Average Q value

[Scott Coutts]

Hi All,

Can anyone tell me the average Q values you get across one or both reads
for a paired end Illumina run (of any length)? Just interested to
compare with others.

Cheers,

Scott.

[Abhishek Pratap]

On Phred scale.. I would say it starts around 33-36 and then depending on the length of reads(cycles) there is a gradual decrease and on a good 50 bp PE run the read 1 last cycle would give me Q median of 22.

For read 2 I would have they end around 18-20. We face issues when the run is 76-100 bp PE the quality tend to fall a bit more there.

Hope this helps.

Cheers,

-Abhi

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