I am running Seurat on publicly available dataset of ~400k cells. More than 80% of the cells are returned as NA when I use percentageFeatureSet(object, pattern = "^MT-"). How should I interpret these result? Does this mean the 80% of cells are of poor quality or have no mitochondrial content?

Any help would be greatly appreciated. Zahra

It means that none of the gene names begin with "MT-".

Can you confirm that the mitochondrial genes for your species do indeed begin with "MT-"?