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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
23051-23100 / 86044 show all | |||||||||||||||
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.5007 | 97.2896 | 99.7423 | 37.1878 | 2728 | 76 | 2709 | 7 | 7 | 100.0000 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 98.3352 | 97.2892 | 99.4041 | 71.1873 | 9044 | 252 | 9174 | 55 | 55 | 100.0000 | |
| dgrover-gatk | INDEL | I6_15 | * | * | 97.9082 | 97.2888 | 98.5355 | 53.2809 | 24150 | 673 | 24155 | 359 | 329 | 91.6435 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.3658 | 97.2888 | 99.4670 | 68.3001 | 933 | 26 | 933 | 5 | 5 | 100.0000 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.3072 | 97.2880 | 99.3480 | 72.0840 | 3659 | 102 | 3657 | 24 | 22 | 91.6667 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.3072 | 97.2880 | 99.3480 | 72.0840 | 3659 | 102 | 3657 | 24 | 22 | 91.6667 | |
| ndellapenna-hhga | SNP | tv | HG002compoundhet | * | 98.0516 | 97.2879 | 98.8274 | 47.0684 | 8681 | 242 | 8681 | 103 | 93 | 90.2913 | |
| eyeh-varpipe | INDEL | * | map_l125_m2_e1 | homalt | 96.9786 | 97.2868 | 96.6724 | 87.1688 | 753 | 21 | 1133 | 39 | 35 | 89.7436 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 93.4354 | 97.2868 | 89.8773 | 59.4527 | 251 | 7 | 293 | 33 | 32 | 96.9697 | |
| cchapple-custom | INDEL | * | map_l125_m2_e1 | homalt | 98.2393 | 97.2868 | 99.2105 | 85.0600 | 753 | 21 | 754 | 6 | 5 | 83.3333 | |
| ghariani-varprowl | SNP | * | map_l250_m1_e0 | * | 95.4295 | 97.2861 | 93.6425 | 90.9971 | 7026 | 196 | 7026 | 477 | 84 | 17.6101 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.4672 | 97.2859 | 99.6775 | 38.9821 | 20037 | 559 | 20088 | 65 | 55 | 84.6154 | |
| ltrigg-rtg1 | SNP | ti | HG002compoundhet | het | 98.5032 | 97.2856 | 99.7516 | 37.6347 | 9247 | 258 | 9237 | 23 | 5 | 21.7391 | |
| gduggal-snapfb | SNP | ti | HG002compoundhet | het | 78.4798 | 97.2856 | 65.7667 | 46.9249 | 9247 | 258 | 9427 | 4907 | 174 | 3.5460 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.4301 | 97.2854 | 97.5753 | 76.8498 | 1326 | 37 | 1328 | 33 | 32 | 96.9697 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 98.0761 | 97.2854 | 98.8798 | 74.4855 | 1326 | 37 | 1324 | 15 | 8 | 53.3333 | |
| jli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 97.5057 | 97.2851 | 97.7273 | 90.8676 | 215 | 6 | 215 | 5 | 2 | 40.0000 | |
| bgallagher-sentieon | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 98.3982 | 97.2851 | 99.5370 | 91.0596 | 215 | 6 | 215 | 1 | 1 | 100.0000 | |
| ndellapenna-hhga | INDEL | D1_5 | map_l100_m2_e0 | * | 97.6927 | 97.2846 | 98.1043 | 82.7144 | 1863 | 52 | 1863 | 36 | 17 | 47.2222 | |
| gduggal-snapvard | SNP | tv | map_siren | het | 94.6657 | 97.2841 | 92.1846 | 72.3745 | 27832 | 777 | 27719 | 2350 | 198 | 8.4255 | |
| eyeh-varpipe | INDEL | I1_5 | map_l100_m2_e1 | het | 96.9546 | 97.2840 | 96.6275 | 81.2002 | 788 | 22 | 1232 | 43 | 28 | 65.1163 | |
| gduggal-snapvard | SNP | tv | map_l150_m2_e0 | het | 88.6343 | 97.2835 | 81.3975 | 85.0700 | 7055 | 197 | 7036 | 1608 | 95 | 5.9080 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.0325 | 97.2835 | 98.7931 | 73.7259 | 1146 | 32 | 1146 | 14 | 13 | 92.8571 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 97.9157 | 97.2833 | 98.5564 | 70.7710 | 752 | 21 | 751 | 11 | 10 | 90.9091 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.4476 | 97.2827 | 97.6130 | 45.1498 | 9201 | 257 | 9201 | 225 | 220 | 97.7778 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.6078 | 97.2827 | 97.9351 | 45.4096 | 9201 | 257 | 9201 | 194 | 187 | 96.3918 | |
| jmaeng-gatk | INDEL | D1_5 | map_l250_m2_e0 | * | 93.4726 | 97.2826 | 89.9497 | 97.0218 | 179 | 5 | 179 | 20 | 1 | 5.0000 | |
| cchapple-custom | INDEL | D1_5 | map_l250_m2_e0 | * | 94.6665 | 97.2826 | 92.1875 | 94.6711 | 179 | 5 | 177 | 15 | 1 | 6.6667 | |
| hfeng-pmm3 | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.3762 | 97.2826 | 99.4947 | 68.4722 | 1969 | 55 | 1969 | 10 | 0 | 0.0000 | |
| jli-custom | INDEL | D1_5 | map_l250_m2_e0 | * | 97.0190 | 97.2826 | 96.7568 | 95.0508 | 179 | 5 | 179 | 6 | 1 | 16.6667 | |
| rpoplin-dv42 | INDEL | D1_5 | map_l250_m2_e0 | * | 98.0822 | 97.2826 | 98.8950 | 95.4061 | 179 | 5 | 179 | 2 | 1 | 50.0000 | |
| gduggal-bwafb | INDEL | D1_5 | map_l250_m2_e0 | * | 97.8142 | 97.2826 | 98.3516 | 95.3737 | 179 | 5 | 179 | 3 | 0 | 0.0000 | |
| ckim-vqsr | SNP | * | segdup | homalt | 98.5850 | 97.2820 | 99.9235 | 88.7282 | 10451 | 292 | 10451 | 8 | 8 | 100.0000 | |
| gduggal-bwavard | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 80.9421 | 97.2812 | 69.3022 | 61.0030 | 10806 | 302 | 10816 | 4791 | 4241 | 88.5201 | |
| ckim-gatk | INDEL | * | map_l250_m2_e0 | * | 92.5287 | 97.2810 | 88.2192 | 97.2498 | 322 | 9 | 322 | 43 | 4 | 9.3023 | |
| ghariani-varprowl | SNP | tv | map_l250_m1_e0 | * | 94.3742 | 97.2799 | 91.6370 | 91.1799 | 2575 | 72 | 2575 | 235 | 32 | 13.6170 | |
| ltrigg-rtg2 | SNP | ti | map_l125_m1_e0 | het | 98.5415 | 97.2791 | 99.8371 | 55.5647 | 17769 | 497 | 17770 | 29 | 4 | 13.7931 | |
| rpoplin-dv42 | INDEL | * | map_l125_m0_e0 | * | 97.5579 | 97.2789 | 97.8385 | 99.0840 | 858 | 24 | 860 | 19 | 7 | 36.8421 | |
| gduggal-snapfb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 46.2642 | 97.2779 | 30.3489 | 80.4847 | 2573 | 72 | 2627 | 6029 | 58 | 0.9620 | |
| ckim-vqsr | INDEL | I16_PLUS | * | het | 98.1949 | 97.2774 | 99.1298 | 76.5400 | 2644 | 74 | 2620 | 23 | 10 | 43.4783 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.6849 | 97.2767 | 98.0965 | 60.4473 | 15610 | 437 | 15615 | 303 | 282 | 93.0693 | |
| ckim-vqsr | INDEL | * | map_l150_m0_e0 | * | 95.5110 | 97.2763 | 93.8086 | 94.9219 | 500 | 14 | 500 | 33 | 2 | 6.0606 | |
| dgrover-gatk | INDEL | * | map_l150_m0_e0 | * | 96.9996 | 97.2763 | 96.7245 | 93.1872 | 500 | 14 | 502 | 17 | 4 | 23.5294 | |
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 96.2853 | 97.2759 | 95.3147 | 68.9687 | 4178 | 117 | 4150 | 204 | 19 | 9.3137 | |
| asubramanian-gatk | INDEL | D6_15 | HG002complexvar | het | 98.2617 | 97.2756 | 99.2679 | 59.9547 | 3035 | 85 | 2983 | 22 | 18 | 81.8182 | |
| ltrigg-rtg2 | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 98.3982 | 97.2756 | 99.5471 | 54.5040 | 3035 | 85 | 3077 | 14 | 13 | 92.8571 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.7783 | 97.2753 | 98.2865 | 69.9578 | 2392 | 67 | 3499 | 61 | 50 | 81.9672 | |
| gduggal-bwafb | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.0894 | 97.2749 | 98.9176 | 66.3428 | 1642 | 46 | 1645 | 18 | 16 | 88.8889 | |
| jli-custom | INDEL | * | map_l125_m0_e0 | het | 97.6068 | 97.2743 | 97.9417 | 88.6222 | 571 | 16 | 571 | 12 | 2 | 16.6667 | |
| cchapple-custom | SNP | * | map_l125_m1_e0 | het | 96.0557 | 97.2739 | 94.8677 | 77.0814 | 27618 | 774 | 27653 | 1496 | 342 | 22.8610 | |