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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
84251-84300 / 86044 show all | |||||||||||||||
| cchapple-custom | SNP | * | map_l100_m1_e0 | * | 97.5223 | 97.7156 | 97.3298 | 67.9657 | 70749 | 1654 | 70750 | 1941 | 403 | 20.7625 | |
| gduggal-snapvard | SNP | * | map_l250_m1_e0 | het | 81.0291 | 96.2566 | 69.9614 | 91.9347 | 4577 | 178 | 4530 | 1945 | 87 | 4.4730 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 90.5655 | 92.3733 | 88.8270 | 56.6366 | 16460 | 1359 | 15479 | 1947 | 1601 | 82.2291 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 84.8407 | 79.4106 | 91.0680 | 42.1071 | 9943 | 2578 | 19902 | 1952 | 731 | 37.4488 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 62.4607 | 73.6600 | 54.2174 | 39.2369 | 481 | 172 | 2314 | 1954 | 1945 | 99.5394 | |
| gduggal-snapplat | INDEL | D1_5 | HG002compoundhet | homalt | 26.1575 | 72.5086 | 15.9570 | 58.0098 | 211 | 80 | 371 | 1954 | 1741 | 89.0993 | |
| ghariani-varprowl | SNP | tv | HG002compoundhet | het | 78.1241 | 90.1776 | 68.9129 | 69.5656 | 4214 | 459 | 4336 | 1956 | 10 | 0.5112 | |
| anovak-vg | INDEL | I6_15 | HG002compoundhet | * | 31.2822 | 22.7666 | 49.9744 | 31.5356 | 1998 | 6778 | 1954 | 1956 | 1488 | 76.0736 | |
| gduggal-snapvard | SNP | * | map_l250_m1_e0 | * | 85.6069 | 95.3199 | 77.6904 | 91.0746 | 6884 | 338 | 6815 | 1957 | 96 | 4.9055 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 89.9539 | 95.3891 | 85.1048 | 47.7198 | 4241 | 205 | 11210 | 1962 | 925 | 47.1458 | |
| cchapple-custom | SNP | * | map_l100_m2_e0 | het | 96.8591 | 97.8857 | 95.8537 | 73.9797 | 45418 | 981 | 45473 | 1967 | 406 | 20.6406 | |
| gduggal-snapvard | INDEL | D6_15 | HG002compoundhet | het | 67.0812 | 63.3178 | 71.3203 | 33.1905 | 542 | 314 | 4894 | 1968 | 1718 | 87.2967 | |
| gduggal-snapvard | INDEL | D6_15 | HG002compoundhet | * | 59.7955 | 51.4782 | 71.3183 | 33.2912 | 4649 | 4382 | 4896 | 1969 | 1719 | 87.3032 | |
| cchapple-custom | SNP | * | map_l100_m2_e0 | * | 97.5457 | 97.7435 | 97.3487 | 69.9609 | 72295 | 1669 | 72297 | 1969 | 408 | 20.7212 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 90.4147 | 91.9985 | 88.8845 | 55.6709 | 14763 | 1284 | 15793 | 1975 | 866 | 43.8481 | |
| ltrigg-rtg1 | SNP | ti | * | het | 99.8539 | 99.8618 | 99.8460 | 16.3632 | 1280123 | 1771 | 1280140 | 1975 | 52 | 2.6329 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 83.3290 | 92.2710 | 75.9669 | 53.2043 | 6196 | 519 | 6246 | 1976 | 523 | 26.4676 | |
| gduggal-snapfb | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 56.0716 | 49.9257 | 63.9431 | 62.6651 | 2017 | 2023 | 3506 | 1977 | 448 | 22.6606 | |
| ciseli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 45.1028 | 77.9188 | 31.7367 | 57.3110 | 921 | 261 | 921 | 1981 | 1814 | 91.5699 | |
| gduggal-snapplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 82.0910 | 79.0543 | 85.3704 | 89.9548 | 11519 | 3052 | 11560 | 1981 | 144 | 7.2691 | |
| gduggal-snapplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 82.0910 | 79.0543 | 85.3704 | 89.9548 | 11519 | 3052 | 11560 | 1981 | 144 | 7.2691 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 36.9440 | 68.9906 | 25.2262 | 52.0434 | 663 | 298 | 669 | 1983 | 1976 | 99.6470 | |
| cchapple-custom | SNP | * | map_l100_m2_e1 | het | 96.8714 | 97.9018 | 95.8624 | 74.0033 | 45914 | 984 | 45967 | 1984 | 408 | 20.5645 | |
| ciseli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 85.2279 | 98.0433 | 75.3754 | 62.9512 | 6063 | 121 | 6073 | 1984 | 52 | 2.6210 | |
| cchapple-custom | SNP | * | map_l100_m2_e1 | * | 97.5551 | 97.7575 | 97.3536 | 69.9828 | 73061 | 1676 | 73060 | 1986 | 410 | 20.6445 | |
| eyeh-varpipe | INDEL | I6_15 | HG002compoundhet | homalt | 2.5353 | 74.1935 | 1.2897 | 22.4317 | 23 | 8 | 26 | 1990 | 1987 | 99.8492 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 90.8245 | 87.6365 | 94.2532 | 40.4574 | 33216 | 4686 | 32687 | 1993 | 1737 | 87.1550 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 47.7195 | 36.5649 | 68.6675 | 29.6562 | 1090 | 1891 | 4370 | 1994 | 1989 | 99.7492 | |
| ciseli-custom | SNP | * | map_l125_m0_e0 | het | 73.0283 | 66.5824 | 80.8560 | 84.3182 | 8432 | 4232 | 8426 | 1995 | 66 | 3.3083 | |
| gduggal-snapvard | SNP | * | map_l250_m2_e0 | het | 81.9515 | 96.3612 | 71.2908 | 92.3358 | 5005 | 189 | 4954 | 1995 | 92 | 4.6115 | |
| 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 | |
| jlack-gatk | SNP | ti | map_l100_m1_e0 | het | 96.3792 | 99.2318 | 93.6859 | 77.4968 | 29712 | 230 | 29705 | 2002 | 175 | 8.7413 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 22.1585 | 18.8343 | 26.9076 | 54.2967 | 740 | 3189 | 737 | 2002 | 1995 | 99.6503 | |
| gduggal-snapvard | SNP | * | map_l250_m2_e1 | het | 82.0702 | 96.3526 | 71.4754 | 92.4111 | 5072 | 192 | 5019 | 2003 | 93 | 4.6430 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 80.0812 | 74.2799 | 86.8654 | 57.3222 | 13126 | 4545 | 13260 | 2005 | 1766 | 88.0798 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 80.0812 | 74.2799 | 86.8654 | 57.3222 | 13126 | 4545 | 13260 | 2005 | 1766 | 88.0798 | |
| ciseli-custom | SNP | * | map_l150_m0_e0 | * | 75.3031 | 70.4787 | 80.8364 | 85.2202 | 8480 | 3552 | 8466 | 2007 | 507 | 25.2616 | |
| gduggal-snapvard | SNP | * | map_l250_m2_e0 | * | 86.3034 | 95.4344 | 78.7671 | 91.5243 | 7525 | 360 | 7449 | 2008 | 101 | 5.0299 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 70.1659 | 88.4506 | 58.1458 | 66.8417 | 2175 | 284 | 2791 | 2009 | 225 | 11.1996 | |
| gduggal-snapvard | SNP | * | map_l250_m2_e1 | * | 86.3822 | 95.4176 | 78.9099 | 91.6016 | 7621 | 366 | 7543 | 2016 | 102 | 5.0595 | |
| jlack-gatk | SNP | ti | map_l100_m1_e0 | * | 97.4794 | 99.0945 | 95.9161 | 72.9428 | 47497 | 434 | 47490 | 2022 | 193 | 9.5450 | |
| ghariani-varprowl | INDEL | D1_5 | HG002complexvar | * | 93.6809 | 93.5932 | 93.7688 | 56.5500 | 30619 | 2096 | 30473 | 2025 | 1375 | 67.9012 | |
| eyeh-varpipe | INDEL | I6_15 | * | homalt | 77.6886 | 84.0359 | 72.2329 | 34.4939 | 5243 | 996 | 5273 | 2027 | 2012 | 99.2600 | |
| 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 | |
| gduggal-snapvard | SNP | tv | map_l100_m1_e0 | het | 92.4877 | 97.3990 | 88.0480 | 78.4967 | 15016 | 401 | 14962 | 2031 | 139 | 6.8439 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 37.5716 | 28.2822 | 55.9480 | 46.5176 | 1788 | 4534 | 2582 | 2033 | 1650 | 81.1608 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 37.5716 | 28.2822 | 55.9480 | 46.5176 | 1788 | 4534 | 2582 | 2033 | 1650 | 81.1608 | |
| jlack-gatk | SNP | ti | map_l100_m2_e0 | het | 96.4036 | 99.2424 | 93.7226 | 78.7202 | 30390 | 232 | 30383 | 2035 | 176 | 8.6487 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 80.9211 | 77.9906 | 84.0804 | 49.2093 | 10751 | 3034 | 10748 | 2035 | 2023 | 99.4103 | |