sinlge-end mapping problem

[cliff]

Hi, All

I have a paired-end dataset by illumina GA. I did two types of mapping using this dataset and BWA:

1: Just use one read to do single-end mapping
2: I merged read1 and read2, and then still do single-end mapping.

Then I used SAMtools to call SNPs. Surprisingly, I found one SNP showing up by using both of mapping but the number of reads mapped to this SNP is the same...

I am confused by this result.. should Type 2 mapping give me more reads mapped to this SNP?

Can anybody help me on this?

Thanks very much!