Identification of candidate genes for drought tolerance by whole-genome resequencing in maize

BMC Plant Biology

Table 1 Summary of SNPs and their distribution in different genomic regions

Chr.	Total SNP		Exonic region				UTR			Splicing sites^e	Intronic region	Promotor	Intergenic region
	Number	Density^a	Nonsyn	Syn	Stop-gain^b	Stop-loss^c	5′-UTR	3′-UTR	5′-UTR/3′-UTR^d
1	2,511,910	8.34	31,289	36,761	619	126	14,036	29,588	631	725	213,368	80,967	2,103,800
2	1,915,130	8.08	25,916	28,767	442	108	10,644	22,370	402	567	150,733	60,545	1,614,636
3	1,862,945	8.03	22,218	25,182	451	106	9,370	18,894	295	494	138,043	55,225	1,592,667
4	1,991,721	8.25	20,323	21,608	456	96	8,740	17,449	458	447	117,866	54,140	1,750,138
5	1,588,421	7.29	22,810	27,197	371	105	10,315	22,646	474	539	142,569	56,768	1,304,627
6	1,270,649	7.51	16,936	19,001	308	77	7,589	14,610	375	424	98,366	43,059	1,069,904
7	1,367,126	7.73	16,692	19,323	301	60	7,361	14,499	301	388	105,085	40,322	1,162,794
8	1,403,887	7.99	18,411	20,233	376	75	43,688	16,400	290	452	111,501	46,710	1,145,751
9	1,267,997	8.09	14,748	17,468	279	71	6,789	14,366	245	355	96,433	38,962	1,078,281
10	1,205,225	8.02	15,871	17,457	240	59	5,978	12,369	120	287	83,062	34,006	1,035,776
Total/Average	16,385,011	7.95	205,214	232,997	3,843	883	124,510	183,191	3,591	4,678	1,257,026	510,704	13,858,374
Percentage	-	-	1.25%	1.42%	0.02%	0.01%	0.76%	1.12%	0.02%	0.03%	7.67%	3.12%	84.58%

Chr chromosome. Nonsyn: nonsynonymous SNPs. Syn synonymous SNPs. ^aDensity: SNP number per Kb. ^b Stop-gain: changes an amino acid to a STOP codon. ^cStop-loss: the mutation results in the loss of a STOP codon. ^d5′-UTR, 3′-UTR: SNPs located in 5′-UTR or 3′-UTR of different transcripts. ^eSplicing sites: SNPs in different genomic regions refer to alternative splicing.

ISSN: 1471-2229