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Sequence quality drops in the 3' end of the left sequence in paired end. What could be the cause?

Hello,

We have received the results of a library sequencing and we have noticed that the sequence quality drops at the 3' end of one of the pairs: enter image description here enter image description here

Moreover, there seems to be a biased base distribution too:

enter image description here

What could be the case? We still have not performed manual filtering of sequences, but I wanted to know what could be causing this.

Anyways, the sequence quality seems somewhat good.

Best,

sequencing
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updated by GenoMax GenoMax • written by eggrandio • eggrandio

But shouldn't quality drop at both 3'ends and not just on the left one?

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written by eggrandio • eggrandio

This may be one of those things that just happens to be a one-time thing with whatever was going on with this run. Was this sample pooled with others you did not prepare/own?

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written by GenoMax GenoMax

What machine? (Nextseq? Novaseq?) what library prep method?

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written by Asaf Asaf

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