# SC-RNA seq percent.mito

Is that possible that the percent.mito level is zero? I have done vlnplot and it shows that its percent.mito level is zero. Does that mean my mitochondrial gene didn't detect?

It is violin plot. And the command is:

• Sorry hua, but I find it difficult to understand. Could you clarify what is "percen.mito" ? It seems like it should be a function or a property of your data but I'm not sure. Also, could you explain what is "VlnPlot" ? It seems like a violin plot, but I'm not sure, perhaps the image didn't get attached (upload just a link and we will add it). – llrs Aug 13 '18 at 15:57
• Your genome likely doesn't title mitochondrial genes MT-something, so you'll need to change how mito.genes is created. – Devon Ryan Aug 14 '18 at 7:22
• Is "percent.mito level" the percent of reads mapping to genes annotated as mitochondrial? Are the mitochondrial genes annotated? Note you have edit button you can use to improve your question. – Kamil S Jaron Aug 14 '18 at 9:19
• You should put "Seurat" in your question, and add a Seurat tag. – swbarnes2 Aug 14 '18 at 16:25

mito.genes <- grep("^mt-", rownames(shox2crepos_mtmg@data), value=TRUE, ignore.case=TRUE)