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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
61951-62000 / 86044 show all | |||||||||||||||
| hfeng-pmm2 | INDEL | * | map_l250_m2_e1 | * | 96.0118 | 97.5976 | 94.4767 | 96.0984 | 325 | 8 | 325 | 19 | 4 | 21.0526 | |
| hfeng-pmm2 | INDEL | * | segdup | * | 99.0994 | 98.9828 | 99.2163 | 94.4475 | 2530 | 26 | 2532 | 20 | 4 | 20.0000 | |
| hfeng-pmm2 | INDEL | * | segdup | homalt | 99.6360 | 99.7917 | 99.4808 | 93.2596 | 958 | 2 | 958 | 5 | 4 | 80.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.8636 | 99.8363 | 99.8908 | 48.6619 | 3660 | 6 | 3660 | 4 | 4 | 100.0000 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 90.1961 | 100.0000 | 82.1429 | 87.8261 | 23 | 0 | 23 | 5 | 4 | 80.0000 | |
| 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 | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 96.0630 | 100.0000 | 92.4242 | 90.7950 | 61 | 0 | 61 | 5 | 4 | 80.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.1550 | 96.9500 | 99.3902 | 75.7157 | 1494 | 47 | 1467 | 9 | 4 | 44.4444 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 88.0000 | 91.6667 | 84.6154 | 79.0323 | 22 | 2 | 22 | 4 | 4 | 100.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.7137 | 96.5174 | 98.9399 | 71.3273 | 582 | 21 | 560 | 6 | 4 | 66.6667 | |
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 94.5603 | 90.2098 | 99.3517 | 87.1432 | 2451 | 266 | 2452 | 16 | 4 | 25.0000 | |
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 91.9578 | 85.8844 | 98.9556 | 88.3338 | 1515 | 249 | 1516 | 16 | 4 | 25.0000 | |
| 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 | |
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 92.3785 | 86.4597 | 99.1673 | 87.8741 | 1309 | 205 | 1310 | 11 | 4 | 36.3636 | |
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.3756 | 97.0003 | 99.7905 | 79.9603 | 10477 | 324 | 10478 | 22 | 4 | 18.1818 | |
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.5896 | 95.5833 | 99.6819 | 79.9854 | 6579 | 304 | 6580 | 21 | 4 | 19.0476 | |
| hfeng-pmm3 | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.8414 | 95.9429 | 99.8165 | 68.2488 | 5983 | 253 | 5983 | 11 | 4 | 36.3636 | |
| hfeng-pmm3 | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.1505 | 98.3978 | 99.9147 | 54.8907 | 17565 | 286 | 17565 | 15 | 4 | 26.6667 | |
| hfeng-pmm3 | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.6122 | 99.3198 | 99.9063 | 37.9962 | 10659 | 73 | 10659 | 10 | 4 | 40.0000 | |
| hfeng-pmm3 | SNP | ti | map_l150_m0_e0 | homalt | 99.6199 | 99.6740 | 99.5658 | 75.7331 | 2752 | 9 | 2752 | 12 | 4 | 33.3333 | |
| hfeng-pmm3 | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.2263 | 98.5599 | 99.9019 | 64.0348 | 17315 | 253 | 17306 | 17 | 4 | 23.5294 | |
| hfeng-pmm3 | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.9108 | 99.8613 | 99.9603 | 61.0721 | 10083 | 14 | 10083 | 4 | 4 | 100.0000 | |
| hfeng-pmm3 | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.1238 | 96.5350 | 99.7657 | 66.1570 | 2981 | 107 | 2981 | 7 | 4 | 57.1429 | |
| hfeng-pmm3 | SNP | tv | map_l100_m0_e0 | het | 99.3072 | 99.2523 | 99.3623 | 70.7621 | 7168 | 54 | 7167 | 46 | 4 | 8.6957 | |
| hfeng-pmm3 | SNP | tv | map_l100_m0_e0 | homalt | 99.6488 | 99.6100 | 99.6877 | 65.3002 | 3831 | 15 | 3831 | 12 | 4 | 33.3333 | |
| hfeng-pmm1 | INDEL | * | map_l150_m2_e1 | * | 97.5801 | 96.5949 | 98.5856 | 88.8230 | 1390 | 49 | 1394 | 20 | 4 | 20.0000 | |
| hfeng-pmm1 | INDEL | * | segdup | * | 99.0215 | 98.9437 | 99.0995 | 94.0294 | 2529 | 27 | 2531 | 23 | 4 | 17.3913 | |
| hfeng-pmm1 | INDEL | * | segdup | homalt | 99.6878 | 99.7917 | 99.5842 | 93.1783 | 958 | 2 | 958 | 4 | 4 | 100.0000 | |
| hfeng-pmm1 | INDEL | D16_PLUS | * | homalt | 99.2597 | 99.0544 | 99.4659 | 65.7799 | 1676 | 16 | 1676 | 9 | 4 | 44.4444 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 98.0433 | 97.5410 | 98.5507 | 69.5460 | 476 | 12 | 476 | 7 | 4 | 57.1429 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.0369 | 98.7990 | 99.2759 | 70.2133 | 1234 | 15 | 1234 | 9 | 4 | 44.4444 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.0336 | 98.8971 | 99.1705 | 63.1579 | 1076 | 12 | 1076 | 9 | 4 | 44.4444 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.0369 | 98.7990 | 99.2759 | 70.2133 | 1234 | 15 | 1234 | 9 | 4 | 44.4444 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 80.8789 | 71.8519 | 92.5000 | 74.9216 | 97 | 38 | 74 | 6 | 4 | 66.6667 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.8909 | 99.8909 | 99.8909 | 48.7917 | 3662 | 4 | 3662 | 4 | 4 | 100.0000 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 96.5336 | 94.5455 | 98.6072 | 76.2252 | 364 | 21 | 354 | 5 | 4 | 80.0000 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.9744 | 98.1557 | 99.8069 | 48.5309 | 3619 | 68 | 3619 | 7 | 4 | 57.1429 | |
| hfeng-pmm1 | INDEL | I16_PLUS | * | het | 98.4241 | 97.9397 | 98.9135 | 73.5192 | 2662 | 56 | 2640 | 29 | 4 | 13.7931 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 90.1961 | 100.0000 | 82.1429 | 88.0342 | 23 | 0 | 23 | 5 | 4 | 80.0000 | |
| 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-pmm1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 96.0630 | 100.0000 | 92.4242 | 91.1409 | 61 | 0 | 61 | 5 | 4 | 80.0000 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.9000 | 98.3483 | 99.4578 | 70.4170 | 1310 | 22 | 1284 | 7 | 4 | 57.1429 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.8185 | 95.8304 | 99.8909 | 57.5027 | 5493 | 239 | 5494 | 6 | 4 | 66.6667 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.5579 | 99.8227 | 99.2945 | 72.0827 | 563 | 1 | 563 | 4 | 4 | 100.0000 | |
| jlack-gatk | INDEL | I1_5 | HG002complexvar | hetalt | 96.7853 | 94.0324 | 99.7041 | 70.7004 | 1623 | 103 | 1685 | 5 | 4 | 80.0000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 94.8351 | 90.2733 | 99.8824 | 28.4609 | 4195 | 452 | 4248 | 5 | 4 | 80.0000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 94.8267 | 90.2557 | 99.8855 | 32.3046 | 4307 | 465 | 4360 | 5 | 4 | 80.0000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.7938 | 100.0000 | 99.5885 | 64.0133 | 968 | 0 | 968 | 4 | 4 | 100.0000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.9127 | 98.8843 | 98.9412 | 74.7999 | 1684 | 19 | 1682 | 18 | 4 | 22.2222 | |
| jlack-gatk | INDEL | I1_5 | map_l100_m2_e0 | het | 95.4195 | 98.1084 | 92.8741 | 89.6484 | 778 | 15 | 782 | 60 | 4 | 6.6667 | |