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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
10501-10550 / 86044 show all | |||||||||||||||
| ckim-isaac | INDEL | I16_PLUS | HG002complexvar | * | 52.2963 | 39.2666 | 78.2675 | 62.9505 | 514 | 795 | 515 | 143 | 46 | 32.1678 | |
| ckim-isaac | INDEL | I1_5 | HG002complexvar | homalt | 94.8874 | 91.2478 | 98.8294 | 44.5077 | 12271 | 1177 | 12242 | 145 | 45 | 31.0345 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 84.9987 | 79.7856 | 90.9408 | 61.8351 | 521 | 132 | 522 | 52 | 45 | 86.5385 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.6427 | 99.5150 | 99.7707 | 54.4892 | 25236 | 123 | 25236 | 58 | 45 | 77.5862 | |
| ckim-isaac | SNP | * | HG002complexvar | homalt | 95.6391 | 91.6604 | 99.9788 | 17.3239 | 264509 | 24066 | 264563 | 56 | 45 | 80.3571 | |
| ckim-isaac | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 97.5405 | 96.0212 | 99.1085 | 32.5488 | 10305 | 427 | 10339 | 93 | 45 | 48.3871 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.3204 | 98.9679 | 99.6754 | 59.9358 | 19657 | 205 | 19650 | 64 | 45 | 70.3125 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.9205 | 98.2346 | 99.6161 | 72.9579 | 15302 | 275 | 15309 | 59 | 45 | 76.2712 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.3708 | 98.3432 | 98.3984 | 72.3852 | 3502 | 59 | 3502 | 57 | 45 | 78.9474 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.2521 | 96.8864 | 99.6568 | 72.9143 | 15092 | 485 | 15100 | 52 | 45 | 86.5385 | |
| ckim-vqsr | INDEL | I6_15 | HG002compoundhet | het | 86.6987 | 97.5962 | 77.9904 | 84.7889 | 203 | 5 | 163 | 46 | 45 | 97.8261 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.5627 | 95.6563 | 99.5467 | 33.3070 | 10020 | 455 | 10102 | 46 | 45 | 97.8261 | |
| gduggal-bwafb | SNP | tv | map_l125_m2_e0 | het | 98.2005 | 98.7742 | 97.6335 | 76.4784 | 10314 | 128 | 10314 | 250 | 45 | 18.0000 | |
| gduggal-bwafb | SNP | tv | map_l125_m2_e1 | het | 98.2193 | 98.7871 | 97.6581 | 76.5519 | 10425 | 128 | 10425 | 250 | 45 | 18.0000 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 83.2899 | 84.1808 | 82.4176 | 55.5375 | 149 | 28 | 225 | 48 | 45 | 93.7500 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 80.5715 | 75.2066 | 86.7606 | 55.0063 | 182 | 60 | 308 | 47 | 45 | 95.7447 | |
| gduggal-bwavard | SNP | * | map_l250_m2_e1 | * | 90.6461 | 97.4959 | 84.6957 | 92.1274 | 7787 | 200 | 7709 | 1393 | 45 | 3.2304 | |
| gduggal-bwavard | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 98.5575 | 98.0766 | 99.0431 | 61.4154 | 6884 | 135 | 6831 | 66 | 45 | 68.1818 | |
| gduggal-bwavard | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 97.8028 | 97.6785 | 97.9275 | 46.3889 | 7279 | 173 | 7182 | 152 | 45 | 29.6053 | |
| gduggal-bwavard | SNP | tv | map_l100_m0_e0 | het | 91.6040 | 98.1446 | 85.8808 | 81.9878 | 7088 | 134 | 7074 | 1163 | 45 | 3.8693 | |
| gduggal-bwavard | SNP | tv | map_l150_m2_e1 | het | 91.8305 | 98.3805 | 86.0982 | 85.8449 | 7229 | 119 | 7209 | 1164 | 45 | 3.8660 | |
| gduggal-bwavard | INDEL | C1_5 | HG002compoundhet | * | 0.0000 | 0.0000 | 48.4848 | 84.1346 | 0 | 1 | 144 | 153 | 45 | 29.4118 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 95.1577 | 91.3256 | 99.3255 | 38.6854 | 2990 | 284 | 8246 | 56 | 45 | 80.3571 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 79.5287 | 70.4992 | 91.2109 | 53.4545 | 1864 | 780 | 467 | 45 | 45 | 100.0000 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 76.6225 | 63.6808 | 96.1659 | 75.3638 | 3384 | 1930 | 3386 | 135 | 45 | 33.3333 | |
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 88.2450 | 80.8166 | 97.1772 | 89.7454 | 8729 | 2072 | 8744 | 254 | 45 | 17.7165 | |
| eyeh-varpipe | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 81.2006 | 94.8980 | 70.9586 | 87.8472 | 1674 | 90 | 1251 | 512 | 45 | 8.7891 | |
| eyeh-varpipe | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 96.0585 | 99.7289 | 92.6487 | 50.1527 | 11402 | 31 | 10889 | 864 | 45 | 5.2083 | |
| eyeh-varpipe | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 84.1712 | 93.6594 | 76.4286 | 83.9334 | 1034 | 70 | 856 | 264 | 45 | 17.0455 | |
| mlin-fermikit | INDEL | D16_PLUS | HG002complexvar | het | 90.4295 | 87.7145 | 93.3180 | 67.0463 | 971 | 136 | 810 | 58 | 45 | 77.5862 | |
| qzeng-custom | INDEL | D16_PLUS | HG002complexvar | het | 88.4674 | 95.9350 | 82.0784 | 59.1925 | 1062 | 45 | 1319 | 288 | 45 | 15.6250 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 79.6041 | 74.3750 | 85.6240 | 66.7717 | 119 | 41 | 542 | 91 | 45 | 49.4505 | |
| qzeng-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 92.8865 | 96.0317 | 89.9408 | 90.7338 | 1694 | 70 | 1824 | 204 | 45 | 22.0588 | |
| qzeng-custom | SNP | ti | HG002compoundhet | het | 98.0838 | 97.7380 | 98.4320 | 42.6883 | 9290 | 215 | 11739 | 187 | 45 | 24.0642 | |
| qzeng-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.8278 | 98.3293 | 99.3313 | 69.2512 | 11359 | 193 | 11290 | 76 | 45 | 59.2105 | |
| qzeng-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.8278 | 98.3293 | 99.3313 | 69.2512 | 11359 | 193 | 11290 | 76 | 45 | 59.2105 | |
| qzeng-custom | SNP | ti | segdup | * | 98.7450 | 98.9558 | 98.5351 | 91.7233 | 19333 | 204 | 19237 | 286 | 45 | 15.7343 | |
| qzeng-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.2810 | 98.6274 | 95.9709 | 85.0094 | 14371 | 200 | 14363 | 603 | 45 | 7.4627 | |
| qzeng-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.2810 | 98.6274 | 95.9709 | 85.0094 | 14371 | 200 | 14363 | 603 | 45 | 7.4627 | |
| qzeng-custom | SNP | tv | map_l125_m2_e1 | homalt | 84.2063 | 73.2631 | 98.9926 | 69.1889 | 4450 | 1624 | 4422 | 45 | 45 | 100.0000 | |
| qzeng-custom | SNP | tv | map_l250_m0_e0 | * | 73.9185 | 63.3987 | 88.6239 | 97.9721 | 485 | 280 | 483 | 62 | 45 | 72.5806 | |
| ltrigg-rtg2 | INDEL | D1_5 | HG002compoundhet | hetalt | 98.0424 | 96.5838 | 99.5458 | 62.4013 | 9867 | 349 | 9863 | 45 | 45 | 100.0000 | |
| ltrigg-rtg2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.3394 | 98.7572 | 97.9251 | 69.6626 | 45134 | 568 | 45544 | 965 | 45 | 4.6632 | |
| ltrigg-rtg2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.3394 | 98.7572 | 97.9251 | 69.6626 | 45134 | 568 | 45544 | 965 | 45 | 4.6632 | |
| mlin-fermikit | INDEL | I1_5 | * | hetalt | 79.4455 | 66.1635 | 99.3997 | 62.4768 | 7407 | 3788 | 7451 | 45 | 45 | 100.0000 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 88.7875 | 97.1564 | 81.7460 | 71.8121 | 205 | 6 | 206 | 46 | 45 | 97.8261 | |
| mlin-fermikit | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 74.3472 | 92.7273 | 62.0482 | 92.1103 | 102 | 8 | 103 | 63 | 45 | 71.4286 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 87.8953 | 92.2197 | 83.9583 | 47.5410 | 403 | 34 | 403 | 77 | 45 | 58.4416 | |
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.7108 | 98.7484 | 98.6731 | 78.8824 | 3866 | 49 | 3867 | 52 | 45 | 86.5385 | |
| ndellapenna-hhga | SNP | tv | * | het | 99.8309 | 99.7335 | 99.9285 | 20.7977 | 590119 | 1577 | 590138 | 422 | 45 | 10.6635 | |