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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
64251-64300 / 86044 show all | |||||||||||||||
| jmaeng-gatk | INDEL | * | lowcmp_AllRepeats_gt200bp_gt95identity_merged | hetalt | 100.0000 | 100.0000 | 100.0000 | 95.6522 | 3 | 0 | 3 | 0 | 0 | ||
| jmaeng-gatk | INDEL | * | lowcmp_AllRepeats_gt200bp_gt95identity_merged | homalt | 100.0000 | 100.0000 | 100.0000 | 99.5117 | 5 | 0 | 5 | 0 | 0 | ||
| jmaeng-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.8577 | 98.4881 | 99.2301 | 73.8561 | 93021 | 1428 | 92930 | 721 | 622 | 86.2691 | |
| jmaeng-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.2695 | 99.3226 | 99.2164 | 76.1399 | 47944 | 327 | 47736 | 377 | 289 | 76.6578 | |
| jmaeng-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.2177 | 93.0272 | 99.6348 | 58.3838 | 14342 | 1075 | 14459 | 53 | 52 | 98.1132 | |
| jmaeng-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.4869 | 99.9155 | 99.0621 | 74.5055 | 30735 | 26 | 30735 | 291 | 281 | 96.5636 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.7771 | 97.1844 | 98.3771 | 67.7791 | 63511 | 1840 | 63286 | 1044 | 906 | 86.7816 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.2920 | 98.3891 | 98.1951 | 74.4975 | 29989 | 491 | 29542 | 543 | 428 | 78.8214 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 95.8097 | 92.2658 | 99.6368 | 36.6287 | 15413 | 1292 | 15635 | 57 | 57 | 100.0000 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.6356 | 99.6862 | 97.6069 | 67.4063 | 18109 | 57 | 18109 | 444 | 421 | 94.8198 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.4267 | 96.6141 | 98.2531 | 76.5682 | 2083 | 73 | 2081 | 37 | 19 | 51.3514 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.5926 | 96.9745 | 98.2186 | 79.0180 | 1218 | 38 | 1213 | 22 | 9 | 40.9091 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 90.1316 | 82.0359 | 100.0000 | 64.7355 | 137 | 30 | 140 | 0 | 0 | ||
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.6450 | 99.3179 | 97.9812 | 73.0406 | 728 | 5 | 728 | 15 | 10 | 66.6667 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_gt200bp_gt95identity_merged | * | 100.0000 | 100.0000 | 100.0000 | 99.4367 | 17 | 0 | 17 | 0 | 0 | ||
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_gt200bp_gt95identity_merged | het | 100.0000 | 100.0000 | 100.0000 | 99.4903 | 10 | 0 | 10 | 0 | 0 | ||
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_gt200bp_gt95identity_merged | hetalt | 100.0000 | 100.0000 | 100.0000 | 94.8276 | 3 | 0 | 3 | 0 | 0 | ||
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_gt200bp_gt95identity_merged | homalt | 100.0000 | 100.0000 | 100.0000 | 99.5992 | 4 | 0 | 4 | 0 | 0 | ||
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.3929 | 99.1600 | 99.6269 | 75.2923 | 5076 | 43 | 5074 | 19 | 13 | 68.4211 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.5824 | 99.4333 | 99.7320 | 76.7777 | 2983 | 17 | 2977 | 8 | 4 | 50.0000 | |
| jmaeng-gatk | SNP | tv | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 92.3077 | 100.0000 | 85.7143 | 92.3077 | 6 | 0 | 6 | 1 | 1 | 100.0000 | |
| jmaeng-gatk | SNP | tv | lowcmp_SimpleRepeat_quadTR_gt200 | * | 0.0000 | 0.0000 | 0.0000 | 0 | 0 | 0 | 0 | 0 | |||
| jmaeng-gatk | SNP | tv | lowcmp_SimpleRepeat_quadTR_gt200 | het | 0.0000 | 0.0000 | 0.0000 | 0 | 0 | 0 | 0 | 0 | |||
| jmaeng-gatk | SNP | tv | lowcmp_SimpleRepeat_quadTR_gt200 | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 0 | 0 | 0 | 0 | |||
| jmaeng-gatk | SNP | tv | lowcmp_SimpleRepeat_quadTR_gt200 | homalt | 0.0000 | 0.0000 | 0.0000 | 0 | 0 | 0 | 0 | 0 | |||
| jmaeng-gatk | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.6666 | 99.6812 | 99.6520 | 39.8884 | 3439 | 11 | 3436 | 12 | 2 | 16.6667 | |
| jmaeng-gatk | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.6261 | 99.8129 | 99.4400 | 42.7465 | 2134 | 4 | 2131 | 12 | 2 | 16.6667 | |
| jmaeng-gatk | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 0.0000 | 100.0000 | 0 | 1 | 0 | 0 | 0 | ||||
| jmaeng-gatk | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.7706 | 99.5423 | 100.0000 | 34.4550 | 1305 | 6 | 1305 | 0 | 0 | ||
| jmaeng-gatk | SNP | tv | lowcmp_SimpleRepeat_triTR_51to200 | * | 100.0000 | 100.0000 | 100.0000 | 98.5507 | 1 | 0 | 1 | 0 | 0 | ||
| jmaeng-gatk | SNP | tv | lowcmp_SimpleRepeat_triTR_51to200 | het | 100.0000 | 100.0000 | 100.0000 | 98.2456 | 1 | 0 | 1 | 0 | 0 | ||
| jmaeng-gatk | SNP | tv | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 0 | 0 | 0 | 0 | |||
| jmaeng-gatk | SNP | tv | lowcmp_SimpleRepeat_triTR_51to200 | homalt | 0.0000 | 100.0000 | 0 | 0 | 0 | 0 | 0 | ||||
| jmaeng-gatk | SNP | tv | map_l100_m0_e0 | * | 81.7650 | 70.7957 | 96.7567 | 85.8314 | 7847 | 3237 | 7846 | 263 | 11 | 4.1825 | |
| jmaeng-gatk | SNP | tv | map_l100_m0_e0 | het | 84.7992 | 76.2808 | 95.4593 | 88.1483 | 5509 | 1713 | 5508 | 262 | 10 | 3.8168 | |
| jmaeng-gatk | SNP | tv | map_l100_m0_e0 | hetalt | 72.0000 | 56.2500 | 100.0000 | 93.2331 | 9 | 7 | 9 | 0 | 0 | ||
| jmaeng-gatk | SNP | tv | map_l100_m0_e0 | homalt | 75.4210 | 60.5564 | 99.9571 | 72.3081 | 2329 | 1517 | 2329 | 1 | 1 | 100.0000 | |
| jmaeng-gatk | SNP | tv | map_l100_m1_e0 | * | 88.1452 | 80.4375 | 97.4866 | 80.6623 | 19708 | 4793 | 19704 | 508 | 16 | 3.1496 | |
| jmaeng-gatk | SNP | tv | map_l100_m1_e0 | het | 91.2990 | 86.7484 | 96.3534 | 83.6231 | 13374 | 2043 | 13370 | 506 | 14 | 2.7668 | |
| jmaeng-gatk | SNP | tv | map_l100_m1_e0 | hetalt | 80.0000 | 68.2927 | 96.5517 | 89.6797 | 28 | 13 | 28 | 1 | 1 | 100.0000 | |
| jmaeng-gatk | SNP | tv | map_l100_m1_e0 | homalt | 82.1629 | 69.7335 | 99.9841 | 67.6746 | 6306 | 2737 | 6306 | 1 | 1 | 100.0000 | |
| jmaeng-gatk | SNP | tv | map_l100_m2_e0 | * | 88.3689 | 80.8253 | 97.4657 | 81.7790 | 20233 | 4800 | 20229 | 526 | 16 | 3.0418 | |
| jmaeng-gatk | SNP | tv | map_l100_m2_e0 | het | 91.4492 | 87.0444 | 96.3236 | 84.5266 | 13733 | 2044 | 13729 | 524 | 14 | 2.6718 | |
| jmaeng-gatk | SNP | tv | map_l100_m2_e0 | hetalt | 80.5556 | 69.0476 | 96.6667 | 90.4762 | 29 | 13 | 29 | 1 | 1 | 100.0000 | |
| jmaeng-gatk | SNP | tv | map_l100_m2_e0 | homalt | 82.5067 | 70.2301 | 99.9845 | 69.8682 | 6471 | 2743 | 6471 | 1 | 1 | 100.0000 | |
| jmaeng-gatk | SNP | tv | map_l100_m2_e1 | * | 88.4662 | 80.9714 | 97.4899 | 81.7669 | 20472 | 4811 | 20468 | 527 | 16 | 3.0361 | |
| jmaeng-gatk | SNP | tv | map_l100_m2_e1 | het | 91.5298 | 87.1628 | 96.3575 | 84.5264 | 13892 | 2046 | 13888 | 525 | 14 | 2.6667 | |
| jmaeng-gatk | SNP | tv | map_l100_m2_e1 | hetalt | 81.0811 | 69.7674 | 96.7742 | 90.1899 | 30 | 13 | 30 | 1 | 1 | 100.0000 | |
| jmaeng-gatk | SNP | tv | map_l100_m2_e1 | homalt | 82.6342 | 70.4150 | 99.9847 | 69.7916 | 6550 | 2752 | 6550 | 1 | 1 | 100.0000 | |
| jmaeng-gatk | SNP | tv | map_l125_m0_e0 | * | 75.4933 | 61.9967 | 96.5015 | 90.4918 | 4111 | 2520 | 4110 | 149 | 7 | 4.6980 | |