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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
78601-78650 / 86044 show all | |||||||||||||||
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 95.9239 | 95.6260 | 96.2236 | 38.3297 | 3498 | 160 | 5784 | 227 | 218 | 96.0352 | |
| anovak-vg | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 59.4656 | 87.5000 | 45.0363 | 57.4665 | 175 | 25 | 186 | 227 | 205 | 90.3084 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.9104 | 91.7791 | 94.0700 | 54.4828 | 3606 | 323 | 3601 | 227 | 215 | 94.7137 | |
| ltrigg-rtg1 | SNP | * | HG002complexvar | het | 99.8148 | 99.6788 | 99.9511 | 18.4181 | 464005 | 1495 | 464235 | 227 | 59 | 25.9912 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.4981 | 97.9421 | 99.0604 | 41.3577 | 24035 | 505 | 24037 | 228 | 220 | 96.4912 | |
| jmaeng-gatk | INDEL | I1_5 | HG002compoundhet | homalt | 73.9819 | 99.3921 | 58.9189 | 89.0727 | 327 | 2 | 327 | 228 | 227 | 99.5614 | |
| mlin-fermikit | SNP | * | segdup | het | 97.6489 | 96.6622 | 98.6560 | 85.6660 | 16739 | 578 | 16736 | 228 | 1 | 0.4386 | |
| mlin-fermikit | INDEL | * | map_l100_m2_e1 | homalt | 77.2097 | 74.0827 | 80.6122 | 81.1659 | 949 | 332 | 948 | 228 | 200 | 87.7193 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 90.7728 | 88.5693 | 93.0888 | 46.5749 | 1170 | 151 | 3071 | 228 | 79 | 34.6491 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 95.3132 | 95.4134 | 95.2131 | 38.5261 | 4535 | 218 | 4535 | 228 | 107 | 46.9298 | |
| ndellapenna-hhga | INDEL | I1_5 | HG002complexvar | * | 98.8448 | 98.3844 | 99.3095 | 53.7677 | 32824 | 539 | 32792 | 228 | 116 | 50.8772 | |
| gduggal-snapplat | INDEL | I6_15 | HG002complexvar | homalt | 34.0455 | 24.6293 | 55.1181 | 60.1881 | 299 | 915 | 280 | 228 | 101 | 44.2982 | |
| gduggal-snapvard | INDEL | D1_5 | map_l150_m1_e0 | * | 86.5802 | 95.6764 | 79.0634 | 89.6914 | 686 | 31 | 861 | 228 | 53 | 23.2456 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.1133 | 95.7268 | 98.5406 | 67.8499 | 15390 | 687 | 15395 | 228 | 206 | 90.3509 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.1133 | 95.7268 | 98.5406 | 67.8499 | 15390 | 687 | 15395 | 228 | 206 | 90.3509 | |
| ciseli-custom | SNP | tv | lowcmp_SimpleRepeat_diTR_51to200 | * | 15.2009 | 76.9231 | 8.4337 | 82.7562 | 20 | 6 | 21 | 228 | 4 | 1.7544 | |
| ciseli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 21.2269 | 13.6601 | 47.5862 | 87.4784 | 209 | 1321 | 207 | 228 | 185 | 81.1404 | |
| ciseli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 21.2269 | 13.6601 | 47.5862 | 87.4784 | 209 | 1321 | 207 | 228 | 185 | 81.1404 | |
| astatham-gatk | INDEL | I1_5 | * | het | 99.5857 | 99.4610 | 99.7107 | 60.4880 | 78615 | 426 | 78596 | 228 | 141 | 61.8421 | |
| bgallagher-sentieon | SNP | ti | map_l125_m1_e0 | * | 99.3257 | 99.4273 | 99.2243 | 71.0550 | 29167 | 168 | 29163 | 228 | 42 | 18.4211 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 63.5445 | 60.9484 | 66.3717 | 63.9745 | 437 | 280 | 450 | 228 | 159 | 69.7368 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 12.5633 | 8.8953 | 21.3793 | 49.9136 | 62 | 635 | 62 | 228 | 224 | 98.2456 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 29.1765 | 45.9259 | 21.3793 | 49.5652 | 62 | 73 | 62 | 228 | 224 | 98.2456 | |
| gduggal-bwavard | SNP | * | segdup | * | 98.3638 | 97.5737 | 99.1668 | 93.3246 | 27386 | 681 | 27135 | 228 | 70 | 30.7018 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.3040 | 97.2229 | 99.4094 | 71.0102 | 32313 | 923 | 38374 | 228 | 113 | 49.5614 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 38.3227 | 27.8708 | 61.3176 | 55.5889 | 233 | 603 | 363 | 229 | 214 | 93.4498 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 86.3046 | 77.4770 | 97.4025 | 63.5175 | 8586 | 2496 | 8587 | 229 | 186 | 81.2227 | |
| gduggal-bwafb | SNP | ti | map_l100_m0_e0 | * | 98.8483 | 98.7506 | 98.9461 | 70.2347 | 21499 | 272 | 21500 | 229 | 69 | 30.1310 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 91.8726 | 90.2567 | 93.5475 | 72.9167 | 3270 | 353 | 3320 | 229 | 219 | 95.6332 | |
| raldana-dualsentieon | SNP | ti | map_l150_m2_e0 | * | 98.9377 | 98.9908 | 98.8846 | 75.4120 | 20305 | 207 | 20301 | 229 | 9 | 3.9301 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 86.7858 | 90.4797 | 83.3817 | 76.0514 | 1226 | 129 | 1149 | 229 | 205 | 89.5197 | |
| mlin-fermikit | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 94.9166 | 92.5873 | 97.3660 | 75.0931 | 8456 | 677 | 8465 | 229 | 6 | 2.6201 | |
| mlin-fermikit | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 94.9166 | 92.5873 | 97.3660 | 75.0931 | 8456 | 677 | 8465 | 229 | 6 | 2.6201 | |
| raldana-dualsentieon | INDEL | * | HG002complexvar | * | 98.9594 | 98.2323 | 99.6974 | 57.2556 | 75578 | 1360 | 75441 | 229 | 196 | 85.5895 | |
| jlack-gatk | SNP | tv | HG002complexvar | * | 99.9000 | 99.8932 | 99.9069 | 22.4572 | 245889 | 263 | 245795 | 229 | 81 | 35.3712 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 95.9795 | 98.7477 | 93.3623 | 66.3775 | 3233 | 41 | 3221 | 229 | 194 | 84.7162 | |
| hfeng-pmm2 | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.8203 | 98.1335 | 99.5168 | 73.5903 | 47370 | 901 | 47163 | 229 | 165 | 72.0524 | |
| hfeng-pmm2 | INDEL | I1_5 | * | het | 99.6023 | 99.4952 | 99.7096 | 59.9116 | 78642 | 399 | 78624 | 229 | 130 | 56.7686 | |
| hfeng-pmm2 | SNP | ti | map_l100_m2_e0 | * | 99.5384 | 99.5445 | 99.5323 | 66.9341 | 48738 | 223 | 48731 | 229 | 30 | 13.1004 | |
| gduggal-snapvard | INDEL | D1_5 | map_l150_m2_e0 | het | 84.3060 | 98.2490 | 73.8286 | 91.1437 | 505 | 9 | 646 | 229 | 52 | 22.7074 | |
| gduggal-snapvard | INDEL | I1_5 | map_l100_m1_e0 | het | 89.7380 | 98.4556 | 82.4387 | 88.3144 | 765 | 12 | 1075 | 229 | 105 | 45.8515 | |
| ghariani-varprowl | INDEL | D1_5 | map_l100_m2_e0 | * | 91.5803 | 94.5692 | 88.7745 | 87.1803 | 1811 | 104 | 1811 | 229 | 65 | 28.3843 | |
| gduggal-snapfb | SNP | ti | map_l250_m1_e0 | * | 94.3297 | 93.7323 | 94.9347 | 89.2465 | 4292 | 287 | 4292 | 229 | 122 | 53.2751 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 35.9715 | 48.9362 | 28.4375 | 54.0890 | 92 | 96 | 91 | 229 | 220 | 96.0699 | |
| ciseli-custom | INDEL | C1_5 | HG002compoundhet | * | 0.0000 | 0.0000 | 10.8949 | 86.7866 | 0 | 1 | 28 | 229 | 83 | 36.2445 | |
| ckim-dragen | SNP | ti | map_l150_m0_e0 | * | 97.7765 | 98.4353 | 97.1264 | 80.6352 | 7738 | 123 | 7740 | 229 | 28 | 12.2271 | |
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.7777 | 99.3930 | 98.1700 | 65.9733 | 12445 | 76 | 12285 | 229 | 215 | 93.8865 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.9340 | 99.3274 | 98.5437 | 62.8374 | 15654 | 106 | 15496 | 229 | 203 | 88.6463 | |
| dgrover-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 95.4266 | 96.8812 | 94.0151 | 79.6225 | 3914 | 126 | 3613 | 230 | 189 | 82.1739 | |
| ckim-vqsr | INDEL | I1_5 | HG002compoundhet | homalt | 73.9572 | 99.6960 | 58.7814 | 88.6470 | 328 | 1 | 328 | 230 | 230 | 100.0000 | |