Table 1. Ciona deep sequencing statistics.

Sample	Total reads	%Reads ≥ MapQ 15	Avg. coverage	% of sites ≥ 10× coverage	Avg. homozygosity(%)
C. intestinalis chm	159,931,687	68.5	34.22	95.42	98.23
MPP C. savignyi bugeye	116,448,947	37.4	13.62	67	96.97
MPP C. savignyi WT-sib	181,200,319	40.3	22.81	76.64	96.45
SPP C. savignyi bugeye	175,967,795	41.1	22.60	77.97	96.71
SPP C. savignyi WT-sib	166,735,236	39.6	20.63	74.42	96.78