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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
16801-16850 / 86044 show all | |||||||||||||||
| ckim-dragen | SNP | * | map_l100_m1_e0 | homalt | 99.6437 | 99.4186 | 99.8698 | 55.6951 | 26846 | 157 | 26851 | 35 | 32 | 91.4286 | |
| ckim-isaac | INDEL | * | map_l100_m2_e0 | het | 84.2881 | 73.9489 | 97.9885 | 86.2255 | 1706 | 601 | 1705 | 35 | 15 | 42.8571 | |
| jlack-gatk | SNP | ti | HG002complexvar | homalt | 99.9491 | 99.9163 | 99.9819 | 18.2375 | 193301 | 162 | 193290 | 35 | 32 | 91.4286 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.6991 | 97.6504 | 99.7706 | 72.0664 | 15211 | 366 | 15219 | 35 | 25 | 71.4286 | |
| hfeng-pmm2 | SNP | tv | segdup | het | 99.5467 | 99.7541 | 99.3402 | 91.9297 | 5274 | 13 | 5270 | 35 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.0292 | 97.0795 | 98.9977 | 67.6517 | 3457 | 104 | 3457 | 35 | 30 | 85.7143 | |
| hfeng-pmm2 | INDEL | I6_15 | HG002complexvar | homalt | 98.4965 | 99.8353 | 97.1933 | 55.2244 | 1212 | 2 | 1212 | 35 | 35 | 100.0000 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.6488 | 94.3546 | 99.0574 | 55.6339 | 3677 | 220 | 3678 | 35 | 28 | 80.0000 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 96.9617 | 96.7357 | 97.1888 | 78.6888 | 1215 | 41 | 1210 | 35 | 17 | 48.5714 | |
| jlack-gatk | INDEL | D6_15 | HG002compoundhet | hetalt | 94.7748 | 90.4552 | 99.5278 | 24.3596 | 7373 | 778 | 7377 | 35 | 30 | 85.7143 | |
| hfeng-pmm1 | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4409 | 98.9502 | 99.9364 | 58.3709 | 55047 | 584 | 55037 | 35 | 12 | 34.2857 | |
| hfeng-pmm1 | SNP | * | map_l100_m1_e0 | homalt | 99.8556 | 99.8408 | 99.8703 | 60.9594 | 26960 | 43 | 26960 | 35 | 17 | 48.5714 | |
| hfeng-pmm1 | SNP | * | map_l100_m2_e0 | homalt | 99.8583 | 99.8438 | 99.8728 | 63.3749 | 27480 | 43 | 27480 | 35 | 17 | 48.5714 | |
| hfeng-pmm1 | SNP | * | map_l100_m2_e1 | homalt | 99.8597 | 99.8453 | 99.8740 | 63.3660 | 27753 | 43 | 27753 | 35 | 17 | 48.5714 | |
| hfeng-pmm1 | SNP | ti | map_l250_m1_e0 | het | 98.6671 | 98.5175 | 98.8172 | 88.8014 | 2924 | 44 | 2924 | 35 | 8 | 22.8571 | |
| hfeng-pmm1 | SNP | ti | map_l250_m2_e0 | het | 98.7844 | 98.6478 | 98.9214 | 88.9993 | 3210 | 44 | 3210 | 35 | 8 | 22.8571 | |
| hfeng-pmm1 | SNP | ti | map_l250_m2_e1 | het | 98.7703 | 98.6056 | 98.9355 | 89.0938 | 3253 | 46 | 3253 | 35 | 8 | 22.8571 | |
| hfeng-pmm3 | SNP | * | map_l100_m1_e0 | homalt | 99.8518 | 99.8334 | 99.8703 | 60.8633 | 26958 | 45 | 26958 | 35 | 17 | 48.5714 | |
| hfeng-pmm3 | SNP | * | map_l100_m2_e0 | homalt | 99.8546 | 99.8365 | 99.8728 | 63.2901 | 27478 | 45 | 27478 | 35 | 17 | 48.5714 | |
| hfeng-pmm3 | SNP | * | map_l100_m2_e1 | homalt | 99.8561 | 99.8381 | 99.8740 | 63.2761 | 27751 | 45 | 27751 | 35 | 17 | 48.5714 | |
| gduggal-bwavard | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | * | 98.7388 | 98.3871 | 99.0930 | 40.5118 | 3843 | 63 | 3824 | 35 | 6 | 17.1429 | |
| gduggal-bwavard | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | het | 98.4421 | 98.3051 | 98.5795 | 46.6205 | 2436 | 42 | 2429 | 35 | 6 | 17.1429 | |
| gduggal-bwafb | INDEL | * | map_l150_m2_e1 | * | 96.4212 | 95.3440 | 97.5230 | 89.5147 | 1372 | 67 | 1378 | 35 | 8 | 22.8571 | |
| gduggal-bwafb | INDEL | D1_5 | map_l100_m2_e1 | * | 97.4531 | 96.7509 | 98.1656 | 84.4194 | 1876 | 63 | 1873 | 35 | 8 | 22.8571 | |
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 43.4690 | 29.6943 | 81.0811 | 66.1792 | 204 | 483 | 150 | 35 | 34 | 97.1429 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 81.1184 | 79.6209 | 82.6733 | 50.0000 | 168 | 43 | 167 | 35 | 34 | 97.1429 | |
| eyeh-varpipe | INDEL | D16_PLUS | HG002compoundhet | het | 53.8274 | 51.6049 | 56.2500 | 59.7990 | 209 | 196 | 45 | 35 | 35 | 100.0000 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 96.4696 | 97.9853 | 95.0000 | 72.7838 | 535 | 11 | 665 | 35 | 35 | 100.0000 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | homalt | 42.6230 | 100.0000 | 27.0833 | 34.2466 | 13 | 0 | 13 | 35 | 31 | 88.5714 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 18.7138 | 10.4396 | 90.2235 | 66.4165 | 247 | 2119 | 323 | 35 | 30 | 85.7143 | |
| eyeh-varpipe | INDEL | I1_5 | segdup | * | 95.8185 | 94.8064 | 96.8525 | 93.2732 | 1004 | 55 | 1077 | 35 | 29 | 82.8571 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 85.0307 | 86.8852 | 83.2536 | 52.9279 | 106 | 16 | 174 | 35 | 33 | 94.2857 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 83.3739 | 71.9097 | 99.1866 | 76.8457 | 4270 | 1668 | 4268 | 35 | 33 | 94.2857 | |
| gduggal-bwaplat | SNP | * | map_l150_m0_e0 | * | 57.1530 | 40.1263 | 99.2803 | 94.5754 | 4828 | 7204 | 4828 | 35 | 15 | 42.8571 | |
| gduggal-bwaplat | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 91.6186 | 84.8043 | 99.6235 | 66.5948 | 9253 | 1658 | 9262 | 35 | 13 | 37.1429 | |
| gduggal-bwaplat | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 91.6939 | 85.0833 | 99.4182 | 67.5827 | 5972 | 1047 | 5981 | 35 | 13 | 37.1429 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 68.7500 | 53.2425 | 97.0034 | 79.7187 | 1133 | 995 | 1133 | 35 | 29 | 82.8571 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 61.6145 | 48.5714 | 84.2342 | 85.1703 | 187 | 198 | 187 | 35 | 5 | 14.2857 | |
| ltrigg-rtg2 | SNP | ti | map_l125_m1_e0 | * | 98.9923 | 98.1217 | 99.8786 | 58.7041 | 28784 | 551 | 28785 | 35 | 10 | 28.5714 | |
| ltrigg-rtg2 | SNP | ti | map_l125_m2_e0 | het | 98.5679 | 97.3564 | 99.8099 | 58.2477 | 18377 | 499 | 18379 | 35 | 4 | 11.4286 | |
| ltrigg-rtg2 | SNP | ti | map_l125_m2_e1 | het | 98.5813 | 97.3804 | 99.8121 | 58.3672 | 18587 | 500 | 18589 | 35 | 4 | 11.4286 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 88.7180 | 93.5323 | 84.3750 | 85.4922 | 188 | 13 | 189 | 35 | 17 | 48.5714 | |
| mlin-fermikit | INDEL | D1_5 | map_l100_m2_e1 | het | 76.7833 | 64.0379 | 95.8629 | 77.1351 | 812 | 456 | 811 | 35 | 19 | 54.2857 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.4473 | 99.1113 | 99.7856 | 56.2027 | 16283 | 146 | 16290 | 35 | 23 | 65.7143 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 98.6796 | 98.9777 | 98.3834 | 43.8974 | 2130 | 22 | 2130 | 35 | 21 | 60.0000 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.7349 | 99.8133 | 99.6566 | 54.0176 | 10159 | 19 | 10157 | 35 | 30 | 85.7143 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 64.0965 | 47.4352 | 98.7989 | 37.2929 | 3403 | 3771 | 2879 | 35 | 30 | 85.7143 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 98.3975 | 98.7234 | 98.0737 | 43.5889 | 464 | 6 | 1782 | 35 | 13 | 37.1429 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | * | het | 97.5719 | 96.3280 | 98.8483 | 63.0112 | 3043 | 116 | 3004 | 35 | 15 | 42.8571 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 94.3219 | 93.9577 | 94.6889 | 71.3603 | 622 | 40 | 624 | 35 | 5 | 14.2857 | |