How Are Sequencing Error Rates Defined?

Question

[Anjan]

Frequently one hears about Illumina's error rate being 0.8% or thereabouts. How is this error rate calculated? A few possibilities come to mind:

1. total number of incorrect bases sequenced as a percentage of total number of sequenced bases.
2. expected percentage of incorrect bases in any given position.
3. percentage of reads with errors as a percentage of the total number of reads.

Will appreciate any pointers. Thanks

Anjan

Answer 1

[Chris Miller]

It may depend on the source, but in my experience, it's defined as the percentage of bases that are incorrectly called. The 0.8% error rate that you describe would mean that of every 1000 bases coming off the sequencer, 8 of them will report the incorrect base.