Dear all,
I have several bacterial strains (very closed to each other) and want to compare SNPs between any two genomes.
several steps in my analysis:
1. mummer (nucmer) to do alignment and identity SNPs. the result is like this:
[P1] [SUB] [P2] | [BUFF] [DIST] | [FRM] [TAGS]
===================================================================
831 T C 831 | 831 831 | 1 1 genome1 genome2
2. remove indels (>1bp).
3. for the remaining SNPs, the SNPs could be determined they are in coding regions or not. for the SNPs in coding regions, I did blast two genes (SNPs inside) to see they are high homologous or not. if yes,
4. two coding sequences were aligned using muscle. then synonymous and nonsynonymous SNPs were told by SNAP.pl.
The result is quite weird because the total number of synonymous SNPs is smaller than the number of nonsynonymous SNPs.
This should be incorrect. But I couldn't figure out where is the problem.
Can anybody help me? May someone give me any clue where the problem is? Many many many thanks.
Salmon
I have several bacterial strains (very closed to each other) and want to compare SNPs between any two genomes.
several steps in my analysis:
1. mummer (nucmer) to do alignment and identity SNPs. the result is like this:
[P1] [SUB] [P2] | [BUFF] [DIST] | [FRM] [TAGS]
===================================================================
831 T C 831 | 831 831 | 1 1 genome1 genome2
2. remove indels (>1bp).
3. for the remaining SNPs, the SNPs could be determined they are in coding regions or not. for the SNPs in coding regions, I did blast two genes (SNPs inside) to see they are high homologous or not. if yes,
4. two coding sequences were aligned using muscle. then synonymous and nonsynonymous SNPs were told by SNAP.pl.
The result is quite weird because the total number of synonymous SNPs is smaller than the number of nonsynonymous SNPs.
This should be incorrect. But I couldn't figure out where is the problem.
Can anybody help me? May someone give me any clue where the problem is? Many many many thanks.
Salmon
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