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

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

Chr. Total SNP Exonic region UTR Splicing sitese Intronic region Promotor Intergenic region
  Number Densitya Nonsyn Syn Stop-gainb Stop-lossc 5′-UTR 3′-UTR 5′-UTR/3′-UTRd     
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%
  1. 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.