Table 1. Total number of reads after quality trimming and proportion mapped to the reference genome before and after masking polymorphic sites.

	Trimmed Reads	tophat2 Initial	tophat2 Masked	bwa mem Initial	bwa mem Masked
Australian
Library 1	31,726,619	0.684	0.472	0.9	0.885
Library 2	33,049,620	0.669	0.455	0.876	0.871
Library 3	32,844,330	0.669	0.455	0.874	0.869
Average		0.674	0.461	0.883	0.875
Timor
Library 1	33,115,938	0.643	0.464	0.883	0.879
Library 2	34,328,721	0.645	0.466	0.883	0.879
Library 3	33,467,969	0.621	0.443	0.864	0.86
Average		0.636	0.458	0.877	0.873