Fig. 3  View of single nucleotide polymorphism (SNP) discovery through mapping short reads from Illumina/Solexa to reference sequence on MAQ software (A) and CLC software (B). (A) Short read 35 bp per read of soybean genome shows completely mapped on the soybean reference sequence. The MAQ software provides a consensus sequence of the genotype sequenced of short read lengths with aligned raw reads to the reference sequence. (B) CLC software is useful for counting reads with DNA variations at each position.