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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
1851-1900 / 86044 show all | |||||||||||||||
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 69.5027 | 72.7855 | 66.5031 | 38.8732 | 11471 | 4289 | 21148 | 10652 | 8272 | 77.6568 | |
| ghariani-varprowl | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 70.0058 | 58.6077 | 86.9078 | 48.1851 | 6070 | 4287 | 6054 | 912 | 765 | 83.8816 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 94.3555 | 90.6219 | 98.4100 | 63.4241 | 41416 | 4286 | 41653 | 673 | 294 | 43.6850 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 94.3555 | 90.6219 | 98.4100 | 63.4241 | 41416 | 4286 | 41653 | 673 | 294 | 43.6850 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 86.8726 | 86.3602 | 87.3912 | 57.0498 | 27124 | 4284 | 27204 | 3925 | 3577 | 91.1338 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 86.8726 | 86.3602 | 87.3912 | 57.0498 | 27124 | 4284 | 27204 | 3925 | 3577 | 91.1338 | |
| raldana-dualsentieon | INDEL | * | * | * | 99.1095 | 98.7566 | 99.4648 | 57.7282 | 340258 | 4284 | 340120 | 1830 | 1626 | 88.8525 | |
| jmaeng-gatk | SNP | tv | map_l125_m1_e0 | * | 83.4629 | 73.2830 | 96.9274 | 85.3732 | 11737 | 4279 | 11735 | 372 | 13 | 3.4946 | |
| jpowers-varprowl | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 70.1373 | 58.7236 | 87.0583 | 47.6620 | 6082 | 4275 | 6061 | 901 | 793 | 88.0133 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 86.7363 | 86.3984 | 87.0769 | 60.8804 | 27136 | 4272 | 28091 | 4169 | 1922 | 46.1022 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 86.7363 | 86.3984 | 87.0769 | 60.8804 | 27136 | 4272 | 28091 | 4169 | 1922 | 46.1022 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 78.7504 | 71.1059 | 88.2367 | 41.6720 | 10513 | 4272 | 11334 | 1511 | 1493 | 98.8087 | |
| anovak-vg | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 47.1342 | 38.1966 | 61.5321 | 37.8247 | 2639 | 4270 | 5213 | 3259 | 2660 | 81.6201 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 59.9212 | 54.8636 | 66.0058 | 31.4666 | 5189 | 4269 | 5194 | 2675 | 2487 | 92.9720 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 83.7356 | 73.4530 | 97.3658 | 70.5818 | 11787 | 4260 | 11791 | 319 | 236 | 73.9812 | |
| ndellapenna-hhga | INDEL | D6_15 | HG002compoundhet | * | 61.2798 | 52.8513 | 72.9065 | 39.3574 | 4773 | 4258 | 4954 | 1841 | 1725 | 93.6991 | |
| gduggal-bwaplat | SNP | ti | map_l150_m1_e0 | homalt | 59.0384 | 41.8998 | 99.9022 | 84.1026 | 3070 | 4257 | 3066 | 3 | 3 | 100.0000 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 28.4562 | 16.8067 | 92.7350 | 41.3166 | 860 | 4257 | 868 | 68 | 64 | 94.1176 | |
| ckim-vqsr | SNP | * | map_l250_m1_e0 | * | 57.9563 | 41.1520 | 97.9565 | 97.0469 | 2972 | 4250 | 2972 | 62 | 0 | 0.0000 | |
| gduggal-bwafb | INDEL | * | HG002complexvar | * | 96.4189 | 94.4813 | 98.4377 | 54.9407 | 72692 | 4246 | 74289 | 1179 | 1015 | 86.0899 | |
| gduggal-snapfb | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 82.7904 | 78.6275 | 87.4187 | 53.2630 | 15617 | 4245 | 16259 | 2340 | 997 | 42.6068 | |
| eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 89.1102 | 86.0761 | 92.3660 | 60.6253 | 26236 | 4244 | 33152 | 2740 | 2400 | 87.5912 | |
| eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 89.1102 | 86.0761 | 92.3660 | 60.6253 | 26236 | 4244 | 33152 | 2740 | 2400 | 87.5912 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 54.5918 | 37.8497 | 97.8929 | 39.6624 | 2584 | 4243 | 2834 | 61 | 58 | 95.0820 | |
| astatham-gatk | SNP | * | map_l100_m0_e0 | het | 88.7308 | 80.0000 | 99.6007 | 77.5238 | 16964 | 4241 | 16960 | 68 | 23 | 33.8235 | |
| ckim-vqsr | SNP | tv | map_l125_m1_e0 | homalt | 43.3097 | 27.6451 | 99.9383 | 87.2272 | 1620 | 4240 | 1620 | 1 | 0 | 0.0000 | |
| ciseli-custom | SNP | tv | map_l125_m2_e1 | * | 79.4183 | 74.5632 | 84.9497 | 78.4301 | 12420 | 4237 | 12412 | 2199 | 540 | 24.5566 | |
| ciseli-custom | SNP | * | map_l125_m0_e0 | het | 73.0283 | 66.5824 | 80.8560 | 84.3182 | 8432 | 4232 | 8426 | 1995 | 66 | 3.3083 | |
| ciseli-custom | INDEL | D1_5 | HG002complexvar | * | 84.6887 | 87.0694 | 82.4348 | 57.7103 | 28483 | 4230 | 28182 | 6005 | 2638 | 43.9301 | |
| ckim-isaac | SNP | tv | map_l125_m2_e1 | het | 74.8404 | 59.9545 | 99.5595 | 75.8491 | 6327 | 4226 | 6329 | 28 | 7 | 25.0000 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 42.0732 | 33.1541 | 57.5573 | 69.3357 | 2096 | 4226 | 2083 | 1536 | 1445 | 94.0755 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 42.0732 | 33.1541 | 57.5573 | 69.3357 | 2096 | 4226 | 2083 | 1536 | 1445 | 94.0755 | |
| gduggal-bwafb | SNP | * | * | * | 99.7820 | 99.8619 | 99.7021 | 21.9848 | 3050417 | 4217 | 3050656 | 9115 | 775 | 8.5025 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 31.6043 | 34.3302 | 29.2795 | 88.3797 | 2204 | 4216 | 2292 | 5536 | 84 | 1.5173 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 31.6043 | 34.3302 | 29.2795 | 88.3797 | 2204 | 4216 | 2292 | 5536 | 84 | 1.5173 | |
| egarrison-hhga | INDEL | D6_15 | * | hetalt | 65.0139 | 48.4952 | 98.5994 | 42.7885 | 3964 | 4210 | 3520 | 50 | 43 | 86.0000 | |
| ciseli-custom | SNP | tv | map_l125_m2_e0 | * | 79.3554 | 74.4800 | 84.9139 | 78.4079 | 12281 | 4208 | 12276 | 2181 | 537 | 24.6217 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 64.3918 | 47.8099 | 98.5834 | 40.4750 | 3853 | 4206 | 3410 | 49 | 42 | 85.7143 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 64.3918 | 47.8099 | 98.5834 | 40.4750 | 3853 | 4206 | 3410 | 49 | 42 | 85.7143 | |
| mlin-fermikit | INDEL | * | HG002complexvar | * | 95.4305 | 94.5346 | 96.3436 | 54.3245 | 72733 | 4205 | 72356 | 2746 | 2618 | 95.3387 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 76.3332 | 62.1432 | 98.9213 | 34.8317 | 6901 | 4204 | 6511 | 71 | 64 | 90.1408 | |
| astatham-gatk | SNP | tv | HG002complexvar | het | 98.5778 | 97.2116 | 99.9829 | 21.9634 | 146528 | 4203 | 146456 | 25 | 11 | 44.0000 | |
| egarrison-hhga | INDEL | D6_15 | HG002compoundhet | hetalt | 65.0591 | 48.4726 | 98.9014 | 28.1522 | 3951 | 4200 | 3511 | 39 | 34 | 87.1795 | |
| mlin-fermikit | SNP | tv | * | homalt | 98.8702 | 98.8876 | 98.8528 | 20.1908 | 372928 | 4195 | 372923 | 4328 | 4101 | 94.7551 | |
| ckim-isaac | SNP | tv | map_l125_m2_e0 | het | 74.7458 | 59.8353 | 99.5540 | 75.8427 | 6248 | 4194 | 6250 | 28 | 7 | 25.0000 | |
| qzeng-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 89.6438 | 88.9452 | 90.3535 | 42.9428 | 33712 | 4190 | 54335 | 5801 | 4069 | 70.1431 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 40.9601 | 29.3830 | 67.5918 | 54.6739 | 1743 | 4189 | 1583 | 759 | 616 | 81.1594 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 85.9444 | 77.0743 | 97.1216 | 57.5074 | 14073 | 4186 | 14070 | 417 | 292 | 70.0240 | |
| ckim-vqsr | SNP | tv | map_l100_m2_e1 | het | 84.3869 | 73.7420 | 98.6235 | 86.5752 | 11753 | 4185 | 11750 | 164 | 1 | 0.6098 | |
| asubramanian-gatk | SNP | * | map_l250_m2_e1 | het | 34.0104 | 20.5167 | 99.3560 | 98.5506 | 1080 | 4184 | 1080 | 7 | 1 | 14.2857 | |