Box plots of GC content at concordant/discordant SNP loci among the NGSs and Omni 2.5-8. A) Box plots of the GC content at the SNP loci showing concordance/discordance between the NGSs and Omni 2.5-8. The box indicates the first and third quartiles and the lines indicate the highest and lowest value that is within 1.5 x inter-quartile range. The graph on the left indicates the distribution of GC content at HiSeq SNP loci. There was no statistically significance difference in GC content between the concordant and discordant SNPs (p = 0.81). The graph on the right indicates the distribution of GC content at Ion Proton and Omni 2.5-8 SNP loci. The difference in GC content between concordant and discordant SNPs was significant (p = 2.2 × 10-16). B) Box plots of the GC content at the SNP loci showing concordance/discordance among the three platforms. The three columns (shaded gray rectangle) from right indicate the distribution of GC content of the discordant SNPs between the NGSs and Omni 2.5-8. The GC content at SNP loci that showed Ion Proton discordance compared with HiSeq and Omni 2.5-8 was significantly different (p = 0.026).