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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
33001-33050 / 86044 show all | |||||||||||||||
| gduggal-bwavard | INDEL | D1_5 | map_l125_m1_e0 | het | 91.0091 | 98.8981 | 84.2857 | 90.2155 | 718 | 8 | 708 | 132 | 17 | 12.8788 | |
| jlack-gatk | INDEL | * | HG002compoundhet | * | 91.0082 | 90.7410 | 91.2769 | 62.3551 | 27186 | 2774 | 27070 | 2587 | 2465 | 95.2841 | |
| gduggal-bwafb | INDEL | I1_5 | HG002compoundhet | hetalt | 91.0057 | 84.5844 | 98.4821 | 73.0807 | 9454 | 1723 | 4282 | 66 | 66 | 100.0000 | |
| qzeng-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 90.9981 | 84.0955 | 99.1351 | 58.5016 | 12965 | 2452 | 4585 | 40 | 31 | 77.5000 | |
| ciseli-custom | SNP | ti | map_l100_m1_e0 | homalt | 90.9965 | 90.6459 | 91.3498 | 59.1340 | 16280 | 1680 | 16242 | 1538 | 1227 | 79.7789 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 90.9953 | 85.7143 | 96.9697 | 69.4444 | 30 | 5 | 32 | 1 | 1 | 100.0000 | |
| ckim-vqsr | INDEL | * | map_l250_m2_e0 | het | 90.9931 | 93.8095 | 88.3408 | 97.8444 | 197 | 13 | 197 | 26 | 1 | 3.8462 | |
| gduggal-snapvard | SNP | ti | map_l125_m0_e0 | * | 90.9915 | 95.2045 | 87.1355 | 81.6073 | 12150 | 612 | 12043 | 1778 | 144 | 8.0990 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 90.9909 | 83.7736 | 99.5690 | 47.3923 | 444 | 86 | 462 | 2 | 1 | 50.0000 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 90.9907 | 84.0382 | 99.1974 | 59.7025 | 616 | 117 | 618 | 5 | 2 | 40.0000 | |
| gduggal-snapvard | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 90.9891 | 97.2501 | 85.4856 | 71.8215 | 34445 | 974 | 34119 | 5793 | 280 | 4.8334 | |
| ghariani-varprowl | INDEL | I1_5 | map_l250_m2_e0 | * | 90.9871 | 93.8053 | 88.3333 | 97.2515 | 106 | 7 | 106 | 14 | 4 | 28.5714 | |
| ltrigg-rtg1 | INDEL | * | map_l100_m2_e1 | hetalt | 90.9869 | 84.0909 | 99.1150 | 91.3476 | 111 | 21 | 112 | 1 | 1 | 100.0000 | |
| gduggal-bwafb | INDEL | D6_15 | * | hetalt | 90.9853 | 84.6464 | 98.3504 | 52.1249 | 6919 | 1255 | 1252 | 21 | 21 | 100.0000 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 90.9774 | 95.2756 | 87.0504 | 53.0405 | 121 | 6 | 121 | 18 | 15 | 83.3333 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 90.9744 | 92.2581 | 89.7260 | 80.4813 | 143 | 12 | 131 | 15 | 3 | 20.0000 | |
| gduggal-bwavard | INDEL | * | map_siren | het | 90.9729 | 98.0035 | 84.8835 | 87.6032 | 4418 | 90 | 4408 | 785 | 417 | 53.1210 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 90.9728 | 84.5626 | 98.4344 | 65.7965 | 493 | 90 | 503 | 8 | 8 | 100.0000 | |
| hfeng-pmm3 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 90.9674 | 84.0188 | 99.1690 | 88.3848 | 715 | 136 | 716 | 6 | 1 | 16.6667 | |
| qzeng-custom | INDEL | * | map_siren | homalt | 90.9652 | 86.4030 | 96.0361 | 77.3592 | 2294 | 361 | 2447 | 101 | 23 | 22.7723 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 90.9626 | 99.2511 | 83.9517 | 58.3543 | 2783 | 21 | 2783 | 532 | 532 | 100.0000 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 90.9582 | 83.4711 | 99.9208 | 44.6727 | 808 | 160 | 10092 | 8 | 8 | 100.0000 | |
| jpowers-varprowl | SNP | ti | map_l250_m0_e0 | het | 90.9574 | 91.5418 | 90.3805 | 95.3348 | 855 | 79 | 855 | 91 | 17 | 18.6813 | |
| gduggal-snapvard | INDEL | D1_5 | segdup | homalt | 90.9566 | 86.6295 | 95.7386 | 91.9173 | 311 | 48 | 337 | 15 | 15 | 100.0000 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 90.9557 | 84.7716 | 98.1132 | 33.9074 | 1002 | 180 | 1092 | 21 | 18 | 85.7143 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 90.9511 | 85.8736 | 96.6667 | 77.4436 | 231 | 38 | 232 | 8 | 5 | 62.5000 | |
| hfeng-pmm3 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 90.9506 | 83.7500 | 99.5058 | 87.7720 | 603 | 117 | 604 | 3 | 1 | 33.3333 | |
| ltrigg-rtg2 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 90.9497 | 87.9032 | 94.2149 | 86.1556 | 109 | 15 | 114 | 7 | 0 | 0.0000 | |
| gduggal-snapplat | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | het | 90.9492 | 84.7458 | 98.1326 | 57.0052 | 2100 | 378 | 2102 | 40 | 4 | 10.0000 | |
| gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 90.9430 | 86.9565 | 95.3125 | 86.7495 | 60 | 9 | 61 | 3 | 2 | 66.6667 | |
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 90.9395 | 84.4821 | 98.4657 | 87.4931 | 38610 | 7092 | 38635 | 602 | 167 | 27.7409 | |
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 90.9395 | 84.4821 | 98.4657 | 87.4931 | 38610 | 7092 | 38635 | 602 | 167 | 27.7409 | |
| asubramanian-gatk | INDEL | D16_PLUS | map_siren | het | 90.9390 | 92.3077 | 89.6104 | 96.4236 | 72 | 6 | 69 | 8 | 1 | 12.5000 | |
| ckim-isaac | INDEL | D6_15 | HG002compoundhet | hetalt | 90.9387 | 83.9774 | 99.1585 | 17.7185 | 6845 | 1306 | 7188 | 61 | 50 | 81.9672 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 90.9278 | 97.6646 | 85.0604 | 50.5657 | 4642 | 111 | 4646 | 816 | 787 | 96.4461 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 90.9276 | 91.7603 | 90.1099 | 64.2202 | 245 | 22 | 246 | 27 | 5 | 18.5185 | |
| rpoplin-dv42 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 90.9269 | 85.8170 | 96.6839 | 77.1395 | 1313 | 217 | 1312 | 45 | 41 | 91.1111 | |
| rpoplin-dv42 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 90.9269 | 85.8170 | 96.6839 | 77.1395 | 1313 | 217 | 1312 | 45 | 41 | 91.1111 | |
| jli-custom | INDEL | D16_PLUS | map_l100_m2_e1 | het | 90.9254 | 90.1961 | 91.6667 | 94.4380 | 46 | 5 | 44 | 4 | 2 | 50.0000 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 90.9226 | 92.4365 | 89.4575 | 60.7169 | 1491 | 122 | 1451 | 171 | 123 | 71.9298 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | het | 90.9225 | 84.6154 | 98.2456 | 43.0000 | 11 | 2 | 56 | 1 | 0 | 0.0000 | |
| gduggal-bwavard | SNP | ti | map_l250_m1_e0 | * | 90.9201 | 97.4012 | 85.2478 | 91.8224 | 4460 | 119 | 4438 | 768 | 26 | 3.3854 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 90.9171 | 92.2101 | 89.6598 | 73.7675 | 28717 | 2426 | 29308 | 3380 | 1164 | 34.4379 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 90.9171 | 92.2101 | 89.6598 | 73.7675 | 28717 | 2426 | 29308 | 3380 | 1164 | 34.4379 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 90.9117 | 92.0249 | 89.8250 | 65.4470 | 5908 | 512 | 5853 | 663 | 643 | 96.9834 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 90.9117 | 92.0249 | 89.8250 | 65.4470 | 5908 | 512 | 5853 | 663 | 643 | 96.9834 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 90.9106 | 86.5682 | 95.7115 | 51.1635 | 5981 | 928 | 4419 | 198 | 174 | 87.8788 | |
| gduggal-bwafb | INDEL | D6_15 | func_cds | homalt | 90.9091 | 83.3333 | 100.0000 | 61.5385 | 10 | 2 | 10 | 0 | 0 | ||
| gduggal-bwafb | INDEL | D6_15 | map_l250_m2_e0 | homalt | 90.9091 | 83.3333 | 100.0000 | 97.7273 | 5 | 1 | 5 | 0 | 0 | ||
| gduggal-bwafb | INDEL | D6_15 | map_l250_m2_e1 | homalt | 90.9091 | 83.3333 | 100.0000 | 97.7679 | 5 | 1 | 5 | 0 | 0 | ||