Yoruban to rCRS Conversion

Human mitochondrial nucleotides are commonly identified using positions derived from the sequence first published by Anderson et al. and later amended by Andrews et al. This sequence, which has become known as the revised Cambridge sequence (rCRS) (accession number NC_012920), has become the standard for notating mtDNA variants. Because the Affymetrix and Illumina data have used notation based on an African Yoruban sequence (accession number AF347015), position values need to be converted.

A pairwise alignment of the rCRS and Yoruban sequence was made using the Seaview (Galtier et al.) program. The presence of three single-nucleotide insertions in the Yoruban sequence and a placeholder position introduced during revision of the original Cambridge sequence cause the nucleotide positions in the two sequences to differ significantly. Corresponding Yoruban positions are mapped to their rCRS equivalent below.

• Anderson, S., Bankier, A. T., Barrell, B. G., de Bruijn, M. H., Coulson, A. R., Drouin, J., Eperon, I. C., Nierlich, D. P., Roe, B. A., Sanger, F., Schreier, P. H., Smith, A. J., Staden, R. and Young, I. G. (1981). "Sequence and organization of the human mitochondrial genome." Nature 290(5806):457-465.
• Andrews, R. M., Kubacka, I., Chinnery, P. F., Lightowlers, R. N., Turnbull, D. M. and Howell, N. (1999). "Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA [letter]." Nature Genetics 23(2):147.
• Galtier, N., Gouy, M. and Gautier, C. (1996) SeaView and Phylo_win, two graphic tools for sequence alignment and molecular phylogeny. Comput. Applic. Biosci., 12, 543-548.

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Diferent alignment protocols in repetitive and polytract regions (D310, 16190-16193) may create slightly different scoring guides, but all should give the same overall positional results.

MSeqDR has an online conversion tool: https://mseqdr.org/mvtool.php

Two manual methods are shown below.

Method 1 (Mitomap v1): Converting from Yoruban positions to rCRS positions

Position Range	Conversion Operation
1-309	identical, no conversion needed
310	Yoruban insertion, position does not exist in rCRS (rCRS annotation=309.1)
311 - 316	decrement by 1
317	Yoruban insertion, position does not exist in rCRS (rCRS annotation=315.1)
318 - 3108	decrement by 2
3109 - 16190	decrement by 1
16191	Yoruban insertion, position does not exist in rCRS (rCRS annotation=16189.1)
16192 - 16571	decrement by 2

* No Yoruban position maps to 3107 in the rCRS since this is merely a placeholder introduced during revision.

Examples for the method above:

• Yoruban position 100 maps to position 100 in the rCRS
• Yoruban position 3100 maps to position 3098 in the rCRS
• Yoruban position 3111 maps to position 3110 in the rCRS
• Yoruban position 16191 does not map to any position in the rCRS, but could be annotated as rCRS 16189.1
• Yoruban position 16225 maps to position 16223 in the rCRS

Method 2 (Mitomap v2, SNPedia's "Standard"): Converting from Yoruban positions to rCRS positions
This yields the identical sequence results as Method 1 due to the 16190-16193 C polytract in the rCRS

Position Range	Conversion Operation
1-309	identical, no conversion needed
310	Yoruban insertion, position does not exist in rCRS (rCRS annotation=309.1)
311 - 316	decrement by 1
317	Yoruban insertion, position does not exist in rCRS (rCRS annotation=315.1)
318 - 3108	decrement by 2
3109 - 16194	decrement by 1
16195	Yoruban insertion, position does not exist in rCRS (rCRS annotation=16193.1)
16196 - 16571	decrement by 2

* No Yoruban position maps to 3107 in the rCRS since this is merely a placeholder introduced during revision.