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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
60301-60350 / 86044 show all | |||||||||||||||
| hfeng-pmm3 | INDEL | D1_5 | map_l125_m1_e0 | * | 98.9456 | 99.0809 | 98.8106 | 83.8505 | 1078 | 10 | 1080 | 13 | 3 | 23.0769 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 63.1996 | 46.4567 | 98.8107 | 36.5459 | 3304 | 3808 | 2908 | 35 | 31 | 88.5714 | |
| jli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.9286 | 99.0462 | 98.8113 | 76.1938 | 1350 | 13 | 1330 | 16 | 10 | 62.5000 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.9663 | 95.1890 | 98.8113 | 52.9502 | 3324 | 168 | 3325 | 40 | 33 | 82.5000 | |
| jli-custom | INDEL | D1_5 | map_l100_m2_e1 | * | 98.6576 | 98.5044 | 98.8114 | 83.1328 | 1910 | 29 | 1912 | 23 | 8 | 34.7826 | |
| dgrover-gatk | INDEL | D1_5 | map_l100_m1_e0 | * | 98.8105 | 98.8095 | 98.8115 | 84.8192 | 1826 | 22 | 1829 | 22 | 5 | 22.7273 | |
| egarrison-hhga | INDEL | I1_5 | map_l125_m2_e1 | het | 98.5192 | 98.2283 | 98.8119 | 87.8019 | 499 | 9 | 499 | 6 | 1 | 16.6667 | |
| raldana-dualsentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.3707 | 95.9702 | 98.8127 | 71.1458 | 1548 | 65 | 1498 | 18 | 13 | 72.2222 | |
| cchapple-custom | INDEL | * | map_l100_m2_e1 | homalt | 98.1532 | 97.5020 | 98.8133 | 82.2920 | 1249 | 32 | 1249 | 15 | 11 | 73.3333 | |
| gduggal-snapfb | SNP | tv | map_l125_m0_e0 | homalt | 96.2107 | 93.7416 | 98.8135 | 84.7573 | 2082 | 139 | 2082 | 25 | 6 | 24.0000 | |
| rpoplin-dv42 | INDEL | D1_5 | map_l100_m2_e1 | * | 98.7364 | 98.6591 | 98.8138 | 83.7031 | 1913 | 26 | 1916 | 23 | 9 | 39.1304 | |
| dgrover-gatk | INDEL | I1_5 | map_l125_m2_e1 | het | 98.4213 | 98.0315 | 98.8142 | 89.0239 | 498 | 10 | 500 | 6 | 0 | 0.0000 | |
| gduggal-bwafb | INDEL | I6_15 | map_siren | * | 89.4095 | 81.6393 | 98.8142 | 76.5306 | 249 | 56 | 250 | 3 | 3 | 100.0000 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 96.8466 | 94.9559 | 98.8142 | 35.1282 | 753 | 40 | 750 | 9 | 9 | 100.0000 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 95.6616 | 92.7039 | 98.8142 | 83.3771 | 216 | 17 | 250 | 3 | 3 | 100.0000 | |
| jpowers-varprowl | INDEL | I1_5 | map_l100_m1_e0 | homalt | 97.6562 | 96.5251 | 98.8142 | 74.0646 | 500 | 18 | 500 | 6 | 5 | 83.3333 | |
| asubramanian-gatk | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.8363 | 98.8582 | 98.8143 | 45.0033 | 6667 | 77 | 6667 | 80 | 1 | 1.2500 | |
| egarrison-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.2514 | 97.6938 | 98.8154 | 81.5275 | 2584 | 61 | 2586 | 31 | 13 | 41.9355 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 63.9253 | 47.2441 | 98.8157 | 36.3273 | 3360 | 3752 | 2837 | 34 | 29 | 85.2941 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 97.0579 | 95.3612 | 98.8161 | 48.1800 | 1254 | 61 | 1252 | 15 | 10 | 66.6667 | |
| dgrover-gatk | INDEL | D6_15 | HG002complexvar | homalt | 99.4048 | 100.0000 | 98.8166 | 62.8338 | 1169 | 0 | 1169 | 14 | 14 | 100.0000 | |
| ckim-isaac | INDEL | I1_5 | map_l150_m2_e0 | * | 77.9463 | 64.3545 | 98.8166 | 91.4754 | 334 | 185 | 334 | 4 | 1 | 25.0000 | |
| raldana-dualsentieon | INDEL | * | map_l100_m0_e0 | homalt | 98.6220 | 98.4283 | 98.8166 | 82.4931 | 501 | 8 | 501 | 6 | 3 | 50.0000 | |
| gduggal-bwafb | SNP | * | map_l125_m2_e1 | * | 98.8522 | 98.8878 | 98.8166 | 74.3375 | 46677 | 525 | 46677 | 559 | 136 | 24.3292 | |
| hfeng-pmm2 | INDEL | I6_15 | * | * | 97.8481 | 96.8980 | 98.8171 | 51.0141 | 24053 | 770 | 24058 | 288 | 265 | 92.0139 | |
| hfeng-pmm1 | SNP | ti | map_l250_m1_e0 | het | 98.6671 | 98.5175 | 98.8172 | 88.8014 | 2924 | 44 | 2924 | 35 | 8 | 22.8571 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 95.8883 | 93.1278 | 98.8175 | 40.7349 | 15557 | 1148 | 16463 | 197 | 178 | 90.3553 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 95.8883 | 93.1278 | 98.8175 | 40.7349 | 15557 | 1148 | 16463 | 197 | 178 | 90.3553 | |
| bgallagher-sentieon | SNP | ti | map_l125_m1_e0 | het | 99.0798 | 99.3430 | 98.8180 | 74.4018 | 18146 | 120 | 18142 | 217 | 33 | 15.2074 | |
| hfeng-pmm1 | INDEL | * | map_l125_m2_e0 | het | 97.3384 | 95.9022 | 98.8183 | 86.3315 | 1334 | 57 | 1338 | 16 | 1 | 6.2500 | |
| gduggal-bwafb | INDEL | I1_5 | map_l100_m2_e1 | * | 97.6023 | 96.4158 | 98.8183 | 83.9763 | 1345 | 50 | 1338 | 16 | 5 | 31.2500 | |
| gduggal-bwafb | INDEL | * | map_l100_m2_e1 | homalt | 98.4321 | 98.0484 | 98.8189 | 84.9917 | 1256 | 25 | 1255 | 15 | 13 | 86.6667 | |
| bgallagher-sentieon | SNP | ti | map_l125_m2_e0 | het | 99.0858 | 99.3537 | 98.8194 | 75.6140 | 18754 | 122 | 18750 | 224 | 33 | 14.7321 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 90.4880 | 83.4521 | 98.8195 | 30.8039 | 11710 | 2322 | 12138 | 145 | 128 | 88.2759 | |
| ndellapenna-hhga | INDEL | D1_5 | map_l100_m1_e0 | homalt | 98.9030 | 98.9865 | 98.8196 | 81.4803 | 586 | 6 | 586 | 7 | 6 | 85.7143 | |
| ckim-isaac | INDEL | I1_5 | map_l125_m1_e0 | * | 82.3612 | 70.6024 | 98.8196 | 86.4457 | 586 | 244 | 586 | 7 | 2 | 28.5714 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 97.5369 | 96.2865 | 98.8203 | 42.9016 | 1089 | 42 | 1089 | 13 | 9 | 69.2308 | |
| jlack-gatk | INDEL | * | map_l125_m2_e0 | homalt | 98.8204 | 98.8204 | 98.8204 | 86.3286 | 754 | 9 | 754 | 9 | 4 | 44.4444 | |
| ndellapenna-hhga | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 98.4390 | 98.0603 | 98.8206 | 66.9267 | 3185 | 63 | 3184 | 38 | 10 | 26.3158 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.6703 | 94.6112 | 98.8210 | 55.5926 | 3687 | 210 | 3688 | 44 | 37 | 84.0909 | |
| qzeng-custom | SNP | tv | map_l150_m2_e0 | homalt | 81.9655 | 70.0220 | 98.8211 | 73.9641 | 2859 | 1224 | 2850 | 34 | 34 | 100.0000 | |
| qzeng-custom | SNP | tv | map_siren | * | 92.0283 | 86.1093 | 98.8212 | 67.3017 | 39550 | 6380 | 39401 | 470 | 339 | 72.1277 | |
| ltrigg-rtg1 | INDEL | * | map_l100_m0_e0 | homalt | 99.0173 | 99.2141 | 98.8212 | 82.1404 | 505 | 4 | 503 | 6 | 3 | 50.0000 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.6974 | 94.6626 | 98.8216 | 55.5793 | 3689 | 208 | 3690 | 44 | 37 | 84.0909 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.9876 | 99.1538 | 98.8219 | 62.9494 | 11014 | 94 | 10989 | 131 | 41 | 31.2977 | |
| dgrover-gatk | INDEL | * | map_l125_m2_e0 | homalt | 98.8867 | 98.9515 | 98.8220 | 87.0968 | 755 | 8 | 755 | 9 | 4 | 44.4444 | |
| jli-custom | INDEL | * | map_l100_m1_e0 | * | 98.4897 | 98.1595 | 98.8222 | 83.0077 | 3520 | 66 | 3524 | 42 | 15 | 35.7143 | |
| jpowers-varprowl | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | het | 98.3094 | 97.8017 | 98.8224 | 46.8984 | 2091 | 47 | 2098 | 25 | 1 | 4.0000 | |
| raldana-dualsentieon | INDEL | I1_5 | map_l100_m2_e0 | * | 98.3491 | 97.8801 | 98.8227 | 82.1466 | 1339 | 29 | 1343 | 16 | 2 | 12.5000 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.6406 | 96.4859 | 98.8233 | 61.6023 | 12081 | 440 | 11926 | 142 | 130 | 91.5493 | |