how to determine a snp ?

[biocc]

hi, i resequenced a mutated bacteria genome, and want to detect the mutation information. at a position, i found half of the reads mapped are different from the reference, and half are the same . so some software reported it as snp, and some not. how to determine it as a SNP. how did this happened.
thanks.

[svl]

It could be a heterozygous SNP. Also errors can/will always occur (in sequencing, mapping), you might want to look at quality values as well.

[ntremblay]

Hi,

if you encounter an interesting SNP in your analysis, the quickest way to determine if it's real or not would be to confirm it with an independant method like PCR + Sanger ...

[drio]

If you have a very small number of SNPs, validate them by eye. Display the alignments at the SNP position and see if the call makes sense. Ultimately of course validate via sanger.

[biocc]

thanks

If you have a very small number of SNPs, validate them by eye. Display the alignments at the SNP position and see if the call makes sense. Ultimately of course validate via sanger.

yes, i did it by eye through Tablet. i found some reads aligned are A and some aligned are G. if all these reads are unique, how should i determinate? thaks

[drio]

Post here a screenshot of the alignments (tablet) for one of the snps and then we can discuss. The original SAM alignments for the SNP would help also.