QuestionsCategory: ChIP-Seq Data AnalysisPipelines and QC: What is “effective genome size”?
stonelakeak@nih.gov Staff asked 5 months ago

What is “effective genome size”?

1 Answers
stonelakeak@nih.gov Staff answered 5 months ago

Effective genome size denotes the portion of the genome that is “mappable” by a sequencing read. There are two common alternative ways to calculate this:
1. The number of non-N bases in the genome.
2. The number of regions (of some size) in the genome that are uniquely mappable (possibly given some maximal edit distance).
Mappability is also affected by sequencing read-length, but typically we use ~2.9Gb and ~2.6Gb as effective genome sizes for human and mouse, respectively.
– answered by Tovah Markowitz, Paul Schaughency, Vishal Koparde.