General mapping rate of human resequencing data against reference in GAiix/Hiseq

[cybog337]

Hi GA/Hiseq users!

I would like to know general mapping rate of human reseq data produced by Hiseq/GA against human reference.
Some site says 95% mapping of >q30, however another site says under 80% or under 75%. I guess what mapping rate is usually acceptable.

Thankm you!!

[simonandrews]

This will depend on the quality of your data and the length of your reads. We see somewhere over 70% mapping from a good 40bp run, but some of the unmapped stuff will be parts which aren't in the assembly. 95% mapping sounds very optimistic even for very long reads with good quality.

For comparison PhiX maps at around 98.5% which suggests that the reduction in human is due to genome complexity and not sequence quality.

[cybog337]

Dear Simon Andrews,
Thank you very much for the reply.
We usually read 100PE using GAIIX or HIseq2000 and mapping rate is 70~80% againt human. Depending your advice, this mapping rate is likely to be normal.