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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
48601-48650 / 86044 show all | |||||||||||||||
| cchapple-custom | INDEL | I1_5 | map_l250_m0_e0 | het | 86.1878 | 86.6667 | 85.7143 | 98.1912 | 13 | 2 | 12 | 2 | 0 | 0.0000 | |
| ckim-gatk | INDEL | I1_5 | map_l250_m0_e0 | het | 81.2500 | 86.6667 | 76.4706 | 98.9875 | 13 | 2 | 13 | 4 | 0 | 0.0000 | |
| gduggal-snapvard | INDEL | I1_5 | map_l250_m0_e0 | het | 70.5302 | 86.6667 | 59.4595 | 98.2596 | 13 | 2 | 22 | 15 | 3 | 20.0000 | |
| gduggal-snapvard | INDEL | I6_15 | map_l125_m1_e0 | het | 65.6975 | 86.6667 | 52.8986 | 82.1244 | 26 | 4 | 73 | 65 | 50 | 76.9231 | |
| gduggal-snapvard | INDEL | I6_15 | map_l125_m2_e0 | het | 66.1017 | 86.6667 | 53.4247 | 82.5150 | 26 | 4 | 78 | 68 | 53 | 77.9412 | |
| gduggal-snapvard | INDEL | I6_15 | map_l125_m2_e1 | het | 66.1017 | 86.6667 | 53.4247 | 82.9240 | 26 | 4 | 78 | 68 | 53 | 77.9412 | |
| ghariani-varprowl | INDEL | I16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 58.1470 | 86.6667 | 43.7500 | 77.4648 | 13 | 2 | 14 | 18 | 17 | 94.4444 | |
| gduggal-snapplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 86.6667 | 86.6667 | 86.6667 | 95.8564 | 13 | 2 | 13 | 2 | 1 | 50.0000 | |
| gduggal-snapplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 86.6667 | 86.6667 | 86.6667 | 95.8564 | 13 | 2 | 13 | 2 | 1 | 50.0000 | |
| gduggal-snapplat | SNP | ti | map_l150_m1_e0 | hetalt | 81.2500 | 86.6667 | 76.4706 | 83.4951 | 13 | 2 | 13 | 4 | 4 | 100.0000 | |
| gduggal-snapplat | SNP | ti | map_l150_m2_e0 | hetalt | 81.2500 | 86.6667 | 76.4706 | 85.8333 | 13 | 2 | 13 | 4 | 4 | 100.0000 | |
| gduggal-snapplat | SNP | ti | map_l150_m2_e1 | hetalt | 81.2500 | 86.6667 | 76.4706 | 85.8333 | 13 | 2 | 13 | 4 | 4 | 100.0000 | |
| gduggal-snapplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 86.6667 | 86.6667 | 86.6667 | 95.8564 | 13 | 2 | 13 | 2 | 1 | 50.0000 | |
| gduggal-snapplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 86.6667 | 86.6667 | 86.6667 | 95.8564 | 13 | 2 | 13 | 2 | 1 | 50.0000 | |
| gduggal-snapfb | INDEL | I1_5 | map_l250_m1_e0 | het | 89.6552 | 86.6667 | 92.8571 | 95.7831 | 52 | 8 | 52 | 4 | 1 | 25.0000 | |
| gduggal-bwavard | INDEL | I1_5 | map_l250_m0_e0 | het | 83.8710 | 86.6667 | 81.2500 | 98.8131 | 13 | 2 | 13 | 3 | 0 | 0.0000 | |
| gduggal-bwaplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 92.8571 | 86.6667 | 100.0000 | 96.9838 | 13 | 2 | 13 | 0 | 0 | ||
| gduggal-bwaplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 92.8571 | 86.6667 | 100.0000 | 96.9838 | 13 | 2 | 13 | 0 | 0 | ||
| gduggal-bwavard | INDEL | D16_PLUS | map_l150_m1_e0 | * | 74.2857 | 86.6667 | 65.0000 | 95.8932 | 13 | 2 | 13 | 7 | 2 | 28.5714 | |
| gduggal-bwafb | INDEL | D6_15 | map_l100_m2_e1 | het | 91.7507 | 86.6667 | 97.4684 | 83.5588 | 117 | 18 | 154 | 4 | 1 | 25.0000 | |
| gduggal-bwaplat | INDEL | I6_15 | func_cds | homalt | 89.6552 | 86.6667 | 92.8571 | 39.1304 | 13 | 2 | 13 | 1 | 1 | 100.0000 | |
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 92.8571 | 86.6667 | 100.0000 | 96.9838 | 13 | 2 | 13 | 0 | 0 | ||
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 92.8571 | 86.6667 | 100.0000 | 96.9838 | 13 | 2 | 13 | 0 | 0 | ||
| eyeh-varpipe | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 73.1615 | 86.6667 | 63.2979 | 89.1767 | 143 | 22 | 119 | 69 | 11 | 15.9420 | |
| gduggal-bwafb | INDEL | I1_5 | map_l250_m1_e0 | het | 92.0354 | 86.6667 | 98.1132 | 96.1398 | 52 | 8 | 52 | 1 | 0 | 0.0000 | |
| ciseli-custom | SNP | * | map_l125_m2_e0 | homalt | 88.1697 | 86.6763 | 89.7155 | 68.5746 | 15060 | 2315 | 15013 | 1721 | 1379 | 80.1278 | |
| ciseli-custom | SNP | * | map_l125_m2_e1 | homalt | 88.1920 | 86.6872 | 89.7500 | 68.5967 | 15198 | 2334 | 15148 | 1730 | 1386 | 80.1156 | |
| asubramanian-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.1790 | 86.6893 | 98.4109 | 40.6421 | 3315 | 509 | 3530 | 57 | 49 | 85.9649 | |
| ckim-isaac | INDEL | D6_15 | * | homalt | 92.2382 | 86.6899 | 98.5453 | 37.3467 | 5484 | 842 | 5487 | 81 | 30 | 37.0370 | |
| ckim-isaac | INDEL | D1_5 | * | hetalt | 92.0397 | 86.6959 | 98.0855 | 45.9935 | 8882 | 1363 | 9222 | 180 | 168 | 93.3333 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 89.3164 | 86.6966 | 92.0994 | 71.2589 | 4438 | 681 | 4523 | 388 | 351 | 90.4639 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 86.4073 | 86.7056 | 86.1111 | 74.4351 | 1337 | 205 | 1364 | 220 | 118 | 53.6364 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 74.8352 | 86.7069 | 65.8228 | 74.0520 | 574 | 88 | 572 | 297 | 264 | 88.8889 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 92.1147 | 86.7089 | 98.2394 | 38.2609 | 548 | 84 | 558 | 10 | 9 | 90.0000 | |
| gduggal-bwaplat | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 92.7883 | 86.7091 | 99.7841 | 61.8573 | 24504 | 3756 | 24493 | 53 | 43 | 81.1321 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 60.3971 | 86.7094 | 46.3362 | 62.7309 | 1083 | 166 | 1075 | 1245 | 1170 | 93.9759 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 60.3971 | 86.7094 | 46.3362 | 62.7309 | 1083 | 166 | 1075 | 1245 | 1170 | 93.9759 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 92.7110 | 86.7096 | 99.6050 | 29.5781 | 1481 | 227 | 1513 | 6 | 6 | 100.0000 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 90.2020 | 86.7117 | 93.9850 | 69.4253 | 385 | 59 | 375 | 24 | 5 | 20.8333 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | map_siren | * | 92.1763 | 86.7133 | 98.3740 | 86.2876 | 124 | 19 | 121 | 2 | 1 | 50.0000 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 89.5255 | 86.7232 | 92.5150 | 65.8836 | 307 | 47 | 309 | 25 | 25 | 100.0000 | |
| gduggal-bwaplat | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 92.4984 | 86.7234 | 99.0973 | 67.6373 | 24247 | 3712 | 24262 | 221 | 75 | 33.9367 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 91.8593 | 86.7265 | 97.6378 | 63.9497 | 869 | 133 | 868 | 21 | 15 | 71.4286 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.8514 | 86.7287 | 99.9044 | 30.7514 | 2052 | 314 | 2090 | 2 | 2 | 100.0000 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 92.0166 | 86.7307 | 97.9886 | 88.3681 | 16981 | 2598 | 17002 | 349 | 101 | 28.9398 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 92.0166 | 86.7307 | 97.9886 | 88.3681 | 16981 | 2598 | 17002 | 349 | 101 | 28.9398 | |
| jli-custom | INDEL | I1_5 | HG002complexvar | hetalt | 92.7842 | 86.7323 | 99.7439 | 70.2420 | 1497 | 229 | 1558 | 4 | 4 | 100.0000 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 91.1773 | 86.7440 | 96.0881 | 48.8639 | 2840 | 434 | 2530 | 103 | 98 | 95.1456 | |
| ciseli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 83.6913 | 86.7444 | 80.8458 | 71.7974 | 1636 | 250 | 1625 | 385 | 278 | 72.2078 | |
| jpowers-varprowl | INDEL | I6_15 | segdup | het | 77.4194 | 86.7470 | 69.9029 | 92.0952 | 72 | 11 | 72 | 31 | 31 | 100.0000 | |