Mapping ratio when alignment 37bp human NGS reads to mouse genome

Question

[Shicheng Guo]

Hi Sequencers:

Is there any empirical intuition what's the appropriate proportion of the reads when we map 37bp human reads to mouse genome?

Best regards

[Brian Bushnell]

No, it depends on a huge number of factors such as the data quality, contamination rate, preprocessing steps, mapping software and parameters, etc. If all of those are good, ~98% is not unreasonable.