Help interpreting samtools tview

[dnusol]

Hi
can anyone help me interpreting the alignment at the position shown in the attached image? I can guess that there is a deletion of two bases but the consensus sequence shows an AA and then follow bases identical to the reference? Why the blue color to those AA's? To me it is not very clear the interpretation of the color code. When I press "?" the final section of help from tview shows:

Underline: secondary or orphan ---what is this?
Blue: 0-9 --- 0-9 what? is it number of reads?


thanks for your help.

D

[dnusol]

Hi, sorry for trying again, but can anyone point me to an explanation of the samtools tview help?? I don´t understand the colour code used and the info displayed when pressing "?" is too limited, at least to me.

Thanks in advance

D.

[jflores]

Hi dnusol,

Very delayed response, hopefully you not only know the answer but can help me a bit.

Underline: secondary or orphan ---what is this?
Blue: 0-9 --- 0-9 what? is it number of reads?

"Blue: 0-9" means all reads/bases (depends on the display mode) with mapping qualities between 0 and 9 will be coloured in blue, and so on with the other colours ,,

Do you know (or anyone else) know what does orphan mean here?

My guess is that underlined reads first of all come from paired-end data and second their pair couldn't be mapped. I'm not sure though ,,

Thanks a lot !


Rodrigo

[Tally]

Hi dnusol,

Very delayed response, hopefully you not only know the answer but can help me a bit.

Underline: secondary or orphan ---what is this?
Blue: 0-9 --- 0-9 what? is it number of reads?

"Blue: 0-9" means all reads/bases (depends on the display mode) with mapping qualities between 0 and 9 will be coloured in blue, and so on with the other colours ,,

Do you know (or anyone else) know what does orphan mean here?

My guess is that underlined reads first of all come from paired-end data and second their pair couldn't be mapped. I'm not sure though ,,



Rodrigo

Dear Rodrigo,
Yes you are correct. The blue means quality of 0-9 and so on for the other colours. Higher scores mean higher qualities.
You were also correct with the orphan reads: These are reads whose pair (from mate paired/paired end data) have not been mapped to the reference sequence. These are not considered by the program when generating the consensus sequence.