PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
14151-14200 / 86044 show all | |||||||||||||||
| ckim-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 91.2201 | 83.9465 | 99.8737 | 37.5887 | 753 | 144 | 791 | 1 | 1 | 100.0000 | |
| ciseli-custom | INDEL | * | HG002compoundhet | homalt | 5.5419 | 79.0087 | 2.8717 | 55.4798 | 542 | 144 | 559 | 18907 | 17855 | 94.4359 | |
| gduggal-bwafb | SNP | tv | map_l100_m0_e0 | * | 98.4300 | 98.7008 | 98.1606 | 72.2063 | 10940 | 144 | 10940 | 205 | 38 | 18.5366 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 69.6394 | 53.9936 | 98.0519 | 57.5172 | 169 | 144 | 302 | 6 | 6 | 100.0000 | |
| eyeh-varpipe | SNP | * | map_l125_m2_e1 | * | 98.7976 | 99.6949 | 97.9163 | 74.9861 | 47058 | 144 | 45676 | 972 | 38 | 3.9095 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 70.2185 | 89.1892 | 57.9025 | 52.1104 | 1188 | 144 | 1176 | 855 | 827 | 96.7251 | |
| gduggal-bwavard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 87.0247 | 88.6166 | 85.4890 | 87.6172 | 1121 | 144 | 1084 | 184 | 65 | 35.3261 | |
| gduggal-snapfb | INDEL | * | map_l125_m2_e1 | * | 94.4490 | 93.5281 | 95.3881 | 87.4419 | 2081 | 144 | 2089 | 101 | 24 | 23.7624 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 85.1218 | 75.0000 | 98.4018 | 76.1827 | 432 | 144 | 431 | 7 | 1 | 14.2857 | |
| gduggal-snapfb | SNP | tv | map_l125_m0_e0 | het | 94.9693 | 96.7280 | 93.2734 | 75.1430 | 4257 | 144 | 4257 | 307 | 123 | 40.0651 | |
| gduggal-snapvard | INDEL | I1_5 | HG002compoundhet | het | 60.6574 | 83.0588 | 47.7728 | 63.6646 | 706 | 144 | 5148 | 5628 | 4753 | 84.4527 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.3852 | 99.0251 | 99.7479 | 54.5094 | 14626 | 144 | 14641 | 37 | 15 | 40.5405 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 82.8480 | 83.5616 | 82.1464 | 73.3422 | 732 | 144 | 819 | 178 | 170 | 95.5056 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 94.0820 | 92.6941 | 95.5121 | 71.6510 | 1827 | 144 | 1809 | 85 | 58 | 68.2353 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 94.0820 | 92.6941 | 95.5121 | 71.6510 | 1827 | 144 | 1809 | 85 | 58 | 68.2353 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 91.2201 | 83.9465 | 99.8737 | 37.5887 | 753 | 144 | 791 | 1 | 1 | 100.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.5108 | 94.0299 | 99.1263 | 61.5359 | 2268 | 144 | 2269 | 20 | 15 | 75.0000 | |
| rpoplin-dv42 | SNP | * | map_l100_m1_e0 | homalt | 99.6291 | 99.4667 | 99.7919 | 61.1512 | 26859 | 144 | 26860 | 56 | 52 | 92.8571 | |
| rpoplin-dv42 | SNP | * | map_l100_m2_e0 | homalt | 99.6325 | 99.4768 | 99.7886 | 63.6376 | 27379 | 144 | 27380 | 58 | 54 | 93.1034 | |
| raldana-dualsentieon | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 93.8925 | 88.9660 | 99.3966 | 87.1383 | 1153 | 143 | 1153 | 7 | 4 | 57.1429 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 81.8346 | 80.5442 | 83.1669 | 54.9775 | 592 | 143 | 583 | 118 | 117 | 99.1525 | |
| ciseli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 86.2310 | 89.4309 | 83.2523 | 73.2130 | 1210 | 143 | 1198 | 241 | 178 | 73.8589 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 56.7644 | 80.9840 | 43.6963 | 58.5880 | 609 | 143 | 610 | 786 | 670 | 85.2417 | |
| ckim-dragen | SNP | tv | * | homalt | 99.9757 | 99.9621 | 99.9894 | 19.9141 | 376980 | 143 | 377083 | 40 | 29 | 72.5000 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 82.7698 | 70.8758 | 99.4609 | 27.5391 | 348 | 143 | 369 | 2 | 2 | 100.0000 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 96.8519 | 95.9843 | 97.7354 | 64.7626 | 3418 | 143 | 3539 | 82 | 70 | 85.3659 | |
| ciseli-custom | SNP | * | map_l250_m0_e0 | homalt | 78.0848 | 77.2655 | 78.9216 | 92.3251 | 486 | 143 | 483 | 129 | 86 | 66.6667 | |
| ciseli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 46.0775 | 80.1389 | 32.3344 | 77.7959 | 577 | 143 | 615 | 1287 | 33 | 2.5641 | |
| hfeng-pmm1 | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.3051 | 98.7492 | 99.8673 | 37.3573 | 11290 | 143 | 11287 | 15 | 0 | 0.0000 | |
| hfeng-pmm2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 90.3644 | 83.1962 | 98.8842 | 87.6910 | 708 | 143 | 709 | 8 | 0 | 0.0000 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.1586 | 95.2030 | 99.1964 | 50.6041 | 2838 | 143 | 2839 | 23 | 18 | 78.2609 | |
| qzeng-custom | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.9643 | 99.4833 | 98.4507 | 67.9503 | 27535 | 143 | 27515 | 433 | 39 | 9.0069 | |
| ndellapenna-hhga | INDEL | D16_PLUS | HG002complexvar | hetalt | 58.9170 | 42.1053 | 98.0769 | 57.6087 | 104 | 143 | 153 | 3 | 2 | 66.6667 | |
| ndellapenna-hhga | INDEL | D6_15 | * | homalt | 95.9125 | 97.7395 | 94.1526 | 53.1263 | 6183 | 143 | 6183 | 384 | 166 | 43.2292 | |
| qzeng-custom | INDEL | * | map_l150_m1_e0 | homalt | 80.5851 | 69.0476 | 96.7517 | 89.5717 | 319 | 143 | 417 | 14 | 7 | 50.0000 | |
| qzeng-custom | INDEL | D6_15 | HG002complexvar | hetalt | 85.8835 | 100.0000 | 870 | 143 | 0 | 0 | 0 | ||||
| mlin-fermikit | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 50.0731 | 34.1014 | 94.1860 | 56.1224 | 74 | 143 | 81 | 5 | 5 | 100.0000 | |
| mlin-fermikit | SNP | * | segdup | homalt | 98.6182 | 98.6689 | 98.5676 | 86.0366 | 10600 | 143 | 10597 | 154 | 135 | 87.6623 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 81.2115 | 77.3016 | 85.5379 | 66.6471 | 487 | 143 | 485 | 82 | 76 | 92.6829 | |
| jli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 90.9027 | 83.6009 | 99.6021 | 25.4941 | 729 | 143 | 751 | 3 | 3 | 100.0000 | |
| jmaeng-gatk | SNP | ti | segdup | * | 98.6795 | 99.2681 | 98.0979 | 93.0686 | 19394 | 143 | 19392 | 376 | 6 | 1.5957 | |
| jpowers-varprowl | INDEL | D1_5 | map_l100_m2_e0 | * | 93.7318 | 92.5326 | 94.9625 | 84.4045 | 1772 | 143 | 1772 | 94 | 63 | 67.0213 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 91.2859 | 84.0580 | 99.8737 | 41.1152 | 754 | 143 | 791 | 1 | 1 | 100.0000 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 46.3519 | 40.9091 | 53.4653 | 59.0264 | 99 | 143 | 108 | 94 | 71 | 75.5319 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.5967 | 99.5697 | 99.6236 | 75.3470 | 33093 | 143 | 33087 | 125 | 100 | 80.0000 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 82.7698 | 70.8758 | 99.4609 | 27.5391 | 348 | 143 | 369 | 2 | 2 | 100.0000 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 91.1683 | 84.8517 | 98.5011 | 38.5122 | 801 | 143 | 920 | 14 | 14 | 100.0000 | |
| egarrison-hhga | SNP | * | map_l250_m2_e0 | het | 98.3259 | 97.2468 | 99.4291 | 88.5758 | 5051 | 143 | 5051 | 29 | 11 | 37.9310 | |
| egarrison-hhga | SNP | ti | map_l125_m0_e0 | het | 98.9821 | 98.2694 | 99.7053 | 75.9224 | 8120 | 143 | 8120 | 24 | 10 | 41.6667 | |
| egarrison-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.7264 | 98.4342 | 99.0203 | 74.1270 | 8990 | 143 | 8995 | 89 | 19 | 21.3483 | |