SNP-based analysis of genetic diversity in anther-derived rice by whole genome sequencing

Rice

Table 3 Distribution of SNPs within genic regions

Cultivar	Gene		Total SNP in gene			Non-synonymous		Synonymous		Non-synonymous SNP/synonymous SNP
Cultivar	(/Total gene #)		Count (/total SNP)		SNP/gene	Count	NS/gene	Count	SY/gene	Non-synonymous SNP/synonymous SNP
Dongjin	4,713	11.2%	31,166	18.2%	6.61^a	4,356	0.92^b	3,802	0.81^c	1.14
Sub total	4,713	11.2%	31,166	18.2%	6.61	4,356	0.92	3,802	0.81	1.14
Sub average	4,713	11.2%	31,166	18.2%	6.61	4,356	0.92	3,802	0.81	1.14
Hwayeong	5,471	13.0%	39,029	17.5%	7.13	5,222	0.95	4,382	0.80	1.19
HY-04	7,507	17.8%	55,668	19.6%	7.42	7,638	1.02	6,368	0.85	1.19
HY-08	6,558	15.6%	47,722	18.4%	7.28	6,448	0.98	5,323	0.81	1.12
BLB	5,764	13.7%	41,214	19.0%	7.15	5,605	0.97	4,773	0.83	1.17
Sub total	25,300	60.1%	183,633	18.7%	7.26	24,913	0.98	20,846	0.82	4.67
Sub average	6,325	15.0%	45,908	18.7%	7.26	6,228	0.98	5,212	0.82	1.16
Total	30,013	71.3%	214,799	18.6%	7.16	29,269	0.98	24,648	0.82	5.81
Average	6,003	14.3%	42,960	18.6%	7.16	5,854	0.98	4,930	0.82	1.16

Total gene count (build 5): 42,088.
a: SNP/Gene : Total SNP frequency in each gene (including CDS, intron, UTR region), 31,166/4,713=6.61.
b: NS/Gene : non-synonymous SNP frequency in each gene, 4,356/4,713=0.92.
c: SY/Gene : Synonymous SNP frequency in each gene, 3,802/4,713=0.81.