Who let M's and R's in the Genome

[Jon_Keats]

Just looking for other peoples input on something

Has anyone notice there are two R and one M IUPAC codes on chromosome 3 in the reference genomes, both NCBI36 and GRCh37. Maybe not surprisingly they sit in the FHIT gene.

Does this worry anyone for genome indexing or the such, seems minor in 3/3billion.

[john_mu]

Yes I noticed that, they are quite odd... I just replace them with N's when doing analysis.

[bioinfosm]

Surprisingly, I noticed this yesterday too!
Not expected, but no clue if it affects things downstream...

[foxyg]

I know in some cases they use N to mask sequence that are repeats.

[Joann]

the other letters in the code

m= a or c, as in amino

r= g or a, as in purine

n= a or g or c or t/u, unknown, or other

[janejane]

m= a or c, as in amino

r= g or a, as in purine

n= a or g or c or t/u, unknown, or other

ah ha, good to know, thanks!

[Joann]

Wait! there's more...

Please see Annex C, Appendix 2, Table 1, page 16 at, for example,

http://www.noip.gov.vn/noip/resource.nsf/vwResourceList/B4F5E35FA26A8AA4472577360013F1D3/$FILE/Standards%20%E2%80%93%20ST25.pdf

for a complete list of nucleotide letter symbols in use per a current international standard.

See also
An extended IUPAC nomenclature code for polymorphic
nucleic acids
doi:10.1093/bioinformatics/btq098

[seq_GA]

Interesting to know something apart from A,T,G,C,N.

But UCSC has them as "N"s

[malachig]

These additional letters are sometimes called 'ambiguiety codes'. Back in the day when a 30X human genome sequence cost a billion dollars instead of several thousand, every piece of sequence information was much more precious. Knowing a position was a purine was better than calling it an N. The codes are also useful for reporting heterozygous genotype information as a single letter. The fact that they still occur in reference genomes is mostly just a nuisance for bioinformatics and thus some resources such as UCSC convert them to N's. I believe human genome sequences retrieved via Ensembl may still contain them though.