Wield MiSeq error rate at the beginning

[feixiang1019]

Recently when we run amplicon libraries on MiSeqs(2 miSeq instruments), we got wield high error rate dots at the beginning of each read. The overall error rate and Q30 was good, we just would like to understand why this was happening. Did anyonce face this before?

Thanks

[Ben3]

feixiang1019 that's very strange. Have you experienced this with any other libraries you have run?

Also, what are the amplicons you are sequencing? Is there a lot of diversity in the sequences?

[JBKri]

We see this all the time with amplicon libraries with low nucleotide diversities. I had the impression this is unavoidable with low diversity libraries.

[Ben3]

JBKri that's what I was expecting. I haven't run amplicons on an Illumina instrument in a while, but I always remember steep drop-offs when there was low diversity.

feixiang1019 if this remains an issue you can add more PhiX to your runs or add in more diverse samples.