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