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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
69101-69150 / 86044 show all | |||||||||||||||
| ckim-gatk | INDEL | D16_PLUS | HG002complexvar | * | 97.6146 | 97.6263 | 97.6030 | 66.9174 | 1604 | 39 | 1588 | 39 | 28 | 71.7949 | |
| hfeng-pmm1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.8444 | 99.6892 | 100.0000 | 52.3753 | 1604 | 5 | 1604 | 0 | 0 | ||
| ckim-vqsr | INDEL | I1_5 | map_siren | het | 97.0962 | 95.4194 | 98.8329 | 85.9291 | 1604 | 77 | 1609 | 19 | 5 | 26.3158 | |
| dgrover-gatk | INDEL | D16_PLUS | HG002complexvar | * | 97.6446 | 97.6263 | 97.6630 | 66.8096 | 1604 | 39 | 1588 | 38 | 27 | 71.0526 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.7823 | 99.6892 | 99.8755 | 54.6328 | 1604 | 5 | 1604 | 2 | 1 | 50.0000 | |
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.7512 | 99.6892 | 99.8133 | 54.3984 | 1604 | 5 | 1604 | 3 | 2 | 66.6667 | |
| qzeng-custom | INDEL | D1_5 | map_l100_m2_e0 | * | 90.1218 | 83.8120 | 97.4590 | 87.8583 | 1605 | 310 | 1841 | 48 | 35 | 72.9167 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.8134 | 99.7514 | 99.8755 | 42.5661 | 1605 | 4 | 1605 | 2 | 2 | 100.0000 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.3153 | 96.9789 | 99.6891 | 57.4040 | 1605 | 50 | 1603 | 5 | 2 | 40.0000 | |
| bgallagher-sentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.8755 | 99.7514 | 100.0000 | 43.3263 | 1605 | 4 | 1605 | 0 | 0 | ||
| astatham-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.8445 | 99.7514 | 99.9377 | 43.3110 | 1605 | 4 | 1605 | 1 | 1 | 100.0000 | |
| rpoplin-dv42 | INDEL | D16_PLUS | HG002compoundhet | hetalt | 90.6567 | 83.2469 | 99.5146 | 24.3343 | 1605 | 323 | 1640 | 8 | 8 | 100.0000 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 90.5141 | 83.1176 | 99.3556 | 34.2956 | 1605 | 326 | 1696 | 11 | 11 | 100.0000 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 90.5141 | 83.1176 | 99.3556 | 34.2956 | 1605 | 326 | 1696 | 11 | 11 | 100.0000 | |
| rpoplin-dv42 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.8755 | 99.7514 | 100.0000 | 52.7941 | 1605 | 4 | 1605 | 0 | 0 | ||
| ckim-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.8445 | 99.7514 | 99.9377 | 43.4109 | 1605 | 4 | 1605 | 1 | 1 | 100.0000 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.8445 | 99.7514 | 99.9377 | 43.6886 | 1605 | 4 | 1605 | 1 | 1 | 100.0000 | |
| raldana-dualsentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.9067 | 99.8135 | 100.0000 | 43.3110 | 1606 | 3 | 1606 | 0 | 0 | ||
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.8756 | 99.8135 | 99.9378 | 52.0442 | 1606 | 3 | 1606 | 1 | 0 | 0.0000 | |
| 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 | |
| hfeng-pmm2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.8756 | 99.8135 | 99.9378 | 53.0803 | 1606 | 3 | 1606 | 1 | 0 | 0.0000 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 92.3449 | 94.3042 | 90.4654 | 62.2051 | 1606 | 97 | 1594 | 168 | 164 | 97.6190 | |
| mlin-fermikit | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.4672 | 99.8135 | 97.1567 | 54.5004 | 1606 | 3 | 1606 | 47 | 36 | 76.5957 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | * | homalt | 97.3031 | 94.9173 | 99.8119 | 53.8350 | 1606 | 86 | 1592 | 3 | 3 | 100.0000 | |
| jmaeng-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.9067 | 99.8135 | 100.0000 | 43.7478 | 1606 | 3 | 1606 | 0 | 0 | ||
| cchapple-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.9067 | 99.8135 | 100.0000 | 43.8707 | 1606 | 3 | 1598 | 0 | 0 | ||
| ckim-isaac | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.5412 | 91.9336 | 99.4434 | 50.8361 | 1607 | 141 | 1608 | 9 | 7 | 77.7778 | |
| rpoplin-dv42 | INDEL | D16_PLUS | * | hetalt | 90.5247 | 83.1350 | 99.3563 | 34.4206 | 1607 | 326 | 1698 | 11 | 11 | 100.0000 | |
| jli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.9067 | 99.8757 | 99.9378 | 47.2268 | 1607 | 2 | 1607 | 1 | 1 | 100.0000 | |
| jpowers-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.9538 | 99.9378 | 97.9890 | 60.2085 | 1608 | 1 | 1608 | 33 | 18 | 54.5455 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 73.6158 | 59.0525 | 97.7135 | 42.8517 | 1608 | 1115 | 1453 | 34 | 29 | 85.2941 | |
| ghariani-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.1063 | 99.9378 | 98.2885 | 58.1479 | 1608 | 1 | 1608 | 28 | 18 | 64.2857 | |
| gduggal-bwafb | INDEL | I1_5 | map_siren | het | 97.2030 | 95.6573 | 98.7995 | 79.6283 | 1608 | 73 | 1646 | 20 | 10 | 50.0000 | |
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 75.5916 | 74.7677 | 76.4339 | 43.0667 | 1609 | 543 | 1839 | 567 | 503 | 88.7125 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 87.0530 | 88.5102 | 85.6431 | 75.6731 | 1610 | 209 | 1718 | 288 | 261 | 90.6250 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 87.0530 | 88.5102 | 85.6431 | 75.6731 | 1610 | 209 | 1718 | 288 | 261 | 90.6250 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 85.8472 | 76.6302 | 97.5845 | 55.5436 | 1610 | 491 | 1616 | 40 | 37 | 92.5000 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 42.7044 | 39.5869 | 46.3548 | 67.9809 | 1610 | 2457 | 1615 | 1869 | 1855 | 99.2509 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.4727 | 88.3644 | 99.2078 | 40.1968 | 1610 | 212 | 1628 | 13 | 12 | 92.3077 | |
| gduggal-bwaplat | INDEL | * | map_l100_m1_e0 | het | 83.2773 | 72.0805 | 98.5924 | 92.9796 | 1611 | 624 | 1611 | 23 | 7 | 30.4348 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 63.8112 | 58.4543 | 70.2490 | 50.9009 | 1611 | 1145 | 1608 | 681 | 680 | 99.8532 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 95.0350 | 97.4018 | 92.7804 | 51.2443 | 1612 | 43 | 2763 | 215 | 42 | 19.5349 | |
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 93.9933 | 91.3832 | 96.7568 | 85.7571 | 1612 | 152 | 1611 | 54 | 24 | 44.4444 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | HG002compoundhet | * | 84.3510 | 75.2217 | 96.0024 | 42.9312 | 1612 | 531 | 1585 | 66 | 64 | 96.9697 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 51.3330 | 45.2682 | 59.2743 | 64.1063 | 1612 | 1949 | 1601 | 1100 | 1012 | 92.0000 | |
| gduggal-snapplat | SNP | tv | map_l250_m2_e1 | het | 86.0422 | 82.0356 | 90.4602 | 95.1420 | 1612 | 353 | 1612 | 170 | 70 | 41.1765 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 72.0736 | 97.5227 | 57.1579 | 53.3629 | 1614 | 41 | 1625 | 1218 | 1207 | 99.0969 | |
| qzeng-custom | SNP | * | map_l250_m2_e0 | homalt | 74.7183 | 60.0894 | 98.7624 | 89.3086 | 1614 | 1072 | 1596 | 20 | 19 | 95.0000 | |
| gduggal-bwavard | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 97.6712 | 95.6754 | 99.7520 | 53.7159 | 1615 | 73 | 1609 | 4 | 3 | 75.0000 | |
| ltrigg-rtg1 | INDEL | I1_5 | map_siren | het | 97.6073 | 96.1333 | 99.1272 | 75.0467 | 1616 | 65 | 1590 | 14 | 0 | 0.0000 | |