Table 1:
The effect of sex chromosome homology on variant calling on the X chromosomea
| Regionb | Length (bp)c | Before Only (per Mb)d | After Only (per Mb)e |
|---|---|---|---|
| PAR1 | 2,589,520 | 0 (0) | 7,563 (2,920.6) |
| PAR2 | 329,516 | 0 (0) | 633 (1921) |
| XTR | 4,287,237 | 40 (9.3) | 366 (85.4) |
| XAR | 55,982,492 | 299 (5.3) | 400 (7.2) |
| XCR | 89,011,795 | 610 (6.9) | 523 (5.9) |
| Total | 152,250,560 | 949 (6.2) | 9,485 (62.3) |
aHigh-coverage whole-genome data from XX individual in Dataset 1.
bPAR1: pseudoautosomal region 1; PAR2: pseudoautosomal region 2; XTR: X-transposed region; XAR: X-added region; XCR: X-conserved region.
cTotal sequence length of region in base pairs.
dTotal number of variants, after filtering, present before but not after Y chromosome masking. Variants per Mb of sequence are presented in parentheses.
eTotal number of variants, after filtering, present after but not before Y chromosome masking. Variants per Mb of sequence are presented in parentheses.