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—Sequence logo of one fragment of an exemplar gene harboring SNPs positions that illustrate sites with high intraspecific variation yet low interspecific variation. Blue stars represent the rare SNPs of MAF <0.01. Red stars represent SNPs of MAF >0.01 but <0.5. Black stars represent cross-species “invariant” SNPs that are consistent throughout the multiple sequence alignment blocks across species. This fragment is located in Chr2: 24,293,421–24,293,580 of the rice genome.
