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Old 09-24-2018, 03:20 AM   #2
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,053

1. Are these amplicons or sequences where there is low nucleotide diversity expected?
2. You possibly have short inserts. Once you go through your inserts you are then sequencing into the adapter on the 3'-end. That leads to low nucleotide diversity and drop-off's in Q-scores.
3. How much phiX is spiked into this run?
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