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Fig. 2 Quality assessment of RRBS sequence data. (a) Sequence content across all bases from the FASTQ file for read 1 showing enrichment for CGG or TGG trinucleotides at the beginning of read 1. This bias is due to MspI digestion, which creates fragments beginning with CGG nucleotides (methylated state) or TGG (unmethylated state). (b) Sequence duplication level of the FASTQ file for Read 1. This is another hallmark of successful MspI digestion as each DNA molecule should produce identical fragments
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