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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
72701-72750 / 86044 show all | |||||||||||||||
| jlack-gatk | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 96.9317 | 95.4084 | 98.5046 | 64.3470 | 5070 | 244 | 5072 | 77 | 69 | 89.6104 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.3261 | 97.7936 | 98.8644 | 77.1834 | 1507 | 34 | 1480 | 17 | 11 | 64.7059 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.5213 | 93.3654 | 99.8981 | 44.6324 | 2913 | 207 | 2942 | 3 | 3 | 100.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 95.5882 | 99.5406 | 91.9378 | 72.4044 | 650 | 3 | 650 | 57 | 55 | 96.4912 | |
| jlack-gatk | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.1906 | 99.8023 | 98.5863 | 61.2684 | 55521 | 110 | 55510 | 796 | 46 | 5.7789 | |
| jlack-gatk | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.7961 | 99.7741 | 97.8371 | 63.8462 | 35339 | 80 | 35328 | 781 | 32 | 4.0973 | |
| jlack-gatk | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 92.3077 | 92.3077 | 92.3077 | 81.4286 | 12 | 1 | 12 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.8935 | 99.8564 | 99.9306 | 55.5702 | 20170 | 29 | 20170 | 14 | 13 | 92.8571 | |
| jlack-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4351 | 99.7890 | 99.0837 | 56.5880 | 27900 | 59 | 27899 | 258 | 21 | 8.1395 | |
| jlack-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.1812 | 99.7479 | 98.6208 | 60.0301 | 17806 | 45 | 17805 | 249 | 13 | 5.2209 | |
| jlack-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 83.3333 | 83.3333 | 83.3333 | 86.0465 | 5 | 1 | 5 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.8960 | 99.8713 | 99.9208 | 48.6105 | 10089 | 13 | 10089 | 8 | 7 | 87.5000 | |
| jli-custom | INDEL | C16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 0.0000 | 0.0000 | 0.0000 | 0 | 0 | 0 | 0 | 0 | |||
| jli-custom | INDEL | C16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 0.0000 | 0.0000 | 0.0000 | 0 | 0 | 0 | 0 | 0 | |||
| jli-custom | INDEL | C16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 0 | 0 | 0 | 0 | |||
| jli-custom | INDEL | C16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 0.0000 | 0 | 0 | 0 | 0 | 0 | |||
| jlack-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.9991 | 96.8351 | 99.1915 | 73.1225 | 15084 | 493 | 15091 | 123 | 94 | 76.4228 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.1869 | 99.2134 | 99.1605 | 78.4314 | 6054 | 48 | 6024 | 51 | 24 | 47.0588 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.1311 | 92.6743 | 99.8558 | 64.0650 | 5503 | 435 | 5540 | 8 | 7 | 87.5000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.9618 | 99.7173 | 98.2178 | 72.3769 | 3527 | 10 | 3527 | 64 | 63 | 98.4375 | |
| jli-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.1076 | 98.6776 | 99.5414 | 71.9967 | 93200 | 1249 | 93118 | 429 | 358 | 83.4499 | |
| jli-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.3482 | 99.1423 | 99.5550 | 73.6647 | 47857 | 414 | 47648 | 213 | 149 | 69.9531 | |
| jli-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.1334 | 94.7850 | 99.6011 | 59.6178 | 14613 | 804 | 14733 | 59 | 58 | 98.3051 | |
| jli-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.6951 | 99.8992 | 99.4918 | 73.2959 | 30730 | 31 | 30737 | 157 | 151 | 96.1783 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 95.1113 | 93.6897 | 96.5766 | 79.4254 | 1069 | 72 | 1072 | 38 | 21 | 55.2632 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 95.3225 | 94.9541 | 95.6938 | 84.8606 | 414 | 22 | 400 | 18 | 4 | 22.2222 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 95.3650 | 91.5952 | 99.4585 | 65.4829 | 534 | 49 | 551 | 3 | 2 | 66.6667 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 93.0769 | 99.1803 | 87.6812 | 86.5889 | 121 | 1 | 121 | 17 | 15 | 88.2353 | |
| hfeng-pmm3 | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4357 | 98.9449 | 99.9314 | 53.1567 | 27664 | 295 | 27664 | 19 | 7 | 36.8421 | |
| hfeng-pmm3 | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.1505 | 98.3978 | 99.9147 | 54.8907 | 17565 | 286 | 17565 | 15 | 4 | 26.6667 | |
| hfeng-pmm3 | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 90.9091 | 83.3333 | 100.0000 | 88.0952 | 5 | 1 | 5 | 0 | 0 | ||
| hfeng-pmm3 | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.9406 | 99.9208 | 99.9604 | 49.7187 | 10094 | 8 | 10094 | 4 | 3 | 75.0000 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.2888 | 95.8808 | 98.7387 | 78.3161 | 1094 | 47 | 1096 | 14 | 11 | 78.5714 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.8944 | 96.5596 | 99.2665 | 83.6203 | 421 | 15 | 406 | 3 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.0122 | 94.5111 | 99.6491 | 66.8219 | 551 | 32 | 568 | 2 | 2 | 100.0000 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 96.4427 | 100.0000 | 93.1298 | 85.5088 | 122 | 0 | 122 | 9 | 9 | 100.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.6199 | 97.4770 | 99.7898 | 71.4168 | 15184 | 393 | 15192 | 32 | 22 | 68.7500 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.2415 | 98.7053 | 99.7836 | 77.2969 | 6023 | 79 | 5994 | 13 | 3 | 23.0769 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.3996 | 94.9310 | 100.0000 | 60.6737 | 5637 | 301 | 5674 | 0 | 0 | ||
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5480 | 99.6325 | 99.4637 | 71.3697 | 3524 | 13 | 3524 | 19 | 19 | 100.0000 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.0502 | 96.8343 | 99.2971 | 55.9217 | 15539 | 508 | 15540 | 110 | 95 | 86.3636 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.2031 | 96.0157 | 98.4203 | 68.4990 | 5374 | 223 | 5358 | 86 | 74 | 86.0465 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.9479 | 95.9924 | 99.9847 | 32.9893 | 6539 | 273 | 6556 | 1 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5197 | 99.6701 | 99.3697 | 56.7552 | 3626 | 12 | 3626 | 23 | 21 | 91.3043 | |
| hfeng-pmm3 | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4564 | 98.9898 | 99.9274 | 58.6346 | 55069 | 562 | 55060 | 40 | 15 | 37.5000 | |
| hfeng-pmm3 | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.1881 | 98.4782 | 99.9083 | 59.9451 | 34880 | 539 | 34871 | 32 | 8 | 25.0000 | |
| hfeng-pmm3 | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.0000 | 92.3077 | 100.0000 | 82.8571 | 12 | 1 | 12 | 0 | 0 | ||
| hfeng-pmm3 | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.9257 | 99.8911 | 99.9604 | 56.1148 | 20177 | 22 | 20177 | 8 | 7 | 87.5000 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.6812 | 95.9164 | 99.5121 | 62.7887 | 5097 | 217 | 5099 | 25 | 19 | 76.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.1550 | 96.9500 | 99.3902 | 75.7157 | 1494 | 47 | 1467 | 9 | 4 | 44.4444 | |