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rCRS is the revised Cambridge Reference Sequence.
The first mitochondrial DNA sequence was produced in a laboratory at Cambridge University over twenty-five years ago using a sample from a person of European descent. Known as the Cambridge Reference Sequence, it became not only a milestone in DNA sequencing but a calibration tool for mitochondrial studies.
Since mitochondria are circular and they have no beginning and end, the ordering of bases is a problem. To fix this, scientists use the revised version of the Cambridge Reference Sequence (rCRS for short) to align other mitochondrial sequences and SNPs. This way, researchers around the globe know that a SNP at 560 on the mitochondria means a SNP corresponding to base 560 counted on the rCRS.
If you are interested in comparing your mitochondrial SNP data to that found in scientific articles or other available resources you should use the rCRS base positions.
Fun fact: the rCRS is assigned to the mitochondrial sequence associated with the H2a2 haplogroup, which is quite rare in England.