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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
65901-65950 / 86044 show all | |||||||||||||||
| rpoplin-dv42 | SNP | tv | map_l100_m2_e1 | homalt | 99.5691 | 99.3550 | 99.7841 | 64.9074 | 9242 | 60 | 9242 | 20 | 18 | 90.0000 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 93.4330 | 91.3758 | 95.5850 | 59.8048 | 445 | 42 | 433 | 20 | 5 | 25.0000 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 70.9431 | 59.3496 | 88.1657 | 78.6885 | 146 | 100 | 149 | 20 | 9 | 45.0000 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 72.3074 | 65.1007 | 81.3084 | 71.2366 | 97 | 52 | 87 | 20 | 14 | 70.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.4848 | 99.7211 | 97.2789 | 61.7387 | 715 | 2 | 715 | 20 | 19 | 95.0000 | |
| ckim-vqsr | INDEL | D1_5 | map_l150_m0_e0 | * | 95.6081 | 97.9239 | 93.3993 | 94.3364 | 283 | 6 | 283 | 20 | 1 | 5.0000 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.8279 | 98.4953 | 99.1628 | 76.9045 | 2422 | 37 | 2369 | 20 | 13 | 65.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 94.9495 | 100.0000 | 90.3846 | 67.5000 | 188 | 0 | 188 | 20 | 19 | 95.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.5108 | 94.0299 | 99.1263 | 61.5359 | 2268 | 144 | 2269 | 20 | 15 | 75.0000 | |
| ckim-vqsr | SNP | ti | HG002complexvar | homalt | 98.3712 | 96.8046 | 99.9893 | 18.7775 | 187281 | 6182 | 187271 | 20 | 20 | 100.0000 | |
| dgrover-gatk | INDEL | * | map_siren | homalt | 99.3423 | 99.4350 | 99.2498 | 81.7385 | 2640 | 15 | 2646 | 20 | 11 | 55.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | HG002compoundhet | homalt | 44.4444 | 100.0000 | 28.5714 | 72.0000 | 8 | 0 | 8 | 20 | 20 | 100.0000 | |
| dgrover-gatk | INDEL | D1_5 | map_siren | het | 99.2553 | 99.3852 | 99.1259 | 82.2139 | 2263 | 14 | 2268 | 20 | 1 | 5.0000 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 82.8484 | 78.1915 | 88.0952 | 60.0000 | 147 | 41 | 148 | 20 | 19 | 95.0000 | |
| ckim-isaac | SNP | tv | HG002complexvar | homalt | 95.1060 | 90.6877 | 99.9768 | 19.5838 | 86254 | 8857 | 86277 | 20 | 16 | 80.0000 | |
| ckim-isaac | SNP | tv | map_l150_m1_e0 | het | 71.1670 | 55.3988 | 99.4831 | 79.3620 | 3848 | 3098 | 3849 | 20 | 6 | 30.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | HG002compoundhet | homalt | 44.4444 | 100.0000 | 28.5714 | 72.5490 | 8 | 0 | 8 | 20 | 20 | 100.0000 | |
| dgrover-gatk | SNP | ti | HG002compoundhet | het | 99.7790 | 99.7685 | 99.7895 | 39.8442 | 9483 | 22 | 9481 | 20 | 14 | 70.0000 | |
| egarrison-hhga | INDEL | D16_PLUS | map_siren | het | 86.5700 | 96.1538 | 78.7234 | 89.0698 | 75 | 3 | 74 | 20 | 14 | 70.0000 | |
| egarrison-hhga | INDEL | D6_15 | map_l100_m2_e1 | * | 90.1715 | 88.0000 | 92.4528 | 85.4555 | 242 | 33 | 245 | 20 | 12 | 60.0000 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 96.1650 | 95.9220 | 96.4093 | 67.7662 | 541 | 23 | 537 | 20 | 9 | 45.0000 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.3607 | 98.5915 | 98.1308 | 64.2380 | 1050 | 15 | 1050 | 20 | 14 | 70.0000 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 91.6667 | 93.6170 | 89.7959 | 66.0312 | 176 | 12 | 176 | 20 | 17 | 85.0000 | |
| egarrison-hhga | SNP | tv | map_l125_m0_e0 | * | 99.1050 | 98.5221 | 99.6948 | 73.4104 | 6533 | 98 | 6533 | 20 | 9 | 45.0000 | |
| anovak-vg | INDEL | C6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 0.0000 | 0.0000 | 83.1933 | 0 | 0 | 0 | 20 | 2 | 10.0000 | ||
| anovak-vg | INDEL | C6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 0.0000 | 0.0000 | 82.6087 | 0 | 0 | 0 | 20 | 2 | 10.0000 | ||
| anovak-vg | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 10.9091 | 6.2500 | 42.8571 | 61.9565 | 12 | 180 | 15 | 20 | 16 | 80.0000 | |
| anovak-vg | INDEL | D6_15 | map_l125_m1_e0 | het | 77.8285 | 81.2500 | 74.6835 | 89.5641 | 52 | 12 | 59 | 20 | 11 | 55.0000 | |
| anovak-vg | INDEL | I6_15 | map_l100_m2_e1 | het | 44.3378 | 34.4262 | 62.2642 | 83.5913 | 21 | 40 | 33 | 20 | 5 | 25.0000 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 97.0857 | 96.0106 | 98.1851 | 47.3483 | 1083 | 45 | 1082 | 20 | 17 | 85.0000 | |
| anovak-vg | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 97.9888 | 97.4071 | 98.5775 | 24.3272 | 1390 | 37 | 1386 | 20 | 20 | 100.0000 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5798 | 99.5507 | 99.6089 | 75.0780 | 5096 | 23 | 5094 | 20 | 10 | 50.0000 | |
| astatham-gatk | INDEL | * | map_l250_m1_e0 | * | 95.1613 | 96.7213 | 93.6508 | 96.0377 | 295 | 10 | 295 | 20 | 4 | 20.0000 | |
| astatham-gatk | INDEL | * | map_l250_m2_e0 | * | 95.3800 | 96.6767 | 94.1176 | 96.2801 | 320 | 11 | 320 | 20 | 4 | 20.0000 | |
| astatham-gatk | INDEL | * | map_l250_m2_e1 | * | 95.4074 | 96.6967 | 94.1520 | 96.3590 | 322 | 11 | 322 | 20 | 4 | 20.0000 | |
| astatham-gatk | SNP | * | map_l125_m1_e0 | homalt | 99.4624 | 99.0476 | 99.8807 | 63.5573 | 16744 | 161 | 16744 | 20 | 16 | 80.0000 | |
| astatham-gatk | SNP | * | map_l125_m2_e0 | homalt | 99.4712 | 99.0619 | 99.8839 | 66.1554 | 17212 | 163 | 17212 | 20 | 16 | 80.0000 | |
| astatham-gatk | SNP | * | map_l125_m2_e1 | homalt | 99.4760 | 99.0703 | 99.8850 | 66.1765 | 17369 | 163 | 17369 | 20 | 16 | 80.0000 | |
| astatham-gatk | SNP | tv | map_l250_m1_e0 | het | 89.4463 | 81.8131 | 98.6505 | 91.5618 | 1462 | 325 | 1462 | 20 | 3 | 15.0000 | |
| astatham-gatk | SNP | tv | map_l250_m2_e0 | het | 89.1403 | 81.2371 | 98.7469 | 92.0672 | 1576 | 364 | 1576 | 20 | 3 | 15.0000 | |
| astatham-gatk | SNP | tv | map_l250_m2_e1 | het | 89.1681 | 81.2723 | 98.7631 | 92.1160 | 1597 | 368 | 1597 | 20 | 3 | 15.0000 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.0742 | 99.2047 | 98.9440 | 72.8770 | 1871 | 15 | 1874 | 20 | 6 | 30.0000 | |
| asubramanian-gatk | INDEL | * | map_siren | homalt | 97.0575 | 94.9906 | 99.2163 | 82.1825 | 2522 | 133 | 2532 | 20 | 9 | 45.0000 | |
| asubramanian-gatk | INDEL | C16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 0.0000 | 0.0000 | 91.2664 | 0 | 0 | 0 | 20 | 0 | 0.0000 | ||
| asubramanian-gatk | INDEL | C16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 81.9820 | 0 | 0 | 0 | 20 | 0 | 0.0000 | ||
| asubramanian-gatk | INDEL | C16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 71.0145 | 0 | 0 | 0 | 20 | 0 | 0.0000 | ||
| asubramanian-gatk | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 66.1017 | 0 | 0 | 0 | 20 | 0 | 0.0000 | ||
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 94.1176 | 95.7529 | 92.5373 | 60.1190 | 248 | 11 | 248 | 20 | 17 | 85.0000 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.2900 | 98.8833 | 99.7000 | 54.0745 | 6641 | 75 | 6647 | 20 | 7 | 35.0000 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 91.9411 | 87.7264 | 96.5812 | 72.9667 | 436 | 61 | 565 | 20 | 19 | 95.0000 | |