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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
44001-44050 / 86044 show all | |||||||||||||||
| jlack-gatk | INDEL | I1_5 | map_l250_m1_e0 | * | 92.3077 | 96.2264 | 88.6957 | 97.0805 | 102 | 4 | 102 | 13 | 2 | 15.3846 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 77.8576 | 69.3798 | 88.6957 | 75.3747 | 179 | 79 | 204 | 26 | 8 | 30.7692 | |
| ckim-gatk | INDEL | D1_5 | map_l150_m2_e1 | het | 93.4998 | 98.8506 | 88.6986 | 93.1423 | 516 | 6 | 518 | 66 | 4 | 6.0606 | |
| asubramanian-gatk | INDEL | * | map_l250_m1_e0 | * | 86.4236 | 84.2623 | 88.6986 | 99.0516 | 257 | 48 | 259 | 33 | 3 | 9.0909 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 58.1841 | 43.2904 | 88.7006 | 71.9789 | 471 | 617 | 471 | 60 | 58 | 96.6667 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 92.5413 | 96.7290 | 88.7011 | 66.3212 | 3519 | 119 | 3517 | 448 | 445 | 99.3304 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 93.5626 | 98.9848 | 88.7036 | 60.4379 | 1170 | 12 | 1170 | 149 | 147 | 98.6577 | |
| gduggal-snapvard | SNP | * | map_l150_m2_e0 | * | 92.3600 | 96.3299 | 88.7044 | 82.4713 | 30683 | 1169 | 30289 | 3857 | 284 | 7.3632 | |
| jpowers-varprowl | INDEL | D1_5 | * | het | 92.8158 | 97.3223 | 88.7081 | 61.6875 | 85229 | 2345 | 85221 | 10848 | 10534 | 97.1055 | |
| raldana-dualsentieon | INDEL | I1_5 | map_l250_m1_e0 | het | 90.1639 | 91.6667 | 88.7097 | 95.3662 | 55 | 5 | 55 | 7 | 0 | 0.0000 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 82.8549 | 77.7251 | 88.7097 | 61.5702 | 164 | 47 | 165 | 21 | 20 | 95.2381 | |
| gduggal-bwafb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 93.4033 | 98.6198 | 88.7109 | 85.7951 | 6788 | 95 | 6813 | 867 | 96 | 11.0727 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 86.4894 | 84.3750 | 88.7125 | 60.9235 | 486 | 90 | 503 | 64 | 41 | 64.0625 | |
| ghariani-varprowl | INDEL | D1_5 | map_l100_m2_e1 | * | 91.5085 | 94.4817 | 88.7167 | 87.2602 | 1832 | 107 | 1832 | 233 | 66 | 28.3262 | |
| ghariani-varprowl | INDEL | D6_15 | HG002complexvar | homalt | 83.9832 | 79.7263 | 88.7204 | 58.7246 | 932 | 237 | 936 | 119 | 92 | 77.3109 | |
| mlin-fermikit | INDEL | I6_15 | map_siren | * | 81.7172 | 75.7377 | 88.7218 | 80.5981 | 231 | 74 | 236 | 30 | 28 | 93.3333 | |
| gduggal-snapplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 51.1782 | 35.9607 | 88.7235 | 60.7545 | 5046 | 8986 | 5067 | 644 | 550 | 85.4037 | |
| ckim-isaac | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 81.4636 | 75.3003 | 88.7258 | 57.0269 | 7585 | 2488 | 7374 | 937 | 772 | 82.3906 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 91.8238 | 95.1411 | 88.7300 | 60.2423 | 10926 | 558 | 10920 | 1387 | 1378 | 99.3511 | |
| eyeh-varpipe | INDEL | D6_15 | map_l125_m1_e0 | * | 86.6250 | 84.6154 | 88.7324 | 87.5548 | 99 | 18 | 126 | 16 | 16 | 100.0000 | |
| gduggal-bwavard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 89.6918 | 90.6694 | 88.7352 | 58.9619 | 447 | 46 | 449 | 57 | 36 | 63.1579 | |
| ciseli-custom | SNP | * | map_l100_m2_e1 | * | 85.2411 | 82.0102 | 88.7370 | 71.8319 | 61292 | 13445 | 61099 | 7755 | 2048 | 26.4088 | |
| mlin-fermikit | INDEL | I16_PLUS | HG002complexvar | * | 84.0504 | 79.8319 | 88.7395 | 68.1648 | 1045 | 264 | 1056 | 134 | 128 | 95.5224 | |
| ciseli-custom | SNP | * | map_l100_m0_e0 | homalt | 87.9778 | 87.2289 | 88.7396 | 61.6447 | 10136 | 1484 | 10103 | 1282 | 1041 | 81.2012 | |
| ltrigg-rtg2 | INDEL | C1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 76.1364 | 66.6667 | 88.7417 | 97.5582 | 2 | 1 | 134 | 17 | 1 | 5.8824 | |
| jlack-gatk | INDEL | D1_5 | segdup | het | 93.5227 | 98.8439 | 88.7451 | 96.2758 | 684 | 8 | 686 | 87 | 3 | 3.4483 | |
| jlack-gatk | INDEL | D1_5 | map_l100_m2_e0 | het | 93.5776 | 98.9650 | 88.7464 | 88.5144 | 1243 | 13 | 1246 | 158 | 10 | 6.3291 | |
| jlack-gatk | SNP | * | map_l150_m1_e0 | het | 93.5301 | 98.8559 | 88.7489 | 85.6678 | 19095 | 221 | 19089 | 2420 | 175 | 7.2314 | |
| eyeh-varpipe | INDEL | I6_15 | map_siren | * | 77.9593 | 69.5082 | 88.7500 | 73.3555 | 212 | 93 | 284 | 36 | 33 | 91.6667 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 64.5118 | 50.6716 | 88.7536 | 66.8832 | 9205 | 8961 | 9186 | 1164 | 976 | 83.8488 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 64.5118 | 50.6716 | 88.7536 | 66.8832 | 9205 | 8961 | 9186 | 1164 | 976 | 83.8488 | |
| ghariani-varprowl | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 93.8322 | 99.5261 | 88.7546 | 70.2144 | 1680 | 8 | 1689 | 214 | 129 | 60.2804 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 92.5136 | 96.5980 | 88.7606 | 66.4930 | 17548 | 618 | 17524 | 2219 | 2149 | 96.8454 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 92.5136 | 96.5980 | 88.7606 | 66.4930 | 17548 | 618 | 17524 | 2219 | 2149 | 96.8454 | |
| gduggal-snapplat | INDEL | D1_5 | map_l100_m0_e0 | het | 84.6379 | 80.8799 | 88.7622 | 92.9498 | 478 | 113 | 545 | 69 | 16 | 23.1884 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 81.1947 | 74.8148 | 88.7640 | 73.9003 | 101 | 34 | 79 | 10 | 8 | 80.0000 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | * | 81.9633 | 76.1261 | 88.7701 | 48.1994 | 169 | 53 | 166 | 21 | 16 | 76.1905 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 91.6966 | 94.8227 | 88.7701 | 73.3903 | 1337 | 73 | 1328 | 168 | 145 | 86.3095 | |
| mlin-fermikit | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 93.0148 | 97.6827 | 88.7726 | 47.1861 | 10117 | 240 | 10097 | 1277 | 1255 | 98.2772 | |
| ghariani-varprowl | INDEL | D1_5 | map_l100_m2_e0 | * | 91.5803 | 94.5692 | 88.7745 | 87.1803 | 1811 | 104 | 1811 | 229 | 65 | 28.3843 | |
| raldana-dualsentieon | INDEL | D16_PLUS | map_l100_m2_e1 | * | 89.2308 | 89.6907 | 88.7755 | 92.8467 | 87 | 10 | 87 | 11 | 4 | 36.3636 | |
| eyeh-varpipe | INDEL | I6_15 | map_l125_m1_e0 | * | 76.9628 | 67.9245 | 88.7755 | 80.5169 | 36 | 17 | 87 | 11 | 9 | 81.8182 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 69.3227 | 56.8627 | 88.7755 | 86.4454 | 87 | 66 | 87 | 11 | 9 | 81.8182 | |
| jlack-gatk | INDEL | D1_5 | map_l100_m2_e1 | het | 93.6001 | 98.9748 | 88.7791 | 88.5873 | 1255 | 13 | 1258 | 159 | 10 | 6.2893 | |
| gduggal-snapvard | SNP | * | map_l150_m2_e1 | * | 92.4051 | 96.3396 | 88.7794 | 82.5294 | 31031 | 1179 | 30628 | 3871 | 287 | 7.4141 | |
| mlin-fermikit | SNP | ti | map_l125_m2_e0 | * | 64.0610 | 50.1091 | 88.7802 | 61.1948 | 15162 | 15096 | 15161 | 1916 | 1690 | 88.2046 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 77.4939 | 68.7532 | 88.7808 | 66.4783 | 1329 | 604 | 1369 | 173 | 122 | 70.5202 | |
| mlin-fermikit | INDEL | I16_PLUS | * | * | 82.9403 | 77.8109 | 88.7937 | 66.6528 | 4962 | 1415 | 4976 | 628 | 607 | 96.6561 | |
| eyeh-varpipe | SNP | tv | map_l150_m0_e0 | het | 93.9083 | 99.6483 | 88.7937 | 84.1222 | 2833 | 10 | 2797 | 353 | 7 | 1.9830 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 93.4540 | 98.6270 | 88.7967 | 40.4203 | 431 | 6 | 428 | 54 | 54 | 100.0000 | |