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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
15501-15550 / 86044 show all | |||||||||||||||
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 95.2832 | 91.6502 | 99.2161 | 44.8245 | 5565 | 507 | 5569 | 44 | 30 | 68.1818 | |
| ciseli-custom | INDEL | I1_5 | map_l100_m2_e0 | homalt | 54.2174 | 40.3013 | 82.8125 | 83.8994 | 214 | 317 | 212 | 44 | 35 | 79.5455 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.3254 | 96.9477 | 97.7059 | 65.2032 | 1874 | 59 | 1874 | 44 | 43 | 97.7273 | |
| anovak-vg | INDEL | I6_15 | map_l100_m2_e1 | * | 53.2425 | 49.1379 | 58.0952 | 82.0819 | 57 | 59 | 61 | 44 | 25 | 56.8182 | |
| anovak-vg | SNP | ti | map_l100_m0_e0 | homalt | 88.2155 | 79.3671 | 99.2843 | 61.2798 | 6170 | 1604 | 6104 | 44 | 41 | 93.1818 | |
| astatham-gatk | INDEL | * | map_l100_m0_e0 | * | 96.7251 | 96.2892 | 97.1649 | 87.6728 | 1505 | 58 | 1508 | 44 | 9 | 20.4545 | |
| astatham-gatk | INDEL | * | map_l125_m2_e0 | * | 96.5138 | 95.1275 | 97.9410 | 89.1008 | 2089 | 107 | 2093 | 44 | 9 | 20.4545 | |
| astatham-gatk | INDEL | * | map_l125_m2_e1 | * | 96.4891 | 95.0562 | 97.9658 | 89.1866 | 2115 | 110 | 2119 | 44 | 9 | 20.4545 | |
| astatham-gatk | INDEL | D1_5 | * | hetalt | 97.2343 | 95.0220 | 99.5520 | 63.2355 | 9735 | 510 | 9778 | 44 | 43 | 97.7273 | |
| astatham-gatk | INDEL | D1_5 | HG002complexvar | hetalt | 95.3253 | 93.9349 | 96.7576 | 72.9412 | 1270 | 82 | 1313 | 44 | 43 | 97.7273 | |
| anovak-vg | INDEL | C6_15 | * | * | 35.2941 | 100.0000 | 21.4286 | 89.7623 | 7 | 0 | 12 | 44 | 5 | 11.3636 | |
| anovak-vg | INDEL | C6_15 | * | het | 31.2500 | 100.0000 | 18.5185 | 88.2096 | 7 | 0 | 10 | 44 | 5 | 11.3636 | |
| anovak-vg | INDEL | D6_15 | map_l100_m1_e0 | * | 69.8276 | 62.7907 | 78.6408 | 85.3172 | 162 | 96 | 162 | 44 | 27 | 61.3636 | |
| anovak-vg | INDEL | D6_15 | map_l100_m2_e0 | * | 69.8453 | 62.5000 | 79.1469 | 85.8199 | 165 | 99 | 167 | 44 | 27 | 61.3636 | |
| anovak-vg | INDEL | D6_15 | map_l100_m2_e1 | * | 69.0673 | 61.0909 | 79.4393 | 85.8746 | 168 | 107 | 170 | 44 | 27 | 61.3636 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 34.8293 | 37.7778 | 32.3077 | 48.0000 | 17 | 28 | 21 | 44 | 33 | 75.0000 | |
| bgallagher-sentieon | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.9298 | 94.4344 | 99.5608 | 32.7290 | 9892 | 583 | 9974 | 44 | 44 | 100.0000 | |
| bgallagher-sentieon | INDEL | * | map_l125_m2_e0 | * | 98.3684 | 98.7250 | 98.0144 | 88.4715 | 2168 | 28 | 2172 | 44 | 9 | 20.4545 | |
| bgallagher-sentieon | INDEL | * | map_l125_m2_e1 | * | 98.3668 | 98.6966 | 98.0392 | 88.5574 | 2196 | 29 | 2200 | 44 | 9 | 20.4545 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.7159 | 97.8795 | 97.5528 | 69.2597 | 1754 | 38 | 1754 | 44 | 33 | 75.0000 | |
| asubramanian-gatk | INDEL | D1_5 | map_l100_m0_e0 | * | 92.4081 | 90.2665 | 94.6537 | 88.7322 | 779 | 84 | 779 | 44 | 5 | 11.3636 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.8231 | 97.4321 | 98.2172 | 67.5349 | 1328 | 35 | 2424 | 44 | 40 | 90.9091 | |
| asubramanian-gatk | SNP | * | map_l100_m1_e0 | het | 63.0315 | 46.0636 | 99.7898 | 86.5707 | 20894 | 24465 | 20888 | 44 | 12 | 27.2727 | |
| bgallagher-sentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 99.4119 | 99.4624 | 99.3614 | 80.8398 | 6846 | 37 | 6846 | 44 | 11 | 25.0000 | |
| bgallagher-sentieon | INDEL | I6_15 | HG002complexvar | homalt | 98.2186 | 99.9176 | 96.5764 | 55.7279 | 1213 | 1 | 1213 | 43 | 43 | 100.0000 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.0609 | 95.3297 | 98.8561 | 56.5082 | 3715 | 182 | 3716 | 43 | 36 | 83.7209 | |
| astatham-gatk | SNP | ti | * | homalt | 99.9764 | 99.9582 | 99.9946 | 15.8604 | 802702 | 336 | 802693 | 43 | 41 | 95.3488 | |
| astatham-gatk | SNP | ti | HG002complexvar | het | 98.7599 | 97.5636 | 99.9860 | 17.3084 | 307097 | 7669 | 307042 | 43 | 17 | 39.5349 | |
| asubramanian-gatk | INDEL | * | map_l150_m0_e0 | * | 90.5945 | 89.6887 | 91.5187 | 98.1956 | 461 | 53 | 464 | 43 | 3 | 6.9767 | |
| asubramanian-gatk | INDEL | D16_PLUS | HG002complexvar | * | 96.5513 | 95.8004 | 97.3142 | 67.2463 | 1574 | 69 | 1558 | 43 | 31 | 72.0930 | |
| anovak-vg | INDEL | I6_15 | map_l100_m2_e0 | * | 53.4759 | 49.1379 | 58.6538 | 81.9130 | 57 | 59 | 61 | 43 | 25 | 58.1395 | |
| anovak-vg | INDEL | I6_15 | segdup | homalt | 59.8909 | 80.8511 | 47.5610 | 87.6506 | 38 | 9 | 39 | 43 | 42 | 97.6744 | |
| anovak-vg | SNP | tv | map_l125_m2_e0 | homalt | 89.0712 | 80.8709 | 99.1223 | 69.1421 | 4866 | 1151 | 4856 | 43 | 32 | 74.4186 | |
| anovak-vg | SNP | tv | map_l125_m2_e1 | homalt | 89.1235 | 80.9516 | 99.1306 | 69.1627 | 4917 | 1157 | 4903 | 43 | 32 | 74.4186 | |
| asubramanian-gatk | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.2719 | 98.8007 | 99.7476 | 56.4979 | 16971 | 206 | 16992 | 43 | 6 | 13.9535 | |
| asubramanian-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 99.0897 | 98.8283 | 99.3524 | 77.3626 | 6579 | 78 | 6597 | 43 | 9 | 20.9302 | |
| bgallagher-sentieon | INDEL | D1_5 | * | hetalt | 96.6974 | 93.9971 | 99.5574 | 61.8361 | 9630 | 615 | 9672 | 43 | 42 | 97.6744 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.9326 | 97.1076 | 98.7718 | 67.6791 | 3458 | 103 | 3458 | 43 | 30 | 69.7674 | |
| hfeng-pmm1 | INDEL | D6_15 | * | homalt | 99.4474 | 99.5732 | 99.3220 | 50.6075 | 6299 | 27 | 6299 | 43 | 42 | 97.6744 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.1261 | 99.3893 | 98.8642 | 54.0422 | 3743 | 23 | 3743 | 43 | 42 | 97.6744 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.1261 | 99.3893 | 98.8642 | 54.0422 | 3743 | 23 | 3743 | 43 | 42 | 97.6744 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.2713 | 95.1718 | 99.4655 | 60.8421 | 8003 | 406 | 8002 | 43 | 27 | 62.7907 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.8197 | 99.8356 | 99.8037 | 72.1124 | 21863 | 36 | 21863 | 43 | 42 | 97.6744 | |
| hfeng-pmm1 | SNP | tv | map_l125_m1_e0 | het | 99.2869 | 99.0026 | 99.5728 | 70.2971 | 10025 | 101 | 10023 | 43 | 11 | 25.5814 | |
| hfeng-pmm1 | SNP | tv | map_l125_m2_e0 | het | 99.3085 | 99.0328 | 99.5858 | 71.6339 | 10341 | 101 | 10339 | 43 | 11 | 25.5814 | |
| hfeng-pmm1 | SNP | tv | map_l125_m2_e1 | het | 99.3110 | 99.0335 | 99.5902 | 71.6922 | 10451 | 102 | 10449 | 43 | 11 | 25.5814 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.7461 | 88.4908 | 97.4313 | 66.6799 | 1630 | 212 | 1631 | 43 | 33 | 76.7442 | |
| jlack-gatk | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.4314 | 99.5510 | 99.3121 | 70.6126 | 6208 | 28 | 6208 | 43 | 21 | 48.8372 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.7497 | 95.9658 | 99.6012 | 27.0945 | 10657 | 448 | 10739 | 43 | 42 | 97.6744 | |
| jlack-gatk | INDEL | D1_5 | HG002compoundhet | hetalt | 95.0540 | 90.9554 | 99.5394 | 57.6003 | 9292 | 924 | 9293 | 43 | 40 | 93.0233 | |