Identification of genes for salt tolerance and yield-related traits in rice plants grown hydroponically and under saline field conditions by genome-wide association study

Rice

Table 2 Distribution of high quality SNP markers in the rice genome

Chr	All SNPs ^a		10% set ^b		SNPs within genes ^c
Chr	No. of SNPs	Spacing (bp)	No. of SNPs	Spacing (bp)	No. of genes	No. of SNPs	Spacing (bp)
1	404,439	107	40,444	1070	5468	128,891	336
2	337,347	107	33,735	1065	4577	105,849	339
3	311,509	117	31,151	1169	4962	94,538	385
4	298,569	119	29,857	1189	3758	98,508	360
5	240,251	125	24,026	1244	3812	73,139	409
6	290,332	108	29,034	1073	3720	91,561	340
7	275,472	108	27,548	1077	3482	88,151	336
8	281,408	101	28,141	1010	3278	90,526	314
9	212,314	108	21,232	1078	2656	67,287	340
10	248,350	93	24,835	934	2724	77,376	299
11	300,367	97	30,037	965	3088	102,704	282
12	255,594	108	25,560	1077	2807	82,874	332
Total	3,455,952	108	345,600	1079	44,332	1,101,404	339

^aAll SNPs with minor allele frequency > 0.05 and missing data rate < 20%; ^bRandomly sampled set of 10% of the SNPs from the complete SNP dataset; ^cAll SNPs distributed in 44,332 annotated genes