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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
6951-7000 / 86044 show all | |||||||||||||||
| ciseli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 93.2663 | 94.0755 | 92.4709 | 53.9758 | 9575 | 603 | 9543 | 777 | 701 | 90.2188 | |
| dgrover-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.8320 | 96.0887 | 99.6397 | 60.4528 | 14814 | 603 | 14932 | 54 | 53 | 98.1481 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 38.3227 | 27.8708 | 61.3176 | 55.5889 | 233 | 603 | 363 | 229 | 214 | 93.4498 | |
| gduggal-bwafb | INDEL | D16_PLUS | * | het | 87.0129 | 80.9433 | 94.0664 | 49.5246 | 2557 | 602 | 3995 | 252 | 244 | 96.8254 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.2868 | 95.8815 | 98.7340 | 45.9174 | 14015 | 602 | 39539 | 507 | 431 | 85.0099 | |
| jpowers-varprowl | SNP | * | map_l125_m0_e0 | het | 95.4272 | 95.2464 | 95.6088 | 82.3444 | 12062 | 602 | 12062 | 554 | 169 | 30.5054 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 76.7383 | 75.0311 | 78.5249 | 51.9191 | 1809 | 602 | 1810 | 495 | 467 | 94.3434 | |
| hfeng-pmm3 | INDEL | D1_5 | * | hetalt | 96.9633 | 94.1240 | 99.9794 | 61.2573 | 9643 | 602 | 9686 | 2 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | HG002compoundhet | hetalt | 96.9544 | 94.1073 | 99.9792 | 56.3965 | 9614 | 602 | 9613 | 2 | 0 | 0.0000 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 93.4760 | 95.9242 | 91.1498 | 55.7793 | 14168 | 602 | 14151 | 1374 | 617 | 44.9054 | |
| ckim-dragen | INDEL | D6_15 | * | * | 97.9198 | 97.6928 | 98.1478 | 56.3201 | 25490 | 602 | 25488 | 481 | 433 | 90.0208 | |
| ckim-isaac | INDEL | * | map_l100_m2_e0 | het | 84.2881 | 73.9489 | 97.9885 | 86.2255 | 1706 | 601 | 1705 | 35 | 15 | 42.8571 | |
| gduggal-bwaplat | INDEL | D16_PLUS | HG002complexvar | * | 76.5914 | 63.4206 | 96.6667 | 72.4490 | 1042 | 601 | 1044 | 36 | 23 | 63.8889 | |
| mlin-fermikit | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 73.6558 | 85.1238 | 64.9109 | 67.0798 | 3439 | 601 | 3241 | 1752 | 1680 | 95.8904 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 43.8001 | 29.2941 | 86.7647 | 51.6014 | 249 | 601 | 236 | 36 | 27 | 75.0000 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.2962 | 90.1200 | 96.7045 | 61.7457 | 5482 | 601 | 5370 | 183 | 171 | 93.4426 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 94.0609 | 90.1200 | 98.3621 | 57.5242 | 5482 | 601 | 5525 | 92 | 66 | 71.7391 | |
| dgrover-gatk | INDEL | I1_5 | HG002compoundhet | * | 96.3058 | 95.1360 | 97.5048 | 66.8717 | 11755 | 601 | 11762 | 301 | 300 | 99.6678 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 82.7602 | 77.8800 | 88.2929 | 83.1252 | 2116 | 601 | 2255 | 299 | 150 | 50.1672 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 74.6510 | 71.8045 | 77.7324 | 73.3424 | 1528 | 600 | 1522 | 436 | 398 | 91.2844 | |
| mlin-fermikit | INDEL | D1_5 | map_l100_m1_e0 | * | 76.7469 | 67.5325 | 88.8730 | 76.4647 | 1248 | 600 | 1246 | 156 | 136 | 87.1795 | |
| ciseli-custom | INDEL | I1_5 | map_siren | homalt | 62.7683 | 50.4950 | 82.9235 | 77.4631 | 612 | 600 | 607 | 125 | 97 | 77.6000 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 92.8801 | 90.1364 | 95.7959 | 52.1555 | 5483 | 600 | 7793 | 342 | 302 | 88.3041 | |
| asubramanian-gatk | INDEL | * | * | homalt | 99.2686 | 99.5207 | 99.0178 | 58.9491 | 124572 | 600 | 124599 | 1236 | 954 | 77.1845 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 94.6607 | 91.0166 | 98.6088 | 31.6968 | 6079 | 600 | 5954 | 84 | 72 | 85.7143 | |
| ltrigg-rtg1 | SNP | * | map_l100_m0_e0 | het | 98.4261 | 97.1705 | 99.7145 | 55.4883 | 20605 | 600 | 20610 | 59 | 8 | 13.5593 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 90.7313 | 91.0661 | 90.3989 | 49.5222 | 6116 | 600 | 6685 | 710 | 208 | 29.2958 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 57.1877 | 67.4267 | 49.6483 | 70.3545 | 1242 | 600 | 1200 | 1217 | 171 | 14.0509 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 14.9034 | 8.1164 | 90.9910 | 51.3158 | 53 | 600 | 101 | 10 | 9 | 90.0000 | |
| gduggal-snapplat | SNP | tv | map_l100_m0_e0 | het | 92.3125 | 91.6921 | 92.9413 | 85.1008 | 6622 | 600 | 6623 | 503 | 271 | 53.8767 | |
| hfeng-pmm2 | INDEL | I6_15 | HG002compoundhet | * | 95.0368 | 93.1632 | 96.9873 | 36.8937 | 8176 | 600 | 8177 | 254 | 252 | 99.2126 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.4715 | 93.5529 | 99.5781 | 31.7934 | 8692 | 599 | 8733 | 37 | 36 | 97.2973 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.4715 | 93.5529 | 99.5781 | 31.7934 | 8692 | 599 | 8733 | 37 | 36 | 97.2973 | |
| qzeng-custom | SNP | * | map_l250_m0_e0 | het | 70.2798 | 60.2258 | 84.3633 | 98.3296 | 907 | 599 | 901 | 167 | 127 | 76.0479 | |
| ckim-isaac | SNP | tv | map_l250_m2_e0 | homalt | 53.0196 | 36.0726 | 100.0000 | 87.3075 | 338 | 599 | 338 | 0 | 0 | ||
| gduggal-snapplat | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 91.6132 | 84.5897 | 99.9088 | 64.9616 | 3288 | 599 | 3285 | 3 | 0 | 0.0000 | |
| eyeh-varpipe | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 16.5137 | 9.1047 | 88.6667 | 60.4222 | 60 | 599 | 133 | 17 | 17 | 100.0000 | |
| eyeh-varpipe | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 16.5137 | 9.1047 | 88.6667 | 60.4222 | 60 | 599 | 133 | 17 | 17 | 100.0000 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 93.1275 | 89.5499 | 97.0028 | 61.5094 | 5133 | 599 | 3463 | 107 | 92 | 85.9813 | |
| qzeng-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.8254 | 98.0798 | 97.5723 | 79.1147 | 30545 | 598 | 30586 | 761 | 104 | 13.6662 | |
| qzeng-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.8254 | 98.0798 | 97.5723 | 79.1147 | 30545 | 598 | 30586 | 761 | 104 | 13.6662 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.3816 | 98.0381 | 96.7339 | 73.7893 | 29882 | 598 | 29440 | 994 | 753 | 75.7545 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.3816 | 98.0381 | 96.7339 | 73.7893 | 29882 | 598 | 29440 | 994 | 753 | 75.7545 | |
| gduggal-snapplat | SNP | tv | map_l150_m2_e1 | homalt | 92.2034 | 85.5346 | 100.0000 | 76.0404 | 3536 | 598 | 3535 | 0 | 0 | ||
| ghariani-varprowl | INDEL | I6_15 | * | het | 73.9358 | 94.0397 | 60.9136 | 54.3281 | 9435 | 598 | 9494 | 6092 | 6035 | 99.0643 | |
| gduggal-snapfb | SNP | ti | map_l100_m2_e1 | het | 97.4111 | 98.0685 | 96.7625 | 68.1401 | 30362 | 598 | 30366 | 1016 | 436 | 42.9134 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.5384 | 98.0960 | 98.9848 | 61.0949 | 30810 | 598 | 30810 | 316 | 292 | 92.4051 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.5384 | 98.0960 | 98.9848 | 61.0949 | 30810 | 598 | 30810 | 316 | 292 | 92.4051 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.4121 | 97.3169 | 99.5323 | 46.2505 | 21653 | 597 | 21709 | 102 | 62 | 60.7843 | |
| gduggal-bwaplat | INDEL | I6_15 | HG002complexvar | het | 84.5433 | 74.6497 | 97.4600 | 66.9103 | 1758 | 597 | 1765 | 46 | 16 | 34.7826 | |