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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
44301-44350 / 86044 show all | |||||||||||||||
| ciseli-custom | INDEL | * | map_siren | het | 76.8656 | 76.7303 | 77.0013 | 84.6311 | 3459 | 1049 | 3482 | 1040 | 630 | 60.5769 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 86.0639 | 76.7320 | 97.9798 | 69.7941 | 1174 | 356 | 1164 | 24 | 19 | 79.1667 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 86.0639 | 76.7320 | 97.9798 | 69.7941 | 1174 | 356 | 1164 | 24 | 19 | 79.1667 | |
| astatham-gatk | SNP | tv | map_l100_m2_e1 | het | 86.7191 | 76.7348 | 99.6902 | 76.6919 | 12230 | 3708 | 12226 | 38 | 10 | 26.3158 | |
| astatham-gatk | SNP | * | map_l100_m1_e0 | het | 86.7442 | 76.7367 | 99.7535 | 74.2815 | 34807 | 10552 | 34796 | 86 | 33 | 38.3721 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 84.1308 | 76.7376 | 93.1005 | 65.8125 | 1082 | 328 | 1093 | 81 | 21 | 25.9259 | |
| gduggal-snapplat | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 85.2074 | 76.7402 | 95.7746 | 76.7746 | 1356 | 411 | 1360 | 60 | 34 | 56.6667 | |
| qzeng-custom | INDEL | * | map_l125_m2_e1 | hetalt | 86.8421 | 76.7442 | 100.0000 | 93.2806 | 33 | 10 | 17 | 0 | 0 | ||
| jpowers-varprowl | INDEL | I6_15 | func_cds | * | 81.4815 | 76.7442 | 86.8421 | 33.3333 | 33 | 10 | 33 | 5 | 5 | 100.0000 | |
| gduggal-bwaplat | SNP | * | map_l100_m2_e0 | het | 86.5211 | 76.7517 | 99.1404 | 84.8771 | 35612 | 10787 | 35636 | 309 | 82 | 26.5372 | |
| gduggal-bwaplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 86.8534 | 76.7619 | 100.0000 | 76.0472 | 403 | 122 | 406 | 0 | 0 | ||
| gduggal-snapplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 86.1165 | 76.7619 | 98.0676 | 77.3770 | 403 | 122 | 406 | 8 | 2 | 25.0000 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 80.6871 | 76.7630 | 85.0340 | 31.9444 | 1328 | 402 | 1375 | 242 | 240 | 99.1736 | |
| qzeng-custom | SNP | tv | map_l125_m2_e0 | het | 85.5513 | 76.7765 | 96.5908 | 86.8303 | 8017 | 2425 | 8018 | 283 | 230 | 81.2721 | |
| ckim-isaac | INDEL | I1_5 | map_siren | hetalt | 85.4934 | 76.7857 | 96.4286 | 82.2410 | 86 | 26 | 81 | 3 | 2 | 66.6667 | |
| gduggal-snapplat | SNP | * | map_l250_m0_e0 | homalt | 86.7142 | 76.7886 | 99.5868 | 94.0431 | 483 | 146 | 482 | 2 | 2 | 100.0000 | |
| qzeng-custom | INDEL | D1_5 | map_l125_m1_e0 | homalt | 86.1830 | 76.7908 | 98.1928 | 83.9614 | 268 | 81 | 326 | 6 | 6 | 100.0000 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 86.7813 | 76.7925 | 99.7573 | 48.6284 | 407 | 123 | 411 | 1 | 1 | 100.0000 | |
| ckim-isaac | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 82.8671 | 76.7932 | 89.9844 | 83.5648 | 1092 | 330 | 1150 | 128 | 68 | 53.1250 | |
| gduggal-bwafb | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 85.9670 | 76.8000 | 97.6190 | 25.0000 | 96 | 29 | 41 | 1 | 1 | 100.0000 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 86.6360 | 76.8019 | 99.3583 | 29.3091 | 1950 | 589 | 2013 | 13 | 11 | 84.6154 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 83.5360 | 76.8142 | 91.5470 | 43.3092 | 2117 | 639 | 2296 | 212 | 212 | 100.0000 | |
| mlin-fermikit | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 86.5177 | 76.8147 | 99.0264 | 30.1942 | 709 | 214 | 712 | 7 | 7 | 100.0000 | |
| anovak-vg | INDEL | D16_PLUS | HG002complexvar | homalt | 75.3150 | 76.8166 | 73.8710 | 63.3570 | 222 | 67 | 229 | 81 | 59 | 72.8395 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 84.1376 | 76.8293 | 92.9825 | 64.4860 | 63 | 19 | 106 | 8 | 8 | 100.0000 | |
| gduggal-bwavard | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | het | 43.6411 | 76.8293 | 30.4762 | 68.5864 | 126 | 38 | 128 | 292 | 286 | 97.9452 | |
| ciseli-custom | SNP | * | map_l125_m2_e0 | * | 81.1188 | 76.8380 | 85.9047 | 77.6345 | 35901 | 10822 | 35830 | 5879 | 1516 | 25.7867 | |
| ghariani-varprowl | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 66.6667 | 76.8421 | 58.8710 | 85.4801 | 73 | 22 | 73 | 51 | 49 | 96.0784 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 85.7593 | 76.8439 | 97.0149 | 63.3307 | 448 | 135 | 455 | 14 | 12 | 85.7143 | |
| qzeng-custom | INDEL | D1_5 | map_l150_m2_e0 | het | 84.9655 | 76.8482 | 95.0000 | 94.5186 | 395 | 119 | 437 | 23 | 19 | 82.6087 | |
| anovak-vg | INDEL | D1_5 | map_l150_m2_e0 | homalt | 85.5172 | 76.8595 | 96.3731 | 89.4304 | 186 | 56 | 186 | 7 | 6 | 85.7143 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 85.8671 | 76.8612 | 97.2637 | 69.0054 | 382 | 115 | 391 | 11 | 10 | 90.9091 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 82.5353 | 76.8626 | 89.1121 | 55.4494 | 3126 | 941 | 3282 | 401 | 398 | 99.2519 | |
| astatham-gatk | SNP | tv | map_l150_m1_e0 | het | 86.7142 | 76.8644 | 99.4596 | 83.0624 | 5339 | 1607 | 5337 | 29 | 8 | 27.5862 | |
| ciseli-custom | SNP | * | map_l100_m0_e0 | * | 81.1632 | 76.8673 | 85.9677 | 74.4366 | 25244 | 7597 | 25198 | 4113 | 1141 | 27.7413 | |
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 82.7354 | 76.8750 | 89.5631 | 81.5825 | 369 | 111 | 369 | 43 | 43 | 100.0000 | |
| astatham-gatk | SNP | ti | map_l100_m1_e0 | het | 86.8541 | 76.8887 | 99.7875 | 73.5726 | 23022 | 6920 | 23015 | 49 | 23 | 46.9388 | |
| gduggal-snapvard | SNP | tv | HG002compoundhet | * | 76.6128 | 76.8912 | 76.3364 | 58.1709 | 6861 | 2062 | 7126 | 2209 | 1084 | 49.0720 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 86.4484 | 76.9057 | 98.6947 | 50.6089 | 1362 | 409 | 1361 | 18 | 16 | 88.8889 | |
| qzeng-custom | SNP | tv | map_l125_m2_e1 | het | 85.6436 | 76.9070 | 96.6195 | 86.8249 | 8116 | 2437 | 8117 | 284 | 231 | 81.3380 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 72.4338 | 76.9090 | 68.4508 | 62.7083 | 2518 | 756 | 2788 | 1285 | 845 | 65.7588 | |
| ciseli-custom | INDEL | D1_5 | map_l250_m0_e0 | homalt | 76.9231 | 76.9231 | 76.9231 | 97.6234 | 10 | 3 | 10 | 3 | 2 | 66.6667 | |
| ciseli-custom | INDEL | D6_15 | map_l150_m1_e0 | homalt | 68.9655 | 76.9231 | 62.5000 | 90.7781 | 20 | 6 | 20 | 12 | 10 | 83.3333 | |
| ciseli-custom | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 55.5556 | 76.9231 | 43.4783 | 70.8861 | 10 | 3 | 10 | 13 | 3 | 23.0769 | |
| ciseli-custom | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 55.5556 | 76.9231 | 43.4783 | 70.8861 | 10 | 3 | 10 | 13 | 3 | 23.0769 | |
| ciseli-custom | SNP | tv | lowcmp_SimpleRepeat_diTR_51to200 | * | 15.2009 | 76.9231 | 8.4337 | 82.7562 | 20 | 6 | 21 | 228 | 4 | 1.7544 | |
| ckim-dragen | INDEL | D1_5 | map_l125_m1_e0 | hetalt | 86.9565 | 76.9231 | 100.0000 | 95.9350 | 10 | 3 | 10 | 0 | 0 | ||
| qzeng-custom | SNP | tv | lowcmp_SimpleRepeat_diTR_51to200 | * | 80.0000 | 76.9231 | 83.3333 | 97.2758 | 20 | 6 | 20 | 4 | 1 | 25.0000 | |
| mlin-fermikit | INDEL | D16_PLUS | map_siren | het | 71.4286 | 76.9231 | 66.6667 | 92.1980 | 60 | 18 | 62 | 31 | 14 | 45.1613 | |
| rpoplin-dv42 | SNP | tv | lowcmp_SimpleRepeat_diTR_51to200 | * | 85.1064 | 76.9231 | 95.2381 | 96.3918 | 20 | 6 | 20 | 1 | 0 | 0.0000 | |