Discovery of Functional SNPs via Genome-Wide Exploration of Malaysian Pigmented Rice Varieties

Table 2

Summary of SNP identification and annotation in Bali, PH9, MRM16, and MRQ100 when compared against Nipponbare reference genome. The number of total annotated SNPs was higher than the total number of quality SNPs due to more than one annotation in a single SNP.

	Bali	PH9	MRM16	MRQ100	Total
Number of raw SNPs	2,394,592	2,227,819	2,740,764	2,380,079	9,743,254
Number of high-quality SNPs	436,322	412,791	469,782	435,382	1,754,277
Intergenic SNPs	328,261	310,712	349,786	327,021	1,315,780
Genic SNPs	149,232	140,677	165,124	149,903	604,936