coverage confusion in mutSig. Why there are covered bases with categ=7 and effect="silent/noncoding"

nzhaonzhao Seattle, WAMember

Dear Mutsig Developers,

I am trying to understand the algorithm more.

I used the coverage file from the TCGA Lung Squamous paper provided from the mutSig website. However, the file really confuses me. When I do a cross tabulation, there are many bases with categ = 7 and effect = "silent" or "noncoding". This doesn't make sense to me because I thought all the 7th category (null mutation) should necessarily fall in the coding region and have a non-silent effect (which is true for the maf file). Could someone explain this a little?

Thanks a lot.

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