Structural variation on Macquarie perch scaffold 633
Manta detected a total of 221 structural variants (42 insertions and 179 deletions) in 90 individuals (47 males, 43 females) spread relatively evenly through 28 positions on scaffold 633 (from 8693 to 274267; Appendix D). Mean detected indel size was 98 bp (range 50-425 bp, despite minimum default size cutoff of 8 bp). None of the structural variants were strongly sex-linked (Fig. D1). In both populations, males had more indels than did females (Dartmouth: 82 vs 58, Yarra: 46 vs 35, respectively) but the difference between the sexes was not significant (per population Fisher test P=0.38, beta-binomial test for pooled populations: P>0.62). Overall, Manta did not show large regions that are haploid in a large proportion of individuals of one sex but not the other.