Relationship of SNP discovery with sequence coverage and read depth in seven flax genotypes. (A) Read depth frequency distribution of 55,465 SNP locations identified by alignment of Illumina GAIIx reads of seven genotypes against the CDC Bethune whole genome shotgun sequence assembly. A minimum of three reads per genotype was required for SNP calling. A log scale was used for the number of SNPs because of the disproportion in the 3-50 reads bin. (B) Correlation of SNP discovery with sequence coverage expressed as genome equivalents (BT-CDC Bethune, MB-Macbeth, SP-SP2047, UG-UGG5-5, DL-Double Low, CT-Crepitam Tabor, G11-G-1186/94, AT-Atlas).