Nucleotides M and R in human reference no. 37

[gene coder]

Thanks. That is what I needed to know.

[Sacha Rybalka]

Hi!
I'm not working with Human genome, but is it not the IUPAC annotation for alternative bases (as S for Strong if G or C)? The wiki page here http://en.wikipedia.org/wiki/Nucleic_acid_notation

[gene coder]

A, C, G and T are "normal" nucleotides and N represents unknown nucleotides in repetitive sequences or SNPs. When checking the reference genome from 1KGP, I found these odd nucleotides: M and R. Does anybody know anything about that?

>>> ref_f = open("human_g1k_v37.fasta", "r")
>>> 
>>> cnt = 0
>>> 
>>> for i in ref_f:
...     cnt += 1
...     if i[0] == ">":
...             print i, 
...             continue
...     
...     n = i.count("A") + i.count("C") + i.count("G") + i.count("T") + i.count("N")
...     
...     if n < len(i) - 1:
...             print cnt, i

yields

...
>3 dna:chromosome chromosome:GRCh37:3:1:198022430:1
9221347 CGCTACATAGCTGMCTTATTATTCGTGGTCCCCTATGACCCCCTGATCATTTTCCCTGAG
9221351 CCRRGCTTGGTTCTAACAATGAATTTAATAAGAATTGTATTTAATCAATGTTTAAATATA
...