Re: [maq-help] Score in dump file with -H

[Heng Li <lh...@gm...>]

Hello Justin,

On 13 Aug 2008, at 05:03, Jeong-Hyeon Justin Choi wrote:

> Hi,
>
> I have question on dump output with the option -H.
> The document said
>
> A readID position strand score
>
> 1. What do scores in the last column mean?

It is the sum of quality values of mismatches, divided by 10.

> 2. Why are there the different scores for a read?

If the read can be mapped to multiple places with different mismatches.

> 3. Is the position is the starting or end position for negative  
> strand?

It is the ending position.

regards,

Heng