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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
16501-16550 / 86044 show all | |||||||||||||||
| gduggal-bwaplat | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 49.0051 | 33.5664 | 90.7407 | 98.6432 | 48 | 95 | 49 | 5 | 3 | 60.0000 | |
| gduggal-bwaplat | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.7591 | 92.2386 | 99.5591 | 69.5815 | 1129 | 95 | 1129 | 5 | 5 | 100.0000 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 95.9405 | 94.8116 | 97.0966 | 77.0267 | 1736 | 95 | 1739 | 52 | 3 | 5.7692 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 76.0161 | 83.1560 | 70.0052 | 27.1233 | 469 | 95 | 5340 | 2288 | 2284 | 99.8252 | |
| gduggal-bwavard | SNP | tv | map_l150_m0_e0 | * | 90.7711 | 97.7240 | 84.7419 | 86.2817 | 4079 | 95 | 4071 | 733 | 21 | 2.8649 | |
| egarrison-hhga | INDEL | D16_PLUS | * | homalt | 94.6666 | 94.3853 | 94.9495 | 59.9952 | 1597 | 95 | 1598 | 85 | 63 | 74.1176 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 92.9921 | 92.3939 | 93.5981 | 64.4892 | 1154 | 95 | 1155 | 79 | 58 | 73.4177 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 92.9921 | 92.3939 | 93.5981 | 64.4892 | 1154 | 95 | 1155 | 79 | 58 | 73.4177 | |
| egarrison-hhga | INDEL | D1_5 | HG002complexvar | homalt | 98.5958 | 99.1036 | 98.0931 | 56.9237 | 10503 | 95 | 10494 | 204 | 148 | 72.5490 | |
| ckim-isaac | INDEL | D1_5 | map_l250_m2_e1 | * | 64.9819 | 48.6486 | 97.8261 | 97.0101 | 90 | 95 | 90 | 2 | 2 | 100.0000 | |
| ckim-vqsr | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.5068 | 99.4678 | 99.5459 | 59.1769 | 17756 | 95 | 17755 | 81 | 6 | 7.4074 | |
| eyeh-varpipe | INDEL | * | map_l100_m1_e0 | het | 96.1706 | 95.7494 | 96.5955 | 81.6758 | 2140 | 95 | 2894 | 102 | 68 | 66.6667 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.6094 | 95.5357 | 95.6831 | 73.2283 | 2033 | 95 | 2017 | 91 | 76 | 83.5165 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 89.8601 | 93.0301 | 86.8990 | 65.5793 | 1268 | 95 | 1247 | 188 | 182 | 96.8085 | |
| mlin-fermikit | SNP | ti | func_cds | * | 99.5022 | 99.3109 | 99.6942 | 17.8687 | 13692 | 95 | 13692 | 42 | 34 | 80.9524 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 80.4044 | 84.5779 | 76.6234 | 63.7476 | 521 | 95 | 590 | 180 | 64 | 35.5556 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 94.5098 | 93.8352 | 95.1942 | 74.3325 | 1446 | 95 | 1446 | 73 | 39 | 53.4247 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 86.9385 | 82.2761 | 92.1610 | 61.6572 | 441 | 95 | 435 | 37 | 30 | 81.0811 | |
| ndellapenna-hhga | SNP | * | map_l100_m1_e0 | homalt | 99.7849 | 99.6482 | 99.9220 | 59.8338 | 26908 | 95 | 26908 | 21 | 19 | 90.4762 | |
| ltrigg-rtg2 | SNP | ti | HG002compoundhet | het | 99.3400 | 99.0005 | 99.6817 | 37.0509 | 9410 | 95 | 9396 | 30 | 8 | 26.6667 | |
| hfeng-pmm3 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 95.7839 | 92.4901 | 99.3209 | 86.5999 | 1170 | 95 | 1170 | 8 | 3 | 37.5000 | |
| hfeng-pmm2 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 93.3244 | 88.0353 | 99.2898 | 87.3699 | 699 | 95 | 699 | 5 | 3 | 60.0000 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 91.2944 | 90.1145 | 92.5056 | 71.8602 | 866 | 95 | 827 | 67 | 61 | 91.0448 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 91.8734 | 84.9684 | 100.0000 | 39.2199 | 537 | 95 | 561 | 0 | 0 | ||
| gduggal-snapfb | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 85.2592 | 83.7329 | 86.8421 | 25.4902 | 489 | 95 | 66 | 10 | 10 | 100.0000 | |
| gduggal-snapfb | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 0.0000 | 0.0000 | 0.0000 | 0 | 95 | 0 | 0 | 0 | |||
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 77.8308 | 85.3621 | 71.5206 | 64.6147 | 554 | 95 | 555 | 221 | 81 | 36.6516 | |
| ghariani-varprowl | INDEL | D6_15 | map_l100_m2_e1 | * | 67.6145 | 65.4545 | 69.9219 | 89.0552 | 180 | 95 | 179 | 77 | 71 | 92.2078 | |
| hfeng-pmm1 | INDEL | * | map_l100_m2_e1 | * | 98.1906 | 97.4707 | 98.9213 | 83.6789 | 3661 | 95 | 3668 | 40 | 9 | 22.5000 | |
| gduggal-snapvard | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 0.0000 | 0.0000 | 24.1758 | 67.1480 | 0 | 95 | 22 | 69 | 23 | 33.3333 | |
| gduggal-snapvard | INDEL | I6_15 | HG002compoundhet | het | 36.3374 | 54.3269 | 27.2981 | 31.6711 | 113 | 95 | 1470 | 3915 | 3322 | 84.8531 | |
| gduggal-snapvard | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.5046 | 97.6173 | 99.4081 | 39.4232 | 3892 | 95 | 3863 | 23 | 9 | 39.1304 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 36.9771 | 25.1969 | 69.4444 | 73.3333 | 32 | 95 | 25 | 11 | 0 | 0.0000 | |
| gduggal-snapplat | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 0.0000 | 0.0000 | 0.0000 | 0 | 95 | 0 | 0 | 0 | |||
| gduggal-snapvard | INDEL | * | map_l125_m1_e0 | homalt | 92.3976 | 87.0219 | 98.4813 | 80.4522 | 637 | 95 | 843 | 13 | 11 | 84.6154 | |
| gduggal-snapfb | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 96.3021 | 99.0596 | 93.6939 | 64.5457 | 10007 | 95 | 10029 | 675 | 110 | 16.2963 | |
| gduggal-snapfb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 59.7519 | 97.7584 | 43.0248 | 79.6303 | 4143 | 95 | 4253 | 5632 | 101 | 1.7933 | |
| gduggal-snapfb | SNP | ti | segdup | * | 99.1459 | 99.5137 | 98.7809 | 90.9477 | 19442 | 95 | 19446 | 240 | 23 | 9.5833 | |
| gduggal-snapplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 39.0387 | 28.0303 | 64.2857 | 93.0175 | 37 | 95 | 36 | 20 | 6 | 30.0000 | |
| gduggal-snapfb | SNP | * | HG002compoundhet | homalt | 96.1466 | 99.1282 | 93.3392 | 44.8696 | 10688 | 94 | 10692 | 763 | 275 | 36.0419 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 55.8708 | 55.0239 | 56.7442 | 69.7183 | 115 | 94 | 122 | 93 | 53 | 56.9892 | |
| gduggal-snapfb | INDEL | D6_15 | map_l100_m2_e0 | * | 76.6354 | 64.3939 | 94.6237 | 81.8182 | 170 | 94 | 176 | 10 | 9 | 90.0000 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 82.7682 | 83.3333 | 82.2107 | 69.9221 | 470 | 94 | 476 | 103 | 33 | 32.0388 | |
| ghariani-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 59.0564 | 88.9542 | 44.2005 | 85.0316 | 757 | 94 | 785 | 991 | 11 | 1.1100 | |
| ghariani-varprowl | SNP | tv | map_l125_m1_e0 | homalt | 98.8683 | 98.3959 | 99.3453 | 69.2128 | 5766 | 94 | 5766 | 38 | 24 | 63.1579 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 0.0000 | 28.7879 | 0.0000 | 0.0000 | 38 | 94 | 0 | 0 | 0 | ||
| gduggal-snapvard | SNP | tv | map_l150_m0_e0 | het | 83.5823 | 96.6936 | 73.6022 | 87.1311 | 2749 | 94 | 2738 | 982 | 41 | 4.1752 | |
| ghariani-varprowl | INDEL | * | map_l100_m0_e0 | * | 90.4000 | 93.9859 | 87.0777 | 93.2660 | 1469 | 94 | 1469 | 218 | 66 | 30.2752 | |
| ghariani-varprowl | INDEL | * | segdup | homalt | 93.7217 | 90.2083 | 97.5197 | 91.8211 | 866 | 94 | 865 | 22 | 17 | 77.2727 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 55.0165 | 87.3144 | 40.1609 | 56.7914 | 647 | 94 | 649 | 967 | 945 | 97.7249 | |