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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
65701-65750 / 86044 show all | |||||||||||||||
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.7108 | 98.7484 | 98.6731 | 78.8824 | 3866 | 49 | 3867 | 52 | 45 | 86.5385 | |
| ndellapenna-hhga | SNP | * | map_l125_m0_e0 | homalt | 99.5815 | 99.2700 | 99.8951 | 66.7961 | 6663 | 49 | 6663 | 7 | 6 | 85.7143 | |
| qzeng-custom | INDEL | D16_PLUS | * | homalt | 83.8251 | 97.1040 | 73.7410 | 65.8948 | 1643 | 49 | 1640 | 584 | 105 | 17.9795 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 88.8820 | 96.0769 | 82.6897 | 71.8992 | 1200 | 49 | 1199 | 251 | 105 | 41.8327 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 88.8820 | 96.0769 | 82.6897 | 71.8992 | 1200 | 49 | 1199 | 251 | 105 | 41.8327 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.0561 | 98.7981 | 99.3154 | 40.3094 | 4028 | 49 | 4062 | 28 | 17 | 60.7143 | |
| qzeng-custom | INDEL | D1_5 | map_l250_m1_e0 | * | 80.9673 | 71.3450 | 93.5897 | 97.5788 | 122 | 49 | 146 | 10 | 9 | 90.0000 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.7953 | 98.1565 | 99.4425 | 52.2443 | 2609 | 49 | 25329 | 142 | 36 | 25.3521 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.0792 | 98.2071 | 95.9770 | 63.3202 | 2684 | 49 | 2672 | 112 | 106 | 94.6429 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 94.7213 | 91.5952 | 98.0684 | 63.9529 | 534 | 49 | 660 | 13 | 13 | 100.0000 | |
| asubramanian-gatk | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.2920 | 98.7455 | 99.8446 | 31.3666 | 3857 | 49 | 3856 | 6 | 1 | 16.6667 | |
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 97.5860 | 95.8996 | 99.3328 | 33.9394 | 1146 | 49 | 1191 | 8 | 8 | 100.0000 | |
| bgallagher-sentieon | SNP | ti | map_l125_m2_e0 | homalt | 99.7354 | 99.5686 | 99.9028 | 65.6605 | 11309 | 49 | 11309 | 11 | 9 | 81.8182 | |
| bgallagher-sentieon | SNP | ti | map_l125_m2_e1 | homalt | 99.7377 | 99.5724 | 99.9037 | 65.6841 | 11409 | 49 | 11409 | 11 | 9 | 81.8182 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 78.8110 | 71.5116 | 87.7698 | 75.9099 | 123 | 49 | 122 | 17 | 11 | 64.7059 | |
| ciseli-custom | INDEL | D1_5 | map_l100_m2_e1 | hetalt | 0.0000 | 3.9216 | 0.0000 | 0.0000 | 2 | 49 | 0 | 0 | 0 | ||
| ciseli-custom | INDEL | D6_15 | map_l100_m2_e1 | het | 63.0961 | 63.7037 | 62.5000 | 90.4573 | 86 | 49 | 90 | 54 | 13 | 24.0741 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 87.1230 | 91.0747 | 83.5000 | 78.7460 | 500 | 49 | 501 | 99 | 52 | 52.5253 | |
| cchapple-custom | INDEL | * | map_l125_m1_e0 | het | 94.5817 | 96.3296 | 92.8962 | 87.3662 | 1286 | 49 | 1360 | 104 | 19 | 18.2692 | |
| cchapple-custom | INDEL | * | map_siren | homalt | 98.6746 | 98.1544 | 99.2003 | 78.4454 | 2606 | 49 | 2605 | 21 | 13 | 61.9048 | |
| cchapple-custom | INDEL | D1_5 | map_l100_m1_e0 | * | 96.7211 | 97.3485 | 96.1018 | 81.7490 | 1799 | 49 | 1775 | 72 | 9 | 12.5000 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.8234 | 96.2133 | 99.4883 | 36.4312 | 1245 | 49 | 1361 | 7 | 7 | 100.0000 | |
| ckim-dragen | INDEL | D1_5 | * | homalt | 99.6542 | 99.8998 | 99.4098 | 63.4062 | 48877 | 49 | 48847 | 290 | 286 | 98.6207 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 97.4000 | 96.5248 | 98.2912 | 75.1339 | 1361 | 49 | 1323 | 23 | 18 | 78.2609 | |
| ckim-dragen | INDEL | D1_5 | map_siren | * | 98.3320 | 98.6115 | 98.0541 | 82.6974 | 3480 | 49 | 3477 | 69 | 7 | 10.1449 | |
| ckim-dragen | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.7746 | 99.8617 | 99.6878 | 62.5042 | 35370 | 49 | 35441 | 111 | 28 | 25.2252 | |
| cchapple-custom | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 99.1597 | 98.9715 | 99.3486 | 67.2313 | 4715 | 49 | 4728 | 31 | 4 | 12.9032 | |
| cchapple-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.5586 | 96.7635 | 98.3668 | 86.6207 | 1465 | 49 | 1566 | 26 | 21 | 80.7692 | |
| ciseli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 82.4034 | 96.8987 | 71.6806 | 60.7006 | 1531 | 49 | 1544 | 610 | 3 | 0.4918 | |
| ckim-dragen | INDEL | * | map_l125_m1_e0 | het | 95.7558 | 96.3296 | 95.1887 | 89.3639 | 1286 | 49 | 1286 | 65 | 7 | 10.7692 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.5458 | 99.2722 | 99.8208 | 49.8653 | 6684 | 49 | 6686 | 12 | 7 | 58.3333 | |
| ckim-vqsr | INDEL | * | map_l100_m0_e0 | * | 96.7114 | 96.8650 | 96.5583 | 90.6490 | 1514 | 49 | 1515 | 54 | 7 | 12.9630 | |
| dgrover-gatk | SNP | * | HG002compoundhet | * | 99.8063 | 99.8102 | 99.8025 | 41.2435 | 25773 | 49 | 25766 | 51 | 36 | 70.5882 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 82.8877 | 86.3510 | 79.6915 | 44.5869 | 310 | 49 | 310 | 79 | 52 | 65.8228 | |
| egarrison-hhga | INDEL | * | map_l125_m2_e0 | * | 98.0153 | 97.7687 | 98.2633 | 98.2577 | 2147 | 49 | 2150 | 38 | 14 | 36.8421 | |
| ckim-vqsr | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.3400 | 98.7394 | 99.9479 | 59.7020 | 3838 | 49 | 3838 | 2 | 2 | 100.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.8234 | 96.2133 | 99.4883 | 36.4312 | 1245 | 49 | 1361 | 7 | 7 | 100.0000 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 99.3603 | 99.2881 | 99.4326 | 81.7523 | 6834 | 49 | 6834 | 39 | 15 | 38.4615 | |
| egarrison-hhga | SNP | ti | segdup | het | 99.5306 | 99.5927 | 99.4687 | 89.2156 | 11981 | 49 | 11981 | 64 | 2 | 3.1250 | |
| eyeh-varpipe | INDEL | * | map_l100_m2_e1 | homalt | 94.8575 | 96.1749 | 93.5757 | 84.5669 | 1232 | 49 | 1879 | 129 | 113 | 87.5969 | |
| eyeh-varpipe | INDEL | * | map_l125_m2_e0 | het | 96.7811 | 96.4774 | 97.0868 | 85.6373 | 1342 | 49 | 1733 | 52 | 30 | 57.6923 | |
| eyeh-varpipe | INDEL | * | map_l125_m2_e1 | het | 96.7368 | 96.5199 | 96.9546 | 85.7560 | 1359 | 49 | 1751 | 55 | 32 | 58.1818 | |
| hfeng-pmm1 | SNP | tv | map_l250_m2_e0 | * | 98.5906 | 98.2998 | 98.8831 | 88.2437 | 2833 | 49 | 2833 | 32 | 7 | 21.8750 | |
| hfeng-pmm1 | SNP | tv | map_l250_m2_e1 | * | 98.6071 | 98.3196 | 98.8962 | 88.3190 | 2867 | 49 | 2867 | 32 | 7 | 21.8750 | |
| hfeng-pmm1 | INDEL | * | map_l150_m2_e1 | * | 97.5801 | 96.5949 | 98.5856 | 88.8230 | 1390 | 49 | 1394 | 20 | 4 | 20.0000 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.3163 | 97.0393 | 99.6273 | 57.4974 | 1606 | 49 | 1604 | 6 | 3 | 50.0000 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 95.3982 | 98.2071 | 92.7456 | 62.2313 | 2684 | 49 | 2672 | 209 | 198 | 94.7368 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 95.3650 | 91.5952 | 99.4585 | 65.4829 | 534 | 49 | 551 | 3 | 2 | 66.6667 | |
| jlack-gatk | SNP | tv | map_l150_m0_e0 | het | 89.8651 | 98.2765 | 82.7801 | 89.5464 | 2794 | 49 | 2793 | 581 | 34 | 5.8520 | |
| hfeng-pmm3 | INDEL | D6_15 | HG002complexvar | hetalt | 97.4277 | 95.1629 | 99.8030 | 47.8149 | 964 | 49 | 1013 | 2 | 1 | 50.0000 | |