PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
82401-82450 / 86044 show all | |||||||||||||||
| jpowers-varprowl | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 0.5082 | 0.0000 | 0.0000 | 9 | 1762 | 0 | 0 | 0 | ||
| anovak-vg | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 76.0027 | 83.0403 | 70.0649 | 36.4124 | 8642 | 1765 | 11127 | 4754 | 3440 | 72.3601 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 17.3710 | 9.5750 | 93.4911 | 35.2490 | 187 | 1766 | 158 | 11 | 11 | 100.0000 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 2.6388 | 1.3951 | 24.3243 | 79.2910 | 25 | 1767 | 27 | 84 | 48 | 57.1429 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 31.1863 | 26.6694 | 37.5453 | 73.7371 | 643 | 1768 | 933 | 1552 | 633 | 40.7861 | |
| ltrigg-rtg1 | INDEL | D1_5 | * | * | 99.2818 | 98.7945 | 99.7740 | 55.6693 | 144976 | 1769 | 144802 | 328 | 127 | 38.7195 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 0.1129 | 0.0000 | 0.0000 | 2 | 1769 | 0 | 0 | 0 | ||
| mlin-fermikit | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 79.6367 | 72.0025 | 89.0817 | 63.6267 | 4552 | 1770 | 4569 | 560 | 555 | 99.1071 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 79.6367 | 72.0025 | 89.0817 | 63.6267 | 4552 | 1770 | 4569 | 560 | 555 | 99.1071 | |
| ltrigg-rtg1 | SNP | ti | * | het | 99.8539 | 99.8618 | 99.8460 | 16.3632 | 1280123 | 1771 | 1280140 | 1975 | 52 | 2.6329 | |
| ghariani-varprowl | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 74.6805 | 73.6967 | 75.6909 | 58.8837 | 4962 | 1771 | 4957 | 1592 | 1522 | 95.6030 | |
| jpowers-varprowl | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 17.1400 | 15.6592 | 18.9300 | 50.8097 | 329 | 1772 | 322 | 1379 | 1373 | 99.5649 | |
| gduggal-bwaplat | SNP | ti | map_l250_m1_e0 | het | 57.3348 | 40.2965 | 99.3367 | 97.5609 | 1196 | 1772 | 1198 | 8 | 2 | 25.0000 | |
| asubramanian-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.2746 | 98.1228 | 98.4270 | 77.7694 | 92676 | 1773 | 96110 | 1536 | 892 | 58.0729 | |
| anovak-vg | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 36.9586 | 26.4511 | 61.3160 | 39.5013 | 638 | 1774 | 1696 | 1070 | 978 | 91.4019 | |
| qzeng-custom | SNP | * | map_l250_m2_e1 | het | 76.4225 | 66.2804 | 90.2293 | 96.3549 | 3489 | 1775 | 3463 | 375 | 310 | 82.6667 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 87.2372 | 87.9811 | 86.5058 | 47.3544 | 13008 | 1777 | 14193 | 2214 | 1144 | 51.6712 | |
| anovak-vg | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 76.9105 | 75.4795 | 78.3969 | 40.0251 | 5470 | 1777 | 5614 | 1547 | 1192 | 77.0524 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 31.7698 | 26.2547 | 40.2181 | 60.9567 | 633 | 1778 | 627 | 932 | 870 | 93.3476 | |
| ckim-isaac | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 96.1945 | 93.5761 | 98.9636 | 58.8872 | 25900 | 1778 | 26068 | 273 | 187 | 68.4982 | |
| jmaeng-gatk | SNP | tv | map_l150_m1_e0 | homalt | 70.8865 | 54.9164 | 99.9539 | 80.1411 | 2167 | 1779 | 2167 | 1 | 1 | 100.0000 | |
| anovak-vg | INDEL | D6_15 | * | homalt | 75.9353 | 71.8780 | 80.4782 | 54.2097 | 4547 | 1779 | 4679 | 1135 | 811 | 71.4537 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 41.1142 | 35.4136 | 49.0020 | 38.2625 | 976 | 1780 | 982 | 1022 | 950 | 92.9550 | |
| gduggal-snapplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 20.4886 | 18.2277 | 23.3898 | 80.8737 | 397 | 1781 | 552 | 1808 | 263 | 14.5465 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 76.0747 | 61.6742 | 99.2486 | 27.4889 | 2866 | 1781 | 2906 | 22 | 22 | 100.0000 | |
| egarrison-hhga | SNP | * | HG002complexvar | het | 99.7873 | 99.6172 | 99.9580 | 18.3902 | 463715 | 1782 | 463738 | 195 | 79 | 40.5128 | |
| qzeng-custom | INDEL | D1_5 | HG002compoundhet | * | 88.1713 | 85.4271 | 91.0977 | 64.3947 | 10452 | 1783 | 11502 | 1124 | 856 | 76.1566 | |
| ckim-gatk | SNP | tv | map_l150_m1_e0 | homalt | 70.8020 | 54.8150 | 99.9538 | 81.0192 | 2163 | 1783 | 2163 | 1 | 0 | 0.0000 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 52.6451 | 49.8736 | 55.7428 | 73.7700 | 1776 | 1785 | 1786 | 1418 | 1371 | 96.6855 | |
| gduggal-snapvard | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 48.6618 | 55.8168 | 43.1327 | 62.9167 | 2255 | 1785 | 5053 | 6662 | 4317 | 64.8004 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 85.4215 | 78.1353 | 94.2062 | 35.5484 | 6386 | 1787 | 2065 | 127 | 67 | 52.7559 | |
| ciseli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 76.7889 | 93.7761 | 65.0122 | 76.1162 | 26925 | 1787 | 27218 | 14648 | 266 | 1.8160 | |
| ciseli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 76.7889 | 93.7761 | 65.0122 | 76.1162 | 26925 | 1787 | 27218 | 14648 | 266 | 1.8160 | |
| ciseli-custom | SNP | * | map_l150_m2_e0 | homalt | 86.5638 | 84.7166 | 88.4932 | 73.1740 | 9911 | 1788 | 9890 | 1286 | 1036 | 80.5599 | |
| raldana-dualsentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.5692 | 95.2826 | 97.8910 | 53.1171 | 36114 | 1788 | 35925 | 774 | 749 | 96.7700 | |
| gduggal-snapfb | INDEL | I1_5 | HG002complexvar | * | 93.5109 | 94.6378 | 92.4106 | 55.4813 | 31574 | 1789 | 31902 | 2620 | 888 | 33.8931 | |
| gduggal-snapplat | SNP | * | HG002compoundhet | het | 76.3438 | 87.3819 | 67.7816 | 62.0964 | 12389 | 1789 | 12564 | 5972 | 438 | 7.3342 | |
| gduggal-snapvard | INDEL | I6_15 | * | het | 64.9859 | 82.1571 | 53.7516 | 42.4853 | 8242 | 1790 | 11591 | 9973 | 7974 | 79.9559 | |
| gduggal-snapfb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 0.0000 | 0.0558 | 0.0000 | 0.0000 | 1 | 1791 | 0 | 0 | 0 | ||
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 71.6772 | 70.5040 | 72.8901 | 52.2851 | 4281 | 1791 | 4802 | 1786 | 1566 | 87.6820 | |
| gduggal-snapplat | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 0.0000 | 0.0000 | 0.0000 | 0 | 1792 | 0 | 0 | 0 | |||
| ckim-isaac | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 91.8499 | 88.8266 | 95.0863 | 43.5099 | 14254 | 1793 | 14165 | 732 | 583 | 79.6448 | |
| ghariani-varprowl | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 33.8478 | 32.4294 | 35.3960 | 74.1660 | 861 | 1794 | 858 | 1566 | 1515 | 96.7433 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 81.9762 | 69.7710 | 99.3570 | 62.1268 | 4143 | 1795 | 4172 | 27 | 27 | 100.0000 | |
| jmaeng-gatk | SNP | tv | map_l150_m2_e0 | homalt | 71.7739 | 55.9882 | 99.9563 | 81.6747 | 2286 | 1797 | 2286 | 1 | 1 | 100.0000 | |
| gduggal-snapvard | SNP | ti | map_l100_m1_e0 | * | 95.0911 | 96.2467 | 93.9630 | 72.8656 | 46132 | 1799 | 45682 | 2935 | 278 | 9.4719 | |
| ckim-gatk | SNP | tv | map_l150_m2_e0 | homalt | 71.6934 | 55.8903 | 99.9562 | 82.4006 | 2282 | 1801 | 2282 | 1 | 0 | 0.0000 | |
| qzeng-custom | SNP | ti | map_l250_m1_e0 | * | 73.1661 | 60.6683 | 92.1490 | 95.6157 | 2778 | 1801 | 2770 | 236 | 199 | 84.3220 | |
| jmaeng-gatk | SNP | tv | map_l150_m1_e0 | het | 83.3948 | 74.0426 | 95.4512 | 90.5818 | 5143 | 1803 | 5141 | 245 | 6 | 2.4490 | |
| gduggal-bwaplat | SNP | tv | map_l250_m1_e0 | * | 48.2541 | 31.8474 | 99.5277 | 97.7346 | 843 | 1804 | 843 | 4 | 1 | 25.0000 | |