666 | 1543 | 663 | 133 | 106 | 79.6992 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 97.7242 | 97.5630 | 97.8859 | 54.6627 | 24741 | 618 | 24632 | 532 | 424 | 79.6992 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 94.6034 | 94.8872 | 94.3212 | 81.3996 | 1262 | 68 | 1063 | 64 | 51 | 79.6875 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 92.1621 | 97.7230 | 87.2000 | 81.7983 | 515 | 12 | 436 | 64 | 51 | 79.6875 | |
| mlin-fermikit | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 85.0654 | 98.4227 | 74.9004 | 87.7501 | 936 | 15 | 940 | 315 | 251 | 79.6825 | |
| qzeng-custom | SNP | ti | map_l100_m2_e1 | * | 87.8109 | 79.2503 | 98.4448 | 76.3141 | 39217 | 10268 | 38930 | 615 | 490 | 79.6748 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 75.1664 | 60.6286 | 98.8753 | 39.2261 | 5633 | 3658 | 5187 | 59 | 47 | 79.6610 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 75.1664 | 60.6286 | 98.8753 | 39.2261 | 5633 | 3658 | 5187 | 59 | 47 | 79.6610 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 94.4657 | 93.1034 | 95.8683 | 72.1692 | 1269 | 94 | 1369 | 59 | 47 | 79.6610 | |
| ltrigg-rtg1 | INDEL | I1_5 | * | homalt | 99.7620 | 99.6227 | 99.9017 | 50.6392 | 60199 | 228 | 59978 | 59 | 47 | 79.6610 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.7409 | 96.6568 | 98.8496 | 59.7558 | 29461 | 1019 | 60407 | 703 | 560 | 79.6586 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.7409 | 96.6568 | 98.8496 | 59.7558 | 29461 | 1019 | 60407 | 703 | 560 | 79.6586 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 37.8106 | 46.6667 | 31.7797 | 37.1505 | 63 | 72 | 300 | 644 | 513 | 79.6584 | |
| anovak-vg | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 28.1418 | 19.8381 | 48.4018 | 54.7521 | 49 | 198 | 106 | 113 | 90 | 79.6460 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 91.8499 | 88.8266 | 95.0863 | 43.5099 | 14254 | 1793 | 14165 | 732 | 583 | 79.6448 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 81.9603 | 79.1667 | 84.9582 | 78.0562 | 304 | 80 | 305 | 54 | 43 | 79.6296 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 81.2239 | 74.1883 | 89.7338 | 67.9659 | 457 | 159 | 472 | 54 | 43 | 79.6296 | |
| ciseli-custom | SNP | ti | map_l100_m2_e1 | homalt | 91.1369 | 90.8132 | 91.4629 | 61.7425 | 16795 | 1699 | 16756 | 1564 | 1245 | 79.6036 | |
| ciseli-custom | SNP | tv | map_l150_m0_e0 | homalt | 82.2034 | 80.3464 | 84.1483 | 77.4538 | 1067 | 261 | 1067 | 201 | 160 | 79.6020 | |
| ciseli-custom | SNP | ti | map_l100_m2_e0 | homalt | 91.1050 | 90.7805 | 91.4319 | 61.7718 | 16621 | 1688 | 16583 | 1554 | 1237 | 79.6010 | |
| anovak-vg | INDEL | * | HG002compoundhet | homalt | 34.7177 | 86.4431 | 21.7206 | 63.7894 | 593 | 93 | 1939 | 6988 | 5562 | 79.5936 | |
| astatham-gatk | INDEL | I1_5 | HG002complexvar | * | 99.6397 | 99.4275 | 99.8527 | 57.1222 | 33172 | 191 | 33219 | 49 | 39 | 79.5918 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 84.4797 | 83.7858 | 85.1852 | 73.6297 | 1142 | 221 | 1127 | 196 | 156 | 79.5918 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 87.9226 | 98.5770 | 79.3467 | 77.1325 | 762 | 11 | 753 | 196 | 156 | 79.5918 | |
| qzeng-custom | SNP | * | HG002compoundhet | homalt | 98.8868 | 98.8963 | 98.8772 | 42.3069 | 10663 | 119 | 8190 | 93 | 74 | 79.5699 | |
| jli-custom | INDEL | I1_5 | * | * | 99.4941 | 99.2055 | 99.7844 | 57.0293 | 149467 | 1197 | 149502 | 323 | 257 | 79.5666 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 26.4385 | 22.6686 | 31.7125 | 37.5578 | 158 | 539 | 300 | 646 | 514 | 79.5666 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 42.8855 | 43.0211 | 42.7507 | 47.9409 | 937 | 1241 | 1778 | 2381 | 1894 | 79.5464 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.5596 | 98.2560 | 98.8651 | 66.9902 | 3831 | 68 | 3833 | 44 | 35 | 79.5455 | |
| ciseli-custom | INDEL | I1_5 | map_l100_m2_e0 | homalt | 54.2174 | 40.3013 | 82.8125 | 83.8994 | 214 | 317 | 212 | 44 | 35 | 79.5455 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.2667 | 99.3211 | 99.2123 | 71.8135 | 5559 | 38 | 5542 | 44 | 35 | 79.5455 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.8440 | 91.1898 | 98.8034 | 58.6110 | 3633 | 351 | 3633 | 44 | 35 | 79.5455 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 30.4360 | 18.8406 | 79.1469 | 74.6699 | 169 | 728 | 167 | 44 | 35 | 79.5455 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 93.4170 | 87.7992 | 99.8027 | 58.9642 | 22265 | 3094 | 22261 | 44 | 35 | 79.5455 | |
| gduggal-snapplat | INDEL | I6_15 | HG002compoundhet | hetalt | 53.1182 | 36.6874 | 96.2041 | 33.7320 | 3132 | 5405 | 3092 | 122 | 97 | 79.5082 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.8272 | 98.5395 | 99.1166 | 73.0877 | 63490 | 941 | 63503 | 566 | 450 | 79.5053 | |
| mlin-fermikit | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 98.5516 | 99.7271 | 97.4035 | 50.4781 | 1462 | 4 | 1463 | 39 | 31 | 79.4872 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.6226 | 99.6991 | 99.5463 | 74.7408 | 33136 | 100 | 33130 | 151 | 120 | 79.4702 | |
| anovak-vg | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 53.2015 | 46.3732 | 62.3880 | 36.5667 | 748 | 865 | 4039 | 2435 | 1935 | 79.4661 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 91.1970 | 96.8085 | 86.2004 | 69.9943 | 455 | 15 | 456 | 73 | 58 | 79.4521 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 79.1674 | 71.9397 | 88.0095 | 54.7793 | 1910 | 745 | 1857 | 253 | 201 | 79.4466 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 96.0352 | 98.6256 | 93.5774 | 85.8273 | 1794 | 25 | 1559 | 107 | 85 | 79.4393 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 96.0352 | 98.6256 | 93.5774 | 85.8273 | 1794 | 25 | 1559 | 107 | 85 | 79.4393 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 36.8196 | 27.4987 | 55.6992 | 44.8224 | 542 | 1429 | 1852 | 1473 | 1170 | 79.4297 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 36.8196 | 27.4987 | 55.6992 | 44.8224 | 542 | 1429 | 1852 | 1473 | 1170 | 79.4297 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 84.1057 | 79.3599 | 89.4551 | 69.7220 | 1711 | 445 | 1773 | 209 | 166 | 79.4258 | |
| ghariani-varprowl | SNP | ti | HG002compoundhet | homalt | 92.9457 | 99.8242 | 86.9540 | 37.0935 | 7381 | 13 | 7385 | 1108 | 880 | 79.4224 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 91.0757 | 96.0870 | 86.5613 | 76.5524 | 221 | 9 | 219 | 34 | 27 | 79.4118 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 90.7836 | 84.1298 | 98.5804 | 37.3201 | 2359 | 445 | 2361 | 34 | 27 | 79.4118 | |
| ckim-vqsr | INDEL | I1_5 | * | * | 99.3579 | 99.0515 | 99.6662 | 59.3791 | 149235 | 1429 | 149282 | 500 | 397 | 79.4000 | |