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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
30601-30650 / 86044 show all | |||||||||||||||
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.8506 | 100.0000 | 97.7273 | 77.7778 | 43 | 0 | 43 | 1 | 1 | 100.0000 | |
| ckim-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 96.1978 | 94.7154 | 97.7273 | 88.5833 | 233 | 13 | 215 | 5 | 3 | 60.0000 | |
| gduggal-snapvard | INDEL | * | map_l250_m1_e0 | homalt | 92.6495 | 88.0734 | 97.7273 | 92.8026 | 96 | 13 | 129 | 3 | 2 | 66.6667 | |
| ghariani-varprowl | SNP | * | map_l100_m1_e0 | * | 98.3728 | 99.0277 | 97.7266 | 70.1377 | 71699 | 704 | 71702 | 1668 | 318 | 19.0647 | |
| ckim-dragen | SNP | tv | map_l125_m1_e0 | * | 98.3749 | 99.0322 | 97.7263 | 73.5955 | 15861 | 155 | 15860 | 369 | 38 | 10.2981 | |
| eyeh-varpipe | INDEL | D1_5 | segdup | * | 97.2740 | 96.8268 | 97.7253 | 93.8542 | 1068 | 35 | 1117 | 26 | 21 | 80.7692 | |
| ckim-vqsr | SNP | * | map_l250_m2_e1 | het | 69.4427 | 53.8564 | 97.7249 | 97.1454 | 2835 | 2429 | 2835 | 66 | 0 | 0.0000 | |
| rpoplin-dv42 | SNP | tv | map_l150_m0_e0 | het | 97.9824 | 98.2413 | 97.7249 | 78.7694 | 2793 | 50 | 2792 | 65 | 38 | 58.4615 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.0612 | 88.8224 | 97.7248 | 55.9006 | 890 | 112 | 902 | 21 | 19 | 90.4762 | |
| jpowers-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 98.8493 | 100.0000 | 97.7247 | 57.8619 | 858 | 0 | 859 | 20 | 12 | 60.0000 | |
| ckim-dragen | SNP | ti | map_l125_m2_e1 | * | 98.4185 | 99.1233 | 97.7236 | 74.4858 | 30301 | 268 | 30308 | 706 | 81 | 11.4731 | |
| gduggal-snapfb | SNP | ti | map_siren | het | 98.2591 | 98.8009 | 97.7232 | 58.6413 | 61634 | 748 | 61636 | 1436 | 494 | 34.4011 | |
| raldana-dualsentieon | INDEL | I1_5 | map_l150_m2_e1 | * | 97.1634 | 96.6102 | 97.7230 | 88.7825 | 513 | 18 | 515 | 12 | 1 | 8.3333 | |
| mlin-fermikit | SNP | * | map_l250_m2_e0 | het | 43.6369 | 28.0901 | 97.7227 | 83.2153 | 1459 | 3735 | 1459 | 34 | 1 | 2.9412 | |
| raldana-dualsentieon | INDEL | D1_5 | map_l150_m1_e0 | het | 97.6164 | 97.5104 | 97.7226 | 86.9141 | 470 | 12 | 472 | 11 | 2 | 18.1818 | |
| gduggal-snapplat | INDEL | D6_15 | HG002compoundhet | hetalt | 51.7417 | 35.1859 | 97.7226 | 44.3646 | 2868 | 5283 | 2875 | 67 | 52 | 77.6119 | |
| ckim-dragen | SNP | * | map_l125_m1_e0 | * | 98.3997 | 99.0866 | 97.7222 | 72.8507 | 44913 | 414 | 44919 | 1047 | 117 | 11.1748 | |
| ciseli-custom | SNP | ti | * | * | 98.3062 | 98.8974 | 97.7221 | 19.7040 | 2062524 | 22994 | 2057571 | 47963 | 7893 | 16.4564 | |
| ckim-isaac | INDEL | D1_5 | map_l100_m0_e0 | het | 83.0777 | 72.2504 | 97.7221 | 87.1675 | 427 | 164 | 429 | 10 | 3 | 30.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.1693 | 98.6207 | 97.7221 | 69.8074 | 429 | 6 | 429 | 10 | 4 | 40.0000 | |
| ckim-dragen | SNP | ti | map_l125_m1_e0 | * | 98.4145 | 99.1171 | 97.7219 | 72.4285 | 29076 | 259 | 29083 | 678 | 79 | 11.6519 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 96.6785 | 95.6573 | 97.7218 | 80.9284 | 815 | 37 | 815 | 19 | 14 | 73.6842 | |
| egarrison-hhga | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 72.8990 | 58.1328 | 97.7209 | 46.5971 | 2223 | 1601 | 2101 | 49 | 43 | 87.7551 | |
| ghariani-varprowl | SNP | ti | map_l125_m1_e0 | * | 98.1866 | 98.6569 | 97.7208 | 74.6512 | 28941 | 394 | 28941 | 675 | 158 | 23.4074 | |
| ckim-vqsr | INDEL | * | map_l100_m1_e0 | * | 97.1981 | 96.6815 | 97.7202 | 88.7691 | 3467 | 119 | 3472 | 81 | 16 | 19.7531 | |
| ghariani-varprowl | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | * | 98.6463 | 99.5904 | 97.7199 | 44.7612 | 3890 | 16 | 3900 | 91 | 9 | 9.8901 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 86.9605 | 78.3357 | 97.7193 | 42.0142 | 546 | 151 | 557 | 13 | 12 | 92.3077 | |
| eyeh-varpipe | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | het | 98.7872 | 99.8789 | 97.7191 | 41.8567 | 2475 | 3 | 2442 | 57 | 4 | 7.0175 | |
| gduggal-bwafb | SNP | ti | segdup | het | 98.5285 | 99.3516 | 97.7189 | 92.3400 | 11952 | 78 | 11952 | 279 | 6 | 2.1505 | |
| gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 97.7933 | 97.8680 | 97.7188 | 57.0996 | 2387 | 52 | 2356 | 55 | 6 | 10.9091 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.5115 | 99.3179 | 97.7181 | 73.3548 | 728 | 5 | 728 | 17 | 13 | 76.4706 | |
| astatham-gatk | INDEL | D1_5 | map_l100_m2_e1 | het | 95.9899 | 94.3218 | 97.7180 | 85.7871 | 1196 | 72 | 1199 | 28 | 4 | 14.2857 | |
| eyeh-varpipe | INDEL | D1_5 | map_l125_m2_e0 | homalt | 98.0337 | 98.3516 | 97.7178 | 87.9259 | 358 | 6 | 471 | 11 | 10 | 90.9091 | |
| dgrover-gatk | INDEL | D16_PLUS | * | * | 97.8781 | 98.0395 | 97.7172 | 70.6733 | 6651 | 133 | 6635 | 155 | 103 | 66.4516 | |
| jli-custom | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 95.1490 | 92.7126 | 97.7169 | 78.3168 | 229 | 18 | 214 | 5 | 2 | 40.0000 | |
| ckim-dragen | SNP | ti | map_l125_m2_e0 | * | 98.4121 | 99.1176 | 97.7165 | 74.4145 | 29991 | 267 | 29998 | 701 | 81 | 11.5549 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 85.2919 | 75.6705 | 97.7165 | 64.9393 | 8690 | 2794 | 8687 | 203 | 174 | 85.7143 | |
| gduggal-bwavard | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.5998 | 97.4834 | 97.7164 | 62.9555 | 54231 | 1400 | 53617 | 1253 | 392 | 31.2849 | |
| ghariani-varprowl | SNP | ti | map_l125_m2_e0 | * | 98.2029 | 98.6946 | 97.7160 | 76.3322 | 29863 | 395 | 29863 | 698 | 158 | 22.6361 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.7335 | 99.7729 | 97.7156 | 45.5716 | 8347 | 19 | 8341 | 195 | 193 | 98.9744 | |
| jlack-gatk | INDEL | D6_15 | HG002complexvar | * | 97.2520 | 96.7937 | 97.7147 | 58.0825 | 5132 | 170 | 5131 | 120 | 96 | 80.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | map_l125_m0_e0 | het | 98.2742 | 98.8406 | 97.7143 | 86.4341 | 341 | 4 | 342 | 8 | 1 | 12.5000 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.5591 | 99.4186 | 97.7143 | 81.1422 | 171 | 1 | 171 | 4 | 1 | 25.0000 | |
| ndellapenna-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 95.6376 | 93.6473 | 97.7143 | 85.3434 | 855 | 58 | 855 | 20 | 10 | 50.0000 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.5591 | 99.4186 | 97.7143 | 81.0401 | 171 | 1 | 171 | 4 | 1 | 25.0000 | |
| ndellapenna-hhga | INDEL | I6_15 | * | * | 96.5902 | 95.4921 | 97.7138 | 48.4477 | 23704 | 1119 | 23721 | 555 | 427 | 76.9369 | |
| ciseli-custom | SNP | ti | func_cds | het | 98.4573 | 99.2121 | 97.7138 | 25.9135 | 8437 | 67 | 8420 | 197 | 2 | 1.0152 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 83.7908 | 73.3408 | 97.7136 | 42.2636 | 5216 | 1896 | 5214 | 122 | 120 | 98.3607 | |
| mlin-fermikit | SNP | ti | map_l250_m1_e0 | het | 42.7481 | 27.3585 | 97.7136 | 79.5371 | 812 | 2156 | 812 | 19 | 1 | 5.2632 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 73.6158 | 59.0525 | 97.7135 | 42.8517 | 1608 | 1115 | 1453 | 34 | 29 | 85.2941 | |