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There are typically three plots: counts per cell, detected genes per cell, and the percentage of mitochondrial counts per cell. If your cells do not express any mitochondrial genes or the IDs in the input file do not match our expected IDs for mitochondrial genes, the plot for the percentage of mitochondrial counts per cell will be absent. 

Mitochondrial genes are defined as genes located on a mitochondrial chromosome in the gene annotation file. The mitochondrial chromosome is identified in the gene annotation file by having "M" or "MT" in its chromosome name. If the gene annotation file does not follow this naming convention for the mitochondrial chromosome, Partek Flow will not be able to identify any mitochondrial genes. If your single cell RNA-Seq data was processed in another program and the count matrix was imported into Partek Flow, be sure that the annotation field that matches your feature IDs was chosen during import; Partek Flow will be unable to identify any mitochondrial genes if the gene symbols in the imported single cell data and the chosen gene/feature annotation do not match. 

Counts is calculated as the sum of the counts for all features in each cell from the input data node. Detected genes is calculated as the number of features in each cell with greater than zero counts. Percentage of mitochondrial counts is calculated as the sum of counts for known mitochondrial genes divided by the sum of counts for all features and multiplied by 100. 

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