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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
31801-31850 / 86044 show all | |||||||||||||||
| jmaeng-gatk | INDEL | * | map_l100_m2_e1 | hetalt | 92.2449 | 85.6061 | 100.0000 | 87.9328 | 113 | 19 | 115 | 0 | 0 | ||
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 92.2413 | 93.5539 | 90.9650 | 64.4972 | 16995 | 1171 | 16995 | 1688 | 1649 | 97.6896 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 92.2413 | 93.5539 | 90.9650 | 64.4972 | 16995 | 1171 | 16995 | 1688 | 1649 | 97.6896 | |
| jlack-gatk | SNP | ti | map_l250_m2_e1 | het | 92.2399 | 98.3631 | 86.8344 | 94.0808 | 3245 | 54 | 3245 | 492 | 42 | 8.5366 | |
| gduggal-snapplat | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 92.2399 | 86.3055 | 99.0506 | 51.0836 | 3441 | 546 | 3443 | 33 | 14 | 42.4242 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 92.2388 | 86.5886 | 98.6779 | 34.8864 | 7244 | 1122 | 7240 | 97 | 80 | 82.4742 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 92.2384 | 96.8903 | 88.0126 | 71.8972 | 592 | 19 | 558 | 76 | 72 | 94.7368 | |
| ckim-isaac | INDEL | D6_15 | * | homalt | 92.2382 | 86.6899 | 98.5453 | 37.3467 | 5484 | 842 | 5487 | 81 | 30 | 37.0370 | |
| ckim-isaac | INDEL | * | HG002complexvar | het | 92.2376 | 90.0654 | 94.5171 | 48.6355 | 41621 | 4591 | 40028 | 2322 | 1017 | 43.7984 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.2374 | 91.8182 | 92.6606 | 88.8205 | 101 | 9 | 101 | 8 | 8 | 100.0000 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 92.2342 | 85.6776 | 99.8774 | 37.7987 | 2333 | 390 | 2444 | 3 | 3 | 100.0000 | |
| jli-custom | INDEL | D16_PLUS | map_l100_m1_e0 | het | 92.2335 | 91.3043 | 93.1818 | 93.9477 | 42 | 4 | 41 | 3 | 2 | 66.6667 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 92.2310 | 86.9440 | 98.2026 | 35.7143 | 606 | 91 | 601 | 11 | 11 | 100.0000 | |
| hfeng-pmm3 | INDEL | D16_PLUS | map_siren | het | 92.2299 | 93.5897 | 90.9091 | 94.3672 | 73 | 5 | 70 | 7 | 1 | 14.2857 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.2288 | 98.9002 | 86.4006 | 59.8278 | 1169 | 13 | 1169 | 184 | 183 | 99.4565 | |
| qzeng-custom | INDEL | I6_15 | HG002complexvar | * | 92.2263 | 91.5275 | 92.9358 | 54.4267 | 4386 | 406 | 4473 | 340 | 144 | 42.3529 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 92.2240 | 99.4840 | 85.9515 | 72.5594 | 21786 | 113 | 22362 | 3655 | 3631 | 99.3434 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 92.2217 | 96.5630 | 88.2540 | 72.0249 | 590 | 21 | 556 | 74 | 70 | 94.5946 | |
| 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 | |
| jlack-gatk | SNP | ti | map_l250_m2_e0 | het | 92.2213 | 98.3712 | 86.7950 | 94.0302 | 3201 | 53 | 3201 | 487 | 40 | 8.2136 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.2212 | 85.5653 | 100.0000 | 31.5699 | 1559 | 263 | 1591 | 0 | 0 | ||
| gduggal-bwavard | INDEL | I1_5 | HG002complexvar | * | 92.2209 | 90.6273 | 93.8716 | 50.7362 | 30236 | 3127 | 29241 | 1909 | 1668 | 87.3756 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.2194 | 86.3886 | 98.8943 | 32.6995 | 1574 | 248 | 1610 | 18 | 16 | 88.8889 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 92.2172 | 86.9261 | 98.1941 | 63.7331 | 871 | 131 | 870 | 16 | 12 | 75.0000 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 92.2162 | 86.6135 | 98.5938 | 42.4667 | 3151 | 487 | 3155 | 45 | 26 | 57.7778 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 92.2149 | 89.1589 | 95.4879 | 47.4893 | 33793 | 4109 | 39553 | 1869 | 1772 | 94.8101 | |
| gduggal-bwafb | INDEL | I1_5 | segdup | hetalt | 92.2122 | 89.5833 | 95.0000 | 97.6771 | 43 | 5 | 19 | 1 | 1 | 100.0000 | |
| ghariani-varprowl | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 92.2109 | 97.6112 | 87.3769 | 74.0644 | 4740 | 116 | 4790 | 692 | 106 | 15.3179 | |
| ckim-isaac | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | het | 92.2085 | 86.7552 | 98.3934 | 61.1512 | 2679 | 409 | 2756 | 45 | 8 | 17.7778 | |
| jmaeng-gatk | INDEL | D1_5 | HG002complexvar | hetalt | 92.2064 | 88.1657 | 96.6354 | 72.5869 | 1192 | 160 | 1235 | 43 | 43 | 100.0000 | |
| ciseli-custom | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 92.2062 | 93.5907 | 90.8621 | 57.8426 | 10572 | 724 | 10550 | 1061 | 847 | 79.8303 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.2061 | 92.0844 | 92.3280 | 55.4245 | 349 | 30 | 349 | 29 | 16 | 55.1724 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 92.2052 | 90.5600 | 93.9113 | 48.2920 | 10754 | 1121 | 12339 | 800 | 737 | 92.1250 | |
| jpowers-varprowl | SNP | * | map_l250_m0_e0 | * | 92.2045 | 93.3489 | 91.0878 | 95.0147 | 1993 | 142 | 1993 | 195 | 31 | 15.8974 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 92.2039 | 88.9215 | 95.7380 | 70.2861 | 1212 | 151 | 1213 | 54 | 33 | 61.1111 | |
| ltrigg-rtg2 | INDEL | I1_5 | map_l250_m1_e0 | het | 92.2036 | 88.3333 | 96.4286 | 92.1897 | 53 | 7 | 54 | 2 | 0 | 0.0000 | |
| gduggal-snapplat | SNP | tv | map_l150_m2_e1 | homalt | 92.2034 | 85.5346 | 100.0000 | 76.0404 | 3536 | 598 | 3535 | 0 | 0 | ||
| ndellapenna-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 92.2021 | 88.9542 | 95.6962 | 86.1888 | 757 | 94 | 756 | 34 | 14 | 41.1765 | |
| jpowers-varprowl | INDEL | * | map_l100_m0_e0 | * | 92.1981 | 91.1068 | 93.3159 | 87.0820 | 1424 | 139 | 1424 | 102 | 64 | 62.7451 | |
| ckim-gatk | INDEL | * | map_l150_m0_e0 | het | 92.1979 | 98.2405 | 86.8557 | 95.3544 | 335 | 6 | 337 | 51 | 1 | 1.9608 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 92.1962 | 96.6768 | 88.1125 | 56.1680 | 5411 | 186 | 12282 | 1657 | 662 | 39.9517 | |
| ltrigg-rtg2 | INDEL | * | map_l250_m0_e0 | het | 92.1945 | 88.6792 | 96.0000 | 94.3883 | 47 | 6 | 48 | 2 | 0 | 0.0000 | |
| qzeng-custom | SNP | tv | map_siren | homalt | 92.1926 | 85.9107 | 99.4656 | 52.8075 | 14811 | 2429 | 14705 | 79 | 75 | 94.9367 | |
| ciseli-custom | SNP | tv | map_siren | homalt | 92.1923 | 91.6589 | 92.7320 | 56.2107 | 15802 | 1438 | 15770 | 1236 | 874 | 70.7120 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 92.1912 | 88.4459 | 96.2678 | 41.3787 | 3261 | 426 | 3250 | 126 | 83 | 65.8730 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 92.1875 | 85.5072 | 100.0000 | 54.9618 | 59 | 10 | 59 | 0 | 0 | ||
| dgrover-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 92.1875 | 100.0000 | 85.5072 | 76.2069 | 59 | 0 | 59 | 10 | 10 | 100.0000 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 92.1875 | 100.0000 | 85.5072 | 75.7042 | 59 | 0 | 59 | 10 | 10 | 100.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 92.1875 | 85.5072 | 100.0000 | 55.6391 | 59 | 10 | 59 | 0 | 0 | ||
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 92.1875 | 85.5072 | 100.0000 | 51.6393 | 59 | 10 | 59 | 0 | 0 | ||