Transcriptome sequencing for SNP discovery across Cucumis melo

BMC Genomics

Table 5 Number of SNPs meeting different criteria for optimizing validation with the sequenom genotyping array

No CS60_MAF¹	Whole collection	No IS60	Variable in all groups
MAF 1	55,000	28,996	9
		(10.21%)
MAF 0.99	108,731	65,500	158
		(23.07%)
MAF 0.98	136,694	86,103	211
		(30.32%)
MAF 0.97	150,590	96,657	231
		(34,04%)
MAF 0.96	160,231	103,976	260
		(36,61%)
MAF 0.95	167,718	109,734	277
		(38,64%)
MAF 0.7	178,107	168,726	431
		(59,42%)

¹ Those SNPs having the filter CS60_MAF in Additional file4 are flanked in a window of 60 bp by other SNPs with values of MAF over the threshold indicated. Columns indicate the number of these SNPs in the whole collection, in the subset free from introns in a flanking window of 60 bp (no IS60), and in the subset variable in all groups. These filters for each SNP of the whole collection are included in Additional file4.

ISSN: 1471-2164