Do eukaryote cells contain DNA that isn't part of a chromosome or located in the mitochondria? I specify eukaryote in the title, but I'm also interested if this question isn't applicable to eukaryote cells in general but is to humans. I was reading "RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays" (John Marioni 2008). In the results it states "By these criteria, 40% of reads mapped uniquely to a genomic location, and of these, 65% mapped to autosomal or sex chromosomes (the remainder mapped almost exclusively to mitochondrial DNA)." I couldn't help but notice the " **almost** exclusively to mitochondrial DNA". Almost exclusively? Can DNA be found in places other than chromosones or mitochondria? Perhaps I'm interpreting the sentence wrong. Any pointers would be appreciated Thanks

In plants, chloroplasts and other plastids contain DNA, but I suppose you are more interested in humans. Quoting from wikipedia,

> In many cells cytoplasmic DNA is also found, which is different from nuclear DNA, both in methylation levels (cytoplasmic has less), and in sequence. EccDNA or extrachromosomal circular DNA is present in all eukaryotic cells, derived from genomic DNA and consists of repetitive sequences of DNA found in both coding and non-coding regions of chromosomes. EccDNA can vary in size from less than 2000 more than 20,000 base pairs. In animals, eccDNA molecules have been shown to contain repetitive sequences that are seen in satellite DNA, 5S ribosomal DNA and telomere DNA. The function of eccDNA has not been widely studied, but it has been proposed that the production of elements of eccDNA from genomic DNA sequences adds to the plasticity of the eukaryotic genome and can influence genome stability, cell aging and the evolution of chromosomes