SNPs local neighborhood - SNP LANE
It is has been suggested that the neighbor bases affect the probability of mutation that drives the origin of SNPs.
However, it may be possible that the genome is not so randomly built.
Therefore a high frequency of C before A or T in the genome woul give the impression that the neighbor C would increase the probability of A to mutate to T and T to A.
This website shows the analysis of the allelic frequency in the SNP neighborhood in several species and regions of genome, such as intron, 5'UTR, 3'UTR and CDS.
Together with similar plot for the baseline frequency in the neighborhood of the pair of bases which comprise a SNP type, e.g. A or T for A/T (W) SNP.
Click here and
- Choose Species: Homo sapiens (under construction), Mus musculus, Rattus norvegicus, Sus scrofa, Bos taurus
- Choose Genomic region (Intron, 5'URT, 3'UTR, CDS)
- Choose type of substitution: W(A/T), S(C/G) | M(A/C), K(G/T) | R(A/G), Y(C/T)
Positions labeled with "*" mean that a chi-square test between the allelic frequencies of that position in SNP data significantly differs from baseline frequencies, e.g. -1*.
Please note that purine lines are continuous and pyrimidine lines are dashed. A and T symbols are in black/grey and C and G in red/orange to distinghish AT from GC rich strands. Mouse over position shows the percentages.