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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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76351-76400 / 86044 show all | |||||||||||||||
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.3623 | 92.9799 | 100.0000 | 31.6887 | 4437 | 335 | 4486 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | I1_5 | * | hetalt | 98.3546 | 97.0076 | 99.7395 | 72.4903 | 10860 | 335 | 11105 | 29 | 29 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I1_5 | HG002compoundhet | hetalt | 98.4111 | 97.0028 | 99.8609 | 64.1248 | 10842 | 335 | 10768 | 15 | 15 | 100.0000 | |
| qzeng-custom | SNP | * | HG002compoundhet | het | 97.8777 | 97.6372 | 98.1193 | 49.7459 | 13843 | 335 | 16591 | 318 | 73 | 22.9560 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.0206 | 93.2787 | 98.9286 | 61.7804 | 4663 | 336 | 4617 | 50 | 35 | 70.0000 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.0206 | 93.2787 | 98.9286 | 61.7804 | 4663 | 336 | 4617 | 50 | 35 | 70.0000 | |
| ndellapenna-hhga | SNP | ti | map_l150_m1_e0 | * | 99.0365 | 98.2955 | 99.7888 | 72.3511 | 19376 | 336 | 19376 | 41 | 23 | 56.0976 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 62.0379 | 61.0660 | 63.0412 | 57.2267 | 527 | 336 | 597 | 350 | 266 | 76.0000 | |
| ghariani-varprowl | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 39.4120 | 30.0000 | 57.4297 | 83.9871 | 144 | 336 | 143 | 106 | 102 | 96.2264 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 61.2790 | 48.5452 | 83.0688 | 66.6372 | 317 | 336 | 314 | 64 | 64 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.2807 | 95.0784 | 99.5875 | 32.3304 | 6491 | 336 | 6518 | 27 | 27 | 100.0000 | |
| jli-custom | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.0633 | 94.3415 | 99.9468 | 62.9123 | 5602 | 336 | 5641 | 3 | 3 | 100.0000 | |
| ltrigg-rtg1 | SNP | * | map_l250_m2_e1 | * | 97.7139 | 95.7932 | 99.7133 | 83.6180 | 7651 | 336 | 7651 | 22 | 11 | 50.0000 | |
| ltrigg-rtg1 | SNP | tv | map_siren | het | 99.1688 | 98.8255 | 99.5144 | 50.4058 | 28273 | 336 | 28278 | 138 | 6 | 4.3478 | |
| gduggal-bwaplat | INDEL | I1_5 | map_l125_m2_e0 | * | 75.4526 | 60.7935 | 99.4275 | 94.2638 | 521 | 336 | 521 | 3 | 1 | 33.3333 | |
| gduggal-bwafb | INDEL | I6_15 | HG002complexvar | hetalt | 81.3403 | 72.5266 | 92.5926 | 62.9291 | 887 | 336 | 300 | 24 | 23 | 95.8333 | |
| egarrison-hhga | INDEL | D16_PLUS | HG002complexvar | * | 85.7883 | 79.5496 | 93.0889 | 62.2772 | 1307 | 336 | 1320 | 98 | 72 | 73.4694 | |
| egarrison-hhga | SNP | * | map_l150_m1_e0 | * | 99.3388 | 98.9023 | 99.7792 | 73.2772 | 30273 | 336 | 30273 | 67 | 32 | 47.7612 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 76.0845 | 61.4679 | 99.8214 | 27.9279 | 536 | 336 | 559 | 1 | 1 | 100.0000 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.0666 | 85.7988 | 99.3224 | 30.2027 | 2030 | 336 | 2052 | 14 | 14 | 100.0000 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.3303 | 92.9589 | 99.9555 | 30.3660 | 4436 | 336 | 4488 | 2 | 2 | 100.0000 | |
| astatham-gatk | SNP | ti | * | homalt | 99.9764 | 99.9582 | 99.9946 | 15.8604 | 802702 | 336 | 802693 | 43 | 41 | 95.3488 | |
| bgallagher-sentieon | SNP | ti | HG002complexvar | * | 99.9558 | 99.9337 | 99.9780 | 17.4939 | 508099 | 337 | 508035 | 112 | 53 | 47.3214 | |
| gduggal-bwaplat | SNP | * | segdup | het | 98.4496 | 98.0539 | 98.8484 | 95.2313 | 16980 | 337 | 16996 | 198 | 12 | 6.0606 | |
| jpowers-varprowl | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 97.2043 | 97.0166 | 97.3928 | 54.4393 | 10959 | 337 | 10945 | 293 | 257 | 87.7133 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 19.1153 | 11.0818 | 69.4915 | 82.2823 | 42 | 337 | 41 | 18 | 11 | 61.1111 | |
| ndellapenna-hhga | SNP | ti | map_l150_m2_e0 | * | 99.0695 | 98.3571 | 99.7923 | 74.0705 | 20175 | 337 | 20175 | 42 | 23 | 54.7619 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 97.8712 | 96.3728 | 99.4169 | 41.9419 | 8954 | 337 | 9036 | 53 | 52 | 98.1132 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 97.8712 | 96.3728 | 99.4169 | 41.9419 | 8954 | 337 | 9036 | 53 | 52 | 98.1132 | |
| mlin-fermikit | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.0726 | 96.5229 | 95.6265 | 68.5165 | 9355 | 337 | 9380 | 429 | 282 | 65.7343 | |
| gduggal-snapvard | SNP | ti | map_l150_m2_e1 | homalt | 97.6162 | 95.6194 | 99.6983 | 73.2617 | 7356 | 337 | 7269 | 22 | 18 | 81.8182 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 18.9387 | 11.0818 | 65.0794 | 81.9484 | 42 | 337 | 41 | 22 | 12 | 54.5455 | |
| gduggal-snapfb | SNP | tv | HG002complexvar | homalt | 99.3543 | 99.6457 | 99.0647 | 24.8993 | 94774 | 337 | 94793 | 895 | 159 | 17.7654 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 36.3779 | 31.5041 | 43.0357 | 63.8943 | 155 | 337 | 241 | 319 | 270 | 84.6395 | |
| ciseli-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 33.7717 | 31.2245 | 36.7713 | 63.1405 | 153 | 337 | 246 | 423 | 326 | 77.0686 | |
| ciseli-custom | INDEL | * | map_l150_m2_e0 | het | 66.9093 | 62.8035 | 71.5895 | 93.6451 | 569 | 337 | 572 | 227 | 132 | 58.1498 | |
| rpoplin-dv42 | INDEL | I16_PLUS | HG002compoundhet | * | 89.3838 | 84.2744 | 95.1528 | 48.3959 | 1806 | 337 | 1806 | 92 | 90 | 97.8261 | |
| ckim-isaac | INDEL | I1_5 | map_l100_m1_e0 | * | 85.2037 | 74.8320 | 98.9130 | 83.0315 | 1002 | 337 | 1001 | 11 | 5 | 45.4545 | |
| hfeng-pmm2 | SNP | ti | map_siren | * | 99.6860 | 99.6642 | 99.7079 | 54.6933 | 100018 | 337 | 100003 | 293 | 39 | 13.3106 | |
| hfeng-pmm3 | INDEL | D1_5 | HG002compoundhet | het | 87.8989 | 80.4977 | 96.7989 | 73.8775 | 1391 | 337 | 1391 | 46 | 42 | 91.3043 | |
| jlack-gatk | SNP | * | map_l100_m1_e0 | het | 95.6776 | 99.2570 | 92.3473 | 78.4943 | 45022 | 337 | 45011 | 3730 | 265 | 7.1046 | |
| hfeng-pmm2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.2945 | 95.0894 | 99.6044 | 78.8532 | 6545 | 338 | 6546 | 26 | 3 | 11.5385 | |
| gduggal-snapvard | SNP | * | map_l250_m1_e0 | * | 85.6069 | 95.3199 | 77.6904 | 91.0746 | 6884 | 338 | 6815 | 1957 | 96 | 4.9055 | |
| gduggal-snapplat | SNP | tv | map_l250_m1_e0 | het | 85.2855 | 81.0856 | 89.9441 | 94.8591 | 1449 | 338 | 1449 | 162 | 67 | 41.3580 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 62.5767 | 48.0000 | 89.8678 | 23.0508 | 312 | 338 | 204 | 23 | 21 | 91.3043 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 90.1510 | 90.4439 | 89.8599 | 72.3577 | 3199 | 338 | 3208 | 362 | 144 | 39.7790 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.0710 | 97.8937 | 98.2489 | 60.0570 | 15709 | 338 | 15710 | 280 | 267 | 95.3571 | |
| gduggal-bwaplat | INDEL | I1_5 | map_l125_m2_e1 | * | 75.7295 | 61.1494 | 99.4393 | 94.2939 | 532 | 338 | 532 | 3 | 1 | 33.3333 | |
| gduggal-bwafb | SNP | ti | map_l125_m1_e0 | * | 98.9304 | 98.8478 | 99.0132 | 72.1354 | 28997 | 338 | 28997 | 289 | 84 | 29.0657 | |
| gduggal-bwavard | SNP | tv | map_l125_m2_e0 | * | 95.0420 | 97.9501 | 92.3015 | 80.3208 | 16151 | 338 | 16102 | 1343 | 73 | 5.4356 | |