Gubbins - Ns in output alignment

[mstagliamonte]

Dear Gubbins Team,

I am trying to use Gubbins to scan for recombination a SNP alignment which contains no missing data. The input alignment has 21,134 sites, the output file (my_output.filtered_polymorphic_sites.fasta) contains 20,174 sites. I initially thought that this was due to the potential recombinant sites being excluded; however I noticed that there are 'Ns' in the output alignment. What are these due to?
I apologize in case this is a duplicated topic, as I found a similar question here: #182 , but there is no answer yet.

Thank you for your kind attention,
Max Tagliamonte

[andrewjpage]

If at a particular site there are SNPs somewhere in the tree and at a different point there is a recombination, the recombination will be masked out with Ns.

[mstagliamonte]

Thank you, @andrewjpage for responding back so quickly.

I am sorry, but I am not sure I understand the answer. If I understand, the alignment is shorter, as some sites were removed because of recombination, but some other sites undergoing recombination were masked instead? I am not sure I understand the difference between the two.

Thank you,
Max

[andrewjpage]

Taking these as input:

sample1

AAC

sample2

AAA

sample3

AGG Gubbins is run and it detects a recombinaton in sample3 at coords 2-3.

sample1

AAC

sample2

AAA

sample3

ANN This recombination then gets masked out. Because there is no longer any variation in coordinate 2, it gets filtered out, but coords 3 have some variation C/A so is kept giving a site with an N:

sample1

AC

sample2

AA

sample3

AN

…

On 19 June 2017 at 22:27, mstagliamonte ***@***.***> wrote: Thank you, @andrewjpage <https://github.com/andrewjpage> for responding back so quickly. I am sorry, but I am not sure I understand the answer. If I understand, the alignment is shorter, as some sites were removed because of recombination, but some other sites undergoing recombination were masked instead? I am not sure I understand the difference between the two. Thank you, Max — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#192 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AABeV2YysHNVy_zcXqdALvS3m-X91Jexks5sFueqgaJpZM4N-upd> .

[mstagliamonte]

Thank you,
I understand now. I appreciate you taking the time to write the explanation, it was really useful.

Have a nice day,
Max

[wanyuac]

I reckon coord 1 in the example above should also be removed and only leave coord 3 in the final alignment, as coord 1 is invariant.