What are the chromosome fragments you see in a genome, and where is the mitochondrial genome?

Question

[cyril-cros]

Hi,

These questions may seem basic but I never saw them mentioned during my classes:

When I look at a genome annotation I see some fragments: chrUn_GL456239, chr1_GL456210_random, chr4_JH584295_random, chr5_GL456354_random. What are they exactly? I used the command cut -f 1 mm10.gtf | uniq to get them, using the mouse genome Ensembl annotation.

Second question: I have never seen any annotation of mitochondrial DNA. Where could I find it? Does sequencing or RNASeq include this data? How to cope with the fact that it has a circular form?

Answer 1

[Devon Ryan]

chr1_GL456210_random is on chromosome 1, but it's unclear exactly where. The various chrUn entries are believed to be part of the human genome, but it's unclear which chromosome.

Mitochondrial DNA is chrM (since you're using UCSC chromosome names, it'll be MT in Gencode or Ensembl).

Edit: Most things don't distinguish between circular and linear DNA. The GTF file you're looking at is no exception.