all depths

[akvarel]

Hello!
I was using Newbler Assembler and Mapper and I got results like alignment depth, total depth, unique depth.

What are the differences between them and what do they mean?

I know that alignment depth is how many times each secuenced base is covered.
What is with others?


Thanks.
Katja

[flxlex]

From the manual:
Unique Depth – the number of non-duplicate reads that align at that position in the alignment
Align Depth – the number of reads (including duplicates) that align at that position in the alignment
This regarding the 454AlignmentInfo.tsv file...

[akvarel]

Thank you but you forgot to write as well what total depth ist.

[flxlex]

Where is this 'Total Depth' reported?