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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
28001-28050 / 86044 show all | |||||||||||||||
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 89.8965 | 92.6829 | 87.2727 | 88.8945 | 190 | 15 | 192 | 28 | 27 | 96.4286 | |
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 89.8965 | 92.6829 | 87.2727 | 88.8945 | 190 | 15 | 192 | 28 | 27 | 96.4286 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 92.2217 | 93.0556 | 91.4027 | 66.4134 | 201 | 15 | 202 | 19 | 19 | 100.0000 | |
| mlin-fermikit | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 85.0654 | 98.4227 | 74.9004 | 87.7501 | 936 | 15 | 940 | 315 | 251 | 79.6825 | |
| mlin-fermikit | SNP | ti | HG002complexvar | hetalt | 96.0000 | 92.7536 | 99.4819 | 33.9041 | 192 | 15 | 192 | 1 | 1 | 100.0000 | |
| ltrigg-rtg2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.2263 | 99.6260 | 98.8298 | 49.0498 | 3996 | 15 | 4054 | 48 | 0 | 0.0000 | |
| ltrigg-rtg2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.0027 | 96.0836 | 100.0000 | 76.6463 | 368 | 15 | 344 | 0 | 0 | ||
| ltrigg-rtg2 | SNP | ti | lowcmp_SimpleRepeat_quadTR_51to200 | het | 80.0241 | 77.2727 | 82.9787 | 93.9040 | 51 | 15 | 39 | 8 | 2 | 25.0000 | |
| ltrigg-rtg2 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 90.9497 | 87.9032 | 94.2149 | 86.1556 | 109 | 15 | 114 | 7 | 0 | 0.0000 | |
| ltrigg-rtg2 | SNP | tv | map_l100_m0_e0 | homalt | 99.7656 | 99.6100 | 99.9217 | 59.8070 | 3831 | 15 | 3829 | 3 | 1 | 33.3333 | |
| ltrigg-rtg2 | SNP | tv | map_l150_m1_e0 | homalt | 99.7842 | 99.6199 | 99.9492 | 67.6001 | 3931 | 15 | 3932 | 2 | 1 | 50.0000 | |
| ltrigg-rtg2 | SNP | tv | map_l150_m2_e0 | homalt | 99.7915 | 99.6326 | 99.9509 | 70.3193 | 4068 | 15 | 4069 | 2 | 1 | 50.0000 | |
| ltrigg-rtg2 | SNP | tv | map_l150_m2_e1 | homalt | 99.7941 | 99.6372 | 99.9515 | 70.3259 | 4119 | 15 | 4123 | 2 | 1 | 50.0000 | |
| mlin-fermikit | INDEL | * | map_l125_m1_e0 | hetalt | 75.7576 | 62.5000 | 96.1538 | 87.0647 | 25 | 15 | 25 | 1 | 0 | 0.0000 | |
| mlin-fermikit | INDEL | D16_PLUS | map_l100_m1_e0 | het | 65.3674 | 67.3913 | 63.4615 | 92.2619 | 31 | 15 | 33 | 19 | 8 | 42.1053 | |
| mlin-fermikit | INDEL | D16_PLUS | map_l100_m1_e0 | hetalt | 57.7428 | 42.3077 | 90.9091 | 78.4314 | 11 | 15 | 10 | 1 | 0 | 0.0000 | |
| mlin-fermikit | INDEL | D16_PLUS | map_l100_m2_e0 | hetalt | 57.8947 | 42.3077 | 91.6667 | 78.1818 | 11 | 15 | 11 | 1 | 0 | 0.0000 | |
| mlin-fermikit | INDEL | D16_PLUS | map_siren | hetalt | 66.6667 | 51.6129 | 94.1176 | 83.1683 | 16 | 15 | 16 | 1 | 0 | 0.0000 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 97.8552 | 97.7169 | 97.9938 | 73.0000 | 642 | 15 | 635 | 13 | 12 | 92.3077 | |
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | hetalt | 0.0000 | 6.2500 | 0.0000 | 0.0000 | 1 | 15 | 0 | 0 | 0 | ||
| anovak-vg | INDEL | * | map_l150_m2_e1 | hetalt | 0.0000 | 34.7826 | 0.0000 | 0.0000 | 8 | 15 | 0 | 0 | 0 | ||
| anovak-vg | INDEL | * | map_l250_m0_e0 | het | 64.3289 | 71.6981 | 58.3333 | 98.2533 | 38 | 15 | 42 | 30 | 12 | 40.0000 | |
| anovak-vg | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | het | 32.5234 | 37.5000 | 28.7129 | 27.3381 | 9 | 15 | 29 | 72 | 60 | 83.3333 | |
| anovak-vg | INDEL | D6_15 | map_l100_m0_e0 | hetalt | 0.0000 | 21.0526 | 0.0000 | 0.0000 | 4 | 15 | 0 | 0 | 0 | ||
| anovak-vg | INDEL | D6_15 | map_l150_m1_e0 | * | 80.4282 | 79.4521 | 81.4286 | 91.4005 | 58 | 15 | 57 | 13 | 8 | 61.5385 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 25.8993 | 40.0000 | 19.1489 | 57.2727 | 10 | 15 | 9 | 38 | 8 | 21.0526 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | het | 10.8696 | 6.2500 | 41.6667 | 53.8462 | 1 | 15 | 5 | 7 | 1 | 14.2857 | |
| asubramanian-gatk | INDEL | D1_5 | map_l250_m1_e0 | het | 83.8428 | 86.4865 | 81.3559 | 96.8108 | 96 | 15 | 96 | 22 | 2 | 9.0909 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.2279 | 99.3671 | 97.1146 | 56.0984 | 2355 | 15 | 2356 | 70 | 66 | 94.2857 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 90.9091 | 84.2105 | 98.7654 | 91.5361 | 80 | 15 | 80 | 1 | 0 | 0.0000 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 89.6330 | 82.7586 | 97.7528 | 84.0215 | 72 | 15 | 87 | 2 | 2 | 100.0000 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 91.2260 | 85.8491 | 97.3214 | 84.7411 | 91 | 15 | 109 | 3 | 3 | 100.0000 | |
| asubramanian-gatk | INDEL | I1_5 | map_l100_m0_e0 | homalt | 96.0199 | 92.7885 | 99.4845 | 82.6009 | 193 | 15 | 193 | 1 | 1 | 100.0000 | |
| asubramanian-gatk | INDEL | I1_5 | map_l250_m2_e0 | het | 82.2581 | 77.2727 | 87.9310 | 97.8716 | 51 | 15 | 51 | 7 | 0 | 0.0000 | |
| asubramanian-gatk | INDEL | I1_5 | map_l250_m2_e1 | het | 82.2581 | 77.2727 | 87.9310 | 97.9454 | 51 | 15 | 51 | 7 | 0 | 0.0000 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 94.0166 | 98.1818 | 90.1905 | 68.4305 | 810 | 15 | 947 | 103 | 102 | 99.0291 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 92.2724 | 89.9329 | 94.7368 | 76.4706 | 134 | 15 | 144 | 8 | 4 | 50.0000 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 94.0166 | 98.1818 | 90.1905 | 68.4305 | 810 | 15 | 947 | 103 | 102 | 99.0291 | |
| asubramanian-gatk | SNP | * | map_l150_m1_e0 | hetalt | 40.0000 | 25.0000 | 100.0000 | 94.6237 | 5 | 15 | 5 | 0 | 0 | ||
| asubramanian-gatk | SNP | * | map_l150_m2_e0 | hetalt | 40.0000 | 25.0000 | 100.0000 | 95.6140 | 5 | 15 | 5 | 0 | 0 | ||
| asubramanian-gatk | SNP | * | map_l150_m2_e1 | hetalt | 40.0000 | 25.0000 | 100.0000 | 95.6140 | 5 | 15 | 5 | 0 | 0 | ||
| asubramanian-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.2864 | 98.6702 | 99.9102 | 42.2199 | 1113 | 15 | 1113 | 1 | 1 | 100.0000 | |
| asubramanian-gatk | SNP | tv | map_l150_m1_e0 | hetalt | 40.0000 | 25.0000 | 100.0000 | 94.6237 | 5 | 15 | 5 | 0 | 0 | ||
| asubramanian-gatk | SNP | tv | map_l150_m2_e0 | hetalt | 40.0000 | 25.0000 | 100.0000 | 95.6140 | 5 | 15 | 5 | 0 | 0 | ||
| asubramanian-gatk | SNP | tv | map_l150_m2_e1 | hetalt | 40.0000 | 25.0000 | 100.0000 | 95.6140 | 5 | 15 | 5 | 0 | 0 | ||
| bgallagher-sentieon | INDEL | * | map_l150_m2_e1 | het | 97.5914 | 98.3766 | 96.8187 | 91.2287 | 909 | 15 | 913 | 30 | 4 | 13.3333 | |
| bgallagher-sentieon | INDEL | D16_PLUS | HG002complexvar | het | 98.0634 | 98.6450 | 97.4886 | 68.5684 | 1092 | 15 | 854 | 22 | 12 | 54.5455 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 92.5887 | 97.7444 | 87.9496 | 86.9299 | 650 | 15 | 489 | 67 | 56 | 83.5821 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 95.7830 | 98.8722 | 92.8811 | 83.4809 | 1315 | 15 | 1109 | 85 | 72 | 84.7059 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.6951 | 99.7767 | 99.6136 | 53.1211 | 6701 | 15 | 6703 | 26 | 9 | 34.6154 | |