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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
12601-12650 / 86044 show all | |||||||||||||||
| ckim-isaac | INDEL | I6_15 | HG002complexvar | hetalt | 70.4127 | 56.1733 | 94.3226 | 46.2179 | 687 | 536 | 731 | 44 | 30 | 68.1818 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.1537 | 99.4096 | 96.9291 | 83.2983 | 1347 | 8 | 1231 | 39 | 30 | 76.9231 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.8082 | 94.2070 | 99.5571 | 26.7517 | 6700 | 412 | 6744 | 30 | 30 | 100.0000 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.7996 | 94.1873 | 99.5608 | 27.3684 | 6757 | 417 | 6801 | 30 | 30 | 100.0000 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5070 | 99.8586 | 99.1578 | 72.7530 | 3532 | 5 | 3532 | 30 | 30 | 100.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.5490 | 95.8600 | 99.2985 | 63.8541 | 5094 | 220 | 5096 | 36 | 30 | 83.3333 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.7315 | 91.7481 | 97.9155 | 67.3720 | 1690 | 152 | 1691 | 36 | 30 | 83.3333 | |
| dgrover-gatk | SNP | * | map_l250_m2_e0 | * | 98.4387 | 98.3513 | 98.5262 | 90.2982 | 7755 | 130 | 7755 | 116 | 30 | 25.8621 | |
| dgrover-gatk | SNP | * | map_l250_m2_e1 | * | 98.4461 | 98.3598 | 98.5325 | 90.3561 | 7856 | 131 | 7856 | 117 | 30 | 25.6410 | |
| dgrover-gatk | SNP | ti | map_l125_m0_e0 | * | 99.0401 | 99.0440 | 99.0361 | 76.9678 | 12640 | 122 | 12638 | 123 | 30 | 24.3902 | |
| dgrover-gatk | SNP | ti | map_l150_m2_e0 | het | 99.0461 | 99.1693 | 98.9232 | 81.0415 | 12774 | 107 | 12770 | 139 | 30 | 21.5827 | |
| dgrover-gatk | SNP | ti | map_l150_m2_e1 | het | 99.0483 | 99.1779 | 98.9191 | 81.1057 | 12908 | 107 | 12904 | 141 | 30 | 21.2766 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 96.3335 | 96.2182 | 96.4490 | 61.4990 | 1552 | 61 | 1521 | 56 | 30 | 53.5714 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 71.1860 | 58.6207 | 90.6077 | 99.6597 | 51 | 36 | 328 | 34 | 30 | 88.2353 | |
| eyeh-varpipe | INDEL | * | map_l125_m1_e0 | het | 96.7178 | 96.4794 | 96.9573 | 84.9956 | 1288 | 47 | 1657 | 52 | 30 | 57.6923 | |
| eyeh-varpipe | INDEL | * | map_l125_m2_e0 | het | 96.7811 | 96.4774 | 97.0868 | 85.6373 | 1342 | 49 | 1733 | 52 | 30 | 57.6923 | |
| egarrison-hhga | INDEL | * | segdup | het | 97.9069 | 98.6357 | 97.1888 | 94.2947 | 1446 | 20 | 1452 | 42 | 30 | 71.4286 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 90.3594 | 93.8224 | 87.1429 | 56.0440 | 243 | 16 | 244 | 36 | 30 | 83.3333 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 84.8057 | 94.4882 | 76.9231 | 49.6774 | 120 | 7 | 120 | 36 | 30 | 83.3333 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.8822 | 98.9362 | 98.8283 | 47.8545 | 3627 | 39 | 3627 | 43 | 30 | 69.7674 | |
| egarrison-hhga | INDEL | I16_PLUS | HG002complexvar | * | 92.4901 | 89.3812 | 95.8231 | 64.9842 | 1170 | 139 | 1170 | 51 | 30 | 58.8235 | |
| egarrison-hhga | INDEL | I1_5 | HG002complexvar | hetalt | 96.4786 | 94.7856 | 98.2332 | 69.9256 | 1636 | 90 | 1668 | 30 | 30 | 100.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.9103 | 98.0469 | 97.7741 | 69.5010 | 1757 | 35 | 1757 | 40 | 30 | 75.0000 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 97.0467 | 94.6710 | 99.5447 | 27.5976 | 6733 | 379 | 6777 | 31 | 30 | 96.7742 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 97.0365 | 94.6613 | 99.5340 | 28.2145 | 6791 | 383 | 6835 | 32 | 30 | 93.7500 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.6664 | 95.9541 | 99.4410 | 50.6296 | 5692 | 240 | 5692 | 32 | 30 | 93.7500 | |
| bgallagher-sentieon | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.6082 | 99.8778 | 99.3401 | 60.0690 | 55563 | 68 | 55552 | 369 | 30 | 8.1301 | |
| bgallagher-sentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.2960 | 99.5274 | 99.0657 | 69.8134 | 45486 | 216 | 45486 | 429 | 30 | 6.9930 | |
| bgallagher-sentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.2960 | 99.5274 | 99.0657 | 69.8134 | 45486 | 216 | 45486 | 429 | 30 | 6.9930 | |
| bgallagher-sentieon | SNP | * | map_l150_m0_e0 | * | 98.7085 | 99.1107 | 98.3096 | 80.7877 | 11925 | 107 | 11922 | 205 | 30 | 14.6341 | |
| bgallagher-sentieon | SNP | ti | map_l150_m2_e0 | het | 98.8935 | 99.2392 | 98.5502 | 79.6724 | 12783 | 98 | 12779 | 188 | 30 | 15.9574 | |
| bgallagher-sentieon | SNP | ti | map_l150_m2_e1 | het | 98.8973 | 99.2470 | 98.5500 | 79.7478 | 12917 | 98 | 12913 | 190 | 30 | 15.7895 | |
| astatham-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.9429 | 98.0986 | 99.8019 | 70.2570 | 44833 | 869 | 44833 | 89 | 30 | 33.7079 | |
| astatham-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.9429 | 98.0986 | 99.8019 | 70.2570 | 44833 | 869 | 44833 | 89 | 30 | 33.7079 | |
| astatham-gatk | SNP | ti | map_siren | het | 90.2825 | 82.3747 | 99.8698 | 61.4644 | 51387 | 10995 | 51378 | 67 | 30 | 44.7761 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 95.8836 | 92.6404 | 99.3621 | 26.9063 | 4305 | 342 | 4829 | 31 | 30 | 96.7742 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 91.8400 | 87.9187 | 96.1276 | 66.5396 | 735 | 101 | 844 | 34 | 30 | 88.2353 | |
| anovak-vg | INDEL | I1_5 | map_l250_m2_e0 | homalt | 68.7117 | 88.8889 | 56.0000 | 95.0723 | 40 | 5 | 42 | 33 | 30 | 90.9091 | |
| anovak-vg | INDEL | I1_5 | map_l250_m2_e1 | homalt | 69.2187 | 89.1304 | 56.5789 | 95.1592 | 41 | 5 | 43 | 33 | 30 | 90.9091 | |
| anovak-vg | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 15.2866 | 9.6774 | 36.3636 | 52.5862 | 18 | 168 | 20 | 35 | 30 | 85.7143 | |
| anovak-vg | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 58.1498 | 70.5882 | 49.4382 | 90.1657 | 72 | 30 | 88 | 90 | 30 | 33.3333 | |
| anovak-vg | SNP | ti | func_cds | homalt | 99.1630 | 98.9384 | 99.3887 | 18.9378 | 5219 | 56 | 5203 | 32 | 30 | 93.7500 | |
| anovak-vg | SNP | tv | map_l125_m1_e0 | homalt | 88.9946 | 80.7338 | 99.1387 | 66.3699 | 4731 | 1129 | 4719 | 41 | 30 | 73.1707 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.9660 | 98.1027 | 97.8297 | 69.4907 | 1758 | 34 | 1758 | 39 | 30 | 76.9231 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.9798 | 94.5444 | 99.5441 | 27.3611 | 6724 | 388 | 6768 | 31 | 30 | 96.7742 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.9771 | 94.5358 | 99.5479 | 27.9803 | 6782 | 392 | 6826 | 31 | 30 | 96.7742 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.6399 | 91.5309 | 97.9675 | 67.1249 | 1686 | 156 | 1687 | 35 | 30 | 85.7143 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.1342 | 96.9891 | 99.3066 | 64.2892 | 5154 | 160 | 5156 | 36 | 30 | 83.3333 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.8462 | 99.3358 | 96.4006 | 82.8203 | 1346 | 9 | 1232 | 46 | 29 | 63.0435 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.9440 | 94.4163 | 99.6108 | 25.7275 | 7643 | 452 | 7678 | 30 | 29 | 96.6667 | |