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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
15901-15950 / 86044 show all | |||||||||||||||
| ltrigg-rtg1 | INDEL | I16_PLUS | HG002complexvar | het | 91.1805 | 84.2105 | 99.4083 | 47.5155 | 560 | 105 | 504 | 3 | 2 | 66.6667 | |
| qzeng-custom | INDEL | D1_5 | HG002compoundhet | het | 92.9212 | 93.9236 | 91.9400 | 64.3165 | 1623 | 105 | 11042 | 968 | 705 | 72.8306 | |
| qzeng-custom | INDEL | I16_PLUS | HG002complexvar | hetalt | 80.5997 | 68.6567 | 97.5728 | 58.5513 | 230 | 105 | 201 | 5 | 5 | 100.0000 | |
| mlin-fermikit | INDEL | D1_5 | map_l250_m2_e0 | * | 56.5892 | 42.9348 | 82.9787 | 91.5996 | 79 | 105 | 78 | 16 | 14 | 87.5000 | |
| qzeng-custom | INDEL | * | map_l250_m1_e0 | * | 75.5265 | 65.5738 | 89.0411 | 97.9332 | 200 | 105 | 260 | 32 | 16 | 50.0000 | |
| ltrigg-rtg2 | INDEL | D6_15 | * | het | 99.2141 | 99.0942 | 99.3342 | 52.7094 | 11487 | 105 | 11339 | 76 | 26 | 34.2105 | |
| ltrigg-rtg2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.1878 | 96.9931 | 99.4123 | 51.7989 | 3387 | 105 | 3383 | 20 | 14 | 70.0000 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 92.7491 | 96.2553 | 89.4894 | 50.3947 | 2699 | 105 | 2699 | 317 | 129 | 40.6940 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 93.4823 | 87.7622 | 100.0000 | 53.9683 | 753 | 105 | 754 | 0 | 0 | ||
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 92.9382 | 92.2964 | 93.5890 | 71.7186 | 1258 | 105 | 1708 | 117 | 101 | 86.3248 | |
| gduggal-bwavard | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.0887 | 98.2753 | 99.9156 | 51.4864 | 5983 | 105 | 5919 | 5 | 4 | 80.0000 | |
| gduggal-snapfb | INDEL | * | HG002compoundhet | homalt | 22.9146 | 84.6939 | 13.2497 | 72.0594 | 581 | 105 | 581 | 3804 | 3669 | 96.4511 | |
| ckim-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7343 | 99.6285 | 99.8404 | 58.9273 | 28155 | 105 | 28158 | 45 | 20 | 44.4444 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 0.0000 | 6.2500 | 0.0000 | 0.0000 | 7 | 105 | 0 | 0 | 0 | ||
| ckim-dragen | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 99.3007 | 99.0279 | 99.5750 | 78.5377 | 10696 | 105 | 10777 | 46 | 21 | 45.6522 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 88.0775 | 95.1208 | 82.0053 | 38.4898 | 2047 | 105 | 3427 | 752 | 750 | 99.7340 | |
| eyeh-varpipe | INDEL | * | map_l100_m2_e1 | het | 96.0818 | 95.5186 | 96.6518 | 82.4853 | 2238 | 105 | 3031 | 105 | 69 | 65.7143 | |
| dgrover-gatk | INDEL | D16_PLUS | * | hetalt | 96.8869 | 94.5680 | 99.3224 | 39.0920 | 1828 | 105 | 2052 | 14 | 14 | 100.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | HG002compoundhet | * | 95.7397 | 95.5147 | 95.9657 | 35.4749 | 2236 | 105 | 2236 | 94 | 91 | 96.8085 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.8591 | 96.7290 | 96.9897 | 63.1840 | 3105 | 105 | 3093 | 96 | 93 | 96.8750 | |
| 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 | |
| dgrover-gatk | SNP | ti | map_l100_m0_e0 | het | 99.1285 | 99.2491 | 99.0081 | 74.4536 | 13878 | 105 | 13875 | 139 | 28 | 20.1439 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 86.6087 | 82.5871 | 91.0420 | 67.8424 | 498 | 105 | 498 | 49 | 34 | 69.3878 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.4731 | 87.4402 | 98.1208 | 65.4453 | 731 | 105 | 731 | 14 | 12 | 85.7143 | |
| raldana-dualsentieon | SNP | tv | map_l100_m1_e0 | het | 99.1452 | 99.3189 | 98.9720 | 68.0652 | 15312 | 105 | 15308 | 159 | 1 | 0.6289 | |
| raldana-dualsentieon | SNP | tv | map_l100_m2_e0 | het | 99.1552 | 99.3345 | 98.9766 | 69.6214 | 15672 | 105 | 15668 | 162 | 1 | 0.6173 | |
| raldana-dualsentieon | SNP | tv | map_l100_m2_e1 | het | 99.1544 | 99.3412 | 98.9684 | 69.6842 | 15833 | 105 | 15829 | 165 | 1 | 0.6061 | |
| raldana-dualsentieon | SNP | tv | map_l150_m2_e1 | * | 99.0225 | 99.0871 | 98.9579 | 75.9025 | 11397 | 105 | 11395 | 120 | 3 | 2.5000 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.7294 | 97.9480 | 99.5234 | 39.3399 | 5012 | 105 | 5012 | 24 | 23 | 95.8333 | |
| rpoplin-dv42 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 86.4388 | 78.8732 | 95.6098 | 71.0452 | 392 | 105 | 392 | 18 | 17 | 94.4444 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 91.3157 | 84.9354 | 98.7324 | 37.8284 | 592 | 105 | 701 | 9 | 9 | 100.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 91.4321 | 87.4402 | 95.8060 | 67.3513 | 731 | 105 | 731 | 32 | 29 | 90.6250 | |
| hfeng-pmm3 | INDEL | I1_5 | HG002compoundhet | het | 91.3786 | 87.6471 | 95.4420 | 86.4242 | 745 | 105 | 691 | 33 | 27 | 81.8182 | |
| hfeng-pmm2 | INDEL | I1_5 | * | homalt | 99.7668 | 99.8262 | 99.7075 | 52.8322 | 60323 | 105 | 60327 | 177 | 174 | 98.3051 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.6222 | 93.5683 | 99.8821 | 33.8144 | 1513 | 104 | 1695 | 2 | 2 | 100.0000 | |
| jlack-gatk | SNP | * | map_l150_m0_e0 | homalt | 98.5532 | 97.4566 | 99.6748 | 74.6529 | 3985 | 104 | 3985 | 13 | 10 | 76.9231 | |
| jlack-gatk | SNP | * | map_l250_m2_e1 | het | 91.1258 | 98.0243 | 85.1345 | 94.1114 | 5160 | 104 | 5160 | 901 | 60 | 6.6593 | |
| jlack-gatk | SNP | ti | map_l125_m0_e0 | het | 93.6780 | 98.7414 | 89.1086 | 85.4382 | 8159 | 104 | 8157 | 997 | 87 | 8.7262 | |
| hfeng-pmm2 | SNP | ti | map_l150_m2_e0 | het | 99.0233 | 99.1926 | 98.8546 | 79.5912 | 12777 | 104 | 12773 | 148 | 13 | 8.7838 | |
| hfeng-pmm2 | SNP | ti | map_l150_m2_e1 | het | 99.0257 | 99.2009 | 98.8512 | 79.6610 | 12911 | 104 | 12907 | 150 | 13 | 8.6667 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.0292 | 97.0795 | 98.9977 | 67.6517 | 3457 | 104 | 3457 | 35 | 30 | 85.7143 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.6223 | 93.5683 | 99.8824 | 33.7490 | 1513 | 104 | 1698 | 2 | 2 | 100.0000 | |
| hfeng-pmm1 | INDEL | I1_5 | HG002compoundhet | het | 90.1398 | 87.7647 | 92.6471 | 86.3079 | 746 | 104 | 693 | 55 | 49 | 89.0909 | |
| hfeng-pmm1 | SNP | ti | map_l125_m0_e0 | het | 99.0169 | 98.7414 | 99.2940 | 75.6362 | 8159 | 104 | 8157 | 58 | 15 | 25.8621 | |
| gduggal-bwavard | SNP | * | map_l250_m1_e0 | het | 86.5001 | 97.8128 | 77.5328 | 92.6635 | 4651 | 104 | 4607 | 1335 | 32 | 2.3970 | |
| gduggal-bwafb | INDEL | I1_5 | map_siren | * | 97.6773 | 96.5391 | 98.8428 | 79.9276 | 2901 | 104 | 2904 | 34 | 18 | 52.9412 | |
| gduggal-bwafb | INDEL | I6_15 | HG002complexvar | homalt | 92.1427 | 91.4333 | 92.8631 | 43.3935 | 1110 | 104 | 1106 | 85 | 84 | 98.8235 | |
| eyeh-varpipe | SNP | ti | map_l125_m2_e1 | * | 99.2798 | 99.6598 | 98.9027 | 74.7802 | 30465 | 104 | 29925 | 332 | 21 | 6.3253 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 35.9600 | 22.9630 | 82.8571 | 58.3333 | 31 | 104 | 29 | 6 | 3 | 50.0000 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 42.5806 | 29.7297 | 75.0000 | 50.4762 | 44 | 104 | 39 | 13 | 10 | 76.9231 | |