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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
23701-23750 / 86044 show all | |||||||||||||||
| ndellapenna-hhga | INDEL | D1_5 | map_l100_m1_e0 | het | 97.7235 | 97.6013 | 97.8459 | 81.5387 | 1180 | 29 | 1181 | 26 | 9 | 34.6154 | |
| ndellapenna-hhga | INDEL | D1_5 | map_l100_m2_e0 | het | 97.8087 | 97.6911 | 97.9266 | 82.2279 | 1227 | 29 | 1228 | 26 | 9 | 34.6154 | |
| ndellapenna-hhga | INDEL | D1_5 | map_l100_m2_e1 | het | 97.7909 | 97.7129 | 97.8690 | 82.3415 | 1239 | 29 | 1240 | 27 | 9 | 33.3333 | |
| ndellapenna-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 82.6785 | 85.8537 | 79.7297 | 84.6367 | 176 | 29 | 177 | 45 | 26 | 57.7778 | |
| ndellapenna-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 82.6785 | 85.8537 | 79.7297 | 84.6367 | 176 | 29 | 177 | 45 | 26 | 57.7778 | |
| mlin-fermikit | INDEL | I6_15 | map_siren | het | 82.8019 | 79.7203 | 86.1314 | 81.4363 | 114 | 29 | 118 | 19 | 17 | 89.4737 | |
| mlin-fermikit | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 98.9788 | 98.1646 | 99.8066 | 46.6460 | 1551 | 29 | 1548 | 3 | 1 | 33.3333 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 93.8778 | 96.0437 | 91.8075 | 72.7305 | 704 | 29 | 706 | 63 | 44 | 69.8413 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 97.6709 | 97.2719 | 98.0732 | 76.6321 | 1034 | 29 | 1018 | 20 | 19 | 95.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 97.6856 | 95.4758 | 100.0000 | 43.1608 | 612 | 29 | 615 | 0 | 0 | ||
| jlack-gatk | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.8935 | 99.8564 | 99.9306 | 55.5702 | 20170 | 29 | 20170 | 14 | 13 | 92.8571 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.3017 | 99.3248 | 99.2786 | 49.2620 | 4266 | 29 | 4266 | 31 | 2 | 6.4516 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.0946 | 96.0916 | 98.1187 | 71.9562 | 713 | 29 | 678 | 13 | 8 | 61.5385 | |
| hfeng-pmm1 | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 82.4859 | 71.5686 | 97.3333 | 92.8910 | 73 | 29 | 73 | 2 | 0 | 0.0000 | |
| hfeng-pmm1 | SNP | * | map_l150_m1_e0 | homalt | 99.7516 | 99.7427 | 99.7604 | 71.3075 | 11244 | 29 | 11244 | 27 | 10 | 37.0370 | |
| hfeng-pmm1 | SNP | * | map_l150_m2_e0 | homalt | 99.7606 | 99.7521 | 99.7692 | 73.4870 | 11670 | 29 | 11670 | 27 | 10 | 37.0370 | |
| hfeng-pmm1 | SNP | * | map_l150_m2_e1 | homalt | 99.7632 | 99.7548 | 99.7717 | 73.5145 | 11798 | 29 | 11798 | 27 | 10 | 37.0370 | |
| hfeng-pmm1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 92.5301 | 86.8778 | 98.9691 | 90.9683 | 192 | 29 | 192 | 2 | 0 | 0.0000 | |
| hfeng-pmm1 | SNP | ti | map_l100_m1_e0 | homalt | 99.8580 | 99.8385 | 99.8775 | 60.1505 | 17931 | 29 | 17931 | 22 | 12 | 54.5455 | |
| hfeng-pmm1 | SNP | ti | map_l100_m2_e0 | homalt | 99.8607 | 99.8416 | 99.8798 | 62.5925 | 18280 | 29 | 18280 | 22 | 12 | 54.5455 | |
| hfeng-pmm1 | SNP | ti | map_l100_m2_e1 | homalt | 99.8621 | 99.8432 | 99.8810 | 62.5754 | 18465 | 29 | 18465 | 22 | 12 | 54.5455 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 90.4918 | 82.6347 | 100.0000 | 69.2140 | 138 | 29 | 141 | 0 | 0 | ||
| jlack-gatk | INDEL | D16_PLUS | HG002complexvar | hetalt | 92.3729 | 88.2591 | 96.8889 | 46.8085 | 218 | 29 | 436 | 14 | 14 | 100.0000 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 92.5616 | 97.8195 | 87.8400 | 82.6726 | 1301 | 29 | 1098 | 152 | 125 | 82.2368 | |
| jlack-gatk | INDEL | D1_5 | map_l100_m2_e1 | * | 95.2916 | 98.5044 | 92.2817 | 87.3451 | 1910 | 29 | 1913 | 160 | 11 | 6.8750 | |
| jlack-gatk | INDEL | D6_15 | * | homalt | 98.1988 | 99.5416 | 96.8918 | 51.5867 | 6297 | 29 | 6297 | 202 | 199 | 98.5149 | |
| jlack-gatk | INDEL | D6_15 | HG002compoundhet | het | 80.7008 | 96.6121 | 69.2893 | 65.6695 | 827 | 29 | 819 | 363 | 325 | 89.5317 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 86.9630 | 95.2537 | 80.0000 | 69.7438 | 582 | 29 | 548 | 137 | 132 | 96.3504 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 89.1470 | 91.9890 | 86.4754 | 82.1898 | 333 | 29 | 211 | 33 | 33 | 100.0000 | |
| hfeng-pmm1 | INDEL | D1_5 | map_l125_m1_e0 | het | 97.4839 | 96.0055 | 99.0085 | 82.7426 | 697 | 29 | 699 | 7 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | D1_5 | map_l125_m2_e0 | het | 97.6108 | 96.2042 | 99.0591 | 83.7802 | 735 | 29 | 737 | 7 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | D1_5 | map_l125_m2_e1 | het | 97.6297 | 96.2338 | 99.0667 | 83.9125 | 741 | 29 | 743 | 7 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.1595 | 95.6456 | 98.7220 | 86.6553 | 637 | 29 | 618 | 8 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.1595 | 95.6456 | 98.7220 | 86.6553 | 637 | 29 | 618 | 8 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 95.9595 | 93.9583 | 98.0477 | 81.2678 | 451 | 29 | 452 | 9 | 7 | 77.7778 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 99.2974 | 99.4333 | 99.1620 | 40.9075 | 5088 | 29 | 5088 | 43 | 42 | 97.6744 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 99.0193 | 98.0576 | 100.0000 | 32.2402 | 1464 | 29 | 1467 | 0 | 0 | ||
| hfeng-pmm3 | INDEL | D6_15 | * | homalt | 99.3845 | 99.5416 | 99.2279 | 50.7795 | 6297 | 29 | 6297 | 49 | 45 | 91.8367 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.0614 | 93.9583 | 98.2609 | 81.1243 | 451 | 29 | 452 | 8 | 7 | 87.5000 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.8501 | 97.8723 | 99.8476 | 77.1269 | 1334 | 29 | 1310 | 2 | 0 | 0.0000 | |
| hfeng-pmm3 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 89.7690 | 82.4242 | 98.5507 | 91.0273 | 136 | 29 | 136 | 2 | 0 | 0.0000 | |
| hfeng-pmm3 | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.3172 | 98.6436 | 100.0000 | 35.7535 | 2109 | 29 | 2106 | 0 | 0 | ||
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.2750 | 99.3899 | 99.1604 | 41.1634 | 4724 | 29 | 4724 | 40 | 40 | 100.0000 | |
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 95.7829 | 92.3684 | 99.4595 | 64.7619 | 351 | 29 | 368 | 2 | 2 | 100.0000 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 81.2903 | 68.4783 | 100.0000 | 58.5526 | 63 | 29 | 63 | 0 | 0 | ||
| hfeng-pmm2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5873 | 99.2770 | 99.8996 | 46.3020 | 3982 | 29 | 3982 | 4 | 0 | 0.0000 | |
| hfeng-pmm2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 87.5596 | 80.9211 | 95.3846 | 90.3561 | 123 | 29 | 124 | 6 | 0 | 0.0000 | |
| hfeng-pmm2 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 85.9729 | 76.6129 | 97.9381 | 89.9168 | 95 | 29 | 95 | 2 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 90.5350 | 91.9220 | 89.1892 | 48.1793 | 330 | 29 | 330 | 40 | 38 | 95.0000 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.9392 | 95.2922 | 98.6441 | 64.3073 | 587 | 29 | 582 | 8 | 8 | 100.0000 | |