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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
72401-72450 / 86044 show all | |||||||||||||||
| eyeh-varpipe | INDEL | * | map_siren | hetalt | 51.9925 | 36.0324 | 93.3333 | 92.3928 | 89 | 158 | 154 | 11 | 9 | 81.8182 | |
| ckim-isaac | INDEL | D1_5 | map_l150_m1_e0 | het | 79.8048 | 67.2199 | 98.1873 | 91.0516 | 324 | 158 | 325 | 6 | 2 | 33.3333 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 73.6851 | 63.7615 | 87.2671 | 74.3426 | 278 | 158 | 281 | 41 | 15 | 36.5854 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 85.2201 | 76.0243 | 96.9466 | 64.6900 | 501 | 158 | 508 | 16 | 13 | 81.2500 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 85.2201 | 76.0243 | 96.9466 | 64.6900 | 501 | 158 | 508 | 16 | 13 | 81.2500 | |
| dgrover-gatk | SNP | * | map_l100_m0_e0 | het | 99.0469 | 99.2549 | 98.8398 | 75.0691 | 21047 | 158 | 21043 | 247 | 48 | 19.4332 | |
| anovak-vg | INDEL | I6_15 | map_siren | * | 52.3607 | 48.1967 | 57.3123 | 74.7000 | 147 | 158 | 145 | 108 | 71 | 65.7407 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 76.5009 | 82.6944 | 71.1705 | 83.8697 | 755 | 158 | 906 | 367 | 155 | 42.2343 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 10.6916 | 5.9524 | 52.4590 | 42.9907 | 10 | 158 | 32 | 29 | 10 | 34.4828 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 80.2738 | 67.8208 | 98.3287 | 28.7698 | 333 | 158 | 353 | 6 | 6 | 100.0000 | |
| asubramanian-gatk | INDEL | D1_5 | map_l100_m2_e0 | het | 91.0865 | 87.4204 | 95.0735 | 88.4658 | 1098 | 158 | 1100 | 57 | 6 | 10.5263 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 95.7443 | 92.7854 | 98.8981 | 31.4540 | 2032 | 158 | 2513 | 28 | 26 | 92.8571 | |
| ckim-dragen | SNP | * | map_l250_m2_e1 | het | 96.3314 | 96.9985 | 95.6733 | 91.4307 | 5106 | 158 | 5108 | 231 | 16 | 6.9264 | |
| ckim-dragen | SNP | * | map_l150_m0_e0 | het | 96.9776 | 97.9975 | 95.9788 | 84.1657 | 7781 | 159 | 7781 | 326 | 26 | 7.9755 | |
| ckim-dragen | SNP | ti | map_l100_m0_e0 | het | 97.6691 | 98.8629 | 96.5038 | 74.2830 | 13824 | 159 | 13829 | 501 | 46 | 9.1816 | |
| ckim-dragen | SNP | ti | map_l150_m1_e0 | het | 97.4739 | 98.7146 | 96.2639 | 80.0619 | 12211 | 159 | 12213 | 474 | 51 | 10.7595 | |
| ciseli-custom | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 82.5695 | 96.6091 | 72.0927 | 44.6474 | 4530 | 159 | 4544 | 1759 | 24 | 1.3644 | |
| cchapple-custom | INDEL | I16_PLUS | HG002compoundhet | * | 94.6047 | 92.5805 | 96.7194 | 51.6153 | 1984 | 159 | 2506 | 85 | 81 | 95.2941 | |
| ndellapenna-hhga | INDEL | D16_PLUS | HG002complexvar | het | 89.4513 | 85.6369 | 93.6214 | 62.1643 | 948 | 159 | 910 | 62 | 44 | 70.9677 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 81.2239 | 74.1883 | 89.7338 | 67.9659 | 457 | 159 | 472 | 54 | 43 | 79.6296 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 94.6844 | 90.6909 | 99.0458 | 31.4136 | 1549 | 159 | 1557 | 15 | 15 | 100.0000 | |
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 68.4814 | 53.3724 | 95.5224 | 60.9709 | 182 | 159 | 192 | 9 | 8 | 88.8889 | |
| mlin-fermikit | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.1967 | 97.8663 | 98.5292 | 39.4229 | 7293 | 159 | 7302 | 109 | 85 | 77.9817 | |
| ndellapenna-hhga | SNP | tv | map_l100_m0_e0 | het | 98.6590 | 97.7984 | 99.5349 | 67.9349 | 7063 | 159 | 7063 | 33 | 13 | 39.3939 | |
| jpowers-varprowl | INDEL | * | map_l100_m2_e1 | het | 91.5148 | 93.2138 | 89.8765 | 87.3477 | 2184 | 159 | 2184 | 246 | 199 | 80.8943 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 96.7268 | 94.6662 | 98.8792 | 50.6141 | 2822 | 159 | 2823 | 32 | 28 | 87.5000 | |
| rpoplin-dv42 | SNP | tv | map_l125_m1_e0 | * | 99.1341 | 99.0072 | 99.2613 | 68.8884 | 15857 | 159 | 15855 | 118 | 69 | 58.4746 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 92.2757 | 91.7744 | 92.7824 | 61.6372 | 1774 | 159 | 1774 | 138 | 138 | 100.0000 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 0.0000 | 31.7597 | 0.0000 | 0.0000 | 74 | 159 | 0 | 0 | 0 | ||
| gduggal-snapvard | SNP | tv | segdup | het | 97.6892 | 96.9926 | 98.3958 | 95.3896 | 5128 | 159 | 5091 | 83 | 12 | 14.4578 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 47.8883 | 35.6275 | 73.0159 | 53.4483 | 88 | 159 | 138 | 51 | 50 | 98.0392 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 63.1130 | 55.0847 | 73.8806 | 56.5640 | 195 | 159 | 198 | 70 | 62 | 88.5714 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 20.7177 | 14.5161 | 36.1702 | 74.1758 | 27 | 159 | 17 | 30 | 17 | 56.6667 | |
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 83.2462 | 89.4980 | 77.8108 | 88.9364 | 1355 | 159 | 1308 | 373 | 121 | 32.4397 | |
| asubramanian-gatk | INDEL | D1_5 | map_l100_m2_e1 | het | 91.0922 | 87.4606 | 95.0385 | 88.5235 | 1109 | 159 | 1111 | 58 | 6 | 10.3448 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.8256 | 93.9864 | 99.8416 | 36.8816 | 2485 | 159 | 2522 | 4 | 4 | 100.0000 | |
| anovak-vg | INDEL | * | map_l100_m2_e0 | homalt | 76.7170 | 87.3910 | 68.3667 | 80.9419 | 1102 | 159 | 1126 | 521 | 485 | 93.0902 | |
| astatham-gatk | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.5088 | 99.0743 | 99.9471 | 55.8025 | 17018 | 159 | 17015 | 9 | 6 | 66.6667 | |
| hfeng-pmm2 | INDEL | D16_PLUS | HG002compoundhet | * | 95.1177 | 93.2080 | 97.1073 | 33.8339 | 2182 | 159 | 2182 | 65 | 63 | 96.9231 | |
| hfeng-pmm2 | INDEL | I16_PLUS | * | hetalt | 95.9205 | 92.4214 | 99.6950 | 58.3968 | 1939 | 159 | 1961 | 6 | 6 | 100.0000 | |
| hfeng-pmm2 | SNP | ti | map_l125_m2_e0 | * | 99.4203 | 99.4745 | 99.3661 | 73.2412 | 30099 | 159 | 30095 | 192 | 23 | 11.9792 | |
| hfeng-pmm2 | SNP | ti | map_l125_m2_e1 | * | 99.4245 | 99.4799 | 99.3693 | 73.2743 | 30410 | 159 | 30406 | 193 | 23 | 11.9171 | |
| hfeng-pmm3 | INDEL | I16_PLUS | HG002compoundhet | * | 95.0875 | 92.5805 | 97.7340 | 52.1790 | 1984 | 159 | 1984 | 46 | 45 | 97.8261 | |
| hfeng-pmm3 | SNP | * | map_l150_m2_e0 | het | 99.2915 | 99.2103 | 99.3729 | 76.6202 | 19974 | 159 | 19968 | 126 | 13 | 10.3175 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.1156 | 95.4467 | 98.8438 | 53.2567 | 3333 | 159 | 3334 | 39 | 32 | 82.0513 | |
| dgrover-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.4591 | 99.4895 | 99.4288 | 67.6195 | 30984 | 159 | 30984 | 178 | 19 | 10.6742 | |
| dgrover-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.4591 | 99.4895 | 99.4288 | 67.6195 | 30984 | 159 | 30984 | 178 | 19 | 10.6742 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 75.8613 | 83.4547 | 69.5344 | 53.8102 | 802 | 159 | 687 | 301 | 288 | 95.6811 | |
| egarrison-hhga | SNP | tv | map_l125_m2_e0 | * | 99.4065 | 99.0357 | 99.7800 | 70.1050 | 16330 | 159 | 16330 | 36 | 17 | 47.2222 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 95.9239 | 95.6260 | 96.2236 | 38.3297 | 3498 | 160 | 5784 | 227 | 218 | 96.0352 | |