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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
49801-49850 / 86044 show all | |||||||||||||||
| eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 86.6959 | 90.9333 | 82.8358 | 66.4682 | 2728 | 272 | 3219 | 667 | 620 | 92.9535 | |
| jpowers-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 86.6965 | 89.5833 | 83.9898 | 89.6733 | 645 | 75 | 661 | 126 | 8 | 6.3492 | |
| gduggal-bwavard | INDEL | * | HG002compoundhet | homalt | 86.6968 | 82.6531 | 91.1565 | 55.5556 | 567 | 119 | 536 | 52 | 47 | 90.3846 | |
| ckim-vqsr | INDEL | I6_15 | HG002compoundhet | het | 86.6987 | 97.5962 | 77.9904 | 84.7889 | 203 | 5 | 163 | 46 | 45 | 97.8261 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 86.6995 | 85.5368 | 87.8943 | 72.5250 | 3099 | 524 | 3093 | 426 | 415 | 97.4178 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 86.7002 | 91.4894 | 82.3875 | 75.9605 | 1247 | 116 | 1263 | 270 | 194 | 71.8519 | |
| astatham-gatk | SNP | tv | map_l100_m2_e0 | het | 86.7029 | 76.7066 | 99.6951 | 76.6657 | 12102 | 3675 | 12098 | 37 | 10 | 27.0270 | |
| asubramanian-gatk | INDEL | * | map_l250_m2_e1 | * | 86.7031 | 84.0841 | 89.4904 | 99.1381 | 280 | 53 | 281 | 33 | 3 | 9.0909 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 86.7133 | 96.8750 | 78.4810 | 46.7416 | 186 | 6 | 186 | 51 | 50 | 98.0392 | |
| astatham-gatk | SNP | tv | map_l150_m1_e0 | het | 86.7142 | 76.8644 | 99.4596 | 83.0624 | 5339 | 1607 | 5337 | 29 | 8 | 27.5862 | |
| gduggal-snapplat | SNP | * | map_l250_m0_e0 | homalt | 86.7142 | 76.7886 | 99.5868 | 94.0431 | 483 | 146 | 482 | 2 | 2 | 100.0000 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 86.7164 | 95.8976 | 79.1397 | 59.1322 | 17088 | 731 | 18434 | 4859 | 4632 | 95.3283 | |
| astatham-gatk | SNP | tv | map_l100_m2_e1 | het | 86.7191 | 76.7348 | 99.6902 | 76.6919 | 12230 | 3708 | 12226 | 38 | 10 | 26.3158 | |
| qzeng-custom | INDEL | D1_5 | map_l125_m2_e0 | het | 86.7233 | 78.9267 | 96.2291 | 92.7251 | 603 | 161 | 689 | 27 | 21 | 77.7778 | |
| ckim-isaac | INDEL | D16_PLUS | segdup | * | 86.7257 | 84.4828 | 89.0909 | 92.1090 | 49 | 9 | 49 | 6 | 3 | 50.0000 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 86.7340 | 86.1272 | 87.3494 | 72.8980 | 298 | 48 | 290 | 42 | 40 | 95.2381 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 86.7363 | 86.3984 | 87.0769 | 60.8804 | 27136 | 4272 | 28091 | 4169 | 1922 | 46.1022 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 86.7363 | 86.3984 | 87.0769 | 60.8804 | 27136 | 4272 | 28091 | 4169 | 1922 | 46.1022 | |
| gduggal-snapvard | INDEL | * | * | homalt | 86.7363 | 77.5779 | 98.3465 | 41.7135 | 97105 | 28066 | 99624 | 1675 | 1571 | 93.7910 | |
| gduggal-bwaplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 86.7364 | 78.3970 | 97.0612 | 92.7953 | 7160 | 1973 | 7167 | 217 | 34 | 15.6682 | |
| gduggal-bwaplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 86.7364 | 78.3970 | 97.0612 | 92.7953 | 7160 | 1973 | 7167 | 217 | 34 | 15.6682 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 86.7395 | 76.5840 | 100.0000 | 47.5746 | 278 | 85 | 281 | 0 | 0 | ||
| jli-custom | INDEL | I6_15 | HG002compoundhet | het | 86.7430 | 93.7500 | 80.7107 | 83.6785 | 195 | 13 | 159 | 38 | 30 | 78.9474 | |
| astatham-gatk | SNP | * | map_l100_m1_e0 | het | 86.7442 | 76.7367 | 99.7535 | 74.2815 | 34807 | 10552 | 34796 | 86 | 33 | 38.3721 | |
| gduggal-bwafb | INDEL | D16_PLUS | map_l125_m1_e0 | het | 86.7470 | 80.0000 | 94.7368 | 83.8983 | 16 | 4 | 18 | 1 | 1 | 100.0000 | |
| gduggal-bwafb | INDEL | D16_PLUS | map_l125_m2_e0 | het | 86.7470 | 80.0000 | 94.7368 | 84.6774 | 16 | 4 | 18 | 1 | 1 | 100.0000 | |
| gduggal-bwafb | INDEL | D16_PLUS | map_l125_m2_e1 | het | 86.7470 | 80.0000 | 94.7368 | 84.8000 | 16 | 4 | 18 | 1 | 1 | 100.0000 | |
| ghariani-varprowl | INDEL | D6_15 | func_cds | * | 86.7470 | 83.7209 | 90.0000 | 58.3333 | 36 | 7 | 36 | 4 | 4 | 100.0000 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | * | 86.7509 | 80.8917 | 93.5252 | 60.6232 | 127 | 30 | 130 | 9 | 4 | 44.4444 | |
| ndellapenna-hhga | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 86.7571 | 85.6250 | 87.9195 | 87.5626 | 137 | 23 | 131 | 18 | 10 | 55.5556 | |
| raldana-dualsentieon | INDEL | D16_PLUS | map_l100_m2_e0 | het | 86.7606 | 91.6667 | 82.3529 | 94.1913 | 44 | 4 | 42 | 9 | 4 | 44.4444 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 86.7610 | 94.3089 | 80.3318 | 79.6037 | 348 | 21 | 339 | 83 | 46 | 55.4217 | |
| raldana-dualsentieon | INDEL | D16_PLUS | map_l100_m0_e0 | het | 86.7624 | 89.4737 | 84.2105 | 95.1157 | 17 | 2 | 16 | 3 | 0 | 0.0000 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 86.7676 | 77.5281 | 98.5075 | 65.9033 | 138 | 40 | 132 | 2 | 2 | 100.0000 | |
| gduggal-snapplat | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 86.7685 | 79.7558 | 95.1333 | 68.7830 | 14502 | 3681 | 14524 | 743 | 84 | 11.3055 | |
| astatham-gatk | SNP | tv | map_l150_m2_e1 | het | 86.7689 | 76.9325 | 99.4894 | 83.9661 | 5653 | 1695 | 5651 | 29 | 8 | 27.5862 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | * | 86.7711 | 82.6667 | 91.3043 | 65.6716 | 62 | 13 | 63 | 6 | 4 | 66.6667 | |
| dgrover-gatk | INDEL | D16_PLUS | map_l100_m2_e0 | * | 86.7725 | 91.1111 | 82.8283 | 95.1111 | 82 | 8 | 82 | 17 | 4 | 23.5294 | |
| mlin-fermikit | INDEL | D6_15 | segdup | * | 86.7731 | 83.7696 | 90.0000 | 91.8182 | 160 | 31 | 162 | 18 | 17 | 94.4444 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 86.7813 | 76.7925 | 99.7573 | 48.6284 | 407 | 123 | 411 | 1 | 1 | 100.0000 | |
| qzeng-custom | INDEL | D1_5 | map_l125_m2_e1 | homalt | 86.7834 | 77.6882 | 98.2906 | 84.8576 | 289 | 83 | 345 | 6 | 6 | 100.0000 | |
| jpowers-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 86.7838 | 93.8345 | 80.7186 | 89.0750 | 2222 | 146 | 2269 | 542 | 180 | 33.2103 | |
| qzeng-custom | INDEL | D1_5 | map_l125_m2_e1 | * | 86.7845 | 78.5653 | 96.9245 | 91.3188 | 909 | 248 | 1040 | 33 | 27 | 81.8182 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 86.7858 | 90.4797 | 83.3817 | 76.0514 | 1226 | 129 | 1149 | 229 | 205 | 89.5197 | |
| astatham-gatk | SNP | tv | map_l150_m2_e0 | het | 86.7915 | 76.9719 | 99.4830 | 83.9440 | 5582 | 1670 | 5580 | 29 | 8 | 27.5862 | |
| astatham-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 86.7925 | 100.0000 | 76.6667 | 88.7640 | 23 | 0 | 23 | 7 | 7 | 100.0000 | |
| astatham-gatk | INDEL | I16_PLUS | map_l100_m2_e0 | * | 86.7925 | 88.4615 | 85.1852 | 96.0641 | 23 | 3 | 23 | 4 | 1 | 25.0000 | |
| astatham-gatk | INDEL | I16_PLUS | map_l100_m2_e1 | * | 86.7925 | 88.4615 | 85.1852 | 96.0813 | 23 | 3 | 23 | 4 | 1 | 25.0000 | |
| jmaeng-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 86.7925 | 100.0000 | 76.6667 | 88.6792 | 23 | 0 | 23 | 7 | 6 | 85.7143 | |
| jmaeng-gatk | INDEL | I6_15 | map_l150_m2_e1 | * | 86.7925 | 85.1852 | 88.4615 | 96.5517 | 23 | 4 | 23 | 3 | 1 | 33.3333 | |