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How Are Sequencing Error Rates Defined?

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

next-gen error
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updated by Chris Miller Chris Miller • written by Anjan Anjan

1 answer

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.

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written by Chris Miller Chris Miller

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