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Why Does The Base Quality Drop Towards The End For Illumina Reads ?
Does anybody knows why, why base quality drops towards the end for Illumina reads?
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The illumina platform uses a so called sequencing by synthesis process. Bases are added one at a time and the consensus is determined in a cluster of identical sequences.
The source of errors can be numerous, here is one review that discusses the issues in more detail:
The challenges of sequencing by synthesis, Nature Biotech, 2009
In a nuthsell a short answer to the best of my understanding is this: Not all sequences in a cluster will grow at the same rate, this will slowly lead to a desynchronization as the errors accumulate. This is why the quality dips towards the end.
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Good question - I have always accepted the phenomenon without really understanding the cause.