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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
10751-10800 / 86044 show all | |||||||||||||||
| gduggal-snapvard | INDEL | I1_5 | map_l150_m2_e1 | het | 87.4676 | 98.7382 | 78.5064 | 92.5981 | 313 | 4 | 431 | 118 | 43 | 36.4407 | |
| gduggal-snapvard | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 82.6781 | 95.0672 | 73.1457 | 83.0764 | 4529 | 235 | 4497 | 1651 | 43 | 2.6045 | |
| gduggal-snapvard | SNP | * | map_l100_m2_e0 | homalt | 98.0484 | 96.3703 | 99.7860 | 62.8472 | 26524 | 999 | 26107 | 56 | 43 | 76.7857 | |
| gduggal-snapvard | SNP | * | map_l100_m2_e1 | homalt | 98.0418 | 96.3556 | 99.7880 | 62.8493 | 26783 | 1013 | 26357 | 56 | 43 | 76.7857 | |
| hfeng-pmm1 | INDEL | * | HG002complexvar | het | 98.8731 | 97.9378 | 99.8265 | 56.4583 | 45259 | 953 | 44888 | 78 | 43 | 55.1282 | |
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 56.5111 | 56.6123 | 56.4103 | 93.4064 | 625 | 479 | 638 | 493 | 43 | 8.7221 | |
| gduggal-snapvard | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 0.0000 | 0.0000 | 38.4615 | 88.9511 | 0 | 0 | 205 | 328 | 43 | 13.1098 | |
| gduggal-snapvard | INDEL | C1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 35.0259 | 100.0000 | 21.2312 | 82.4631 | 1 | 0 | 169 | 627 | 43 | 6.8581 | |
| gduggal-snapvard | INDEL | C6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 0.0000 | 0.0000 | 47.2362 | 89.5263 | 0 | 0 | 94 | 105 | 43 | 40.9524 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 2.7260 | 1.4416 | 25.0000 | 74.2765 | 19 | 1299 | 20 | 60 | 43 | 71.6667 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 4.9557 | 2.7624 | 24.0506 | 74.0984 | 10 | 352 | 19 | 60 | 43 | 71.6667 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 22.5181 | 16.0393 | 37.7778 | 69.3878 | 98 | 513 | 85 | 140 | 43 | 30.7143 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 47.4332 | 31.5939 | 95.1220 | 44.9136 | 1114 | 2412 | 1092 | 56 | 43 | 76.7857 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 47.4332 | 31.5939 | 95.1220 | 44.9136 | 1114 | 2412 | 1092 | 56 | 43 | 76.7857 | |
| gduggal-snapplat | SNP | * | map_l250_m0_e0 | * | 83.7909 | 76.0187 | 93.3333 | 96.5523 | 1623 | 512 | 1624 | 116 | 43 | 37.0690 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 65.7529 | 52.8540 | 86.9801 | 38.4187 | 963 | 859 | 481 | 72 | 43 | 59.7222 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.5493 | 93.8357 | 99.4245 | 23.8294 | 7596 | 499 | 7602 | 44 | 43 | 97.7273 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.5181 | 93.7722 | 99.4296 | 26.3580 | 7664 | 509 | 7670 | 44 | 43 | 97.7273 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.1200 | 95.0044 | 99.3320 | 25.8972 | 6542 | 344 | 6543 | 44 | 43 | 97.7273 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 94.9354 | 94.1445 | 95.7397 | 51.4296 | 1238 | 77 | 1236 | 55 | 43 | 78.1818 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.5900 | 96.6582 | 98.5399 | 68.6164 | 3442 | 119 | 3442 | 51 | 43 | 84.3137 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 74.0331 | 94.3662 | 60.9091 | 53.7815 | 67 | 4 | 67 | 43 | 43 | 100.0000 | |
| raldana-dualsentieon | SNP | * | * | het | 99.8865 | 99.8694 | 99.9036 | 19.2179 | 1871141 | 2446 | 1871016 | 1806 | 43 | 2.3810 | |
| rpoplin-dv42 | SNP | tv | map_l125_m0_e0 | het | 98.3333 | 98.5458 | 98.1217 | 74.3380 | 4337 | 64 | 4336 | 83 | 43 | 51.8072 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.4712 | 96.1968 | 98.7798 | 51.8157 | 5514 | 218 | 5505 | 68 | 43 | 63.2353 | |
| egarrison-hhga | INDEL | I6_15 | HG002complexvar | homalt | 96.2063 | 97.0346 | 95.3921 | 53.5137 | 1178 | 36 | 1180 | 57 | 43 | 75.4386 | |
| dgrover-gatk | INDEL | D1_5 | * | hetalt | 97.3217 | 95.1977 | 99.5427 | 63.5299 | 9753 | 492 | 9795 | 45 | 43 | 95.5556 | |
| dgrover-gatk | INDEL | D1_5 | HG002complexvar | hetalt | 95.3242 | 93.9349 | 96.7552 | 73.1272 | 1270 | 82 | 1312 | 44 | 43 | 97.7273 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 75.4098 | 97.1831 | 61.6071 | 52.3404 | 69 | 2 | 69 | 43 | 43 | 100.0000 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | het | 68.1120 | 71.9512 | 64.6617 | 69.6347 | 118 | 46 | 86 | 47 | 43 | 91.4894 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 92.0106 | 92.2964 | 91.7266 | 69.6573 | 1258 | 105 | 1275 | 115 | 43 | 37.3913 | |
| egarrison-hhga | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 72.8990 | 58.1328 | 97.7209 | 46.5971 | 2223 | 1601 | 2101 | 49 | 43 | 87.7551 | |
| ckim-vqsr | INDEL | D1_5 | * | hetalt | 96.5103 | 93.6457 | 99.5557 | 62.7258 | 9594 | 651 | 9636 | 43 | 43 | 100.0000 | |
| ckim-vqsr | INDEL | D1_5 | HG002complexvar | hetalt | 92.5788 | 88.8314 | 96.6563 | 72.4212 | 1201 | 151 | 1243 | 43 | 43 | 100.0000 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 75.4098 | 97.1831 | 61.6071 | 52.7426 | 69 | 2 | 69 | 43 | 43 | 100.0000 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.0580 | 99.2555 | 98.8612 | 71.4717 | 3733 | 28 | 3733 | 43 | 43 | 100.0000 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.0580 | 99.2555 | 98.8612 | 71.4717 | 3733 | 28 | 3733 | 43 | 43 | 100.0000 | |
| egarrison-hhga | INDEL | D6_15 | * | hetalt | 65.0139 | 48.4952 | 98.5994 | 42.7885 | 3964 | 4210 | 3520 | 50 | 43 | 86.0000 | |
| egarrison-hhga | INDEL | D6_15 | HG002complexvar | homalt | 95.9329 | 97.8614 | 94.0789 | 59.2766 | 1144 | 25 | 1144 | 72 | 43 | 59.7222 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 87.5573 | 82.7344 | 92.9773 | 75.9228 | 944 | 197 | 940 | 71 | 43 | 60.5634 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 90.3952 | 98.3425 | 83.6364 | 84.1954 | 356 | 6 | 230 | 45 | 43 | 95.5556 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.5292 | 96.8794 | 96.1816 | 74.8551 | 1366 | 44 | 1335 | 53 | 43 | 81.1321 | |
| astatham-gatk | INDEL | D1_5 | * | hetalt | 97.2343 | 95.0220 | 99.5520 | 63.2355 | 9735 | 510 | 9778 | 44 | 43 | 97.7273 | |
| astatham-gatk | INDEL | D1_5 | HG002complexvar | hetalt | 95.3253 | 93.9349 | 96.7576 | 72.9412 | 1270 | 82 | 1313 | 44 | 43 | 97.7273 | |
| astatham-gatk | SNP | * | map_l125_m1_e0 | * | 91.2465 | 84.0779 | 99.7513 | 74.8310 | 38110 | 7217 | 38104 | 95 | 43 | 45.2632 | |
| astatham-gatk | SNP | * | map_l125_m2_e0 | * | 91.3143 | 84.1877 | 99.7590 | 76.2743 | 39335 | 7388 | 39329 | 95 | 43 | 45.2632 | |
| astatham-gatk | SNP | * | map_l125_m2_e1 | * | 91.3125 | 84.1829 | 99.7615 | 76.3148 | 39736 | 7466 | 39730 | 95 | 43 | 45.2632 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.3254 | 96.9477 | 97.7059 | 65.2032 | 1874 | 59 | 1874 | 44 | 43 | 97.7273 | |
| anovak-vg | INDEL | D1_5 | map_l125_m0_e0 | * | 80.9550 | 82.0565 | 79.8828 | 90.2159 | 407 | 89 | 409 | 103 | 43 | 41.7476 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 15.5475 | 9.5361 | 42.0635 | 45.6897 | 37 | 351 | 53 | 73 | 43 | 58.9041 | |