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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
26451-26500 / 86044 show all | |||||||||||||||
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 96.5189 | 98.9555 | 94.1994 | 86.2906 | 1800 | 19 | 1559 | 96 | 69 | 71.8750 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 96.5189 | 98.9555 | 94.1994 | 86.2906 | 1800 | 19 | 1559 | 96 | 69 | 71.8750 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 83.4086 | 85.9259 | 81.0345 | 77.7778 | 116 | 19 | 94 | 22 | 21 | 95.4545 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.7468 | 99.7171 | 99.7766 | 54.5091 | 6697 | 19 | 6699 | 15 | 8 | 53.3333 | |
| ckim-vqsr | INDEL | D1_5 | map_l100_m0_e0 | het | 96.0537 | 96.7851 | 95.3333 | 90.9829 | 572 | 19 | 572 | 28 | 2 | 7.1429 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 98.9445 | 98.1905 | 99.7101 | 62.5272 | 1031 | 19 | 1032 | 3 | 3 | 100.0000 | |
| ckim-vqsr | SNP | ti | map_l100_m1_e0 | hetalt | 51.2821 | 34.4828 | 100.0000 | 93.5065 | 10 | 19 | 10 | 0 | 0 | ||
| ckim-vqsr | SNP | ti | map_l100_m2_e0 | hetalt | 53.6585 | 36.6667 | 100.0000 | 93.6416 | 11 | 19 | 11 | 0 | 0 | ||
| astatham-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 83.4086 | 85.9259 | 81.0345 | 77.5629 | 116 | 19 | 94 | 22 | 21 | 95.4545 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.1994 | 99.4197 | 97.0087 | 68.4176 | 3255 | 19 | 3243 | 100 | 97 | 97.0000 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.9371 | 98.3926 | 99.4876 | 28.2475 | 1163 | 19 | 1165 | 6 | 6 | 100.0000 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.0806 | 99.4197 | 96.7771 | 68.3987 | 3255 | 19 | 3243 | 108 | 105 | 97.2222 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.7407 | 99.3048 | 96.2251 | 62.9649 | 2714 | 19 | 2702 | 106 | 102 | 96.2264 | |
| bgallagher-sentieon | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 99.0857 | 99.0613 | 99.1102 | 68.1518 | 2005 | 19 | 2005 | 18 | 4 | 22.2222 | |
| bgallagher-sentieon | SNP | ti | map_l150_m0_e0 | homalt | 99.5462 | 99.3118 | 99.7817 | 72.6486 | 2742 | 19 | 2742 | 6 | 5 | 83.3333 | |
| bgallagher-sentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 99.2817 | 99.2817 | 99.2817 | 83.4450 | 2626 | 19 | 2626 | 19 | 6 | 31.5789 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.7335 | 99.7729 | 97.7156 | 45.5716 | 8347 | 19 | 8341 | 195 | 193 | 98.9744 | |
| astatham-gatk | SNP | * | map_l250_m0_e0 | homalt | 97.9920 | 96.9793 | 99.0260 | 91.4528 | 610 | 19 | 610 | 6 | 5 | 83.3333 | |
| astatham-gatk | SNP | tv | map_l250_m1_e0 | homalt | 98.5866 | 97.7804 | 99.4062 | 85.3845 | 837 | 19 | 837 | 5 | 4 | 80.0000 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 97.8256 | 96.4486 | 99.2424 | 73.9001 | 516 | 19 | 524 | 4 | 4 | 100.0000 | |
| anovak-vg | INDEL | * | func_cds | homalt | 87.7119 | 91.5929 | 84.1463 | 33.8710 | 207 | 19 | 207 | 39 | 35 | 89.7436 | |
| anovak-vg | INDEL | D16_PLUS | map_siren | homalt | 59.9144 | 44.1176 | 93.3333 | 91.0180 | 15 | 19 | 14 | 1 | 1 | 100.0000 | |
| anovak-vg | INDEL | D6_15 | map_l150_m2_e1 | * | 79.8957 | 77.6471 | 82.2785 | 91.1236 | 66 | 19 | 65 | 14 | 9 | 64.2857 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 91.7468 | 88.1250 | 95.6790 | 89.0392 | 141 | 19 | 155 | 7 | 5 | 71.4286 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 96.2980 | 98.3871 | 94.2957 | 66.7441 | 1159 | 19 | 1620 | 98 | 95 | 96.9388 | |
| asubramanian-gatk | INDEL | I1_5 | map_l125_m1_e0 | homalt | 97.0079 | 94.1896 | 100.0000 | 84.1944 | 308 | 19 | 309 | 0 | 0 | ||
| asubramanian-gatk | INDEL | I1_5 | map_l125_m2_e0 | homalt | 97.1342 | 94.4282 | 100.0000 | 85.3437 | 322 | 19 | 322 | 0 | 0 | ||
| asubramanian-gatk | INDEL | I1_5 | map_l125_m2_e1 | homalt | 97.1514 | 94.4606 | 100.0000 | 85.5551 | 324 | 19 | 324 | 0 | 0 | ||
| asubramanian-gatk | INDEL | I1_5 | map_l150_m0_e0 | * | 91.8129 | 89.2045 | 94.5783 | 94.1487 | 157 | 19 | 157 | 9 | 0 | 0.0000 | |
| asubramanian-gatk | INDEL | I1_5 | map_l250_m2_e0 | * | 87.8505 | 83.1858 | 93.0693 | 97.3379 | 94 | 19 | 94 | 7 | 0 | 0.0000 | |
| asubramanian-gatk | INDEL | I1_5 | map_l250_m2_e1 | * | 87.9630 | 83.3333 | 93.1373 | 97.3953 | 95 | 19 | 95 | 7 | 0 | 0.0000 | |
| asubramanian-gatk | INDEL | I1_5 | segdup | * | 98.7667 | 98.2059 | 99.3340 | 95.0336 | 1040 | 19 | 1044 | 7 | 2 | 28.5714 | |
| asubramanian-gatk | SNP | ti | HG002complexvar | hetalt | 94.4724 | 90.8213 | 98.4293 | 40.4984 | 188 | 19 | 188 | 3 | 0 | 0.0000 | |
| asubramanian-gatk | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 99.1770 | 98.4477 | 99.9171 | 58.7551 | 1205 | 19 | 1205 | 1 | 1 | 100.0000 | |
| asubramanian-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5884 | 99.5263 | 99.6506 | 48.9164 | 3992 | 19 | 3993 | 14 | 1 | 7.1429 | |
| asubramanian-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.1239 | 97.7673 | 98.4831 | 88.4750 | 832 | 19 | 844 | 13 | 7 | 53.8462 | |
| asubramanian-gatk | SNP | ti | map_l100_m1_e0 | hetalt | 51.2821 | 34.4828 | 100.0000 | 89.3617 | 10 | 19 | 10 | 0 | 0 | ||
| asubramanian-gatk | SNP | ti | map_l100_m2_e0 | hetalt | 53.6585 | 36.6667 | 100.0000 | 89.6226 | 11 | 19 | 11 | 0 | 0 | ||
| asubramanian-gatk | SNP | ti | map_l100_m2_e1 | hetalt | 55.8140 | 38.7097 | 100.0000 | 88.7850 | 12 | 19 | 12 | 0 | 0 | ||
| bgallagher-sentieon | INDEL | * | map_l150_m1_e0 | * | 97.9979 | 98.5800 | 97.4227 | 90.0883 | 1319 | 19 | 1323 | 35 | 7 | 20.0000 | |
| bgallagher-sentieon | INDEL | * | map_l150_m2_e0 | * | 98.0622 | 98.6506 | 97.4808 | 90.7478 | 1389 | 19 | 1393 | 36 | 7 | 19.4444 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 96.5857 | 94.5714 | 98.6877 | 35.6419 | 331 | 19 | 376 | 5 | 5 | 100.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.8275 | 97.5066 | 98.1506 | 66.5044 | 743 | 19 | 743 | 14 | 8 | 57.1429 | |
| anovak-vg | INDEL | I16_PLUS | segdup | het | 34.4828 | 20.8333 | 100.0000 | 91.2281 | 5 | 19 | 5 | 0 | 0 | ||
| anovak-vg | INDEL | I1_5 | map_l125_m1_e0 | homalt | 68.2142 | 94.1896 | 53.4687 | 80.5464 | 308 | 19 | 316 | 275 | 253 | 92.0000 | |
| anovak-vg | INDEL | I1_5 | segdup | homalt | 68.8866 | 95.9831 | 53.7209 | 91.7355 | 454 | 19 | 462 | 398 | 376 | 94.4724 | |
| anovak-vg | SNP | ti | map_l100_m1_e0 | hetalt | 0.0000 | 34.4828 | 0.0000 | 0.0000 | 10 | 19 | 0 | 0 | 0 | ||
| anovak-vg | SNP | ti | map_l100_m2_e0 | hetalt | 0.0000 | 36.6667 | 0.0000 | 0.0000 | 11 | 19 | 0 | 0 | 0 | ||
| astatham-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.5706 | 99.1399 | 92.2494 | 66.0177 | 2190 | 19 | 2190 | 184 | 181 | 98.3696 | |
| astatham-gatk | INDEL | * | segdup | het | 98.4019 | 98.7040 | 98.1017 | 95.1947 | 1447 | 19 | 1447 | 28 | 2 | 7.1429 | |