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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
4601-4650 / 86044 show all | |||||||||||||||
| gduggal-bwavard | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 0.0000 | 0.1674 | 0.0000 | 0.0000 | 2 | 1193 | 0 | 0 | 0 | ||
| gduggal-snapfb | SNP | * | map_l150_m1_e0 | * | 96.2111 | 96.1025 | 96.3199 | 76.8067 | 29416 | 1193 | 29419 | 1124 | 527 | 46.8861 | |
| ckim-isaac | SNP | ti | HG002compoundhet | homalt | 91.0386 | 83.8788 | 99.5347 | 26.2921 | 6202 | 1192 | 6203 | 29 | 24 | 82.7586 | |
| ciseli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 59.8797 | 85.7519 | 46.0008 | 48.3317 | 7174 | 1192 | 7166 | 8412 | 7803 | 92.7603 | |
| gduggal-snapfb | SNP | * | map_l100_m0_e0 | * | 96.4309 | 96.3734 | 96.4883 | 71.4997 | 31650 | 1191 | 31653 | 1152 | 513 | 44.5312 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 75.7234 | 65.8935 | 89.0004 | 54.7661 | 2301 | 1191 | 2306 | 285 | 284 | 99.6491 | |
| hfeng-pmm2 | INDEL | * | HG002complexvar | * | 99.1003 | 98.4520 | 99.7572 | 57.3339 | 75747 | 1191 | 75614 | 184 | 143 | 77.7174 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.1302 | 92.8764 | 99.6203 | 36.5800 | 15515 | 1190 | 15743 | 60 | 60 | 100.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.1302 | 92.8764 | 99.6203 | 36.5800 | 15515 | 1190 | 15743 | 60 | 60 | 100.0000 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 95.7763 | 96.4226 | 95.1386 | 69.4450 | 32047 | 1189 | 32017 | 1636 | 1576 | 96.3325 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 94.5490 | 94.0187 | 95.0853 | 75.2577 | 18674 | 1188 | 18786 | 971 | 814 | 83.8311 | |
| jpowers-varprowl | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 0.0000 | 0.5858 | 0.0000 | 0.0000 | 7 | 1188 | 0 | 0 | 0 | ||
| ghariani-varprowl | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 0.0000 | 0.5858 | 0.0000 | 0.0000 | 7 | 1188 | 0 | 0 | 0 | ||
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.1399 | 92.8943 | 99.6204 | 36.5756 | 15518 | 1187 | 15746 | 60 | 60 | 100.0000 | |
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.1399 | 92.8943 | 99.6204 | 36.5756 | 15518 | 1187 | 15746 | 60 | 60 | 100.0000 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 92.7620 | 87.2242 | 99.0507 | 45.1542 | 8104 | 1187 | 2713 | 26 | 26 | 100.0000 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 92.7620 | 87.2242 | 99.0507 | 45.1542 | 8104 | 1187 | 2713 | 26 | 26 | 100.0000 | |
| qzeng-custom | SNP | ti | map_l250_m2_e1 | het | 74.8760 | 64.0800 | 90.0468 | 96.4938 | 2114 | 1185 | 2117 | 234 | 196 | 83.7607 | |
| jpowers-varprowl | SNP | ti | HG002compoundhet | * | 92.4932 | 93.2258 | 91.7721 | 42.7151 | 16294 | 1184 | 16396 | 1470 | 904 | 61.4966 | |
| ciseli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 79.2334 | 93.9527 | 68.5015 | 74.7853 | 18395 | 1184 | 18642 | 8572 | 188 | 2.1932 | |
| ciseli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 79.2334 | 93.9527 | 68.5015 | 74.7853 | 18395 | 1184 | 18642 | 8572 | 188 | 2.1932 | |
| qzeng-custom | SNP | ti | map_l150_m0_e0 | homalt | 72.5105 | 57.1894 | 99.0446 | 79.2025 | 1579 | 1182 | 1555 | 15 | 15 | 100.0000 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 62.4770 | 93.3666 | 46.9454 | 60.6415 | 16637 | 1182 | 16660 | 18828 | 18130 | 96.2928 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 53.5889 | 45.7759 | 64.6178 | 56.5306 | 997 | 1181 | 2071 | 1134 | 332 | 29.2769 | |
| anovak-vg | SNP | tv | map_l100_m1_e0 | het | 79.8335 | 92.3396 | 70.3109 | 72.6600 | 14236 | 1181 | 14226 | 6007 | 1268 | 21.1087 | |
| mlin-fermikit | SNP | * | map_l250_m0_e0 | het | 35.3963 | 21.6467 | 97.0238 | 84.3210 | 326 | 1180 | 326 | 10 | 1 | 10.0000 | |
| gduggal-bwavard | SNP | tv | map_siren | * | 96.6959 | 97.4309 | 95.9719 | 67.9885 | 44750 | 1180 | 44530 | 1869 | 157 | 8.4002 | |
| gduggal-bwavard | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 0.0000 | 0.2538 | 0.0000 | 0.0000 | 3 | 1179 | 0 | 0 | 0 | ||
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 79.5052 | 66.5627 | 98.6958 | 53.7549 | 2347 | 1179 | 2346 | 31 | 28 | 90.3226 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 79.5052 | 66.5627 | 98.6958 | 53.7549 | 2347 | 1179 | 2346 | 31 | 28 | 90.3226 | |
| gduggal-snapvard | SNP | * | map_l150_m2_e1 | * | 92.4051 | 96.3396 | 88.7794 | 82.5294 | 31031 | 1179 | 30628 | 3871 | 287 | 7.4141 | |
| ndellapenna-hhga | SNP | * | map_siren | * | 99.5283 | 99.1937 | 99.8651 | 53.0102 | 145049 | 1179 | 145051 | 196 | 89 | 45.4082 | |
| gduggal-bwaplat | INDEL | * | map_l100_m2_e0 | * | 80.6607 | 68.1018 | 98.8989 | 92.5303 | 2515 | 1178 | 2515 | 28 | 11 | 39.2857 | |
| gduggal-bwafb | INDEL | I16_PLUS | * | hetalt | 59.7317 | 43.8513 | 93.6441 | 57.0909 | 920 | 1178 | 221 | 15 | 15 | 100.0000 | |
| gduggal-bwaplat | SNP | ti | map_l250_m2_e0 | homalt | 49.2891 | 32.7044 | 100.0000 | 95.1810 | 572 | 1177 | 571 | 0 | 0 | ||
| qzeng-custom | SNP | ti | map_l250_m2_e0 | het | 74.6630 | 63.8291 | 89.9265 | 96.4842 | 2077 | 1177 | 2080 | 233 | 195 | 83.6910 | |
| ckim-isaac | INDEL | I1_5 | HG002complexvar | homalt | 94.8874 | 91.2478 | 98.8294 | 44.5077 | 12271 | 1177 | 12242 | 145 | 45 | 31.0345 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 70.7753 | 78.9709 | 64.1209 | 53.4898 | 4420 | 1177 | 8614 | 4820 | 4189 | 86.9087 | |
| gduggal-bwafb | INDEL | I16_PLUS | HG002compoundhet | hetalt | 60.2626 | 43.8127 | 96.4912 | 42.7136 | 917 | 1176 | 220 | 8 | 8 | 100.0000 | |
| gduggal-bwaplat | INDEL | * | HG002complexvar | hetalt | 79.9153 | 68.2076 | 96.4751 | 78.0617 | 2523 | 1176 | 2518 | 92 | 88 | 95.6522 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 43.8454 | 39.1619 | 49.8013 | 62.4191 | 757 | 1176 | 752 | 758 | 719 | 94.8549 | |
| egarrison-hhga | INDEL | D16_PLUS | HG002compoundhet | * | 61.7860 | 49.7651 | 81.4641 | 41.2623 | 1165 | 1176 | 1213 | 276 | 256 | 92.7536 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 0.0000 | 0.5922 | 0.0000 | 0.0000 | 7 | 1175 | 0 | 0 | 0 | ||
| ckim-dragen | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.1935 | 96.8999 | 97.4889 | 57.0530 | 36727 | 1175 | 36532 | 941 | 927 | 98.5122 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 0.0000 | 0.5922 | 0.0000 | 0.0000 | 7 | 1175 | 0 | 0 | 0 | ||
| jpowers-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 52.8814 | 39.9386 | 78.2347 | 54.0553 | 780 | 1173 | 780 | 217 | 203 | 93.5484 | |
| jlack-gatk | INDEL | I6_15 | * | * | 96.1308 | 95.2745 | 97.0025 | 53.1865 | 23650 | 1173 | 23656 | 731 | 625 | 85.4993 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 52.8148 | 39.9386 | 77.9441 | 54.2466 | 780 | 1173 | 781 | 221 | 203 | 91.8552 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.1875 | 96.2685 | 98.1242 | 59.9927 | 30236 | 1172 | 30236 | 578 | 510 | 88.2353 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.1875 | 96.2685 | 98.1242 | 59.9927 | 30236 | 1172 | 30236 | 578 | 510 | 88.2353 | |