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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
11751-11800 / 86044 show all | |||||||||||||||
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 65.8537 | 49.2027 | 99.5392 | 51.5625 | 216 | 223 | 216 | 1 | 1 | 100.0000 | |
| gduggal-bwaplat | SNP | ti | segdup | het | 98.4906 | 98.1463 | 98.8374 | 94.7165 | 11807 | 223 | 11817 | 139 | 6 | 4.3166 | |
| hfeng-pmm2 | INDEL | I16_PLUS | * | * | 97.5355 | 96.5031 | 98.5902 | 69.5601 | 6154 | 223 | 6154 | 88 | 61 | 69.3182 | |
| hfeng-pmm2 | SNP | ti | map_l100_m2_e0 | * | 99.5384 | 99.5445 | 99.5323 | 66.9341 | 48738 | 223 | 48731 | 229 | 30 | 13.1004 | |
| hfeng-pmm2 | SNP | ti | map_l100_m2_e1 | * | 99.5423 | 99.5494 | 99.5352 | 66.9275 | 49262 | 223 | 49255 | 230 | 30 | 13.0435 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.2031 | 96.0157 | 98.4203 | 68.4990 | 5374 | 223 | 5358 | 86 | 74 | 86.0465 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 85.1178 | 74.4266 | 99.3958 | 24.0826 | 649 | 223 | 658 | 4 | 4 | 100.0000 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.5003 | 95.5391 | 97.4811 | 71.7827 | 4776 | 223 | 4760 | 123 | 101 | 82.1138 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.5003 | 95.5391 | 97.4811 | 71.7827 | 4776 | 223 | 4760 | 123 | 101 | 82.1138 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 93.4664 | 90.7546 | 96.3452 | 62.2067 | 2189 | 223 | 2188 | 83 | 56 | 67.4699 | |
| ckim-isaac | INDEL | D1_5 | map_l125_m2_e0 | het | 82.3461 | 70.8115 | 98.3696 | 88.9842 | 541 | 223 | 543 | 9 | 3 | 33.3333 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 89.1325 | 94.2362 | 84.5533 | 48.1916 | 3646 | 223 | 3246 | 593 | 548 | 92.4115 | |
| egarrison-hhga | INDEL | D16_PLUS | * | het | 92.0708 | 92.9408 | 91.2170 | 67.2524 | 2936 | 223 | 3043 | 293 | 261 | 89.0785 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.4424 | 99.5121 | 99.3729 | 70.5814 | 45479 | 223 | 45479 | 287 | 31 | 10.8014 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.4424 | 99.5121 | 99.3729 | 70.5814 | 45479 | 223 | 45479 | 287 | 31 | 10.8014 | |
| anovak-vg | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 93.6443 | 95.4077 | 91.9449 | 64.3247 | 4633 | 223 | 4874 | 427 | 230 | 53.8642 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 92.7600 | 86.9438 | 99.4102 | 29.9035 | 1485 | 223 | 1517 | 9 | 8 | 88.8889 | |
| bgallagher-sentieon | SNP | * | map_l100_m1_e0 | het | 99.2217 | 99.5084 | 98.9366 | 68.7750 | 45136 | 223 | 45125 | 485 | 63 | 12.9897 | |
| bgallagher-sentieon | SNP | ti | map_l100_m2_e1 | * | 99.4649 | 99.5494 | 99.3806 | 66.3075 | 49262 | 223 | 49255 | 307 | 50 | 16.2866 | |
| bgallagher-sentieon | SNP | ti | map_l100_m2_e0 | * | 99.4612 | 99.5466 | 99.3760 | 66.3096 | 48739 | 222 | 48732 | 306 | 50 | 16.3399 | |
| astatham-gatk | SNP | ti | HG002compoundhet | het | 98.7553 | 97.6644 | 99.8709 | 39.9910 | 9283 | 222 | 9281 | 12 | 11 | 91.6667 | |
| jlack-gatk | SNP | * | map_l150_m2_e0 | het | 93.6840 | 98.8973 | 88.9927 | 86.5727 | 19911 | 222 | 19905 | 2462 | 176 | 7.1487 | |
| jlack-gatk | SNP | * | map_l150_m2_e1 | het | 93.7014 | 98.9098 | 89.0141 | 86.6201 | 20141 | 222 | 20135 | 2485 | 178 | 7.1630 | |
| jpowers-varprowl | SNP | * | segdup | * | 98.1671 | 99.2090 | 97.1467 | 91.9113 | 27845 | 222 | 27851 | 818 | 71 | 8.6797 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 86.2358 | 92.6000 | 80.6901 | 73.5018 | 2778 | 222 | 2783 | 666 | 652 | 97.8979 | |
| jpowers-varprowl | INDEL | * | map_siren | homalt | 94.9463 | 91.6384 | 98.5020 | 74.3563 | 2433 | 222 | 2433 | 37 | 25 | 67.5676 | |
| jpowers-varprowl | INDEL | D1_5 | map_siren | * | 94.5668 | 93.7093 | 95.4401 | 81.4755 | 3307 | 222 | 3307 | 158 | 114 | 72.1519 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.8537 | 97.8565 | 99.8715 | 37.6633 | 10135 | 222 | 10103 | 13 | 13 | 100.0000 | |
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 76.8434 | 94.7617 | 64.6239 | 86.6785 | 4016 | 222 | 3986 | 2182 | 61 | 2.7956 | |
| ghariani-varprowl | SNP | * | map_l100_m0_e0 | homalt | 98.8809 | 98.0895 | 99.6851 | 64.3445 | 11398 | 222 | 11398 | 36 | 21 | 58.3333 | |
| ghariani-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 81.6587 | 97.5693 | 70.2096 | 85.8214 | 8911 | 222 | 8977 | 3809 | 26 | 0.6826 | |
| ghariani-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 81.6587 | 97.5693 | 70.2096 | 85.8214 | 8911 | 222 | 8977 | 3809 | 26 | 0.6826 | |
| cchapple-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.3696 | 99.2268 | 97.5271 | 78.9884 | 28490 | 222 | 28632 | 726 | 57 | 7.8512 | |
| cchapple-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.3696 | 99.2268 | 97.5271 | 78.9884 | 28490 | 222 | 28632 | 726 | 57 | 7.8512 | |
| ciseli-custom | INDEL | * | map_l150_m0_e0 | * | 63.1351 | 56.8093 | 71.0462 | 94.9719 | 292 | 222 | 292 | 119 | 60 | 50.4202 | |
| ckim-dragen | SNP | ti | map_l100_m0_e0 | * | 98.3169 | 98.9803 | 97.6623 | 69.9393 | 21549 | 222 | 21557 | 516 | 60 | 11.6279 | |
| gduggal-bwaplat | INDEL | I1_5 | map_l100_m2_e1 | homalt | 74.0396 | 58.8889 | 99.6865 | 89.4161 | 318 | 222 | 318 | 1 | 1 | 100.0000 | |
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 46.1240 | 34.8974 | 68.0000 | 71.9101 | 119 | 222 | 17 | 8 | 8 | 100.0000 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 96.6052 | 94.2754 | 99.0530 | 53.1678 | 3656 | 222 | 3661 | 35 | 17 | 48.5714 | |
| ckim-isaac | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 96.7084 | 94.4652 | 99.0608 | 42.7483 | 3789 | 222 | 3797 | 36 | 12 | 33.3333 | |
| ckim-isaac | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 84.2675 | 79.8913 | 89.1509 | 81.5972 | 882 | 222 | 945 | 115 | 66 | 57.3913 | |
| raldana-dualsentieon | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.7835 | 87.9479 | 98.1818 | 64.9979 | 1620 | 222 | 1620 | 30 | 27 | 90.0000 | |
| rpoplin-dv42 | SNP | ti | map_l150_m2_e0 | * | 99.1376 | 98.9177 | 99.3584 | 75.0879 | 20290 | 222 | 20286 | 131 | 93 | 70.9924 | |
| qzeng-custom | INDEL | I1_5 | map_l100_m2_e0 | het | 80.9908 | 72.0050 | 92.5390 | 89.7242 | 571 | 222 | 831 | 67 | 13 | 19.4030 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 68.8811 | 63.9610 | 74.6212 | 70.9571 | 394 | 222 | 394 | 134 | 130 | 97.0149 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.9726 | 98.5812 | 99.3672 | 71.8268 | 15356 | 221 | 15545 | 99 | 39 | 39.3939 | |
| cchapple-custom | SNP | * | map_l250_m2_e0 | het | 95.2059 | 95.7451 | 94.6728 | 91.6166 | 4973 | 221 | 4976 | 280 | 64 | 22.8571 | |
| cchapple-custom | SNP | tv | map_l100_m1_e0 | homalt | 98.7629 | 97.5561 | 100.0000 | 57.4941 | 8822 | 221 | 8817 | 0 | 0 | ||
| cchapple-custom | SNP | tv | map_l100_m2_e0 | homalt | 98.7862 | 97.6015 | 100.0000 | 60.2310 | 8993 | 221 | 8987 | 0 | 0 | ||
| ciseli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 0.0000 | 5.1502 | 0.0000 | 0.0000 | 12 | 221 | 0 | 0 | 0 | ||