Illumina quality values for v.3 chemistry

[GenoMax]

I tried to search for a previous post on this but topic did not find one. Would be glad if someone else knows of a previous post on this topic and posts the relevant link.

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We recently discovered that for v.3 chemistry (Illumina) the range of normal quality values was expanded. The new range now covers quality values from "b" to "m" (max quality is now 45?).

Previously illumina scores used the mapping scale (Phred+64). Anyone know what the new mapping scale is?


Note: This should become a non-issue with pipeline v.1.8 (which will produce sanger quality values as default).

[HESmith]

I was told that the base-calling algorithms for the latest version of RTA have been improved, which is why the qualities can be assigned with greater confidence (i.e., higher q-scores). CASAVA 1.8 will convert to the standard PHRED offset (+33), but the top score will still be 45.

[maubp]

Confirmed on this thread that currently Illumina are seeing PHRED 41 in testing and hope to go higher: http://seqanswers.com/forums/showpos...6&postcount=62