YFull: FAQ↩ Back 

Q: What kind of mtDNA results does a YFull client receive, and how are they presented?

A: In all MT reports, mtDNA results are presented through comparison with two reference sequences: the rCRS (Revised Cambridge Reference Sequence) and the RSRS (Reconstructed Sapiens Reference Sequence). The rCRS is an earlier reference sequence based on a European individual from haplogroup H2a2a1, while the RSRS is a newer reference constructed to reflect the genome of the 'mitochondrial Eve', representing a more ancient lineage. 

In the "Hg and SNPs" report, all positive SNPs are displayed. The primary report for interpreting mtDNA results is the "M-report"t," which lists all mutations across the various regions of mitochondrial DNA. It highlights mutations across different regions depending on the frequency of polymorphisms.

The HVR1 (16024-16383) and HVR2 (57-574) are hypervariable regions of mtDNA, known for their high mutation rates.

The CR (575-16000) represents the coding region, encompassing nearly the entire rest of the mtDNA genome. 

In the "MTree matches" tab, all of a client's SNPs are categorized based on whether they are found in other samples along the path from the 'Mitochondrial Eve' to the client's sample, and those that are not present in other samples. This categorization aids in discerning the unique and shared characteristics of the client's mtDNA, offering insights into their maternal ancestry.

The "Extras" section details the sample's private mutations, which are unique SNPs not currently used in the construction of the MTree. These mutations could potentially be integrated into the Mtree as more data becomes available and further analysis is conducted. 

Furthermore, the "Mt matches" report lists all samples with SNPs that match those of the client.

References:

For constructing the MTree YFull uses data from their customers and data from GenBank The initial version of MTree was based on the PhyloTree 17 of van Oven (18 Feb 2016). See van Oven M, Kayser M. 2009. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30(2):E386-E394. PhyloTree.org. doi:10.1002/humu.20921

Also, YFull used some information from Ian Logan's website.

The formula of calculation of the phylogenetic weight of mutation based on HaploGrep principes See Weissensteiner H., Pacher D., Kloss-Brandstätter A., Forer L., Specht G., Bandelt H.-J., Kronenberg F., Salas A., Schönherr S. 2016. HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucl. Acids. Res. 2016 Apr 15; doi:10.1093/nar/gkw233

For the mtDNA haplogroup classification, YFull uses Kulczynski distance. See Kloss-Brandstätter A., Pacher D., Schönherr S., Weissensteiner H., Binna R., Specht G., Kronenberg F. 2011. HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups< Hum Mutat. 2011 Jan;32(1):25-32. doi: 10.1002/humu.21382. Epub 2010 Nov 16.

Last updated May 29, 2024.