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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
20251-20300 / 86044 show all | |||||||||||||||
| ltrigg-rtg1 | INDEL | I16_PLUS | * | hetalt | 85.7294 | 75.3098 | 99.4953 | 51.3953 | 1580 | 518 | 1577 | 8 | 8 | 100.0000 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.8242 | 94.2928 | 99.4953 | 23.7079 | 6493 | 393 | 6506 | 33 | 33 | 100.0000 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.8165 | 94.2782 | 99.4953 | 23.7106 | 6492 | 394 | 6505 | 33 | 33 | 100.0000 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 97.0717 | 94.7636 | 99.4951 | 30.0679 | 7637 | 422 | 7685 | 39 | 38 | 97.4359 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 97.0717 | 94.7636 | 99.4951 | 30.0679 | 7637 | 422 | 7685 | 39 | 38 | 97.4359 | |
| jli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.6207 | 99.7468 | 99.4949 | 51.0355 | 1576 | 4 | 1576 | 8 | 0 | 0.0000 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 98.9834 | 98.4772 | 99.4949 | 54.7945 | 194 | 3 | 197 | 1 | 1 | 100.0000 | |
| jpowers-varprowl | SNP | ti | * | het | 99.4145 | 99.3343 | 99.4948 | 22.7953 | 1273353 | 8534 | 1273511 | 6466 | 293 | 4.5314 | |
| mlin-fermikit | INDEL | * | HG002compoundhet | hetalt | 77.7377 | 63.7887 | 99.4948 | 53.3255 | 16062 | 9118 | 16150 | 82 | 81 | 98.7805 | |
| hfeng-pmm3 | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.3762 | 97.2826 | 99.4947 | 68.4722 | 1969 | 55 | 1969 | 10 | 0 | 0.0000 | |
| jli-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 98.5010 | 97.5270 | 99.4946 | 34.2043 | 1262 | 32 | 1378 | 7 | 7 | 100.0000 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.7472 | 94.1475 | 99.4946 | 23.8423 | 6483 | 403 | 6496 | 33 | 33 | 100.0000 | |
| gduggal-snapfb | SNP | tv | map_l100_m2_e1 | homalt | 98.4024 | 97.3339 | 99.4946 | 73.1383 | 9054 | 248 | 9055 | 46 | 9 | 19.5652 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 94.4663 | 89.9219 | 99.4945 | 27.8754 | 6451 | 723 | 6495 | 33 | 28 | 84.8485 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.1839 | 94.9785 | 99.4942 | 28.3420 | 9949 | 526 | 10032 | 51 | 50 | 98.0392 | |
| gduggal-bwafb | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.2945 | 99.0956 | 99.4942 | 40.3814 | 6684 | 61 | 6688 | 34 | 20 | 58.8235 | |
| bgallagher-sentieon | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 99.2848 | 99.0764 | 99.4941 | 66.4545 | 4720 | 44 | 4720 | 24 | 5 | 20.8333 | |
| rpoplin-dv42 | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 99.3435 | 99.1935 | 99.4939 | 70.5690 | 984 | 8 | 983 | 5 | 1 | 20.0000 | |
| cchapple-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.6621 | 99.8310 | 99.4938 | 54.7565 | 2954 | 5 | 2948 | 15 | 1 | 6.6667 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.1601 | 96.8618 | 99.4937 | 40.9343 | 17686 | 573 | 17687 | 90 | 86 | 95.5556 | |
| ckim-dragen | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 98.8470 | 98.2089 | 99.4934 | 48.2524 | 2906 | 53 | 2946 | 15 | 4 | 26.6667 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.5924 | 95.7627 | 99.4934 | 31.8370 | 904 | 40 | 982 | 5 | 5 | 100.0000 | |
| dgrover-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 99.4814 | 99.4694 | 99.4934 | 82.7155 | 4124 | 22 | 4124 | 21 | 7 | 33.3333 | |
| ckim-vqsr | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.9263 | 98.3656 | 99.4933 | 72.9052 | 30634 | 509 | 30634 | 156 | 20 | 12.8205 | |
| ckim-vqsr | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.9263 | 98.3656 | 99.4933 | 72.9052 | 30634 | 509 | 30634 | 156 | 20 | 12.8205 | |
| astatham-gatk | INDEL | D1_5 | map_l100_m1_e0 | homalt | 99.4932 | 99.4932 | 99.4932 | 83.1098 | 589 | 3 | 589 | 3 | 2 | 66.6667 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 94.3126 | 89.6450 | 99.4931 | 30.6266 | 2121 | 245 | 2159 | 11 | 11 | 100.0000 | |
| eyeh-varpipe | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7221 | 99.9521 | 99.4931 | 42.7028 | 6265 | 3 | 6281 | 32 | 9 | 28.1250 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 94.2777 | 89.5819 | 99.4931 | 26.8704 | 6492 | 755 | 6477 | 33 | 25 | 75.7576 | |
| bgallagher-sentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.4720 | 99.4510 | 99.4930 | 87.3253 | 2355 | 13 | 2355 | 12 | 11 | 91.6667 | |
| jmaeng-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.1788 | 98.8665 | 99.4930 | 89.4926 | 785 | 9 | 785 | 4 | 4 | 100.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 94.0410 | 89.1557 | 99.4928 | 31.2609 | 1151 | 140 | 1177 | 6 | 5 | 83.3333 | |
| ndellapenna-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.2048 | 98.9185 | 99.4928 | 63.7700 | 1372 | 15 | 1373 | 7 | 2 | 28.5714 | |
| hfeng-pmm3 | SNP | ti | map_l250_m2_e1 | homalt | 99.5488 | 99.6050 | 99.4927 | 87.7689 | 1765 | 7 | 1765 | 9 | 2 | 22.2222 | |
| hfeng-pmm2 | SNP | ti | map_l250_m2_e1 | homalt | 99.5488 | 99.6050 | 99.4927 | 87.8092 | 1765 | 7 | 1765 | 9 | 2 | 22.2222 | |
| hfeng-pmm1 | SNP | ti | map_l250_m2_e1 | homalt | 99.5205 | 99.5485 | 99.4924 | 87.8161 | 1764 | 8 | 1764 | 9 | 2 | 22.2222 | |
| ltrigg-rtg2 | INDEL | I1_5 | map_l150_m2_e0 | homalt | 99.2481 | 99.0050 | 99.4924 | 85.2434 | 199 | 2 | 196 | 1 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 99.4924 | 99.4924 | 99.4924 | 60.6000 | 196 | 1 | 196 | 1 | 1 | 100.0000 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 75.7488 | 61.1544 | 99.4924 | 57.4514 | 392 | 249 | 392 | 2 | 2 | 100.0000 | |
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 95.0365 | 90.9628 | 99.4922 | 86.4235 | 2154 | 214 | 2155 | 11 | 4 | 36.3636 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5214 | 99.5507 | 99.4922 | 74.9449 | 5096 | 23 | 5094 | 26 | 13 | 50.0000 | |
| jli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 97.6090 | 95.7958 | 99.4921 | 26.3939 | 6813 | 299 | 6856 | 35 | 34 | 97.1429 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 97.4314 | 95.4545 | 99.4920 | 57.5943 | 1176 | 56 | 1175 | 6 | 5 | 83.3333 | |
| ckim-isaac | SNP | tv | map_l150_m2_e1 | het | 71.6314 | 55.9608 | 99.4920 | 80.5897 | 4112 | 3236 | 4113 | 21 | 6 | 28.5714 | |
| jli-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.6951 | 99.8992 | 99.4918 | 73.2959 | 30730 | 31 | 30737 | 157 | 151 | 96.1783 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.7194 | 96.0089 | 99.4918 | 41.3653 | 19774 | 822 | 19775 | 101 | 87 | 86.1386 | |
| ghariani-varprowl | SNP | tv | map_l125_m0_e0 | homalt | 98.1984 | 96.9383 | 99.4917 | 74.3206 | 2153 | 68 | 2153 | 11 | 4 | 36.3636 | |
| mlin-fermikit | INDEL | I1_5 | HG002compoundhet | hetalt | 79.4743 | 66.1627 | 99.4916 | 57.4825 | 7395 | 3782 | 7437 | 38 | 38 | 100.0000 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.5638 | 99.6361 | 99.4916 | 74.0824 | 1369 | 5 | 1370 | 7 | 0 | 0.0000 | |
| ckim-gatk | INDEL | D1_5 | map_l100_m1_e0 | homalt | 99.3232 | 99.1554 | 99.4915 | 83.5517 | 587 | 5 | 587 | 3 | 2 | 66.6667 | |