Low sequence diversity is the source of the erratic signal intensity in the beginning of Read 1 (shown in the first 25bp in the figure below). This low diversity occurs during sequencing of the adapter present in Archer libraries. The MBC adapter has a number of bases that are common for all of your samples. It is that “common” region that contributes to the low read diversity in the first 25 bases. Addition of PhiX to the library pool increases sequence diversity and reduces error rates when sequencing through this region.
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