mismatches in maqView (why > 2)

[saima]

i think that maq map command with n -2 determines that the maximum number of mismatches in alignment reads will be not greater than 2, but my output is showing a large number of mismatches (in red color) in a single read. why is this so?

can ruan jue or any one else reply

thanks
saima

[lh3]

2 mismatches are guaranteed in the first 28bp. Occasionally you see 3. For whole reads, you may see even more mismatches.

[saima]

thanks a lot.

i think you mean first 28 bps of every read but i am receiving mismatches in start of reads even.

i wish i could show u my output, if could be attached here.

[saima]

to lh3(about mismatches in maqview)

Hi lh3,

here is my output attached (under attach files), you can see many mismatches even in first 28 bps of many reads.

[Janet]

lots of mismatches in maqview

I am having the same problem but my mismatches are all shown in lowercase, therefore have lower Quality?
Can anyone explain this?