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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
12751-12800 / 86044 show all | |||||||||||||||
| rpoplin-dv42 | SNP | ti | map_l250_m2_e1 | het | 98.3298 | 98.1510 | 98.5093 | 88.6573 | 3238 | 61 | 3238 | 49 | 29 | 59.1837 | |
| hfeng-pmm3 | INDEL | I6_15 | * | het | 98.8597 | 98.1362 | 99.5939 | 56.2294 | 9846 | 187 | 9811 | 40 | 29 | 72.5000 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.0322 | 99.6364 | 96.4789 | 69.7121 | 822 | 3 | 822 | 30 | 29 | 96.6667 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.0322 | 99.6364 | 96.4789 | 69.7121 | 822 | 3 | 822 | 30 | 29 | 96.6667 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.4932 | 99.8351 | 99.1537 | 57.8723 | 3632 | 6 | 3632 | 31 | 29 | 93.5484 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.7125 | 97.6953 | 99.7510 | 72.1894 | 15218 | 359 | 15225 | 38 | 29 | 76.3158 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.2559 | 99.3087 | 99.2032 | 69.9329 | 3735 | 26 | 3735 | 30 | 29 | 96.6667 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.2559 | 99.3087 | 99.2032 | 69.9329 | 3735 | 26 | 3735 | 30 | 29 | 96.6667 | |
| hfeng-pmm2 | SNP | * | map_siren | homalt | 99.9075 | 99.9003 | 99.9148 | 53.4382 | 55101 | 55 | 55092 | 47 | 29 | 61.7021 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 96.6892 | 96.0886 | 97.2973 | 79.6160 | 1302 | 53 | 1188 | 33 | 29 | 87.8788 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 96.4907 | 96.3100 | 96.6721 | 79.6867 | 1305 | 50 | 1191 | 41 | 29 | 70.7317 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 95.2809 | 97.0252 | 93.5982 | 46.7059 | 424 | 13 | 424 | 29 | 29 | 100.0000 | |
| hfeng-pmm1 | INDEL | I1_5 | HG002complexvar | * | 99.5778 | 99.2956 | 99.8615 | 56.6148 | 33128 | 235 | 33171 | 46 | 29 | 63.0435 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.0351 | 96.4286 | 97.6493 | 76.4347 | 2079 | 77 | 2077 | 50 | 29 | 58.0000 | |
| jlack-gatk | INDEL | D1_5 | HG002complexvar | het | 99.5570 | 99.5377 | 99.5763 | 55.9428 | 20669 | 96 | 20681 | 88 | 29 | 32.9545 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 95.2929 | 93.9216 | 96.7048 | 85.0071 | 1437 | 93 | 1438 | 49 | 29 | 59.1837 | |
| hfeng-pmm1 | INDEL | I6_15 | HG002compoundhet | het | 80.0927 | 79.8077 | 80.3797 | 86.5646 | 166 | 42 | 127 | 31 | 29 | 93.5484 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.3774 | 93.8671 | 99.0257 | 55.4228 | 3658 | 239 | 3659 | 36 | 29 | 80.5556 | |
| hfeng-pmm1 | SNP | * | map_l125_m1_e0 | het | 99.2507 | 98.9117 | 99.5921 | 70.2654 | 28083 | 309 | 28077 | 115 | 29 | 25.2174 | |
| hfeng-pmm1 | SNP | * | map_l125_m2_e0 | het | 99.2641 | 98.9290 | 99.6016 | 71.5339 | 29004 | 314 | 28998 | 116 | 29 | 25.0000 | |
| hfeng-pmm1 | SNP | * | map_l125_m2_e1 | het | 99.2688 | 98.9372 | 99.6025 | 71.5784 | 29325 | 315 | 29319 | 117 | 29 | 24.7863 | |
| hfeng-pmm1 | SNP | ti | * | het | 99.9312 | 99.8931 | 99.9694 | 16.7684 | 1280521 | 1370 | 1280470 | 392 | 29 | 7.3980 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 95.2929 | 93.9216 | 96.7048 | 85.0071 | 1437 | 93 | 1438 | 49 | 29 | 59.1837 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 91.4321 | 87.4402 | 95.8060 | 67.3513 | 731 | 105 | 731 | 32 | 29 | 90.6250 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 97.0680 | 94.6510 | 99.6117 | 25.8826 | 7662 | 433 | 7696 | 30 | 29 | 96.6667 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 97.0455 | 94.6164 | 99.6025 | 28.0867 | 7733 | 440 | 7768 | 31 | 29 | 93.5484 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.6223 | 93.7986 | 99.6213 | 24.3454 | 7593 | 502 | 7628 | 29 | 29 | 100.0000 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.5969 | 93.7477 | 99.6247 | 26.3674 | 7662 | 511 | 7698 | 29 | 29 | 100.0000 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.9180 | 98.7044 | 99.1325 | 79.1132 | 28340 | 372 | 28340 | 248 | 29 | 11.6935 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.9180 | 98.7044 | 99.1325 | 79.1132 | 28340 | 372 | 28340 | 248 | 29 | 11.6935 | |
| ckim-isaac | SNP | ti | HG002complexvar | homalt | 95.8992 | 92.1386 | 99.9798 | 16.1839 | 178255 | 15209 | 178286 | 36 | 29 | 80.5556 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 80.4772 | 76.5586 | 84.8185 | 64.9306 | 307 | 94 | 257 | 46 | 29 | 63.0435 | |
| ckim-isaac | INDEL | D6_15 | HG002compoundhet | homalt | 40.0881 | 54.1667 | 31.8182 | 65.3543 | 13 | 11 | 14 | 30 | 29 | 96.6667 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 92.9688 | 92.3674 | 93.5780 | 71.2618 | 714 | 59 | 714 | 49 | 29 | 59.1837 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 62.7001 | 46.0184 | 98.3531 | 38.3761 | 2196 | 2576 | 1911 | 32 | 29 | 90.6250 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.2214 | 97.1584 | 99.3078 | 64.5805 | 5163 | 151 | 5165 | 36 | 29 | 80.5556 | |
| dgrover-gatk | SNP | * | map_l150_m0_e0 | * | 98.7537 | 98.7949 | 98.7125 | 82.2666 | 11887 | 145 | 11884 | 155 | 29 | 18.7097 | |
| dgrover-gatk | SNP | * | map_l250_m1_e0 | * | 98.3434 | 98.2276 | 98.4594 | 89.8378 | 7094 | 128 | 7094 | 111 | 29 | 26.1261 | |
| dgrover-gatk | SNP | ti | map_l150_m1_e0 | het | 99.0308 | 99.1431 | 98.9188 | 80.0370 | 12264 | 106 | 12260 | 134 | 29 | 21.6418 | |
| dgrover-gatk | SNP | tv | map_l100_m1_e0 | * | 99.4329 | 99.4817 | 99.3842 | 68.2243 | 24374 | 127 | 24370 | 151 | 29 | 19.2053 | |
| dgrover-gatk | SNP | tv | map_l100_m2_e0 | * | 99.4410 | 99.4927 | 99.3893 | 69.7626 | 24906 | 127 | 24902 | 153 | 29 | 18.9542 | |
| dgrover-gatk | SNP | tv | map_l100_m2_e1 | * | 99.4445 | 99.4977 | 99.3914 | 69.7839 | 25156 | 127 | 25152 | 154 | 29 | 18.8312 | |
| egarrison-hhga | INDEL | * | map_l100_m1_e0 | het | 97.5114 | 97.9418 | 97.0848 | 83.6025 | 2189 | 46 | 2198 | 66 | 29 | 43.9394 | |
| egarrison-hhga | INDEL | * | map_l100_m2_e0 | het | 97.5246 | 97.9627 | 97.0903 | 84.4521 | 2260 | 47 | 2269 | 68 | 29 | 42.6471 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 95.3978 | 94.1426 | 96.6870 | 72.1399 | 1109 | 69 | 1109 | 38 | 29 | 76.3158 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 93.8528 | 89.4478 | 98.7142 | 36.5693 | 2365 | 279 | 2380 | 31 | 29 | 93.5484 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 90.8228 | 92.2830 | 89.4081 | 69.5735 | 287 | 24 | 287 | 34 | 29 | 85.2941 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.2341 | 97.7771 | 98.6954 | 80.9079 | 6730 | 153 | 6733 | 89 | 29 | 32.5843 | |
| gduggal-snapvard | INDEL | I6_15 | map_l150_m2_e0 | * | 61.1650 | 72.0000 | 53.1646 | 88.2789 | 18 | 7 | 42 | 37 | 29 | 78.3784 | |
| gduggal-snapvard | INDEL | I6_15 | map_l150_m2_e0 | het | 64.5327 | 93.3333 | 49.3151 | 88.3013 | 14 | 1 | 36 | 37 | 29 | 78.3784 | |