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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
6351-6400 / 86044 show all | |||||||||||||||
| ckim-isaac | INDEL | * | HG002compoundhet | hetalt | 88.0188 | 79.0747 | 99.2444 | 32.7152 | 19911 | 5269 | 20095 | 153 | 126 | 82.3529 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5991 | 99.7991 | 99.4000 | 72.8360 | 21855 | 44 | 21701 | 131 | 126 | 96.1832 | |
| ckim-dragen | SNP | tv | * | het | 99.7113 | 99.9417 | 99.4820 | 27.9772 | 591351 | 345 | 591544 | 3080 | 126 | 4.0909 | |
| ckim-gatk | INDEL | D1_5 | * | het | 99.6268 | 99.8162 | 99.4381 | 60.7761 | 87413 | 161 | 87419 | 494 | 126 | 25.5061 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 96.5054 | 94.3089 | 98.8067 | 30.3644 | 10473 | 632 | 11178 | 135 | 126 | 93.3333 | |
| asubramanian-gatk | INDEL | D1_5 | * | het | 99.3754 | 99.1025 | 99.6499 | 59.9427 | 86788 | 786 | 86804 | 305 | 126 | 41.3115 | |
| anovak-vg | INDEL | I16_PLUS | HG002compoundhet | * | 11.6860 | 7.0929 | 33.1593 | 41.3476 | 152 | 1991 | 127 | 256 | 126 | 49.2188 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 91.7145 | 87.1038 | 96.8405 | 38.5031 | 5167 | 765 | 5180 | 169 | 126 | 74.5562 | |
| dgrover-gatk | SNP | ti | * | * | 99.9570 | 99.9639 | 99.9500 | 17.7617 | 2084759 | 752 | 2084696 | 1042 | 126 | 12.0921 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 80.9329 | 94.5455 | 70.7469 | 64.8688 | 312 | 18 | 341 | 141 | 126 | 89.3617 | |
| jpowers-varprowl | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 92.9799 | 99.5261 | 87.2417 | 71.6212 | 1680 | 8 | 1689 | 247 | 126 | 51.0121 | |
| gduggal-bwavard | SNP | * | map_l150_m2_e0 | het | 93.0021 | 97.9685 | 88.5150 | 85.7521 | 19724 | 409 | 19491 | 2529 | 126 | 4.9822 | |
| gduggal-bwaplat | INDEL | I1_5 | HG002complexvar | het | 91.7425 | 85.6452 | 98.7744 | 60.7292 | 15578 | 2611 | 15555 | 193 | 126 | 65.2850 | |
| gduggal-bwaplat | INDEL | I1_5 | HG002compoundhet | * | 82.1492 | 71.0667 | 97.3270 | 74.9005 | 8781 | 3575 | 8775 | 241 | 126 | 52.2822 | |
| gduggal-bwafb | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.7961 | 98.2976 | 95.3398 | 72.9184 | 9527 | 165 | 9554 | 467 | 126 | 26.9807 | |
| gduggal-bwafb | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.8088 | 99.1429 | 96.5101 | 64.4371 | 17698 | 153 | 17754 | 642 | 126 | 19.6262 | |
| hfeng-pmm1 | INDEL | I1_5 | HG002compoundhet | homalt | 83.5249 | 99.3921 | 72.0264 | 83.4186 | 327 | 2 | 327 | 127 | 126 | 99.2126 | |
| jlack-gatk | SNP | ti | map_l150_m2_e0 | * | 96.1925 | 98.6739 | 93.8329 | 83.2384 | 20240 | 272 | 20236 | 1330 | 126 | 9.4737 | |
| hfeng-pmm2 | INDEL | D1_5 | HG002compoundhet | * | 95.6235 | 92.5950 | 98.8568 | 63.0617 | 11329 | 906 | 11328 | 131 | 126 | 96.1832 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.0894 | 96.6856 | 99.5346 | 57.0832 | 30367 | 1041 | 30368 | 142 | 126 | 88.7324 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.0894 | 96.6856 | 99.5346 | 57.0832 | 30367 | 1041 | 30368 | 142 | 126 | 88.7324 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 92.5616 | 97.8195 | 87.8400 | 82.6726 | 1301 | 29 | 1098 | 152 | 125 | 82.2368 | |
| hfeng-pmm3 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 94.1239 | 92.6980 | 95.5943 | 77.1597 | 3745 | 295 | 3450 | 159 | 125 | 78.6164 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.6110 | 96.3981 | 98.8550 | 60.6748 | 12070 | 451 | 11914 | 138 | 125 | 90.5797 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.0835 | 99.3208 | 98.8474 | 56.8151 | 11406 | 78 | 11406 | 133 | 125 | 93.9850 | |
| jlack-gatk | SNP | ti | map_l150_m1_e0 | * | 96.1043 | 98.6353 | 93.7000 | 82.0564 | 19443 | 269 | 19439 | 1307 | 125 | 9.5639 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 28.7100 | 20.4082 | 48.3974 | 46.2069 | 150 | 585 | 151 | 161 | 125 | 77.6398 | |
| anovak-vg | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 23.7087 | 15.9091 | 46.5116 | 54.5317 | 133 | 703 | 140 | 161 | 125 | 77.6398 | |
| anovak-vg | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 97.8222 | 97.8503 | 97.7942 | 34.8099 | 6600 | 145 | 6606 | 149 | 125 | 83.8926 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 95.7607 | 94.8001 | 96.7410 | 36.3288 | 3865 | 212 | 3859 | 130 | 125 | 96.1538 | |
| mlin-fermikit | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.6168 | 96.8493 | 96.3855 | 66.9947 | 4703 | 153 | 4720 | 177 | 125 | 70.6215 | |
| ndellapenna-hhga | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 79.7416 | 66.9975 | 98.4728 | 66.8746 | 10329 | 5088 | 9672 | 150 | 125 | 83.3333 | |
| qzeng-custom | SNP | tv | map_l250_m2_e0 | * | 77.9675 | 67.2797 | 92.6923 | 95.3450 | 1939 | 943 | 1928 | 152 | 125 | 82.2368 | |
| qzeng-custom | SNP | tv | map_l250_m2_e1 | * | 78.0956 | 67.4211 | 92.7860 | 95.3708 | 1966 | 950 | 1955 | 152 | 125 | 82.2368 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 87.8155 | 85.8877 | 89.8319 | 60.6862 | 1132 | 186 | 1122 | 127 | 125 | 98.4252 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.7464 | 96.5472 | 98.9758 | 64.1922 | 13282 | 475 | 13239 | 137 | 125 | 91.2409 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.7464 | 96.5472 | 98.9758 | 64.1922 | 13282 | 475 | 13239 | 137 | 125 | 91.2409 | |
| gduggal-snapvard | SNP | tv | map_l125_m2_e1 | * | 93.1692 | 96.8962 | 89.7183 | 79.8287 | 16140 | 517 | 16082 | 1843 | 125 | 6.7824 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 68.3405 | 57.5940 | 84.0173 | 50.8840 | 766 | 564 | 1167 | 222 | 125 | 56.3063 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.6041 | 96.4619 | 98.7737 | 60.3970 | 12078 | 443 | 11921 | 148 | 125 | 84.4595 | |
| gduggal-snapfb | SNP | ti | map_l250_m2_e1 | het | 94.1247 | 95.4229 | 92.8614 | 87.6593 | 3148 | 151 | 3148 | 242 | 125 | 51.6529 | |
| ckim-gatk | SNP | * | map_siren | * | 94.1020 | 89.7981 | 98.8391 | 66.9681 | 131310 | 14918 | 131287 | 1542 | 125 | 8.1064 | |
| ckim-dragen | SNP | ti | HG002complexvar | het | 99.9189 | 99.9266 | 99.9111 | 17.5776 | 314535 | 231 | 314661 | 280 | 125 | 44.6429 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 93.9836 | 91.7841 | 96.2911 | 69.5456 | 3452 | 309 | 3453 | 133 | 125 | 93.9850 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 93.9836 | 91.7841 | 96.2911 | 69.5456 | 3452 | 309 | 3453 | 133 | 125 | 93.9850 | |
| gduggal-bwavard | SNP | * | map_l100_m0_e0 | het | 93.1046 | 97.6656 | 88.9506 | 81.2913 | 20710 | 495 | 20488 | 2545 | 125 | 4.9116 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 73.9449 | 73.7705 | 74.1201 | 54.7329 | 360 | 128 | 358 | 125 | 125 | 100.0000 | |
| eyeh-varpipe | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 48.5484 | 60.8696 | 40.3756 | 32.1656 | 14 | 9 | 86 | 127 | 125 | 98.4252 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 83.9473 | 78.4628 | 90.2562 | 82.3482 | 1858 | 510 | 1973 | 213 | 125 | 58.6854 | |
| dgrover-gatk | INDEL | D1_5 | * | het | 99.7614 | 99.7979 | 99.7250 | 59.4296 | 87397 | 177 | 87406 | 241 | 125 | 51.8672 | |