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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
15251-15300 / 86044 show all | |||||||||||||||
| egarrison-hhga | SNP | ti | map_l100_m2_e0 | het | 99.3933 | 98.9779 | 99.8123 | 65.4669 | 30309 | 313 | 30310 | 57 | 18 | 31.5789 | |
| egarrison-hhga | SNP | ti | map_l100_m2_e1 | het | 99.3984 | 98.9890 | 99.8111 | 65.4651 | 30647 | 313 | 30648 | 58 | 18 | 31.0345 | |
| eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 56.2806 | 41.3174 | 88.2353 | 79.4355 | 69 | 98 | 135 | 18 | 18 | 100.0000 | |
| eyeh-varpipe | INDEL | * | map_l150_m1_e0 | het | 96.7203 | 96.6082 | 96.8326 | 87.6550 | 826 | 29 | 1070 | 35 | 18 | 51.4286 | |
| eyeh-varpipe | INDEL | * | map_l150_m2_e0 | het | 96.7930 | 96.5784 | 97.0085 | 88.1973 | 875 | 31 | 1135 | 35 | 18 | 51.4286 | |
| eyeh-varpipe | INDEL | * | map_l150_m2_e1 | het | 96.7897 | 96.5368 | 97.0439 | 88.2865 | 892 | 32 | 1149 | 35 | 18 | 51.4286 | |
| eyeh-varpipe | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 32.3529 | 97.2222 | 0 | 0 | 11 | 23 | 18 | 78.2609 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 91.9368 | 91.0345 | 92.8571 | 60.6373 | 396 | 39 | 390 | 30 | 18 | 60.0000 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 95.1367 | 94.4039 | 95.8810 | 72.5157 | 388 | 23 | 419 | 18 | 18 | 100.0000 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 82.4180 | 70.7101 | 98.7723 | 34.9310 | 1673 | 693 | 1770 | 22 | 18 | 81.8182 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 90.9557 | 84.7716 | 98.1132 | 33.9074 | 1002 | 180 | 1092 | 21 | 18 | 85.7143 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 80.4824 | 75.1220 | 86.6667 | 77.3014 | 154 | 51 | 156 | 24 | 18 | 75.0000 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 80.4824 | 75.1220 | 86.6667 | 77.3014 | 154 | 51 | 156 | 24 | 18 | 75.0000 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 71.9593 | 58.1340 | 94.4123 | 59.6109 | 486 | 350 | 490 | 29 | 18 | 62.0690 | |
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 51.7766 | 41.1290 | 69.8630 | 99.9464 | 51 | 73 | 51 | 22 | 18 | 81.8182 | |
| anovak-vg | INDEL | D1_5 | segdup | homalt | 93.5483 | 94.1504 | 92.9539 | 93.9028 | 338 | 21 | 343 | 26 | 18 | 69.2308 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 9.4937 | 5.5556 | 32.6087 | 59.8253 | 23 | 391 | 30 | 62 | 18 | 29.0323 | |
| anovak-vg | SNP | ti | map_l150_m0_e0 | homalt | 84.9295 | 74.3209 | 99.0709 | 76.2265 | 2052 | 709 | 2026 | 19 | 18 | 94.7368 | |
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.5583 | 99.5229 | 99.5937 | 62.9090 | 11055 | 53 | 11030 | 45 | 18 | 40.0000 | |
| astatham-gatk | INDEL | * | map_l100_m2_e0 | * | 96.5801 | 95.1530 | 98.0507 | 86.7138 | 3514 | 179 | 3521 | 70 | 18 | 25.7143 | |
| astatham-gatk | INDEL | * | map_l100_m2_e1 | * | 96.5544 | 95.0745 | 98.0811 | 86.7793 | 3571 | 185 | 3578 | 70 | 18 | 25.7143 | |
| astatham-gatk | SNP | * | map_l125_m0_e0 | het | 89.5045 | 81.3803 | 99.4306 | 82.1625 | 10306 | 2358 | 10303 | 59 | 18 | 30.5085 | |
| astatham-gatk | SNP | ti | HG002compoundhet | * | 99.2746 | 98.6669 | 99.8899 | 35.7263 | 17245 | 233 | 17243 | 19 | 18 | 94.7368 | |
| astatham-gatk | SNP | ti | map_l150_m1_e0 | het | 85.9873 | 75.6508 | 99.5954 | 82.9552 | 9358 | 3012 | 9354 | 38 | 18 | 47.3684 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 93.0029 | 89.2396 | 97.0976 | 37.9705 | 622 | 75 | 736 | 22 | 18 | 81.8182 | |
| asubramanian-gatk | INDEL | D6_15 | HG002complexvar | het | 98.2617 | 97.2756 | 99.2679 | 59.9547 | 3035 | 85 | 2983 | 22 | 18 | 81.8182 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 88.2241 | 93.9024 | 83.1933 | 72.9545 | 77 | 5 | 99 | 20 | 18 | 90.0000 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 86.3432 | 96.6102 | 78.0488 | 75.0760 | 57 | 2 | 64 | 18 | 18 | 100.0000 | |
| bgallagher-sentieon | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 96.7166 | 95.4426 | 98.0251 | 79.9026 | 1089 | 52 | 1092 | 22 | 18 | 81.8182 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.0886 | 98.9484 | 99.2292 | 67.4228 | 3858 | 41 | 3862 | 30 | 18 | 60.0000 | |
| bgallagher-sentieon | SNP | * | map_l100_m1_e0 | homalt | 99.7886 | 99.6630 | 99.9146 | 57.7258 | 26912 | 91 | 26912 | 23 | 18 | 78.2609 | |
| bgallagher-sentieon | SNP | * | map_l100_m2_e0 | homalt | 99.7908 | 99.6657 | 99.9162 | 60.2352 | 27431 | 92 | 27431 | 23 | 18 | 78.2609 | |
| bgallagher-sentieon | SNP | * | map_l100_m2_e1 | homalt | 99.7911 | 99.6654 | 99.9170 | 60.2187 | 27703 | 93 | 27703 | 23 | 18 | 78.2609 | |
| astatham-gatk | INDEL | D16_PLUS | HG002compoundhet | homalt | 47.0588 | 100.0000 | 30.7692 | 73.1959 | 8 | 0 | 8 | 18 | 18 | 100.0000 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.5527 | 99.7211 | 97.4114 | 61.5908 | 715 | 2 | 715 | 19 | 18 | 94.7368 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 96.5536 | 96.0864 | 97.0255 | 75.2541 | 712 | 29 | 685 | 21 | 18 | 85.7143 | |
| astatham-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.3282 | 96.4052 | 98.2690 | 85.0309 | 1475 | 55 | 1476 | 26 | 18 | 69.2308 | |
| astatham-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.3282 | 96.4052 | 98.2690 | 85.0309 | 1475 | 55 | 1476 | 26 | 18 | 69.2308 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 95.1899 | 100.0000 | 90.8213 | 67.6056 | 188 | 0 | 188 | 19 | 18 | 94.7368 | |
| asubramanian-gatk | SNP | tv | HG002complexvar | * | 98.0754 | 96.2442 | 99.9776 | 22.6117 | 236907 | 9245 | 236824 | 53 | 18 | 33.9623 | |
| asubramanian-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.9673 | 98.9982 | 98.9364 | 66.6862 | 17392 | 176 | 17395 | 187 | 18 | 9.6257 | |
| asubramanian-gatk | SNP | tv | * | homalt | 98.7491 | 97.5342 | 99.9946 | 20.2324 | 367824 | 9299 | 367810 | 20 | 17 | 85.0000 | |
| bgallagher-sentieon | INDEL | * | map_l100_m1_e0 | * | 98.3343 | 98.6615 | 98.0094 | 85.1549 | 3538 | 48 | 3545 | 72 | 17 | 23.6111 | |
| bgallagher-sentieon | INDEL | * | map_l100_m2_e0 | * | 98.3285 | 98.6461 | 98.0129 | 85.9953 | 3643 | 50 | 3650 | 74 | 17 | 22.9730 | |
| bgallagher-sentieon | INDEL | * | map_l100_m2_e1 | * | 98.3429 | 98.6422 | 98.0454 | 86.0496 | 3705 | 51 | 3712 | 74 | 17 | 22.9730 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 96.0600 | 98.8417 | 93.4307 | 60.0583 | 256 | 3 | 256 | 18 | 17 | 94.4444 | |
| astatham-gatk | SNP | ti | HG002complexvar | het | 98.7599 | 97.5636 | 99.9860 | 17.3084 | 307097 | 7669 | 307042 | 43 | 17 | 39.5349 | |
| astatham-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.9634 | 98.0991 | 99.8431 | 67.2451 | 30551 | 592 | 30551 | 48 | 17 | 35.4167 | |
| astatham-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.9634 | 98.0991 | 99.8431 | 67.2451 | 30551 | 592 | 30551 | 48 | 17 | 35.4167 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.4435 | 99.1224 | 99.7666 | 66.9356 | 28012 | 248 | 28207 | 66 | 17 | 25.7576 | |