Meaning Of '0' Quality Score In Maq?

Question

[Paul]

If a read has a zero quality score in MAQ does that mean:

a) The read aligns to multiple positions b) The read aligns to nowhere

I think it's either one or both of these but I'd hope someone can clear it up for me?

Answer 1

[User 59]

It means the reads map to multiple positions in this case - equally well.

And a quick check of the MAQ FAQ would have shown this:

"What happens to the reads that can be mapped to many positions?

If a read can be mapped to several equally best positions, Maq will randomly choose one position and give the alignment a zero mapping quality."

[User 59]

Well they could be from paralagous genes or repetitive sequences. It's kind of hard to just make a general rule on non-specific matches. Have a read of this: http://www.nature.com/nmeth/journal/v5/n7/full/nmeth.1226.html

[Paul]

Oh right, dunno how I missed that, is there really any point in filtering these out if this is the case? I'm analyzing some rna-seq data.