Calculating the Uniqueness of MAQ SNP output
Hi All,
I have learnt a lot from reading the forumn posts. Thank you all for your contributions.
I have a question on the calculation of SNP Uniqueness from the MAQ SNP output in column 7.
It states in the Maq manual that the value in column 7 represents the average number of hits of reads covering this position. This number represents the uniqueness factor of that SNP, and thus influences on the chance of the SNP being true.
Is it true that a higher number in column 7 would mean that a SNP is less unique?
I also realised from my dataset that this number can go below the value 1 with majority of them being zero. What does that mean and how can that be possible?
If a SNP is made from 5 read; each read only matches to one location on the reference genome, we should get (1+1+1+1+1)/5 = 1
Can someone enlighten me on this? Am I calculating and interpretating the value wrongly?
Thanks all.
I have learnt a lot from reading the forumn posts. Thank you all for your contributions.
I have a question on the calculation of SNP Uniqueness from the MAQ SNP output in column 7.
It states in the Maq manual that the value in column 7 represents the average number of hits of reads covering this position. This number represents the uniqueness factor of that SNP, and thus influences on the chance of the SNP being true.
Is it true that a higher number in column 7 would mean that a SNP is less unique?
I also realised from my dataset that this number can go below the value 1 with majority of them being zero. What does that mean and how can that be possible?
If a SNP is made from 5 read; each read only matches to one location on the reference genome, we should get (1+1+1+1+1)/5 = 1
Can someone enlighten me on this? Am I calculating and interpretating the value wrongly?
Thanks all.