What are the unmapped reads

[beelu]

Hi All,

In a normal run, we have 85% pass filter, then probably 80% mappable reads. Any idea what the good quality un-mappable reads are??

[lh3]

1. Overestimated base quality. The reads are bad in fact.
2. Some aligners apply filters before alignment (e.g. polyA).
3. Some aligners may drop reads with extremely high copy number
4. The reference genome is imperfect.