Why Does The Base Quality Drop Towards The End For Illumina Reads ?

Question

[jack]

Does anybody knows why, why base quality drops towards the end for Illumina reads?

[Ian]

Good question - I have always accepted the phenomenon without really understanding the cause.

Answer 1

[Istvan Albert]

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.

Answer 2

[lakhujanivijay]

See this post: Why does base quality of reads generally decreases at the end of the read?

Answer 3

[andrew.j.skelton73]

I'd highly recommend you check out this - The site as a whole is useful for explaining common things you'd see in sequencing, like primer bias.

[lakhujanivijay]

Link looks broken, can you check?

[andrew.j.skelton73]

Seems to be down at the moment