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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
82351-82400 / 86044 show all | |||||||||||||||
| gduggal-snapfb | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 87.7974 | 81.4329 | 95.2411 | 80.6685 | 7570 | 1726 | 3002 | 150 | 102 | 68.0000 | |
| gduggal-bwafb | INDEL | I1_5 | * | hetalt | 90.3216 | 84.5735 | 96.9081 | 78.3569 | 9468 | 1727 | 4294 | 137 | 135 | 98.5401 | |
| gduggal-snapvard | INDEL | D1_5 | * | het | 88.4948 | 98.0268 | 80.6523 | 58.4318 | 85844 | 1728 | 115949 | 27815 | 21843 | 78.5296 | |
| gduggal-snapvard | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 23.1444 | 17.6107 | 33.7493 | 43.2911 | 370 | 1731 | 649 | 1274 | 1040 | 81.6327 | |
| gduggal-bwafb | SNP | ti | * | het | 99.7363 | 99.8649 | 99.6080 | 22.2231 | 1280165 | 1732 | 1280284 | 5038 | 382 | 7.5824 | |
| hfeng-pmm1 | SNP | * | HG002complexvar | * | 99.8780 | 99.7704 | 99.9859 | 18.8078 | 752649 | 1732 | 752504 | 106 | 51 | 48.1132 | |
| qzeng-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 90.4993 | 83.4558 | 98.8412 | 37.5745 | 8742 | 1733 | 2900 | 34 | 26 | 76.4706 | |
| gduggal-bwavard | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 18.9766 | 17.5155 | 20.7036 | 55.4928 | 368 | 1733 | 359 | 1375 | 1359 | 98.8364 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 75.6874 | 87.3937 | 66.7467 | 68.5588 | 12021 | 1734 | 12511 | 6233 | 2150 | 34.4938 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 75.6874 | 87.3937 | 66.7467 | 68.5588 | 12021 | 1734 | 12511 | 6233 | 2150 | 34.4938 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 2.0892 | 0.0000 | 0.0000 | 37 | 1734 | 0 | 0 | 0 | ||
| ciseli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 60.9265 | 84.9007 | 47.5105 | 54.7800 | 9750 | 1734 | 9733 | 10753 | 9871 | 91.7976 | |
| anovak-vg | INDEL | D6_15 | HG002complexvar | * | 72.7472 | 67.2954 | 79.1602 | 52.2024 | 3568 | 1734 | 3582 | 943 | 676 | 71.6861 | |
| ltrigg-rtg2 | SNP | ti | * | het | 99.8504 | 99.8647 | 99.8361 | 15.7716 | 1280159 | 1735 | 1280167 | 2101 | 75 | 3.5697 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.4936 | 95.9940 | 99.0408 | 57.8182 | 41599 | 1736 | 41405 | 401 | 351 | 87.5312 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 0.0000 | 4.7201 | 0.0000 | 0.0000 | 86 | 1736 | 0 | 0 | 0 | ||
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 91.2469 | 84.8746 | 98.6537 | 45.5252 | 9747 | 1737 | 9746 | 133 | 101 | 75.9398 | |
| gduggal-snapfb | INDEL | I6_15 | * | homalt | 78.8948 | 72.1430 | 87.0410 | 39.6459 | 4501 | 1738 | 4480 | 667 | 645 | 96.7016 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 56.6451 | 52.8614 | 61.0122 | 54.6408 | 1949 | 1738 | 1953 | 1248 | 1228 | 98.3974 | |
| ghariani-varprowl | SNP | * | HG002complexvar | het | 99.2312 | 99.6262 | 98.8393 | 22.3346 | 463752 | 1740 | 464023 | 5449 | 138 | 2.5326 | |
| ciseli-custom | INDEL | I6_15 | HG002complexvar | het | 39.0345 | 26.1146 | 77.2559 | 60.9179 | 615 | 1740 | 625 | 184 | 138 | 75.0000 | |
| gduggal-snapfb | INDEL | I6_15 | HG002complexvar | * | 72.9303 | 63.6686 | 85.3453 | 43.1989 | 3051 | 1741 | 3040 | 522 | 491 | 94.0613 | |
| gduggal-snapplat | SNP | * | map_l150_m0_e0 | * | 89.5961 | 85.5219 | 94.0779 | 88.4577 | 10290 | 1742 | 10294 | 648 | 357 | 55.0926 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 0.0000 | 20.4566 | 0.0000 | 0.0000 | 448 | 1742 | 0 | 0 | 0 | ||
| hfeng-pmm2 | SNP | * | HG002complexvar | * | 99.8743 | 99.7689 | 99.9799 | 18.8346 | 752638 | 1743 | 752495 | 151 | 59 | 39.0728 | |
| jli-custom | INDEL | * | HG002compoundhet | * | 95.6209 | 94.1822 | 97.1042 | 61.3856 | 28217 | 1743 | 28100 | 838 | 804 | 95.9427 | |
| astatham-gatk | SNP | tv | map_l150_m2_e1 | * | 91.6416 | 84.8374 | 99.6324 | 80.3148 | 9758 | 1744 | 9756 | 36 | 13 | 36.1111 | |
| asubramanian-gatk | SNP | * | map_l250_m0_e0 | * | 30.8789 | 18.2670 | 99.7442 | 99.0504 | 390 | 1745 | 390 | 1 | 1 | 100.0000 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 59.5457 | 53.6378 | 66.9161 | 58.0784 | 2020 | 1746 | 2146 | 1061 | 754 | 71.0650 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 59.5457 | 53.6378 | 66.9161 | 58.0784 | 2020 | 1746 | 2146 | 1061 | 754 | 71.0650 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 86.6613 | 87.3341 | 85.9988 | 44.9670 | 12039 | 1746 | 13212 | 2151 | 1124 | 52.2548 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 78.1128 | 65.0730 | 97.6884 | 78.4680 | 3253 | 1746 | 3254 | 77 | 59 | 76.6234 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 78.1128 | 65.0730 | 97.6884 | 78.4680 | 3253 | 1746 | 3254 | 77 | 59 | 76.6234 | |
| gduggal-bwavard | INDEL | I1_5 | * | het | 92.1214 | 97.7872 | 87.0762 | 61.9735 | 77292 | 1749 | 76863 | 11408 | 10744 | 94.1795 | |
| gduggal-bwaplat | SNP | * | map_l250_m1_e0 | homalt | 44.8992 | 28.9484 | 100.0000 | 95.4511 | 713 | 1750 | 712 | 0 | 0 | ||
| ckim-vqsr | SNP | tv | map_l125_m0_e0 | het | 74.6025 | 60.2363 | 97.9675 | 92.7270 | 2651 | 1750 | 2651 | 55 | 0 | 0.0000 | |
| ltrigg-rtg1 | INDEL | I1_5 | * | * | 99.3139 | 98.8385 | 99.7940 | 55.2555 | 148913 | 1750 | 148225 | 306 | 127 | 41.5033 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 56.7870 | 50.7723 | 64.4183 | 57.0048 | 1808 | 1753 | 1805 | 997 | 979 | 98.1946 | |
| ciseli-custom | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 79.6648 | 84.2067 | 75.5878 | 57.5613 | 9352 | 1754 | 9484 | 3063 | 1008 | 32.9089 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 57.4030 | 44.5498 | 80.6804 | 63.6484 | 1410 | 1755 | 1328 | 318 | 230 | 72.3270 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 85.8383 | 78.3200 | 94.9533 | 28.7854 | 6340 | 1755 | 2032 | 108 | 63 | 58.3333 | |
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 23.1772 | 16.4208 | 39.3809 | 42.5111 | 345 | 1756 | 458 | 705 | 585 | 82.9787 | |
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 82.7666 | 91.0205 | 75.8851 | 82.6190 | 17820 | 1758 | 17704 | 5626 | 180 | 3.1994 | |
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 82.7666 | 91.0205 | 75.8851 | 82.6190 | 17820 | 1758 | 17704 | 5626 | 180 | 3.1994 | |
| ciseli-custom | SNP | * | map_l150_m1_e0 | homalt | 86.3052 | 84.4052 | 88.2927 | 70.7708 | 9515 | 1758 | 9495 | 1259 | 1014 | 80.5401 | |
| ckim-vqsr | SNP | tv | map_l125_m0_e0 | homalt | 34.4391 | 20.8014 | 100.0000 | 91.7691 | 462 | 1759 | 462 | 0 | 0 | ||
| gduggal-snapvard | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 73.1367 | 73.8749 | 72.4131 | 44.0488 | 4974 | 1759 | 7145 | 2722 | 2236 | 82.1455 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 0.5647 | 0.0000 | 0.0000 | 10 | 1761 | 0 | 0 | 0 | ||
| qzeng-custom | SNP | * | map_l250_m2_e0 | het | 76.2572 | 66.0955 | 90.1111 | 96.3398 | 3433 | 1761 | 3408 | 374 | 309 | 82.6203 | |
| gduggal-bwafb | SNP | * | HG002complexvar | * | 99.8109 | 99.7664 | 99.8554 | 20.0831 | 752623 | 1762 | 752783 | 1090 | 464 | 42.5688 | |