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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
70151-70200 / 86044 show all | |||||||||||||||
| ciseli-custom | INDEL | I1_5 | map_siren | * | 68.4975 | 64.7920 | 72.6525 | 80.4862 | 1947 | 1058 | 1942 | 731 | 614 | 83.9945 | |
| gduggal-snapvard | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 75.9223 | 95.2075 | 63.1339 | 85.1688 | 1927 | 97 | 1942 | 1134 | 22 | 1.9400 | |
| gduggal-snapfb | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 92.5726 | 90.3810 | 94.8730 | 43.3628 | 1945 | 207 | 1943 | 105 | 74 | 70.4762 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.2343 | 99.5392 | 98.9313 | 39.6684 | 1944 | 9 | 1944 | 21 | 20 | 95.2381 | |
| qzeng-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 96.4272 | 98.7275 | 94.2317 | 67.6240 | 1862 | 24 | 1944 | 119 | 18 | 15.1261 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 95.3176 | 99.5904 | 91.3963 | 41.9328 | 1945 | 8 | 1944 | 183 | 182 | 99.4536 | |
| ciseli-custom | SNP | ti | map_l250_m2_e0 | het | 64.2691 | 59.7419 | 69.5388 | 93.5208 | 1944 | 1310 | 1945 | 852 | 20 | 2.3474 | |
| dgrover-gatk | INDEL | D16_PLUS | HG002compoundhet | hetalt | 97.0887 | 94.7095 | 99.5904 | 26.5237 | 1826 | 102 | 1945 | 8 | 8 | 100.0000 | |
| bgallagher-sentieon | INDEL | I16_PLUS | HG002compoundhet | * | 93.0399 | 90.7606 | 95.4367 | 53.0631 | 1945 | 198 | 1945 | 93 | 93 | 100.0000 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 89.0334 | 80.6002 | 99.4376 | 31.3443 | 1907 | 459 | 1945 | 11 | 10 | 90.9091 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.3868 | 99.5904 | 99.1841 | 39.0236 | 1945 | 8 | 1945 | 16 | 16 | 100.0000 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.9210 | 92.2462 | 93.6058 | 72.7642 | 1963 | 165 | 1947 | 133 | 117 | 87.9699 | |
| jmaeng-gatk | INDEL | I16_PLUS | * | hetalt | 95.5588 | 91.7541 | 99.6928 | 55.4720 | 1925 | 173 | 1947 | 6 | 5 | 83.3333 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 44.3676 | 44.4859 | 44.2500 | 32.4739 | 1073 | 1339 | 1947 | 2453 | 2342 | 95.4749 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 73.2113 | 82.3308 | 65.9106 | 63.8478 | 1752 | 376 | 1947 | 1007 | 294 | 29.1956 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.2106 | 99.7440 | 98.6829 | 40.0729 | 1948 | 5 | 1948 | 26 | 25 | 96.1538 | |
| ckim-vqsr | INDEL | I16_PLUS | HG002compoundhet | hetalt | 95.7976 | 92.0210 | 99.8974 | 44.8061 | 1926 | 167 | 1948 | 2 | 2 | 100.0000 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 89.4563 | 82.1519 | 98.1864 | 56.4502 | 1947 | 423 | 1949 | 36 | 33 | 91.6667 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 93.8172 | 88.6758 | 99.5914 | 32.3428 | 1942 | 248 | 1950 | 8 | 8 | 100.0000 | |
| ckim-gatk | INDEL | I16_PLUS | HG002compoundhet | hetalt | 95.8494 | 92.1166 | 99.8975 | 44.7808 | 1928 | 165 | 1950 | 2 | 2 | 100.0000 | |
| jli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.1609 | 99.8464 | 98.4848 | 39.5973 | 1950 | 3 | 1950 | 30 | 30 | 100.0000 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.3615 | 99.8976 | 96.8719 | 41.6063 | 1951 | 2 | 1951 | 63 | 62 | 98.4127 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.3863 | 99.8976 | 96.9200 | 41.5335 | 1951 | 2 | 1951 | 62 | 62 | 100.0000 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.3615 | 99.8976 | 96.8719 | 41.6063 | 1951 | 2 | 1951 | 63 | 62 | 98.4127 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 97.6232 | 99.8976 | 95.4501 | 41.3150 | 1951 | 2 | 1951 | 93 | 92 | 98.9247 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.3863 | 99.8976 | 96.9200 | 41.4826 | 1951 | 2 | 1951 | 62 | 62 | 100.0000 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.3623 | 99.9488 | 96.8254 | 41.7173 | 1952 | 1 | 1952 | 64 | 62 | 96.8750 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.2138 | 99.9488 | 96.5381 | 40.8253 | 1952 | 1 | 1952 | 70 | 69 | 98.5714 | |
| gduggal-bwafb | INDEL | D16_PLUS | HG002compoundhet | * | 82.3584 | 75.6514 | 90.3704 | 28.6893 | 1771 | 570 | 1952 | 208 | 208 | 100.0000 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 56.6451 | 52.8614 | 61.0122 | 54.6408 | 1949 | 1738 | 1953 | 1248 | 1228 | 98.3974 | |
| anovak-vg | INDEL | I6_15 | HG002compoundhet | * | 31.2822 | 22.7666 | 49.9744 | 31.5356 | 1998 | 6778 | 1954 | 1956 | 1488 | 76.0736 | |
| ckim-vqsr | INDEL | I16_PLUS | * | hetalt | 95.6650 | 91.9924 | 99.6430 | 54.9403 | 1930 | 168 | 1954 | 7 | 6 | 85.7143 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.5176 | 92.5752 | 96.5432 | 70.8171 | 1970 | 158 | 1955 | 70 | 56 | 80.0000 | |
| hfeng-pmm2 | INDEL | I16_PLUS | HG002compoundhet | hetalt | 96.0539 | 92.4510 | 99.9489 | 46.1750 | 1935 | 158 | 1955 | 1 | 1 | 100.0000 | |
| qzeng-custom | SNP | tv | map_l250_m2_e1 | * | 78.0956 | 67.4211 | 92.7860 | 95.3708 | 1966 | 950 | 1955 | 152 | 125 | 82.2368 | |
| ckim-gatk | INDEL | I16_PLUS | * | hetalt | 95.7167 | 92.0877 | 99.6434 | 54.9150 | 1932 | 166 | 1956 | 7 | 6 | 85.7143 | |
| ckim-dragen | INDEL | I16_PLUS | HG002compoundhet | * | 93.5490 | 91.3672 | 95.8374 | 52.5778 | 1958 | 185 | 1957 | 85 | 85 | 100.0000 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 55.8931 | 39.9329 | 93.1051 | 68.6867 | 1071 | 1611 | 1958 | 145 | 138 | 95.1724 | |
| jli-custom | INDEL | D16_PLUS | HG002compoundhet | hetalt | 97.5241 | 95.5394 | 99.5931 | 24.6166 | 1842 | 86 | 1958 | 8 | 8 | 100.0000 | |
| gduggal-bwaplat | SNP | ti | map_l250_m2_e0 | * | 56.1308 | 39.0775 | 99.5931 | 97.1311 | 1957 | 3051 | 1958 | 8 | 2 | 25.0000 | |
| asubramanian-gatk | SNP | tv | map_l150_m2_e0 | het | 42.5209 | 27.0270 | 99.6439 | 95.4728 | 1960 | 5292 | 1959 | 7 | 1 | 14.2857 | |
| hfeng-pmm3 | INDEL | I16_PLUS | HG002compoundhet | hetalt | 96.1827 | 92.6899 | 99.9490 | 46.0226 | 1940 | 153 | 1960 | 1 | 1 | 100.0000 | |
| gduggal-bwafb | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 82.5111 | 88.7732 | 77.0743 | 58.5831 | 1961 | 248 | 1960 | 583 | 573 | 98.2847 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 94.3169 | 89.7764 | 99.3411 | 33.3446 | 6182 | 704 | 1960 | 13 | 13 | 100.0000 | |
| hfeng-pmm2 | INDEL | I16_PLUS | * | hetalt | 95.9205 | 92.4214 | 99.6950 | 58.3968 | 1939 | 159 | 1961 | 6 | 6 | 100.0000 | |
| hfeng-pmm2 | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.0002 | 96.8379 | 99.1907 | 64.6712 | 1960 | 64 | 1961 | 16 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.9251 | 92.9511 | 96.9847 | 70.2893 | 1978 | 150 | 1962 | 61 | 54 | 88.5246 | |
| hfeng-pmm1 | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.2228 | 96.9368 | 99.5434 | 64.5886 | 1962 | 62 | 1962 | 9 | 0 | 0.0000 | |
| anovak-vg | SNP | * | map_l250_m2_e1 | homalt | 84.0320 | 72.8109 | 99.3418 | 88.4510 | 1979 | 739 | 1962 | 13 | 9 | 69.2308 | |
| astatham-gatk | INDEL | I16_PLUS | HG002compoundhet | hetalt | 96.1827 | 92.6899 | 99.9491 | 45.9080 | 1940 | 153 | 1962 | 1 | 1 | 100.0000 | |