Additional file 3 of A novel method for effectively selecting fragments not associated with restriction sites for whole-genome genotyping

Additional file 3: Figure S8. Sequencing yields of the maize genetic population.Sequencing yields of different sequencing strategies in the CIMBL83/GEMS41 population.Sequencing yields of different sequencing strategies in the CML496/GEMS41 population. For boxplots, center line is the median; box limits represent upper and lower quartiles. Different methods use different REs. Figure S9. iRAD significantly reduces the number of reads containing restriction enzyme recognition sites.Proportion of reads without AluI recognition sites in the CIMBL83/GEMS41 populationand CML496/GEMS41 populationwith Panel_A, Panel_B and AIO-seq.Proportion of reads without HindIII recognition sites in the CIMBL83/GEMS41 populationand CML496/GEMS41 populationwith Panel_A, Panel_B and AIO-seq. Different methods use different REs. Figure S10. iRAD-seq can enhance the depth of the obtained SNPs.The number of SNPs at different depths. The data used in the experiment was 0.5 Gb, 1.5 Gb, and 2.0 Gb. SNP number at different depths. Log10: n is the number of SNPs. For boxplots, center line is the median; box limits represent upper and lower quartiles. Employ the t-test to assess differences in different method, p < 0.0001. Different methods use different REs.

附加文件3：图S8。玉米遗传群体的测序产出：分别展示CIMBL83/GEMS41群体与CML496/GEMS41群体中不同测序策略的测序产出。箱线图中，中线代表中位数，箱体上下限分别对应上四分位数与下四分位数。不同实验方法采用不同的限制性内切酶（restriction enzyme, RE）。
图S9。iRAD可显著降低含限制性内切酶识别位点的测序读段数量：分别展示CIMBL83/GEMS41与CML496/GEMS41群体中，采用Panel_A、Panel_B及AIO-seq时，不含AluI识别位点的读段占比，以及不含HindIII识别位点的读段占比。不同实验方法采用不同的限制性内切酶。
图S10。iRAD-seq可提升所获单核苷酸多态性（Single Nucleotide Polymorphism, SNP）的测序深度。本实验所用测序数据量分别为0.5 Gb、1.5 Gb及2.0 Gb，分析不同测序深度下的SNP数量，纵轴采用Log10标度，n代表SNP的计数。箱线图中，中线为中位数，箱体上下限代表上下四分位数。采用t检验评估不同方法间的组间差异，p < 0.0001。不同实验方法采用不同的限制性内切酶。