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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
21001-21050 / 86044 show all | |||||||||||||||
| qzeng-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 62.5431 | 70.2703 | 56.3470 | 39.8682 | 104 | 44 | 617 | 478 | 306 | 64.0167 | |
| ndellapenna-hhga | INDEL | * | map_l100_m0_e0 | * | 97.2514 | 97.1849 | 97.3180 | 98.3412 | 1519 | 44 | 1524 | 42 | 9 | 21.4286 | |
| ndellapenna-hhga | INDEL | D6_15 | map_siren | * | 91.7468 | 91.3556 | 92.1415 | 83.5594 | 465 | 44 | 469 | 40 | 20 | 50.0000 | |
| qzeng-custom | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.3797 | 98.5411 | 94.3110 | 80.2460 | 2972 | 44 | 2984 | 180 | 15 | 8.3333 | |
| qzeng-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.5943 | 98.9387 | 96.2859 | 86.8966 | 4102 | 44 | 4122 | 159 | 29 | 18.2390 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.3687 | 96.7718 | 97.9730 | 70.6802 | 1319 | 44 | 1305 | 27 | 14 | 51.8519 | |
| ndellapenna-hhga | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.7605 | 99.6030 | 99.9185 | 55.4188 | 11040 | 44 | 11040 | 9 | 6 | 66.6667 | |
| ndellapenna-hhga | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 97.8073 | 97.0976 | 98.5274 | 67.7670 | 1472 | 44 | 1472 | 22 | 11 | 50.0000 | |
| qzeng-custom | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 97.4130 | 95.2329 | 99.6951 | 36.9231 | 879 | 44 | 327 | 1 | 1 | 100.0000 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 98.9775 | 98.7855 | 99.1701 | 81.3679 | 3579 | 44 | 3585 | 30 | 6 | 20.0000 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.7996 | 97.7237 | 97.8756 | 64.8324 | 1889 | 44 | 1889 | 41 | 41 | 100.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.5292 | 96.8794 | 96.1816 | 74.8551 | 1366 | 44 | 1335 | 53 | 43 | 81.1321 | |
| bgallagher-sentieon | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 99.2848 | 99.0764 | 99.4941 | 66.4545 | 4720 | 44 | 4720 | 24 | 5 | 20.8333 | |
| bgallagher-sentieon | SNP | * | segdup | * | 99.5028 | 99.8432 | 99.1647 | 90.1877 | 28023 | 44 | 28017 | 236 | 12 | 5.0848 | |
| bgallagher-sentieon | SNP | tv | map_l100_m0_e0 | het | 98.6394 | 99.3908 | 97.8993 | 74.3366 | 7178 | 44 | 7177 | 154 | 21 | 13.6364 | |
| astatham-gatk | INDEL | D1_5 | map_l125_m2_e0 | * | 96.9583 | 96.1505 | 97.7798 | 88.0289 | 1099 | 44 | 1101 | 25 | 5 | 20.0000 | |
| astatham-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.2539 | 96.1437 | 98.3900 | 80.1773 | 1097 | 44 | 1100 | 18 | 16 | 88.8889 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.7550 | 98.6561 | 96.8703 | 68.6124 | 3230 | 44 | 3219 | 104 | 99 | 95.1923 | |
| asubramanian-gatk | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.4451 | 98.8964 | 100.0000 | 34.3864 | 3943 | 44 | 3946 | 0 | 0 | ||
| anovak-vg | INDEL | D1_5 | map_l250_m1_e0 | * | 72.2457 | 74.2690 | 70.3297 | 96.0219 | 127 | 44 | 128 | 54 | 24 | 44.4444 | |
| gduggal-snapplat | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 0.0000 | 0.0000 | 0.0000 | 0 | 44 | 0 | 0 | 0 | |||
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 17.2414 | 10.2041 | 55.5556 | 59.0909 | 5 | 44 | 5 | 4 | 3 | 75.0000 | |
| gduggal-snapplat | INDEL | D6_15 | map_l100_m1_e0 | homalt | 47.6190 | 31.2500 | 100.0000 | 93.2692 | 20 | 44 | 14 | 0 | 0 | ||
| gduggal-snapplat | SNP | * | HG002compoundhet | hetalt | 97.1488 | 94.8956 | 99.5116 | 22.8814 | 818 | 44 | 815 | 4 | 4 | 100.0000 | |
| gduggal-snapfb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 0.0000 | 0.0000 | 0.0000 | 0 | 44 | 0 | 0 | 0 | |||
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 92.1833 | 90.4762 | 93.9560 | 39.3333 | 418 | 44 | 171 | 11 | 10 | 90.9091 | |
| gduggal-snapfb | INDEL | D1_5 | map_l100_m2_e0 | het | 95.7149 | 96.4968 | 94.9456 | 82.1389 | 1212 | 44 | 1221 | 65 | 8 | 12.3077 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 66.7366 | 54.6392 | 85.7143 | 3.4483 | 53 | 44 | 24 | 4 | 4 | 100.0000 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 35.4132 | 25.4237 | 58.3333 | 64.1791 | 15 | 44 | 14 | 10 | 10 | 100.0000 | |
| gduggal-snapfb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 17.3977 | 88.6010 | 9.6459 | 80.7136 | 342 | 44 | 365 | 3419 | 49 | 1.4332 | |
| gduggal-snapfb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 41.5632 | 96.5217 | 26.4836 | 86.5727 | 1221 | 44 | 1254 | 3481 | 67 | 1.9247 | |
| gduggal-snapfb | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 88.7788 | 99.0616 | 80.4299 | 50.4389 | 4645 | 44 | 4677 | 1138 | 26 | 2.2847 | |
| ghariani-varprowl | INDEL | * | map_l100_m2_e0 | het | 90.5891 | 98.0928 | 84.1518 | 89.9495 | 2263 | 44 | 2262 | 426 | 198 | 46.4789 | |
| ghariani-varprowl | INDEL | D16_PLUS | HG002compoundhet | het | 34.2987 | 89.1358 | 21.2349 | 37.1418 | 361 | 44 | 368 | 1365 | 1360 | 99.6337 | |
| ghariani-varprowl | INDEL | D1_5 | map_l100_m2_e1 | homalt | 95.2066 | 92.9032 | 97.6271 | 78.5766 | 576 | 44 | 576 | 14 | 2 | 14.2857 | |
| ghariani-varprowl | INDEL | I1_5 | map_l100_m1_e0 | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 44 | 0 | 0 | 0 | |||
| ghariani-varprowl | INDEL | I1_5 | map_l100_m2_e0 | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 44 | 0 | 0 | 0 | |||
| ghariani-varprowl | INDEL | I6_15 | segdup | hetalt | 0.0000 | 2.2222 | 0.0000 | 0.0000 | 1 | 44 | 0 | 0 | 0 | ||
| ghariani-varprowl | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.0759 | 98.6453 | 88.1018 | 77.5526 | 3204 | 44 | 3221 | 435 | 34 | 7.8161 | |
| ghariani-varprowl | SNP | ti | map_l250_m0_e0 | * | 94.5118 | 96.7883 | 92.3398 | 94.5924 | 1326 | 44 | 1326 | 110 | 17 | 15.4545 | |
| hfeng-pmm1 | INDEL | * | HG002complexvar | homalt | 99.7782 | 99.8372 | 99.7192 | 55.9241 | 26983 | 44 | 26991 | 76 | 70 | 92.1053 | |
| gduggal-snapplat | SNP | tv | HG002compoundhet | hetalt | 97.1488 | 94.8956 | 99.5116 | 22.8814 | 818 | 44 | 815 | 4 | 4 | 100.0000 | |
| gduggal-snapvard | INDEL | D16_PLUS | map_l100_m2_e0 | het | 13.5593 | 8.3333 | 36.3636 | 95.1754 | 4 | 44 | 4 | 7 | 2 | 28.5714 | |
| gduggal-snapvard | INDEL | D1_5 | map_siren | hetalt | 0.0000 | 47.6190 | 0.0000 | 0.0000 | 40 | 44 | 0 | 0 | 0 | ||
| gduggal-snapvard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 0.0000 | 15.3846 | 0.0000 | 0.0000 | 8 | 44 | 0 | 0 | 0 | ||
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.6139 | 95.3390 | 100.0000 | 30.9052 | 900 | 44 | 977 | 0 | 0 | ||
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 96.8420 | 95.3291 | 98.4036 | 71.9360 | 898 | 44 | 863 | 14 | 8 | 57.1429 | |
| rpoplin-dv42 | SNP | tv | map_l125_m0_e0 | homalt | 98.8647 | 98.0189 | 99.7251 | 70.7294 | 2177 | 44 | 2177 | 6 | 6 | 100.0000 | |
| raldana-dualsentieon | SNP | ti | map_l125_m1_e0 | homalt | 99.7597 | 99.6016 | 99.9183 | 62.2389 | 11001 | 44 | 11001 | 9 | 8 | 88.8889 | |
| raldana-dualsentieon | SNP | ti | map_l125_m2_e0 | homalt | 99.7663 | 99.6126 | 99.9205 | 64.9616 | 11314 | 44 | 11314 | 9 | 8 | 88.8889 | |