In a previous post I described how our 5% bleach solution for post-run washes had gone bad. Recently I did three MiSeq runs in a row with various amplicons. This was a chance for me to investigate potential carryover contamination between runs, as usually much time passes and multiple washes occur between runs. I was surprised to find a correlation between amplicon read numbers between the first two runs. Carryover levels were around 0.02% , whereas Illumina's Technical Support Note indicates "as low as 0.001% " after carrying out the bleach post-run wash. Between the second and third runs I did the post-run wash twice; this seems to have eliminated any carryover. The current batch of bleach arrived ~8 months ago; this is already too long ago it seems.
