Whole-Genome Characteristics and Polymorphic Analysis of Vietnamese Rice Landraces as a Comprehensive Information Resource for Marker-Assisted Selection

Table 3

Number of SNP effects annotated by SnpEff. SNPs were classified into various genomic regions (intergenic regions, intron, and exon) and effect terms by types. The total of intergenic, intronic, and exonic SNPs was more than the total number of SNPs due to overlapping gene models in the GFF file.

	indica 12		indica 13		indica 15		japonica 11		japonica 14
Intergenic	1,374,419	68.45	1,329,647	69.46	1,527,754	68.16	488,888	66.10	454,811	65.83
Genic	633,408	31.55	584,505	30.54	713,664	31.84	250,766	33.90	236,104	34.17
Intron & regulatory sequences	288,375	45.53	279,350	47.79	320,956	44.97	109,191	43.54	101,187	42.86
UTRs	85,749	13.54	82,611	14.13	96,948	13.58	29,587	11.80	28,138	11.92
CDS	259,284	40.93	222,544	38.07	295,760	41.44	111,988	44.66	106,779	45.23
Nonsynonymous	151,998	58.62	131,754	59.20	172,767	58.41	66,645	59.51	63,962	59.90
Synonymous	107,286	41.38	90,790	40.80	122,993	41.59	45,343	40.49	42,817	40.10