PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
9751-9800 / 86044 show all | |||||||||||||||
| ckim-isaac | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 92.1781 | 91.6618 | 92.7003 | 64.7784 | 1561 | 142 | 1562 | 123 | 54 | 43.9024 | |
| egarrison-hhga | SNP | ti | HG002compoundhet | homalt | 99.3116 | 99.4861 | 99.1378 | 31.0451 | 7356 | 38 | 7359 | 64 | 54 | 84.3750 | |
| egarrison-hhga | SNP | ti | map_siren | * | 99.6715 | 99.4669 | 99.8769 | 52.8764 | 99820 | 535 | 99821 | 123 | 54 | 43.9024 | |
| eyeh-varpipe | INDEL | C1_5 | HG002complexvar | hetalt | 0.0000 | 0.0000 | 88.8235 | 85.1744 | 0 | 0 | 453 | 57 | 54 | 94.7368 | |
| ckim-vqsr | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.3917 | 93.3580 | 99.6293 | 58.1709 | 14393 | 1024 | 14513 | 54 | 54 | 100.0000 | |
| egarrison-hhga | INDEL | * | map_siren | het | 97.9497 | 98.4472 | 97.4573 | 81.1814 | 4438 | 70 | 4446 | 116 | 54 | 46.5517 | |
| astatham-gatk | INDEL | I6_15 | * | het | 98.9793 | 98.7242 | 99.2358 | 59.2368 | 9905 | 128 | 9869 | 76 | 54 | 71.0526 | |
| anovak-vg | SNP | * | map_l150_m1_e0 | homalt | 87.8735 | 78.8344 | 99.2540 | 70.4677 | 8887 | 2386 | 8781 | 66 | 54 | 81.8182 | |
| astatham-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.7545 | 95.9460 | 99.6325 | 60.1730 | 14792 | 625 | 14910 | 55 | 54 | 98.1818 | |
| anovak-vg | INDEL | * | func_cds | * | 81.4334 | 80.2247 | 82.6790 | 38.5816 | 357 | 88 | 358 | 75 | 54 | 72.0000 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 77.8733 | 76.5766 | 79.2148 | 62.9281 | 340 | 104 | 343 | 90 | 54 | 60.0000 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 55.0270 | 47.1042 | 66.1538 | 55.0691 | 122 | 137 | 129 | 66 | 54 | 81.8182 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.4411 | 98.4169 | 87.1495 | 60.2600 | 373 | 6 | 373 | 55 | 54 | 98.1818 | |
| asubramanian-gatk | SNP | * | HG002complexvar | * | 98.2310 | 96.5837 | 99.9354 | 19.5730 | 728609 | 25772 | 728466 | 471 | 54 | 11.4650 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.9536 | 94.8907 | 99.1081 | 52.4443 | 6556 | 353 | 6556 | 59 | 54 | 91.5254 | |
| bgallagher-sentieon | SNP | ti | HG002complexvar | * | 99.9558 | 99.9337 | 99.9780 | 17.4939 | 508099 | 337 | 508035 | 112 | 53 | 47.3214 | |
| bgallagher-sentieon | SNP | tv | * | het | 99.8318 | 99.9594 | 99.7045 | 23.0898 | 591456 | 240 | 591385 | 1753 | 53 | 3.0234 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 92.3763 | 96.3910 | 88.6827 | 87.4183 | 641 | 24 | 478 | 61 | 53 | 86.8852 | |
| asubramanian-gatk | INDEL | I6_15 | * | het | 98.1049 | 97.0796 | 99.1521 | 59.9730 | 9740 | 293 | 9706 | 83 | 53 | 63.8554 | |
| anovak-vg | SNP | ti | map_l125_m2_e1 | homalt | 90.0123 | 82.2569 | 99.3822 | 67.2869 | 9425 | 2033 | 9330 | 58 | 53 | 91.3793 | |
| anovak-vg | SNP | tv | map_l250_m0_e0 | * | 73.9996 | 77.6471 | 70.6794 | 95.9856 | 594 | 171 | 593 | 246 | 53 | 21.5447 | |
| anovak-vg | INDEL | * | map_l150_m0_e0 | homalt | 74.0771 | 78.6585 | 70.0000 | 91.3793 | 129 | 35 | 133 | 57 | 53 | 92.9825 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 71.2981 | 57.7309 | 93.2011 | 73.4101 | 2300 | 1684 | 2303 | 168 | 53 | 31.5476 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 82.2975 | 70.7032 | 98.4402 | 61.5346 | 8396 | 3479 | 8394 | 133 | 53 | 39.8496 | |
| gduggal-bwaplat | INDEL | D6_15 | HG002complexvar | homalt | 88.8329 | 83.9179 | 94.3595 | 65.4443 | 981 | 188 | 987 | 59 | 53 | 89.8305 | |
| gduggal-bwaplat | INDEL | D6_15 | HG002compoundhet | homalt | 37.8738 | 75.0000 | 25.3333 | 81.1558 | 18 | 6 | 19 | 56 | 53 | 94.6429 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 85.9154 | 76.4472 | 98.0606 | 64.1454 | 2879 | 887 | 2882 | 57 | 53 | 92.9825 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 85.9154 | 76.4472 | 98.0606 | 64.1454 | 2879 | 887 | 2882 | 57 | 53 | 92.9825 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 79.1172 | 68.0571 | 94.4698 | 74.1440 | 1860 | 873 | 1862 | 109 | 53 | 48.6239 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 80.1285 | 70.1493 | 93.4180 | 55.0363 | 423 | 180 | 809 | 57 | 53 | 92.9825 | |
| gduggal-bwafb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 97.2224 | 95.1576 | 99.3788 | 72.1373 | 16153 | 822 | 16158 | 101 | 53 | 52.4752 | |
| gduggal-bwafb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 97.2224 | 95.1576 | 99.3788 | 72.1373 | 16153 | 822 | 16158 | 101 | 53 | 52.4752 | |
| qzeng-custom | INDEL | * | map_l100_m1_e0 | het | 83.3456 | 79.6421 | 87.4105 | 89.3842 | 1780 | 455 | 2319 | 334 | 53 | 15.8683 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 77.1546 | 63.0485 | 99.3919 | 33.0569 | 8678 | 5086 | 8826 | 54 | 53 | 98.1481 | |
| mlin-fermikit | INDEL | D6_15 | map_siren | * | 81.1872 | 77.0138 | 85.8388 | 82.0071 | 392 | 117 | 394 | 65 | 53 | 81.5385 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 96.3080 | 97.8404 | 94.8229 | 62.8918 | 1042 | 23 | 1044 | 57 | 53 | 92.9825 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | * | homalt | 94.2470 | 92.2486 | 96.3340 | 45.0988 | 1440 | 121 | 1419 | 54 | 53 | 98.1481 | |
| ltrigg-rtg2 | SNP | * | segdup | * | 99.1371 | 99.6722 | 98.6078 | 87.3153 | 27975 | 92 | 27977 | 395 | 53 | 13.4177 | |
| qzeng-custom | INDEL | D6_15 | HG002complexvar | homalt | 94.3279 | 97.3482 | 91.4894 | 56.3918 | 1138 | 31 | 1161 | 108 | 53 | 49.0741 | |
| ciseli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 31.2957 | 79.5337 | 19.4805 | 82.5076 | 307 | 79 | 315 | 1302 | 53 | 4.0707 | |
| ciseli-custom | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 97.2393 | 99.5982 | 94.9895 | 38.3851 | 2727 | 11 | 2711 | 143 | 53 | 37.0629 | |
| ciseli-custom | SNP | ti | map_l250_m0_e0 | homalt | 80.1652 | 78.8991 | 81.4727 | 91.7012 | 344 | 92 | 343 | 78 | 53 | 67.9487 | |
| ckim-dragen | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.4729 | 99.1955 | 97.7608 | 76.5892 | 28481 | 231 | 28728 | 658 | 53 | 8.0547 | |
| ckim-dragen | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.4729 | 99.1955 | 97.7608 | 76.5892 | 28481 | 231 | 28728 | 658 | 53 | 8.0547 | |
| cchapple-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.3852 | 95.7925 | 99.0319 | 61.6504 | 6056 | 266 | 6342 | 62 | 53 | 85.4839 | |
| cchapple-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.3852 | 95.7925 | 99.0319 | 61.6504 | 6056 | 266 | 6342 | 62 | 53 | 85.4839 | |
| ciseli-custom | INDEL | * | map_l150_m1_e0 | homalt | 63.4966 | 53.8961 | 77.2586 | 91.1399 | 249 | 213 | 248 | 73 | 53 | 72.6027 | |
| rpoplin-dv42 | INDEL | * | HG002complexvar | homalt | 99.6016 | 99.4265 | 99.7773 | 55.5190 | 26872 | 155 | 26879 | 60 | 53 | 88.3333 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 95.7880 | 95.3926 | 96.1867 | 75.7339 | 1470 | 71 | 1463 | 58 | 53 | 91.3793 | |
| raldana-dualsentieon | SNP | * | * | homalt | 99.9888 | 99.9827 | 99.9949 | 17.0955 | 1179957 | 204 | 1179943 | 60 | 53 | 88.3333 | |