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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
23951-24000 / 86044 show all | |||||||||||||||
| jli-custom | INDEL | * | map_l125_m2_e0 | het | 98.3415 | 97.9871 | 98.6985 | 86.8786 | 1363 | 28 | 1365 | 18 | 4 | 22.2222 | |
| jli-custom | INDEL | * | map_l125_m2_e1 | het | 98.3616 | 98.0114 | 98.7143 | 86.9876 | 1380 | 28 | 1382 | 18 | 4 | 22.2222 | |
| jli-custom | INDEL | * | map_l150_m2_e1 | * | 98.2943 | 98.0542 | 98.5356 | 89.3280 | 1411 | 28 | 1413 | 21 | 8 | 38.0952 | |
| hfeng-pmm1 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 86.4865 | 77.4194 | 97.9592 | 90.1210 | 96 | 28 | 96 | 2 | 0 | 0.0000 | |
| hfeng-pmm2 | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 84.9320 | 77.4194 | 94.0594 | 99.9207 | 96 | 28 | 95 | 6 | 0 | 0.0000 | |
| hfeng-pmm2 | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 78.1011 | 67.8161 | 92.0635 | 99.9065 | 59 | 28 | 58 | 5 | 0 | 0.0000 | |
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 95.4401 | 91.7889 | 99.3939 | 60.5263 | 313 | 28 | 328 | 2 | 2 | 100.0000 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.7467 | 97.8979 | 99.6103 | 71.3232 | 1304 | 28 | 1278 | 5 | 4 | 80.0000 | |
| hfeng-pmm2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.3754 | 98.8773 | 99.8785 | 57.1429 | 2466 | 28 | 2466 | 3 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 97.0242 | 95.4545 | 98.6464 | 64.6742 | 588 | 28 | 583 | 8 | 8 | 100.0000 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.3410 | 99.5071 | 99.1754 | 50.3830 | 5653 | 28 | 5653 | 47 | 47 | 100.0000 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 95.7835 | 93.2367 | 98.4733 | 73.1190 | 386 | 28 | 387 | 6 | 4 | 66.6667 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 97.7987 | 95.6923 | 100.0000 | 23.4223 | 622 | 28 | 631 | 0 | 0 | ||
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 95.9022 | 93.2367 | 98.7245 | 72.6257 | 386 | 28 | 387 | 5 | 4 | 80.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.7466 | 97.5243 | 100.0000 | 41.8848 | 1103 | 28 | 1110 | 0 | 0 | ||
| hfeng-pmm3 | SNP | * | map_l125_m0_e0 | homalt | 99.5977 | 99.5828 | 99.6125 | 70.7306 | 6684 | 28 | 6684 | 26 | 9 | 34.6154 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 94.0695 | 89.1473 | 99.5671 | 45.7746 | 230 | 28 | 230 | 1 | 1 | 100.0000 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 91.1111 | 85.4167 | 97.6190 | 27.2727 | 164 | 28 | 164 | 4 | 4 | 100.0000 | |
| ckim-isaac | INDEL | D6_15 | map_l150_m1_e0 | het | 43.1373 | 28.2051 | 91.6667 | 96.4072 | 11 | 28 | 11 | 1 | 1 | 100.0000 | |
| ckim-isaac | INDEL | I1_5 | map_l150_m0_e0 | het | 84.7826 | 73.5849 | 100.0000 | 94.4681 | 78 | 28 | 78 | 0 | 0 | ||
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.0580 | 99.2555 | 98.8612 | 71.4717 | 3733 | 28 | 3733 | 43 | 43 | 100.0000 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.0580 | 99.2555 | 98.8612 | 71.4717 | 3733 | 28 | 3733 | 43 | 43 | 100.0000 | |
| ckim-vqsr | INDEL | I6_15 | HG002complexvar | het | 99.2942 | 98.8110 | 99.7821 | 59.6661 | 2327 | 28 | 2290 | 5 | 4 | 80.0000 | |
| ckim-vqsr | SNP | * | map_l100_m1_e0 | hetalt | 48.1481 | 31.7073 | 100.0000 | 94.6058 | 13 | 28 | 13 | 0 | 0 | ||
| ckim-vqsr | SNP | * | map_l100_m2_e0 | hetalt | 50.0000 | 33.3333 | 100.0000 | 94.9640 | 14 | 28 | 14 | 0 | 0 | ||
| ckim-vqsr | SNP | * | map_l100_m2_e1 | hetalt | 51.7241 | 34.8837 | 100.0000 | 94.6237 | 15 | 28 | 15 | 0 | 0 | ||
| ckim-vqsr | SNP | ti | * | hetalt | 97.3638 | 95.1890 | 99.6403 | 53.2773 | 554 | 28 | 554 | 2 | 2 | 100.0000 | |
| ckim-vqsr | SNP | ti | HG002compoundhet | hetalt | 97.5221 | 95.1641 | 100.0000 | 22.7209 | 551 | 28 | 551 | 0 | 0 | ||
| egarrison-hhga | INDEL | D6_15 | map_l100_m2_e1 | hetalt | 74.8782 | 61.6438 | 95.3488 | 77.1277 | 45 | 28 | 41 | 2 | 1 | 50.0000 | |
| ckim-isaac | SNP | ti | HG002complexvar | hetalt | 92.7461 | 86.4734 | 100.0000 | 28.1124 | 179 | 28 | 179 | 0 | 0 | ||
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.3728 | 99.7562 | 97.0272 | 61.9399 | 11456 | 28 | 11456 | 351 | 343 | 97.7208 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.3738 | 95.1973 | 99.6522 | 66.4723 | 555 | 28 | 573 | 2 | 2 | 100.0000 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 95.4319 | 93.2367 | 97.7330 | 74.4530 | 386 | 28 | 388 | 9 | 9 | 100.0000 | |
| dgrover-gatk | SNP | ti | map_l250_m2_e0 | homalt | 99.1074 | 98.3991 | 99.8260 | 86.5878 | 1721 | 28 | 1721 | 3 | 2 | 66.6667 | |
| dgrover-gatk | SNP | ti | map_l250_m2_e1 | homalt | 99.1191 | 98.4199 | 99.8283 | 86.6233 | 1744 | 28 | 1744 | 3 | 2 | 66.6667 | |
| ckim-vqsr | SNP | tv | map_l100_m1_e0 | hetalt | 48.1481 | 31.7073 | 100.0000 | 94.6058 | 13 | 28 | 13 | 0 | 0 | ||
| ckim-vqsr | SNP | tv | map_l100_m2_e0 | hetalt | 50.0000 | 33.3333 | 100.0000 | 94.9640 | 14 | 28 | 14 | 0 | 0 | ||
| ckim-vqsr | SNP | tv | map_l100_m2_e1 | hetalt | 51.7241 | 34.8837 | 100.0000 | 94.6237 | 15 | 28 | 15 | 0 | 0 | ||
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 96.7853 | 97.1074 | 96.4652 | 83.3460 | 940 | 28 | 846 | 31 | 21 | 67.7419 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.8747 | 99.8104 | 99.9390 | 55.0186 | 14742 | 28 | 14744 | 9 | 4 | 44.4444 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 93.3545 | 97.0864 | 89.8990 | 74.7771 | 933 | 28 | 890 | 100 | 90 | 90.0000 | |
| ltrigg-rtg2 | SNP | ti | map_l125_m0_e0 | homalt | 99.6428 | 99.3765 | 99.9105 | 65.1370 | 4463 | 28 | 4463 | 4 | 4 | 100.0000 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 97.5368 | 96.9631 | 98.1174 | 69.9601 | 894 | 28 | 886 | 17 | 14 | 82.3529 | |
| qzeng-custom | INDEL | D1_5 | map_l150_m0_e0 | homalt | 79.8653 | 67.0588 | 98.7179 | 91.2752 | 57 | 28 | 77 | 1 | 1 | 100.0000 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | * | 79.6385 | 80.2817 | 79.0055 | 39.4649 | 114 | 28 | 143 | 38 | 18 | 47.3684 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 86.6593 | 88.6640 | 84.7432 | 65.8939 | 219 | 28 | 561 | 101 | 76 | 75.2475 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 89.9699 | 84.9462 | 95.6250 | 69.2308 | 158 | 28 | 153 | 7 | 5 | 71.4286 | |
| ndellapenna-hhga | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.4850 | 99.2977 | 99.6730 | 35.9284 | 3959 | 28 | 3962 | 13 | 12 | 92.3077 | |
| qzeng-custom | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 87.3874 | 77.6000 | 100.0000 | 66.6667 | 97 | 28 | 1 | 0 | 0 | ||
| qzeng-custom | INDEL | * | map_l250_m0_e0 | * | 73.8916 | 64.1026 | 87.2093 | 99.0927 | 50 | 28 | 75 | 11 | 6 | 54.5455 | |