PrecisionFDA
Truth Challenge
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Explore HG002 comparison results
Use this interactive explorer to filter all results across submission entries and multiple dimensions.
| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
84201-84250 / 86044 show all | |||||||||||||||
| mlin-fermikit | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 94.5891 | 93.3138 | 95.8997 | 71.5881 | 60123 | 4308 | 60061 | 2568 | 2492 | 97.0405 | |
| anovak-vg | SNP | ti | HG002compoundhet | * | 77.8164 | 75.3290 | 80.4737 | 38.3806 | 13166 | 4312 | 13522 | 3281 | 2578 | 78.5736 | |
| jmaeng-gatk | SNP | tv | map_l125_m2_e1 | * | 84.0047 | 74.0950 | 96.9745 | 86.2788 | 12342 | 4315 | 12340 | 385 | 14 | 3.6364 | |
| gduggal-bwaplat | SNP | ti | map_l150_m2_e0 | homalt | 60.4067 | 43.2904 | 99.9090 | 85.1344 | 3297 | 4319 | 3293 | 3 | 3 | 100.0000 | |
| ckim-vqsr | SNP | tv | map_l125_m2_e1 | homalt | 44.7879 | 28.8607 | 99.9430 | 87.9632 | 1753 | 4321 | 1753 | 1 | 0 | 0.0000 | |
| gduggal-snapvard | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 58.7303 | 0.0000 | 0.0000 | 6152 | 4323 | 0 | 0 | 0 | ||
| ckim-gatk | SNP | tv | map_l125_m2_e0 | * | 83.8704 | 73.7765 | 97.1641 | 86.1398 | 12165 | 4324 | 12163 | 355 | 14 | 3.9437 | |
| ckim-isaac | SNP | tv | map_l100_m2_e0 | homalt | 69.2951 | 53.0280 | 99.9591 | 61.2002 | 4886 | 4328 | 4886 | 2 | 2 | 100.0000 | |
| gduggal-snapvard | SNP | tv | HG002complexvar | het | 97.6940 | 97.1254 | 98.2693 | 25.4121 | 146401 | 4333 | 143709 | 2531 | 919 | 36.3098 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 63.0485 | 48.1459 | 91.3123 | 63.3492 | 4025 | 4335 | 4015 | 382 | 317 | 82.9843 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 63.0485 | 48.1459 | 91.3123 | 63.3492 | 4025 | 4335 | 4015 | 382 | 317 | 82.9843 | |
| anovak-vg | SNP | * | map_l150_m1_e0 | * | 79.3251 | 85.8375 | 73.7311 | 78.7422 | 26274 | 4335 | 25974 | 9254 | 2118 | 22.8874 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 63.1364 | 48.1459 | 91.6819 | 62.9404 | 4025 | 4335 | 4012 | 364 | 316 | 86.8132 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 63.1364 | 48.1459 | 91.6819 | 62.9404 | 4025 | 4335 | 4012 | 364 | 316 | 86.8132 | |
| ckim-gatk | SNP | tv | map_l125_m2_e1 | * | 83.9775 | 73.9449 | 97.1598 | 86.1410 | 12317 | 4340 | 12315 | 360 | 15 | 4.1667 | |
| gduggal-bwaplat | SNP | ti | map_l150_m2_e1 | homalt | 60.6049 | 43.4941 | 99.9103 | 85.0982 | 3346 | 4347 | 3342 | 3 | 3 | 100.0000 | |
| mlin-fermikit | SNP | tv | map_l100_m0_e0 | het | 56.5874 | 39.7258 | 98.3185 | 59.7124 | 2869 | 4353 | 2865 | 49 | 0 | 0.0000 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 77.1368 | 72.0532 | 82.9923 | 72.5173 | 11223 | 4353 | 45225 | 9268 | 7975 | 86.0488 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 33.2123 | 28.3742 | 40.0394 | 54.5997 | 1726 | 4357 | 3049 | 4566 | 3071 | 67.2580 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 86.9809 | 86.1182 | 87.8610 | 55.6334 | 27048 | 4360 | 27135 | 3749 | 3406 | 90.8509 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 86.9809 | 86.1182 | 87.8610 | 55.6334 | 27048 | 4360 | 27135 | 3749 | 3406 | 90.8509 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 65.7740 | 85.6857 | 53.3715 | 63.8640 | 26117 | 4363 | 26223 | 22910 | 22642 | 98.8302 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 65.7740 | 85.6857 | 53.3715 | 63.8640 | 26117 | 4363 | 26223 | 22910 | 22642 | 98.8302 | |
| ndellapenna-hhga | SNP | * | * | het | 99.8554 | 99.7670 | 99.9441 | 18.2036 | 1869221 | 4366 | 1869241 | 1046 | 128 | 12.2371 | |
| mlin-fermikit | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 89.0060 | 88.0657 | 89.9667 | 48.3054 | 32225 | 4367 | 32137 | 3584 | 3498 | 97.6004 | |
| ckim-isaac | SNP | tv | map_l100_m2_e1 | homalt | 69.3075 | 53.0424 | 99.9595 | 61.1858 | 4934 | 4368 | 4934 | 2 | 2 | 100.0000 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 80.3731 | 72.7114 | 89.8397 | 50.0523 | 11668 | 4379 | 12441 | 1407 | 1388 | 98.6496 | |
| gduggal-bwaplat | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 74.5401 | 60.5690 | 96.8890 | 74.8497 | 6728 | 4380 | 6727 | 216 | 42 | 19.4444 | |
| qzeng-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 90.0572 | 89.8904 | 90.2247 | 50.1569 | 38954 | 4381 | 59902 | 6490 | 4175 | 64.3297 | |
| gduggal-snapvard | INDEL | D6_15 | HG002compoundhet | * | 59.7955 | 51.4782 | 71.3183 | 33.2912 | 4649 | 4382 | 4896 | 1969 | 1719 | 87.3032 | |
| astatham-gatk | SNP | * | map_l100_m0_e0 | * | 92.7245 | 86.6569 | 99.7057 | 72.7426 | 28459 | 4382 | 28455 | 84 | 35 | 41.6667 | |
| mlin-fermikit | SNP | tv | map_l150_m1_e0 | het | 53.4835 | 36.7982 | 97.8528 | 67.3388 | 2556 | 4390 | 2552 | 56 | 0 | 0.0000 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 51.7828 | 35.4521 | 96.0081 | 54.3492 | 2415 | 4397 | 2862 | 119 | 117 | 98.3193 | |
| gduggal-snapplat | SNP | * | map_l100_m1_e0 | * | 95.4122 | 93.9174 | 96.9553 | 75.8528 | 67999 | 4404 | 68019 | 2136 | 1080 | 50.5618 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 40.0753 | 30.3227 | 59.0755 | 67.9189 | 1917 | 4405 | 1917 | 1328 | 1307 | 98.4187 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 40.0753 | 30.3227 | 59.0755 | 67.9189 | 1917 | 4405 | 1917 | 1328 | 1307 | 98.4187 | |
| gduggal-bwaplat | INDEL | I1_5 | HG002complexvar | * | 92.5060 | 86.7938 | 99.0230 | 59.4097 | 28957 | 4406 | 28886 | 285 | 203 | 71.2281 | |
| ckim-vqsr | SNP | ti | map_l150_m0_e0 | * | 60.7533 | 43.9130 | 98.5441 | 93.9394 | 3452 | 4409 | 3452 | 51 | 0 | 0.0000 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 33.6989 | 27.4371 | 43.6639 | 50.1227 | 1669 | 4414 | 2219 | 2863 | 2250 | 78.5889 | |
| ckim-vqsr | SNP | ti | map_l100_m0_e0 | het | 80.8690 | 68.4116 | 98.8733 | 87.2610 | 9566 | 4417 | 9565 | 109 | 1 | 0.9174 | |
| gduggal-snapvard | INDEL | D6_15 | * | homalt | 45.1606 | 30.1454 | 89.9777 | 38.5773 | 1907 | 4419 | 1616 | 180 | 176 | 97.7778 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 35.8293 | 22.1968 | 92.8622 | 57.9026 | 1261 | 4420 | 1301 | 100 | 93 | 93.0000 | |
| gduggal-bwavard | SNP | * | map_siren | * | 97.0294 | 96.9773 | 97.0815 | 65.0881 | 141808 | 4420 | 139841 | 4204 | 408 | 9.7050 | |
| ckim-vqsr | SNP | ti | map_l150_m1_e0 | het | 77.8168 | 64.2603 | 98.6225 | 90.8714 | 7949 | 4421 | 7947 | 111 | 1 | 0.9009 | |
| jmaeng-gatk | SNP | * | map_l100_m0_e0 | homalt | 76.4825 | 61.9363 | 99.9583 | 70.3301 | 7197 | 4423 | 7197 | 3 | 3 | 100.0000 | |
| gduggal-snapplat | SNP | * | map_l100_m2_e0 | * | 95.4808 | 94.0120 | 96.9962 | 77.3300 | 69535 | 4429 | 69555 | 2154 | 1085 | 50.3714 | |
| anovak-vg | SNP | tv | * | homalt | 99.0679 | 98.8237 | 99.3132 | 19.4559 | 372687 | 4436 | 371341 | 2568 | 1960 | 76.3240 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 0.0000 | 4.4114 | 0.0000 | 0.0000 | 205 | 4442 | 0 | 0 | 0 | ||
| gduggal-snapplat | SNP | * | map_l100_m2_e1 | * | 95.5097 | 94.0511 | 97.0142 | 77.3448 | 70291 | 4446 | 70312 | 2164 | 1091 | 50.4159 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 25.1673 | 16.3154 | 55.0168 | 69.5072 | 867 | 4447 | 817 | 668 | 604 | 90.4192 | |