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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
12251-12300 / 86044 show all | |||||||||||||||
| ciseli-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 63.3990 | 50.8728 | 84.1085 | 55.4404 | 204 | 197 | 217 | 41 | 32 | 78.0488 | |
| ciseli-custom | INDEL | D6_15 | segdup | * | 68.3802 | 65.4450 | 71.5909 | 94.3207 | 125 | 66 | 126 | 50 | 32 | 64.0000 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 26.6490 | 16.9856 | 61.8182 | 56.0000 | 71 | 347 | 68 | 42 | 32 | 76.1905 | |
| ciseli-custom | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 72.9289 | 95.5040 | 58.9859 | 74.2486 | 1933 | 91 | 1966 | 1367 | 32 | 2.3409 | |
| cchapple-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.0840 | 95.2463 | 98.9940 | 50.7712 | 3326 | 166 | 3444 | 35 | 32 | 91.4286 | |
| cchapple-custom | SNP | * | HG002complexvar | homalt | 99.8273 | 99.6680 | 99.9871 | 18.5601 | 287616 | 958 | 286343 | 37 | 32 | 86.4865 | |
| ciseli-custom | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 8.4568 | 34.6774 | 4.8156 | 99.4220 | 43 | 81 | 47 | 929 | 32 | 3.4446 | |
| ciseli-custom | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | homalt | 36.2774 | 80.9524 | 23.3766 | 99.8723 | 17 | 4 | 18 | 59 | 32 | 54.2373 | |
| ciseli-custom | INDEL | * | map_l250_m1_e0 | het | 57.5615 | 54.7368 | 60.6936 | 97.5902 | 104 | 86 | 105 | 68 | 32 | 47.0588 | |
| ckim-dragen | SNP | tv | map_l100_m1_e0 | het | 98.0692 | 99.1503 | 97.0114 | 73.5010 | 15286 | 131 | 15289 | 471 | 32 | 6.7941 | |
| ckim-dragen | SNP | tv | map_l100_m2_e0 | het | 98.0513 | 99.1697 | 96.9579 | 75.2085 | 15646 | 131 | 15649 | 491 | 32 | 6.5173 | |
| ckim-dragen | SNP | tv | map_l100_m2_e1 | het | 98.0614 | 99.1655 | 96.9816 | 75.2723 | 15805 | 133 | 15808 | 492 | 32 | 6.5041 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.7140 | 95.9777 | 99.5142 | 33.0521 | 6538 | 274 | 6555 | 32 | 32 | 100.0000 | |
| ckim-gatk | SNP | ti | map_l150_m1_e0 | het | 84.9286 | 75.4406 | 97.1464 | 89.3093 | 9332 | 3038 | 9328 | 274 | 32 | 11.6788 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.4003 | 99.3113 | 99.4894 | 56.4059 | 6633 | 46 | 6625 | 34 | 32 | 94.1176 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.3919 | 95.3611 | 99.5111 | 32.7822 | 6496 | 316 | 6513 | 32 | 32 | 100.0000 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 96.1405 | 97.7087 | 94.6218 | 72.0263 | 597 | 14 | 563 | 32 | 32 | 100.0000 | |
| ckim-dragen | INDEL | I1_5 | HG002compoundhet | het | 97.0139 | 98.3529 | 95.7108 | 85.3685 | 836 | 14 | 781 | 35 | 32 | 91.4286 | |
| ckim-dragen | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 92.7152 | 99.5261 | 86.7769 | 70.8785 | 210 | 1 | 210 | 32 | 32 | 100.0000 | |
| ckim-dragen | SNP | * | map_l100_m1_e0 | homalt | 99.6437 | 99.4186 | 99.8698 | 55.6951 | 26846 | 157 | 26851 | 35 | 32 | 91.4286 | |
| ckim-dragen | SNP | * | map_l250_m2_e1 | * | 97.2818 | 97.6712 | 96.8956 | 89.8498 | 7801 | 186 | 7803 | 250 | 32 | 12.8000 | |
| anovak-vg | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 97.9539 | 97.6909 | 98.2183 | 50.5289 | 2200 | 52 | 2205 | 40 | 32 | 80.0000 | |
| anovak-vg | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 96.7969 | 96.8324 | 96.7615 | 60.7624 | 2415 | 79 | 2450 | 82 | 32 | 39.0244 | |
| anovak-vg | SNP | tv | func_cds | * | 98.2741 | 97.7580 | 98.7957 | 36.4158 | 4273 | 98 | 4266 | 52 | 32 | 61.5385 | |
| anovak-vg | SNP | tv | map_l125_m2_e0 | homalt | 89.0712 | 80.8709 | 99.1223 | 69.1421 | 4866 | 1151 | 4856 | 43 | 32 | 74.4186 | |
| anovak-vg | SNP | tv | map_l125_m2_e1 | homalt | 89.1235 | 80.9516 | 99.1306 | 69.1627 | 4917 | 1157 | 4903 | 43 | 32 | 74.4186 | |
| bgallagher-sentieon | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.7043 | 99.9506 | 99.4592 | 57.8271 | 6069 | 3 | 6069 | 33 | 32 | 96.9697 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.7313 | 99.3358 | 96.1778 | 82.5839 | 1346 | 9 | 1233 | 49 | 32 | 65.3061 | |
| bgallagher-sentieon | INDEL | D6_15 | HG002compoundhet | hetalt | 96.6337 | 93.8535 | 99.5837 | 23.7576 | 7650 | 501 | 7654 | 32 | 32 | 100.0000 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.0553 | 90.6080 | 97.7752 | 66.9888 | 1669 | 173 | 1670 | 38 | 32 | 84.2105 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 97.5355 | 100.0000 | 95.1895 | 73.1086 | 653 | 0 | 653 | 33 | 32 | 96.9697 | |
| bgallagher-sentieon | SNP | * | map_l250_m2_e0 | * | 98.4835 | 98.8332 | 98.1363 | 89.4731 | 7793 | 92 | 7793 | 148 | 32 | 21.6216 | |
| bgallagher-sentieon | SNP | * | map_l250_m2_e1 | * | 98.4903 | 98.8356 | 98.1475 | 89.5400 | 7894 | 93 | 7894 | 149 | 32 | 21.4765 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.1515 | 96.1503 | 98.1737 | 71.9585 | 2073 | 83 | 2204 | 41 | 32 | 78.0488 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.9355 | 96.4181 | 99.5014 | 33.6275 | 6568 | 244 | 6585 | 33 | 32 | 96.9697 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.4789 | 99.8586 | 99.1021 | 72.7252 | 3532 | 5 | 3532 | 32 | 32 | 100.0000 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.9885 | 94.6447 | 99.4513 | 62.5582 | 5620 | 318 | 6163 | 34 | 32 | 94.1176 | |
| anovak-vg | INDEL | * | map_l250_m1_e0 | homalt | 71.5666 | 73.3945 | 69.8276 | 95.2322 | 80 | 29 | 81 | 35 | 32 | 91.4286 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 88.7453 | 86.9963 | 90.5660 | 76.6520 | 475 | 71 | 480 | 50 | 32 | 64.0000 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 78.0662 | 93.4911 | 67.0103 | 81.9367 | 158 | 11 | 65 | 32 | 32 | 100.0000 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.4023 | 95.4216 | 99.4669 | 60.8921 | 8024 | 385 | 8023 | 43 | 32 | 74.4186 | |
| hfeng-pmm1 | INDEL | I6_15 | HG002complexvar | homalt | 98.6168 | 99.8353 | 97.4277 | 55.0578 | 1212 | 2 | 1212 | 32 | 32 | 100.0000 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 97.6744 | 99.2727 | 96.1268 | 69.7551 | 819 | 6 | 819 | 33 | 32 | 96.9697 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 97.6744 | 99.2727 | 96.1268 | 69.7551 | 819 | 6 | 819 | 33 | 32 | 96.9697 | |
| hfeng-pmm1 | SNP | * | HG002complexvar | homalt | 99.9818 | 99.9754 | 99.9882 | 20.0017 | 288503 | 71 | 288488 | 34 | 32 | 94.1176 | |
| hfeng-pmm1 | SNP | * | map_l100_m1_e0 | het | 99.4173 | 99.1159 | 99.7205 | 63.9471 | 44958 | 401 | 44947 | 126 | 32 | 25.3968 | |
| hfeng-pmm1 | SNP | * | map_l100_m2_e0 | het | 99.4228 | 99.1250 | 99.7224 | 65.3363 | 45993 | 406 | 45982 | 128 | 32 | 25.0000 | |
| hfeng-pmm1 | SNP | * | map_l100_m2_e1 | het | 99.4258 | 99.1322 | 99.7211 | 65.3522 | 46491 | 407 | 46480 | 130 | 32 | 24.6154 | |
| hfeng-pmm1 | SNP | ti | map_l100_m1_e0 | * | 99.5693 | 99.3532 | 99.7862 | 62.2569 | 47621 | 310 | 47614 | 102 | 32 | 31.3725 | |
| hfeng-pmm1 | SNP | ti | map_l100_m2_e0 | * | 99.5722 | 99.3566 | 99.7887 | 64.0145 | 48646 | 315 | 48639 | 103 | 32 | 31.0680 | |