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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
61251-61300 / 86044 show all | |||||||||||||||
| jmaeng-gatk | INDEL | I1_5 | HG002complexvar | hetalt | 91.9469 | 85.2839 | 99.7392 | 69.0289 | 1472 | 254 | 1530 | 4 | 4 | 100.0000 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.3451 | 96.0317 | 98.6949 | 65.7350 | 605 | 25 | 605 | 8 | 4 | 50.0000 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.2047 | 98.8739 | 99.5378 | 72.9132 | 1317 | 15 | 1292 | 6 | 4 | 66.6667 | |
| jmaeng-gatk | INDEL | I1_5 | map_l100_m1_e0 | homalt | 99.3263 | 99.6139 | 99.0403 | 80.7962 | 516 | 2 | 516 | 5 | 4 | 80.0000 | |
| jmaeng-gatk | INDEL | I1_5 | map_l100_m2_e0 | homalt | 99.3427 | 99.6234 | 99.0637 | 82.1345 | 529 | 2 | 529 | 5 | 4 | 80.0000 | |
| jmaeng-gatk | INDEL | I1_5 | map_l100_m2_e1 | homalt | 99.3536 | 99.6296 | 99.0792 | 82.1733 | 538 | 2 | 538 | 5 | 4 | 80.0000 | |
| jmaeng-gatk | INDEL | I1_5 | map_siren | homalt | 99.5051 | 99.4224 | 99.5878 | 78.4891 | 1205 | 7 | 1208 | 5 | 4 | 80.0000 | |
| jmaeng-gatk | INDEL | I6_15 | HG002complexvar | het | 99.1867 | 98.5563 | 99.8253 | 59.8421 | 2321 | 34 | 2285 | 4 | 4 | 100.0000 | |
| jmaeng-gatk | INDEL | I6_15 | map_siren | homalt | 97.2678 | 98.8889 | 95.6989 | 85.7143 | 89 | 1 | 89 | 4 | 4 | 100.0000 | |
| jmaeng-gatk | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.9505 | 98.4748 | 99.4309 | 69.9164 | 2970 | 46 | 2970 | 17 | 4 | 23.5294 | |
| jmaeng-gatk | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.7211 | 99.6873 | 99.7550 | 36.7324 | 7332 | 23 | 7328 | 18 | 4 | 22.2222 | |
| jmaeng-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 99.2650 | 98.9969 | 99.5345 | 87.4939 | 1283 | 13 | 1283 | 6 | 4 | 66.6667 | |
| jmaeng-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 99.1765 | 99.0599 | 99.2933 | 88.5872 | 843 | 8 | 843 | 6 | 4 | 66.6667 | |
| ltrigg-rtg1 | INDEL | * | map_l100_m2_e0 | homalt | 99.0050 | 98.5726 | 99.4413 | 82.1306 | 1243 | 18 | 1246 | 7 | 4 | 57.1429 | |
| ltrigg-rtg1 | INDEL | * | map_l100_m2_e1 | homalt | 99.0206 | 98.5948 | 99.4501 | 82.2479 | 1263 | 18 | 1266 | 7 | 4 | 57.1429 | |
| ltrigg-rtg1 | INDEL | C16_PLUS | * | * | 0.0000 | 0.0000 | 93.1507 | 95.5569 | 0 | 0 | 68 | 5 | 4 | 80.0000 | |
| ltrigg-rtg1 | INDEL | C16_PLUS | HG002compoundhet | * | 0.0000 | 0.0000 | 87.5000 | 88.7324 | 0 | 0 | 28 | 4 | 4 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | HG002compoundhet | homalt | 73.6842 | 87.5000 | 63.6364 | 59.2593 | 7 | 1 | 7 | 4 | 4 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.4377 | 95.6458 | 99.2980 | 71.4667 | 1296 | 59 | 1273 | 9 | 4 | 44.4444 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 97.6072 | 95.6801 | 99.6135 | 53.2309 | 1041 | 47 | 1031 | 4 | 4 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 96.5360 | 94.4171 | 98.7522 | 73.2347 | 575 | 34 | 554 | 7 | 4 | 57.1429 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 87.2734 | 78.1321 | 98.8372 | 30.2231 | 343 | 96 | 340 | 4 | 4 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 96.8866 | 95.1220 | 98.7179 | 46.1140 | 312 | 16 | 308 | 4 | 4 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.4520 | 98.9651 | 99.9438 | 27.8836 | 7172 | 75 | 7111 | 4 | 4 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 90.5529 | 87.3239 | 94.0299 | 48.4615 | 62 | 9 | 63 | 4 | 4 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 91.7858 | 86.9565 | 97.1831 | 21.9780 | 140 | 21 | 138 | 4 | 4 | 100.0000 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 75.2837 | 62.1359 | 95.4887 | 76.4184 | 128 | 78 | 127 | 6 | 4 | 66.6667 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 85.2043 | 75.0733 | 98.4962 | 64.0541 | 256 | 85 | 262 | 4 | 4 | 100.0000 | |
| ltrigg-rtg1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 94.6243 | 90.3481 | 99.3255 | 49.4027 | 571 | 61 | 589 | 4 | 4 | 100.0000 | |
| ltrigg-rtg1 | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.2468 | 97.8723 | 98.6242 | 69.6350 | 1334 | 29 | 1362 | 19 | 4 | 21.0526 | |
| ltrigg-rtg1 | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.2639 | 98.7961 | 99.7361 | 66.9655 | 2626 | 32 | 2646 | 7 | 4 | 57.1429 | |
| jli-custom | INDEL | I6_15 | map_siren | * | 96.1474 | 94.0984 | 98.2877 | 81.5307 | 287 | 18 | 287 | 5 | 4 | 80.0000 | |
| jli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 97.6684 | 97.6684 | 97.6684 | 90.9048 | 377 | 9 | 377 | 9 | 4 | 44.4444 | |
| jli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 97.4820 | 98.1884 | 96.7857 | 90.8765 | 271 | 5 | 271 | 9 | 4 | 44.4444 | |
| jli-custom | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.8148 | 99.6933 | 99.9367 | 55.5774 | 11050 | 34 | 11048 | 7 | 4 | 57.1429 | |
| jli-custom | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.9097 | 99.9179 | 99.9015 | 54.3245 | 6083 | 5 | 6083 | 6 | 4 | 66.6667 | |
| jli-custom | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.2134 | 99.9065 | 98.5299 | 39.2599 | 18166 | 17 | 18163 | 271 | 4 | 1.4760 | |
| jli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.8440 | 99.7316 | 99.9566 | 64.4687 | 11521 | 31 | 11521 | 5 | 4 | 80.0000 | |
| jli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.0950 | 99.1848 | 99.0054 | 86.2506 | 1095 | 9 | 1095 | 11 | 4 | 36.3636 | |
| jli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.8235 | 99.1667 | 98.4828 | 87.3627 | 714 | 6 | 714 | 11 | 4 | 36.3636 | |
| jli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.8440 | 99.7316 | 99.9566 | 64.4687 | 11521 | 31 | 11521 | 5 | 4 | 80.0000 | |
| jli-custom | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | * | 99.7828 | 99.7106 | 99.8551 | 69.0939 | 4823 | 14 | 4823 | 7 | 4 | 57.1429 | |
| jli-custom | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.7298 | 99.6506 | 99.8091 | 71.0989 | 3137 | 11 | 3137 | 6 | 4 | 66.6667 | |
| jli-custom | SNP | ti | map_l150_m0_e0 | homalt | 99.6006 | 99.3481 | 99.8544 | 71.0140 | 2743 | 18 | 2743 | 4 | 4 | 100.0000 | |
| jli-custom | SNP | ti | segdup | homalt | 99.9200 | 99.8934 | 99.9467 | 87.3710 | 7497 | 8 | 7497 | 4 | 4 | 100.0000 | |
| jli-custom | SNP | tv | HG002compoundhet | homalt | 99.8081 | 99.7934 | 99.8228 | 43.2831 | 3381 | 7 | 3380 | 6 | 4 | 66.6667 | |
| jli-custom | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.8860 | 99.8316 | 99.9405 | 61.6312 | 10080 | 17 | 10080 | 6 | 4 | 66.6667 | |
| jli-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.1690 | 99.0514 | 99.2868 | 87.9764 | 1253 | 12 | 1253 | 9 | 4 | 44.4444 | |
| jli-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.9924 | 98.9924 | 98.9924 | 89.0195 | 786 | 8 | 786 | 8 | 4 | 50.0000 | |
| jli-custom | SNP | tv | map_l100_m0_e0 | homalt | 99.6481 | 99.4020 | 99.8955 | 59.7962 | 3823 | 23 | 3823 | 4 | 4 | 100.0000 | |