PrecisionFDA
Truth Challenge
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
22951-23000 / 86044 show all | |||||||||||||||
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 91.9908 | 86.2661 | 98.5294 | 74.4040 | 201 | 32 | 201 | 3 | 2 | 66.6667 | |
| ndellapenna-hhga | INDEL | * | map_l100_m2_e1 | hetalt | 83.8498 | 75.7576 | 93.8776 | 89.0990 | 100 | 32 | 92 | 6 | 2 | 33.3333 | |
| ndellapenna-hhga | INDEL | * | segdup | hetalt | 85.5736 | 75.3846 | 98.9474 | 95.6039 | 98 | 32 | 94 | 1 | 1 | 100.0000 | |
| ndellapenna-hhga | INDEL | D1_5 | map_siren | het | 98.4865 | 98.5946 | 98.3786 | 78.7325 | 2245 | 32 | 2245 | 37 | 15 | 40.5405 | |
| mlin-fermikit | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.4225 | 97.6048 | 97.2409 | 55.7572 | 1304 | 32 | 1304 | 37 | 14 | 37.8378 | |
| mlin-fermikit | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 96.9376 | 96.2573 | 97.6275 | 55.5145 | 823 | 32 | 823 | 20 | 1 | 5.0000 | |
| ltrigg-rtg2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.3336 | 98.6760 | 100.0000 | 74.6486 | 2385 | 32 | 2381 | 0 | 0 | ||
| ltrigg-rtg2 | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.0316 | 99.5706 | 98.4983 | 37.0609 | 7420 | 32 | 7412 | 113 | 2 | 1.7699 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 84.5227 | 93.4426 | 77.1574 | 75.5280 | 456 | 32 | 456 | 135 | 119 | 88.1481 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 48.0237 | 81.0651 | 34.1176 | 68.8073 | 137 | 32 | 58 | 112 | 111 | 99.1071 | |
| mlin-fermikit | INDEL | D16_PLUS | map_l100_m2_e0 | * | 59.1325 | 64.4444 | 54.6296 | 93.1904 | 58 | 32 | 59 | 49 | 15 | 30.6122 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 51.5152 | 34.6939 | 100.0000 | 32.0000 | 17 | 32 | 17 | 0 | 0 | ||
| mlin-fermikit | INDEL | D1_5 | map_l150_m0_e0 | homalt | 65.0307 | 62.3529 | 67.9487 | 83.1533 | 53 | 32 | 53 | 25 | 21 | 84.0000 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 76.3336 | 82.0225 | 71.3826 | 66.3055 | 146 | 32 | 222 | 89 | 24 | 26.9663 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 94.0840 | 93.1034 | 95.0855 | 69.5114 | 432 | 32 | 445 | 23 | 15 | 65.2174 | |
| ndellapenna-hhga | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 79.5193 | 68.6275 | 94.5205 | 91.5704 | 70 | 32 | 69 | 4 | 3 | 75.0000 | |
| ndellapenna-hhga | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.7217 | 99.5441 | 99.8999 | 60.0411 | 6987 | 32 | 6987 | 7 | 4 | 57.1429 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 92.7811 | 94.6932 | 90.9448 | 44.0938 | 571 | 32 | 3706 | 369 | 326 | 88.3469 | |
| raldana-dualsentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.2372 | 99.7214 | 96.7966 | 60.1274 | 11452 | 32 | 11452 | 379 | 372 | 98.1530 | |
| raldana-dualsentieon | INDEL | * | map_l150_m2_e0 | het | 96.9552 | 96.4680 | 97.4473 | 88.6581 | 874 | 32 | 878 | 23 | 2 | 8.6957 | |
| raldana-dualsentieon | INDEL | * | segdup | * | 99.0001 | 98.7480 | 99.2534 | 93.8102 | 2524 | 32 | 2526 | 19 | 11 | 57.8947 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 88.5260 | 93.1770 | 84.3173 | 80.1174 | 437 | 32 | 457 | 85 | 70 | 82.3529 | |
| anovak-vg | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 52.0833 | 43.8596 | 64.1026 | 99.3572 | 25 | 32 | 25 | 14 | 11 | 78.5714 | |
| anovak-vg | INDEL | D6_15 | map_l100_m0_e0 | * | 75.4516 | 68.9320 | 83.3333 | 89.1892 | 71 | 32 | 70 | 14 | 12 | 85.7143 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.3072 | 99.1321 | 99.4829 | 51.2667 | 3655 | 32 | 3655 | 19 | 16 | 84.2105 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.8489 | 98.6987 | 98.9996 | 76.4157 | 2427 | 32 | 2375 | 24 | 15 | 62.5000 | |
| bgallagher-sentieon | SNP | ti | map_l125_m0_e0 | homalt | 99.5535 | 99.2875 | 99.8209 | 66.4916 | 4459 | 32 | 4459 | 8 | 6 | 75.0000 | |
| bgallagher-sentieon | SNP | ti | map_l250_m1_e0 | het | 98.1612 | 98.9218 | 97.4121 | 90.4001 | 2936 | 32 | 2936 | 78 | 16 | 20.5128 | |
| bgallagher-sentieon | SNP | ti | map_l250_m2_e0 | het | 98.3066 | 99.0166 | 97.6068 | 90.7462 | 3222 | 32 | 3222 | 79 | 16 | 20.2532 | |
| bgallagher-sentieon | SNP | tv | map_l250_m1_e0 | het | 97.5542 | 98.2093 | 96.9078 | 89.8378 | 1755 | 32 | 1755 | 56 | 8 | 14.2857 | |
| bgallagher-sentieon | SNP | tv | map_l250_m2_e0 | het | 97.6459 | 98.3505 | 96.9512 | 90.3681 | 1908 | 32 | 1908 | 60 | 9 | 15.0000 | |
| bgallagher-sentieon | SNP | tv | map_l250_m2_e1 | het | 97.6756 | 98.3715 | 96.9895 | 90.4284 | 1933 | 32 | 1933 | 60 | 9 | 15.0000 | |
| bgallagher-sentieon | INDEL | * | map_l100_m2_e0 | het | 98.0419 | 98.6129 | 97.4776 | 86.6167 | 2275 | 32 | 2280 | 59 | 11 | 18.6441 | |
| bgallagher-sentieon | INDEL | * | map_l100_m2_e1 | het | 98.0718 | 98.6342 | 97.5158 | 86.6842 | 2311 | 32 | 2316 | 59 | 11 | 18.6441 | |
| astatham-gatk | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.1992 | 98.5033 | 99.9050 | 39.1794 | 2106 | 32 | 2103 | 2 | 1 | 50.0000 | |
| asubramanian-gatk | INDEL | * | map_l250_m1_e0 | het | 83.2020 | 83.1579 | 83.2461 | 97.3234 | 158 | 32 | 159 | 32 | 3 | 9.3750 | |
| astatham-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 97.3654 | 95.1442 | 99.6928 | 71.1308 | 627 | 32 | 649 | 2 | 2 | 100.0000 | |
| astatham-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 97.3654 | 95.1442 | 99.6928 | 71.1308 | 627 | 32 | 649 | 2 | 2 | 100.0000 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.8693 | 98.6987 | 99.0405 | 76.6032 | 2427 | 32 | 2374 | 23 | 15 | 65.2174 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 96.9530 | 95.0769 | 98.9045 | 23.1047 | 618 | 32 | 632 | 7 | 5 | 71.4286 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 93.0561 | 88.8112 | 97.7273 | 51.9782 | 254 | 32 | 344 | 8 | 8 | 100.0000 | |
| asubramanian-gatk | SNP | ti | * | hetalt | 95.6522 | 94.5017 | 96.8310 | 46.4151 | 550 | 32 | 550 | 18 | 1 | 5.5556 | |
| asubramanian-gatk | SNP | ti | HG002compoundhet | hetalt | 95.8808 | 94.4732 | 97.3310 | 25.3652 | 547 | 32 | 547 | 15 | 0 | 0.0000 | |
| asubramanian-gatk | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.2451 | 98.5461 | 99.9540 | 42.2689 | 2169 | 32 | 2172 | 1 | 1 | 100.0000 | |
| ghariani-varprowl | INDEL | D6_15 | map_siren | homalt | 85.5895 | 75.3846 | 98.9899 | 78.1457 | 98 | 32 | 98 | 1 | 0 | 0.0000 | |
| ghariani-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 94.7282 | 99.1860 | 90.6540 | 71.0721 | 3899 | 32 | 3909 | 403 | 1 | 0.2481 | |
| ghariani-varprowl | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | * | 97.1636 | 99.0725 | 95.3268 | 47.5871 | 3418 | 32 | 3427 | 168 | 33 | 19.6429 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.4096 | 99.6175 | 99.2025 | 47.1436 | 8334 | 32 | 8334 | 67 | 66 | 98.5075 | |
| hfeng-pmm1 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.5421 | 99.6910 | 99.3935 | 43.8031 | 10325 | 32 | 10325 | 63 | 62 | 98.4127 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 81.9563 | 92.6437 | 73.4797 | 72.5162 | 403 | 32 | 435 | 157 | 14 | 8.9172 | |