Table 3.
FMR1 and FMR2 full-mutations detected by ExpansionHunter, GangSTR, and TREDPARSE with lowered repeat length threshold
| Aligner | Isaac | BWA | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Locus | FMR1 (n = 18) | FMR2 (n = 3) | FMR1 (n = 18) | FMR2 (n = 3) | ||||||||||
| FM threshold | 54 repeats | 60 repeats | 54 repeats | 60 repeats | ||||||||||
| Allelic classification | FM | IM | NL | FP | FM | NL | FP | FM | IM | NL | FP | FM | NL | FP |
| EH_v2 | 18 | . | . | 20 | 3 | . | 0 | 18 | . | . | 16 | 3 | . | 0 |
| EH_v3 | 18 | . | . | 22 | 3 | . | 0 | 18 | . | . | 22 | 3 | . | 0 |
| GangSTR | 4 | . | 14 | 7 | 0 | 3 | 0 | 3 | . | 15 | 0 | 0 | 3 | 0 |
| TREDPARSE | 15 | 1 | 2 | 8 | 0 | 3 | 0 | 16 | . | 2 | 13 | 0 | 3 | 0 |
The number of full-mutations (FMs) misclassified as normal (NL; < 45 repeats for FMR1 and < 31 repeats for FMR2) or intermediate (IM; 45–54 repeats for FMR1) allele are shown. The true number (n) of known FM alleles in the FMR1 and FMR2 genes is indicated in parenthesis. False-positive (FP) calls made by the tools are also reported