Fig. 4

Comparison of graphical genotype of SNPs detected bwa + GATK and bidirectional alignment. a map of bwa + GATK data, b map of bidirectional alignment data. For GATK results, SNP positions which show 40 or more read depth and 1000 or more quality were selected. For SNPs detected by bidirectional alignment, SNPs marked ‘M’, i.e., ‘homozygous’ were selected. Upper side of the chromosomal map is plotted with SNPs from ‘Norin8’. Lower side is ‘Koshihikari’. Common SNPs between ‘Norin8’ and ‘Koshihikari’ are indicated with dark blue. ‘Norin8’ or ‘Koshihikari’ specific SNPs are indicated with salmon pink. Regions without color indicate the same region with ‘Nipponbare’ reference genome