Table 1. Percent mapped reads for sequencing libraries.

Sample	# Reads	# Mapped Reads	% Mapped
D. sechellia C1	19,222,060	18,496,450	96.23
D. sechellia C2	20,704,811	19,440,620	93.89
D. sechellia C3	17,696,868	17,123,579	96.76
D. sechellia LD1	19,576,162	18,341,777	93.69
D. sechellia LD2	14,508,205	12,988,684	89.53
D. sechellia LD3	17,432,600	16,040,372	92.01
D. simulans C1	28,056,123	26,210,691	93.42
D. simulans C2	26,058,213	24,449,785	93.83
D. simulans C3	24,095,284	22,589,715	93.75
D. simulans LD1	17,841,650	16,739,731	93.82
D. simulans LD2	14,608,378	13,562,252	92.84
D. simulans LD3	17,628,201	16,471,452	93.44
D. melanogaster C1	21,999,530	20,633,866	93.79
D. melanogaster C2	20,950,464	19,779,953	94.41
D. melanogaster C3	22,157,160	20,919,514	94.41
D. melanogaster LD1	39,619,560	37,618,491	94.95
D. melanogaster LD2	23,214,861	21,991,775	94.73
D. melanogaster LD3	18,976,326	17,855,382	94.09