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Can anyone tell me the exact meaning of the following features "nnei","x","X" in the MutSig output analysis.
Also, are indels included in the MutSig calculation?
Many thanks for your help
These values give insight into how the background mutation rate is calculated for a given gene.
nnei gives the number of neighboring genes that are pooled together to compute the background mutation rate for that gene; these genes are not necessarily adjacent on the genome, but rather they have nearby covariate values. x gives the number of mutated bases in these neigboring genes that are either silent or non-coding, while X gives the total number of bases related to these neighboring genes.
Indels are counted as Null mutations.