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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
1851-1900 / 86044 show all | |||||||||||||||
| asubramanian-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 94.2414 | 93.9394 | 94.5455 | 90.9836 | 155 | 10 | 156 | 9 | 2 | 22.2222 | |
| asubramanian-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_gt200bp_gt95identity_merged | * | 0.0000 | 100.0000 | 0 | 0 | 0 | 0 | 0 | ||||
| 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 | |
| asubramanian-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.1886 | 98.1028 | 98.2745 | 88.1406 | 1241 | 24 | 1253 | 22 | 8 | 36.3636 | |
| asubramanian-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.9023 | 98.7458 | 99.0593 | 82.5203 | 4094 | 52 | 4107 | 39 | 10 | 25.6410 | |
| asubramanian-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.2216 | 97.3921 | 99.0654 | 77.9808 | 14191 | 380 | 14204 | 134 | 16 | 11.9403 | |
| asubramanian-gatk | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 99.1035 | 98.9086 | 99.2991 | 66.9100 | 4803 | 53 | 4817 | 34 | 12 | 35.2941 | |
| asubramanian-gatk | SNP | tv | lowcmp_SimpleRepeat_diTR_51to200 | * | 90.5660 | 92.3077 | 88.8889 | 96.6165 | 24 | 2 | 24 | 3 | 0 | 0.0000 | |
| asubramanian-gatk | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.3827 | 98.8452 | 99.9260 | 60.8128 | 10785 | 126 | 10801 | 8 | 5 | 62.5000 | |
| asubramanian-gatk | SNP | tv | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 0.0000 | 100.0000 | 0 | 0 | 0 | 0 | 0 | ||||
| asubramanian-gatk | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.4177 | 98.8728 | 97.9668 | 40.4008 | 7368 | 84 | 7372 | 153 | 3 | 1.9608 | |
| asubramanian-gatk | SNP | tv | lowcmp_SimpleRepeat_quadTR_51to200 | * | 97.6190 | 97.6190 | 97.6190 | 89.3939 | 41 | 1 | 41 | 1 | 0 | 0.0000 | |
| asubramanian-gatk | SNP | tv | lowcmp_SimpleRepeat_quadTR_gt200 | * | 0.0000 | 0.0000 | 0.0000 | 0 | 0 | 0 | 0 | 0 | |||
| asubramanian-gatk | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.4476 | 99.1594 | 99.7375 | 38.8443 | 3421 | 29 | 3420 | 9 | 2 | 22.2222 | |
| asubramanian-gatk | SNP | tv | lowcmp_SimpleRepeat_triTR_51to200 | * | 100.0000 | 100.0000 | 100.0000 | 98.5714 | 1 | 0 | 1 | 0 | 0 | ||
| asubramanian-gatk | SNP | tv | map_l100_m0_e0 | * | 43.7760 | 28.0314 | 99.8714 | 92.3134 | 3107 | 7977 | 3107 | 4 | 1 | 25.0000 | |
| asubramanian-gatk | SNP | tv | map_l100_m1_e0 | * | 57.1254 | 40.0024 | 99.8777 | 86.7426 | 9801 | 14700 | 9799 | 12 | 2 | 16.6667 | |
| asubramanian-gatk | SNP | tv | map_l100_m2_e0 | * | 58.0625 | 40.9300 | 99.8635 | 87.2733 | 10246 | 14787 | 10244 | 14 | 2 | 14.2857 | |
| asubramanian-gatk | SNP | tv | map_l100_m2_e1 | * | 58.2603 | 41.1264 | 99.8655 | 87.2297 | 10398 | 14885 | 10396 | 14 | 2 | 14.2857 | |
| asubramanian-gatk | SNP | tv | map_l125_m0_e0 | * | 34.3571 | 20.7510 | 99.7825 | 95.7011 | 1376 | 5255 | 1376 | 3 | 1 | 33.3333 | |
| asubramanian-gatk | SNP | tv | map_l125_m1_e0 | * | 45.0440 | 29.0834 | 99.8285 | 92.0394 | 4658 | 11358 | 4657 | 8 | 1 | 12.5000 | |
| asubramanian-gatk | SNP | tv | map_l125_m2_e0 | * | 46.3923 | 30.2201 | 99.7997 | 92.3039 | 4983 | 11506 | 4982 | 10 | 2 | 20.0000 | |
| asubramanian-gatk | SNP | tv | map_l125_m2_e1 | * | 46.6345 | 30.4256 | 99.8030 | 92.2720 | 5068 | 11589 | 5067 | 10 | 2 | 20.0000 | |
| asubramanian-gatk | SNP | tv | map_l150_m0_e0 | * | 29.8574 | 17.5611 | 99.5924 | 97.2219 | 733 | 3441 | 733 | 3 | 1 | 33.3333 | |
| asubramanian-gatk | SNP | tv | map_l150_m1_e0 | * | 37.4814 | 23.0755 | 99.7622 | 94.8394 | 2518 | 8394 | 2517 | 6 | 1 | 16.6667 | |
| asubramanian-gatk | SNP | tv | map_l150_m2_e0 | * | 39.2587 | 24.4386 | 99.7483 | 94.9137 | 2775 | 8580 | 2774 | 7 | 1 | 14.2857 | |
| asubramanian-gatk | SNP | tv | map_l150_m2_e1 | * | 39.5063 | 24.6305 | 99.7534 | 94.8804 | 2833 | 8669 | 2832 | 7 | 1 | 14.2857 | |
| asubramanian-gatk | SNP | tv | map_l250_m0_e0 | * | 28.2828 | 16.4706 | 100.0000 | 99.1823 | 126 | 639 | 126 | 0 | 0 | ||
| asubramanian-gatk | SNP | tv | map_l250_m1_e0 | * | 27.4267 | 15.9048 | 99.5272 | 98.5741 | 421 | 2226 | 421 | 2 | 0 | 0.0000 | |
| asubramanian-gatk | SNP | tv | map_l250_m2_e0 | * | 28.9950 | 16.9674 | 99.5927 | 98.5624 | 489 | 2393 | 489 | 2 | 0 | 0.0000 | |
| asubramanian-gatk | SNP | tv | map_l250_m2_e1 | * | 29.3068 | 17.1811 | 99.6024 | 98.5560 | 501 | 2415 | 501 | 2 | 0 | 0.0000 | |
| asubramanian-gatk | SNP | tv | map_siren | * | 72.2865 | 56.6449 | 99.8618 | 75.5276 | 26017 | 19913 | 26011 | 36 | 12 | 33.3333 | |
| asubramanian-gatk | SNP | tv | segdup | * | 97.9981 | 96.6831 | 99.3493 | 93.1884 | 8249 | 283 | 8245 | 54 | 6 | 11.1111 | |
| asubramanian-gatk | SNP | tv | segdupwithalt | * | 0.0000 | 100.0000 | 0 | 0 | 0 | 0 | 0 | ||||
| asubramanian-gatk | SNP | tv | tech_badpromoters | * | 97.9021 | 97.2222 | 98.5915 | 53.5948 | 70 | 2 | 70 | 1 | 1 | 100.0000 | |
| bgallagher-sentieon | INDEL | * | * | * | 99.2678 | 99.2143 | 99.3213 | 59.6036 | 341835 | 2707 | 341703 | 2335 | 1924 | 82.3983 | |
| bgallagher-sentieon | INDEL | * | HG002complexvar | * | 99.4954 | 99.3774 | 99.6137 | 58.2041 | 76459 | 479 | 76328 | 296 | 257 | 86.8243 | |
| bgallagher-sentieon | INDEL | * | HG002compoundhet | * | 93.7345 | 93.5147 | 93.9554 | 62.6967 | 28017 | 1943 | 27901 | 1795 | 1783 | 99.3315 | |
| bgallagher-sentieon | INDEL | * | decoy | * | 100.0000 | 100.0000 | 100.0000 | 99.9337 | 10 | 0 | 10 | 0 | 0 | ||
| bgallagher-sentieon | INDEL | * | func_cds | * | 99.5531 | 99.7753 | 99.3318 | 44.7724 | 444 | 1 | 446 | 3 | 1 | 33.3333 | |
| bgallagher-sentieon | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.1594 | 93.5769 | 94.7492 | 68.8883 | 9426 | 647 | 9275 | 514 | 466 | 90.6615 | |
| bgallagher-sentieon | INDEL | * | lowcmp_AllRepeats_gt200bp_gt95identity_merged | * | 97.5610 | 100.0000 | 95.2381 | 99.3365 | 20 | 0 | 20 | 1 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.0261 | 98.9285 | 99.1239 | 73.3821 | 93437 | 1012 | 93346 | 825 | 733 | 88.8485 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.9919 | 97.7475 | 98.2375 | 67.0385 | 63879 | 1472 | 63652 | 1142 | 1030 | 90.1926 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.5826 | 97.4026 | 97.7633 | 76.4020 | 2100 | 56 | 2098 | 48 | 23 | 47.9167 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_gt200bp_gt95identity_merged | * | 97.1429 | 100.0000 | 94.4444 | 99.4067 | 17 | 0 | 17 | 1 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5214 | 99.5507 | 99.4922 | 74.9449 | 5096 | 23 | 5094 | 26 | 13 | 50.0000 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.7380 | 99.8068 | 99.6692 | 75.6445 | 3616 | 7 | 3616 | 12 | 6 | 50.0000 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.1903 | 92.5366 | 93.8532 | 64.0267 | 5629 | 454 | 5512 | 361 | 345 | 95.5679 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_gt200bp_gt95identity_merged | * | 100.0000 | 100.0000 | 100.0000 | 97.7273 | 3 | 0 | 3 | 0 | 0 | ||