I'm not sure I entirely understand your question, but there doesn't appear to be anything wrong with the output you posted. It indicates that you have 7 mutations in LATS1, all SNVs. If you had 2 indels and 2 SNVs, the total mutations would still be 7. According to the FDR values, this gene is mutated more frequently than would be expected, based on the background mutation rate in the samples. - Chris Miller