Additional file 2 of A novel method for effectively selecting fragments not associated with restriction sites for whole-genome genotyping

Additional file 2: Figure S4. Evaluation of RE efficiency.Proportion of reads without RE recognition sites with Panel_A and Panel_B in maize and rice.Proportion of reads without each RE recognition sites with Panel_A and Panel_B in maize and rice. Panel_A: MseI, MspI and AluI; Panel_B: MseI, MspI and HindIII. Figure S5. Consistency of coverage among 4 repeats when using varying sequencing data sizes. Pairwise Spearman correlation of the mean coverage between replicates with 100 kb windows. Panel_A: MseI, MspI and AluI; Panel_B: MseI, MspI and HindIII. Figure S6. The overlap of SNPs among 4 repeats when using varying sequencing data sizes. Panel_A: MseI, MspI and AluI; Panel_B: MseI, MspI and HindIII. Figure S7. Application of iRAD-seq in maize germplasm.Sequencing yields of 132 maize germplasms.1812 high-quality SNPs of 139 maize germplasms widespread in the genome. Panel_A: MseI, MspI and AluI.