Why higher read counts in chromosome M/MT

Question

[Lou11]

I'm looking at x30 whole genome sequencing in IGV (bam) and the mitochondrial chromosome coverage track shows 1000-7000 for the read counts. Does MT DNA typically give this degree of increased read counts compared to the autosomal DNA? IGV also shows a large amount of tandem duplication reads across the entire chromosome.

This is my first time viewing the M chromosome so I'm unsure if this is how it should look?

Many thanks for any input.

Answer 1

[Jeremy Leipzig]

mitochondria outnumber nuclei by 100-2500 depending on the cell

[Lou11]

Many thanks!

[ATpoint]

This, and the fact that chrM is only about 17kb whereas autosomes are several orders of magnitude larger.

Answer 2

[wakaruszka]

Hi. What you are actually seeing are not tandem duplicate reads. Note that the human mitochondrial genome is circular, but in IGV the reads are mapped in a line. Therefore, paired reads that span the boundary of first and last positions in the circular mtDNA will be mapped at opposite ends in the linear reference genome in IGV. Their orientation will be inverted, and they will have a large insert size. So large that it spans the molecular mtDNA.

So the green inverted paired reads in the mt-genome in IGV are common. They result from mapping of the circular mtDNA to the linear reference genome.