Table 2.

Summary of re-sequencing data and reads mapping onto the Nipponbare genome

	S24	Huaye 3	Huaye 4
Total reads	79,619,359	95,853,301	77,152,550
High-quality reads	77,907,543	95,453,868	75,256,129
Clean bases	19,629,347,386	28,611,001,160	18,960,007,854
Percent of bases ≥ Q20 (%)	96.55	94.67	92.47
Percent of bases ≥ Q30 (%)	89.6	87.98	86.85
Mapped (%)	96.54	97.71	97.83
Properly mapped (%)	89.76	90.34	91.17
Coverage ratio 10× (%)	91.71	91.47	87.52
GC content (%)	43.46	44.97	41.43
Average coverage depth	44	65	42