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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
7751-7800 / 86044 show all | |||||||||||||||
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 88.2450 | 80.8166 | 97.1772 | 89.7454 | 8729 | 2072 | 8744 | 254 | 45 | 17.7165 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.7097 | 93.6390 | 99.9886 | 31.7888 | 8700 | 591 | 8743 | 1 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.7097 | 93.6390 | 99.9886 | 31.7888 | 8700 | 591 | 8743 | 1 | 0 | 0.0000 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.6089 | 93.9727 | 99.3973 | 31.2378 | 8731 | 560 | 8741 | 53 | 52 | 98.1132 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.6089 | 93.9727 | 99.3973 | 31.2378 | 8731 | 560 | 8741 | 53 | 52 | 98.1132 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.4888 | 93.5852 | 99.5783 | 30.8129 | 8695 | 596 | 8738 | 37 | 37 | 100.0000 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.4888 | 93.5852 | 99.5783 | 30.8129 | 8695 | 596 | 8738 | 37 | 37 | 100.0000 | |
| ltrigg-rtg1 | SNP | tv | HG002compoundhet | * | 98.9891 | 98.2741 | 99.7146 | 44.8855 | 8769 | 154 | 8736 | 25 | 5 | 20.0000 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.1607 | 93.4776 | 99.0024 | 33.2299 | 8685 | 606 | 8733 | 88 | 82 | 93.1818 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.1607 | 93.4776 | 99.0024 | 33.2299 | 8685 | 606 | 8733 | 88 | 82 | 93.1818 | |
| 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 | |
| ckim-vqsr | SNP | tv | HG002compoundhet | * | 98.8066 | 97.8931 | 99.7373 | 49.7301 | 8735 | 188 | 8732 | 23 | 15 | 65.2174 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 63.9682 | 59.1207 | 69.6815 | 44.3739 | 8741 | 6044 | 8729 | 3798 | 3701 | 97.4460 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 67.5308 | 74.8546 | 61.5124 | 50.8317 | 4376 | 1470 | 8728 | 5461 | 4703 | 86.1198 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 67.5308 | 74.8546 | 61.5124 | 50.8317 | 4376 | 1470 | 8728 | 5461 | 4703 | 86.1198 | |
| gduggal-bwaplat | INDEL | D1_5 | HG002compoundhet | * | 81.6558 | 71.3118 | 95.5098 | 73.5540 | 8725 | 3510 | 8721 | 410 | 263 | 64.1463 | |
| mlin-fermikit | SNP | ti | map_l125_m2_e1 | het | 62.3819 | 45.6908 | 98.2867 | 64.4551 | 8721 | 10366 | 8720 | 152 | 7 | 4.6053 | |
| gduggal-snapvard | SNP | tv | map_l100_m1_e0 | homalt | 98.2646 | 96.7599 | 99.8168 | 61.4274 | 8750 | 293 | 8718 | 16 | 10 | 62.5000 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.5598 | 93.3484 | 100.0000 | 31.4834 | 8673 | 618 | 8716 | 0 | 0 | ||
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.5598 | 93.3484 | 100.0000 | 31.4834 | 8673 | 618 | 8716 | 0 | 0 | ||
| eyeh-varpipe | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 58.5321 | 47.8735 | 75.2959 | 43.8204 | 2544 | 2770 | 8714 | 2859 | 2841 | 99.3704 | |
| ckim-isaac | SNP | tv | map_l125_m1_e0 | * | 70.3696 | 54.3831 | 99.6682 | 71.7978 | 8710 | 7306 | 8712 | 29 | 9 | 31.0345 | |
| gduggal-bwaplat | SNP | * | map_l125_m2_e1 | homalt | 66.3796 | 49.6863 | 99.9655 | 80.4451 | 8711 | 8821 | 8704 | 3 | 3 | 100.0000 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 91.7464 | 96.2737 | 87.6259 | 45.7712 | 3152 | 122 | 8703 | 1229 | 548 | 44.5891 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 85.2919 | 75.6705 | 97.7165 | 64.9393 | 8690 | 2794 | 8687 | 203 | 174 | 85.7143 | |
| ndellapenna-hhga | SNP | tv | HG002compoundhet | * | 98.0516 | 97.2879 | 98.8274 | 47.0684 | 8681 | 242 | 8681 | 103 | 93 | 90.2913 | |
| gduggal-snapplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 79.2090 | 80.0667 | 78.3696 | 91.0972 | 8648 | 2153 | 8681 | 2396 | 141 | 5.8848 | |
| gduggal-bwaplat | SNP | ti | HG002compoundhet | het | 83.6361 | 90.0158 | 78.1008 | 46.8217 | 8556 | 949 | 8677 | 2433 | 181 | 7.4394 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 84.3874 | 97.5345 | 74.3636 | 48.4035 | 8189 | 207 | 8676 | 2991 | 2903 | 97.0578 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 46.9955 | 42.3432 | 52.7964 | 40.4686 | 8721 | 11875 | 8666 | 7748 | 7585 | 97.8962 | |
| jli-custom | INDEL | D6_15 | HG002compoundhet | * | 96.8618 | 95.8809 | 97.8630 | 33.8766 | 8659 | 372 | 8655 | 189 | 186 | 98.4127 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 86.2248 | 91.8756 | 81.2289 | 81.5160 | 8391 | 742 | 8646 | 1998 | 399 | 19.9700 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 86.2248 | 91.8756 | 81.2289 | 81.5160 | 8391 | 742 | 8646 | 1998 | 399 | 19.9700 | |
| gduggal-snapplat | SNP | ti | HG002compoundhet | het | 78.6871 | 89.5844 | 70.1534 | 57.2786 | 8515 | 990 | 8645 | 3678 | 282 | 7.6672 | |
| mlin-fermikit | SNP | tv | map_l100_m2_e0 | het | 70.4610 | 54.8457 | 98.5073 | 60.6122 | 8653 | 7124 | 8645 | 131 | 2 | 1.5267 | |
| ckim-gatk | SNP | * | map_l125_m0_e0 | het | 79.9330 | 68.2249 | 96.4920 | 90.8886 | 8640 | 4024 | 8637 | 314 | 30 | 9.5541 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 45.8395 | 42.0033 | 50.4468 | 47.0151 | 8651 | 11945 | 8637 | 8484 | 8329 | 98.1730 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 65.9654 | 55.6526 | 80.9698 | 74.3202 | 8669 | 6908 | 8633 | 2029 | 1680 | 82.7994 | |
| ciseli-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 71.8331 | 93.3976 | 58.3587 | 78.4954 | 8530 | 603 | 8633 | 6160 | 87 | 1.4123 | |
| ciseli-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 71.8331 | 93.3976 | 58.3587 | 78.4954 | 8530 | 603 | 8633 | 6160 | 87 | 1.4123 | |
| jmaeng-gatk | SNP | * | map_l125_m0_e0 | het | 79.8036 | 68.1775 | 96.2100 | 91.1308 | 8634 | 4030 | 8631 | 340 | 27 | 7.9412 | |
| ckim-isaac | INDEL | I6_15 | * | het | 88.7567 | 85.9065 | 91.8024 | 48.2080 | 8619 | 1414 | 8623 | 770 | 554 | 71.9481 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 83.6639 | 97.9752 | 73.0007 | 49.9045 | 8226 | 170 | 8617 | 3187 | 3103 | 97.3643 | |
| ltrigg-rtg2 | INDEL | D6_15 | HG002compoundhet | * | 97.5434 | 95.9362 | 99.2054 | 30.5780 | 8664 | 367 | 8615 | 69 | 63 | 91.3043 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 80.5008 | 99.2225 | 67.7227 | 54.9332 | 8295 | 65 | 8615 | 4106 | 4035 | 98.2708 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 80.5008 | 99.2225 | 67.7227 | 54.9332 | 8295 | 65 | 8615 | 4106 | 4035 | 98.2708 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 70.7753 | 78.9709 | 64.1209 | 53.4898 | 4420 | 1177 | 8614 | 4820 | 4189 | 86.9087 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 95.8359 | 92.4591 | 99.4688 | 63.5748 | 8595 | 701 | 8613 | 46 | 42 | 91.3043 | |
| asubramanian-gatk | SNP | tv | HG002compoundhet | * | 98.0032 | 96.5370 | 99.5145 | 49.4980 | 8614 | 309 | 8609 | 42 | 11 | 26.1905 | |