Table 3. The frequency of SNP bases substitution between wild rice lines and reference genomes.

Sample	Base	93–11 reference genome				Nipponbare reference genome
		A	C	G	T	A	C	G	T
Huaye 1	A	—	51,853	237,959	59,654	—	46,564	203,260	53,572
	C	55,295	—	36,627	227,188	48,371	—	31,605	220,915
	G	227,618	36,423	—	55,377	220,817	31,596	—	48,437
	T	59,790	237,539	52,375	—	53,574	204,496	46,101	—
Huaye 2	A	—	41,232	187,341	46,372	—	53,349	232,858	59,193
	C	44,710	—	29,937	181,480	55,466	—	36,871	254,857
	G	182,044	29,718	—	44,940	256,021	36,976	—	55,386
	T	46,780	187,690	41,228	—	59,793	234,656	52,533	—

Rows with gray color indicate the reference bases, and columns with gray color indicate the substituted bases. For example, Row 'A' column 'T' indicates how many 'A' bases have been replaced by 'T' bases. Red cell means the higher bases substitution, and the green means the lower bases substitution.