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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
16401-16450 / 86044 show all | |||||||||||||||
| astatham-gatk | SNP | tv | map_l100_m2_e1 | het | 86.7191 | 76.7348 | 99.6902 | 76.6919 | 12230 | 3708 | 12226 | 38 | 10 | 26.3158 | |
| anovak-vg | INDEL | * | map_l250_m0_e0 | * | 64.4116 | 67.9487 | 61.2245 | 98.1965 | 53 | 25 | 60 | 38 | 20 | 52.6316 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 25.8993 | 40.0000 | 19.1489 | 57.2727 | 10 | 15 | 9 | 38 | 8 | 21.0526 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 28.0467 | 29.2683 | 26.9231 | 53.5714 | 12 | 29 | 14 | 38 | 20 | 52.6316 | |
| asubramanian-gatk | SNP | * | HG002compoundhet | hetalt | 95.0437 | 94.5476 | 95.5451 | 26.8439 | 815 | 47 | 815 | 38 | 0 | 0.0000 | |
| asubramanian-gatk | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 98.2626 | 98.6842 | 97.8446 | 62.1511 | 1725 | 23 | 1725 | 38 | 1 | 2.6316 | |
| asubramanian-gatk | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.1453 | 98.8584 | 99.4339 | 36.2670 | 6668 | 77 | 6675 | 38 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.5254 | 93.7213 | 99.5026 | 29.5295 | 7553 | 506 | 7601 | 38 | 37 | 97.3684 | |
| 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 | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 96.6140 | 98.9214 | 94.4118 | 67.8183 | 642 | 7 | 642 | 38 | 38 | 100.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | HG002compoundhet | hetalt | 96.7320 | 94.0192 | 99.6060 | 57.1663 | 9605 | 611 | 9606 | 38 | 38 | 100.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.2540 | 95.0409 | 99.5726 | 63.0163 | 8835 | 461 | 8854 | 38 | 38 | 100.0000 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.5254 | 93.7213 | 99.5026 | 29.5295 | 7553 | 506 | 7601 | 38 | 37 | 97.3684 | |
| anovak-vg | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 47.6190 | 44.4444 | 51.2821 | 43.8849 | 12 | 15 | 40 | 38 | 35 | 92.1053 | |
| anovak-vg | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 67.0246 | 87.7551 | 54.2169 | 78.5530 | 43 | 6 | 45 | 38 | 31 | 81.5789 | |
| anovak-vg | SNP | * | map_l125_m0_e0 | homalt | 85.5602 | 75.1937 | 99.2421 | 70.8421 | 5047 | 1665 | 4976 | 38 | 33 | 86.8421 | |
| anovak-vg | SNP | tv | func_cds | het | 97.9570 | 97.3654 | 98.5557 | 42.0612 | 2587 | 70 | 2593 | 38 | 21 | 55.2632 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 97.2183 | 97.1882 | 97.2484 | 66.9538 | 1348 | 39 | 1343 | 38 | 14 | 36.8421 | |
| astatham-gatk | INDEL | * | map_l150_m2_e1 | * | 96.4999 | 95.6915 | 97.3221 | 91.2120 | 1377 | 62 | 1381 | 38 | 8 | 21.0526 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.0605 | 98.0859 | 98.0352 | 64.9002 | 1896 | 37 | 1896 | 38 | 35 | 92.1053 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 97.0603 | 94.6723 | 99.5719 | 32.5070 | 8796 | 495 | 8838 | 38 | 37 | 97.3684 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 97.0603 | 94.6723 | 99.5719 | 32.5070 | 8796 | 495 | 8838 | 38 | 37 | 97.3684 | |
| astatham-gatk | INDEL | D6_15 | HG002complexvar | hetalt | 94.7783 | 93.2873 | 96.3178 | 48.2447 | 945 | 68 | 994 | 38 | 37 | 97.3684 | |
| asubramanian-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 44.7761 | 100.0000 | 28.8462 | 82.9508 | 15 | 0 | 15 | 37 | 0 | 0.0000 | |
| asubramanian-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 44.7761 | 100.0000 | 28.8462 | 82.9508 | 15 | 0 | 15 | 37 | 0 | 0.0000 | |
| astatham-gatk | SNP | ti | map_l100_m0_e0 | het | 88.3269 | 79.3034 | 99.6674 | 77.0849 | 11089 | 2894 | 11086 | 37 | 16 | 43.2432 | |
| astatham-gatk | SNP | tv | HG002complexvar | * | 99.1122 | 98.2547 | 99.9847 | 22.3181 | 241856 | 4296 | 241769 | 37 | 21 | 56.7568 | |
| astatham-gatk | SNP | tv | map_l100_m1_e0 | het | 86.5303 | 76.4416 | 99.6869 | 75.5609 | 11785 | 3632 | 11781 | 37 | 10 | 27.0270 | |
| astatham-gatk | SNP | tv | map_l100_m2_e0 | het | 86.7029 | 76.7066 | 99.6951 | 76.6657 | 12102 | 3675 | 12098 | 37 | 10 | 27.0270 | |
| asubramanian-gatk | INDEL | C16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 0.0000 | 0.0000 | 85.0806 | 0 | 0 | 0 | 37 | 0 | 0.0000 | ||
| asubramanian-gatk | INDEL | C6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 0.0000 | 0.0000 | 76.5823 | 0 | 0 | 0 | 37 | 0 | 0.0000 | ||
| asubramanian-gatk | INDEL | D16_PLUS | * | hetalt | 95.6218 | 93.1712 | 98.2048 | 39.4536 | 1801 | 132 | 2024 | 37 | 31 | 83.7838 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 95.6445 | 93.2160 | 98.2030 | 39.3698 | 1800 | 131 | 2022 | 37 | 31 | 83.7838 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 95.6445 | 93.2160 | 98.2030 | 39.3698 | 1800 | 131 | 2022 | 37 | 31 | 83.7838 | |
| anovak-vg | INDEL | * | map_l250_m2_e0 | homalt | 72.3983 | 74.7826 | 70.1613 | 95.5950 | 86 | 29 | 87 | 37 | 34 | 91.8919 | |
| anovak-vg | INDEL | * | map_l250_m2_e1 | homalt | 72.6272 | 75.0000 | 70.4000 | 95.6911 | 87 | 29 | 88 | 37 | 34 | 91.8919 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 90.6611 | 90.9091 | 90.4145 | 54.4274 | 340 | 34 | 349 | 37 | 21 | 56.7568 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 95.4177 | 95.2047 | 95.6316 | 62.5883 | 814 | 41 | 810 | 37 | 17 | 45.9459 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.8091 | 97.3562 | 98.2662 | 76.6111 | 2099 | 57 | 2097 | 37 | 20 | 54.0541 | |
| astatham-gatk | INDEL | * | map_l125_m2_e0 | het | 94.9267 | 92.7390 | 97.2201 | 89.8845 | 1290 | 101 | 1294 | 37 | 5 | 13.5135 | |
| astatham-gatk | INDEL | * | map_l125_m2_e1 | het | 94.9130 | 92.6847 | 97.2511 | 89.9694 | 1305 | 103 | 1309 | 37 | 5 | 13.5135 | |
| astatham-gatk | INDEL | * | map_l150_m2_e0 | * | 96.6049 | 95.8807 | 97.3400 | 91.1929 | 1350 | 58 | 1354 | 37 | 7 | 18.9189 | |
| astatham-gatk | INDEL | * | segdup | * | 98.7115 | 98.8654 | 98.5581 | 94.6872 | 2527 | 29 | 2529 | 37 | 10 | 27.0270 | |
| bgallagher-sentieon | INDEL | * | map_l100_m0_e0 | het | 97.4344 | 98.4329 | 96.4559 | 87.7838 | 1005 | 16 | 1007 | 37 | 4 | 10.8108 | |
| bgallagher-sentieon | INDEL | * | map_l150_m2_e1 | * | 97.9994 | 98.5407 | 97.4640 | 90.7582 | 1418 | 21 | 1422 | 37 | 8 | 21.6216 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.4715 | 93.5529 | 99.5781 | 31.7934 | 8692 | 599 | 8733 | 37 | 36 | 97.2973 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.4715 | 93.5529 | 99.5781 | 31.7934 | 8692 | 599 | 8733 | 37 | 36 | 97.2973 | |
| bgallagher-sentieon | INDEL | D6_15 | HG002complexvar | hetalt | 94.0808 | 91.9052 | 96.3618 | 47.7926 | 931 | 82 | 980 | 37 | 37 | 100.0000 | |
| hfeng-pmm1 | SNP | tv | map_l100_m0_e0 | het | 99.2295 | 98.9754 | 99.4850 | 70.4702 | 7148 | 74 | 7147 | 37 | 11 | 29.7297 | |
| hfeng-pmm2 | INDEL | * | map_l100_m0_e0 | het | 97.3349 | 98.2370 | 96.4491 | 87.4337 | 1003 | 18 | 1005 | 37 | 3 | 8.1081 | |