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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
30201-30250 / 86044 show all | |||||||||||||||
| jli-custom | INDEL | * | map_l100_m0_e0 | het | 97.8452 | 97.8452 | 97.8452 | 85.1642 | 999 | 22 | 999 | 22 | 5 | 22.7273 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.2034 | 96.5701 | 97.8450 | 55.8440 | 36602 | 1300 | 36414 | 802 | 774 | 96.5087 | |
| asubramanian-gatk | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 98.2626 | 98.6842 | 97.8446 | 62.1511 | 1725 | 23 | 1725 | 38 | 1 | 2.6316 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 95.0193 | 92.3530 | 97.8441 | 60.3645 | 12705 | 1052 | 12662 | 279 | 130 | 46.5950 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 95.0193 | 92.3530 | 97.8441 | 60.3645 | 12705 | 1052 | 12662 | 279 | 130 | 46.5950 | |
| gduggal-snapplat | INDEL | D1_5 | map_l100_m2_e1 | homalt | 88.9945 | 81.6129 | 97.8441 | 87.0712 | 506 | 114 | 590 | 13 | 1 | 7.6923 | |
| rpoplin-dv42 | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.4674 | 99.0988 | 97.8440 | 74.2336 | 47836 | 435 | 47787 | 1053 | 987 | 93.7322 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.6538 | 97.4644 | 97.8440 | 54.1303 | 10801 | 281 | 10801 | 238 | 235 | 98.7395 | |
| eyeh-varpipe | INDEL | I1_5 | map_l125_m2_e0 | * | 97.6374 | 97.4329 | 97.8428 | 85.0133 | 835 | 22 | 1270 | 28 | 19 | 67.8571 | |
| ndellapenna-hhga | INDEL | D1_5 | HG002complexvar | * | 97.3122 | 96.7874 | 97.8426 | 54.8110 | 31664 | 1051 | 31656 | 698 | 573 | 82.0917 | |
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 95.8427 | 93.9232 | 97.8424 | 72.3914 | 4034 | 261 | 4036 | 89 | 6 | 6.7416 | |
| raldana-dualsentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 89.4737 | 82.4242 | 97.8417 | 90.5954 | 136 | 29 | 136 | 3 | 1 | 33.3333 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 97.5084 | 97.1778 | 97.8412 | 76.7438 | 1033 | 30 | 1269 | 28 | 22 | 78.5714 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 72.9624 | 58.1711 | 97.8403 | 43.0063 | 1584 | 1139 | 1495 | 33 | 31 | 93.9394 | |
| qzeng-custom | INDEL | * | HG002complexvar | het | 97.8163 | 97.7928 | 97.8398 | 56.2530 | 45192 | 1020 | 49233 | 1087 | 393 | 36.1546 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 97.0658 | 96.3042 | 97.8396 | 70.2140 | 3622 | 139 | 3623 | 80 | 65 | 81.2500 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 97.0658 | 96.3042 | 97.8396 | 70.2140 | 3622 | 139 | 3623 | 80 | 65 | 81.2500 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.7705 | 99.7193 | 97.8396 | 67.4095 | 18115 | 51 | 18115 | 400 | 388 | 97.0000 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.7705 | 99.7193 | 97.8396 | 67.4095 | 18115 | 51 | 18115 | 400 | 388 | 97.0000 | |
| qzeng-custom | SNP | ti | map_l100_m2_e0 | het | 87.5433 | 79.2078 | 97.8395 | 80.9563 | 24255 | 6367 | 24137 | 533 | 415 | 77.8612 | |
| hfeng-pmm1 | INDEL | * | map_l150_m0_e0 | * | 97.1639 | 96.4981 | 97.8389 | 90.4125 | 496 | 18 | 498 | 11 | 4 | 36.3636 | |
| gduggal-bwafb | INDEL | * | map_l100_m0_e0 | * | 96.4693 | 95.1376 | 97.8389 | 85.1430 | 1487 | 76 | 1494 | 33 | 7 | 21.2121 | |
| rpoplin-dv42 | INDEL | * | map_l125_m0_e0 | * | 97.5579 | 97.2789 | 97.8385 | 99.0840 | 858 | 24 | 860 | 19 | 7 | 36.8421 | |
| jpowers-varprowl | SNP | tv | map_l250_m0_e0 | homalt | 95.7672 | 93.7824 | 97.8378 | 95.4944 | 181 | 12 | 181 | 4 | 0 | 0.0000 | |
| jlack-gatk | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.7961 | 99.7741 | 97.8371 | 63.8462 | 35339 | 80 | 35328 | 781 | 32 | 4.0973 | |
| ghariani-varprowl | INDEL | * | map_l100_m2_e1 | homalt | 94.7241 | 91.8033 | 97.8369 | 80.2368 | 1176 | 105 | 1176 | 26 | 9 | 34.6154 | |
| asubramanian-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.7580 | 97.6793 | 97.8367 | 88.4863 | 1389 | 33 | 1402 | 31 | 10 | 32.2581 | |
| gduggal-bwavard | INDEL | D6_15 | HG002complexvar | homalt | 86.1695 | 76.9889 | 97.8360 | 44.7799 | 900 | 269 | 859 | 19 | 14 | 73.6842 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.7250 | 99.6324 | 97.8339 | 67.7720 | 1084 | 4 | 1084 | 24 | 21 | 87.5000 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.7250 | 99.6324 | 97.8339 | 67.7720 | 1084 | 4 | 1084 | 24 | 21 | 87.5000 | |
| gduggal-bwafb | INDEL | D1_5 | map_l125_m2_e1 | * | 97.7499 | 97.6664 | 97.8336 | 87.0352 | 1130 | 27 | 1129 | 25 | 3 | 12.0000 | |
| ckim-gatk | SNP | * | map_l125_m2_e1 | * | 84.7700 | 74.7850 | 97.8324 | 85.1204 | 35300 | 11902 | 35294 | 782 | 60 | 7.6726 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.2176 | 96.6110 | 97.8319 | 41.8109 | 19898 | 698 | 19899 | 441 | 420 | 95.2381 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 94.5966 | 91.5686 | 97.8316 | 84.9216 | 1401 | 129 | 1534 | 34 | 25 | 73.5294 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 94.5966 | 91.5686 | 97.8316 | 84.9216 | 1401 | 129 | 1534 | 34 | 25 | 73.5294 | |
| raldana-dualsentieon | INDEL | I1_5 | map_l125_m2_e1 | het | 97.5364 | 97.2441 | 97.8304 | 85.6618 | 494 | 14 | 496 | 11 | 0 | 0.0000 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 83.9148 | 73.4651 | 97.8302 | 47.7704 | 706 | 255 | 2074 | 46 | 36 | 78.2609 | |
| ckim-gatk | SNP | ti | map_l125_m0_e0 | * | 77.0822 | 63.5950 | 97.8298 | 88.5344 | 8116 | 4646 | 8114 | 180 | 23 | 12.7778 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.9660 | 98.1027 | 97.8297 | 69.4907 | 1758 | 34 | 1758 | 39 | 30 | 76.9231 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.5824 | 99.3478 | 97.8288 | 50.3389 | 4722 | 31 | 4731 | 105 | 95 | 90.4762 | |
| ghariani-varprowl | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 98.7332 | 99.6556 | 97.8277 | 50.1744 | 4051 | 14 | 4053 | 90 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.8151 | 99.8240 | 97.8265 | 57.8124 | 5671 | 10 | 5671 | 126 | 125 | 99.2063 | |
| dgrover-gatk | INDEL | D1_5 | map_l100_m2_e0 | hetalt | 94.6463 | 91.6667 | 97.8261 | 90.8367 | 44 | 4 | 45 | 1 | 0 | 0.0000 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 85.9048 | 76.5734 | 97.8261 | 53.6290 | 219 | 67 | 225 | 5 | 5 | 100.0000 | |
| ckim-isaac | INDEL | D1_5 | map_l250_m2_e0 | * | 65.2174 | 48.9130 | 97.8261 | 96.9405 | 90 | 94 | 90 | 2 | 2 | 100.0000 | |
| ckim-isaac | INDEL | D1_5 | map_l250_m2_e1 | * | 64.9819 | 48.6486 | 97.8261 | 97.0101 | 90 | 95 | 90 | 2 | 2 | 100.0000 | |
| ckim-isaac | INDEL | D6_15 | segdup | homalt | 93.7500 | 90.0000 | 97.8261 | 86.1862 | 45 | 5 | 45 | 1 | 0 | 0.0000 | |
| egarrison-hhga | INDEL | * | map_l150_m1_e0 | * | 97.6046 | 97.3842 | 97.8261 | 98.6310 | 1303 | 35 | 1305 | 29 | 10 | 34.4828 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.9011 | 100.0000 | 97.8261 | 83.7456 | 45 | 0 | 45 | 1 | 1 | 100.0000 | |
| ckim-vqsr | INDEL | I1_5 | map_l250_m2_e0 | homalt | 98.9011 | 100.0000 | 97.8261 | 95.2675 | 45 | 0 | 45 | 1 | 1 | 100.0000 | |