Table 3 FMR1 and FMR2 full-mutations detected by ExpansionHunter, GangSTR, and TREDPARSE with lowered repeat length threshold
From: Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions
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 |