Understanding pilon correction on the reference sequence

Question

[andres.firrincieli]

Hello,

I need some clarification about specific kind fix made by pilon on the reference sequence:

ref             -GGAGTGCTCCGGGCGGGTGACCCGGCACCACCACGACAGCGCCTGCTGCTGTGGACCGA
fix             CGGAGTGCTCCGGGCGGGTGACCCGGCACCACCACGACAGCGCCTGCTGCTGTGGACCGA
                 ***********************************************************

ref             TCAGCTGGTCCGGTTCCCGAAGGTGACTGTCTCGCAGCGTGGTCGCGTCGTCGCGACCAC
fix             TCAGCTGGTCCGGTTCCCGAAGGTGACTGTCTCGCAGCGTGGTCGCGTCGTCGCGACCAC
                ************************************************************

ref             GCTGCTGCCCTGGGCCGCCTCACCGGGACGGGTCTTCCGGGTGCCGTGGTCGATCATGGA
fix             GCTGCTGCCCTGGGCCGCCTCACCGGGACGGGTCTTCCGGGTGCCGTGGTCGATCATGGA
                ************************************************************

ref             CGCCGTCGACCCGGCACTGGGGCCCGTGACCGTCGGACTGGCCAACGCACCTCGTCGGGG
fix             CGCCGTCGACCCGGCACTGGGGCCCGTGACCGTCGGACTGGCCAACGCACCTCGTCGGGG
                ************************************************************

ref             AACCACGCCCAATGCGGTCGGGGAATTCATTCCCTCCCGCTGCAACTGAGCACACCCCCG
fix             AACCACGCCCAATGCGGTCGGGGAATTCATTCCCTCCCGCTGCAACTGAGCACACCCCCG
                ************************************************************

ref             ACACGCACTCTCGTTCAGCACTACCCCGCACACAGATTGTCGACAGTAAACTTCGATCGA
fix             ACACGCACTCTCGTTCAGCACTACCCCGCACACAGATTGTCGACAGTAAACTTCGATCGA
                ************************************************************

ref             TCGGAAGACACATGACGGAAGTACAGGGCGGTTTGCACGGTCCCGAGATGCGGCGGGCCA
fix             TCGGAAGACACATGACGGAAGTACAGGGCGGTTTGCACGGTCCCGAGATGCGGCGGGCCA
                ************************************************************

ref             TCACGGCCGCCGCGATCGGAAACTTCATCACCTGGTTCGACTTCGCGGCATACGGATTTC
fix             TCACGGCCGCCGCGATCGGAAACTTCATCACCTGGTTCGACTTCGCGGCATACGGATTTC
                ************************************************************

ref             TCGCCGTCCTGCTCGGCCAGATCTTCTTT-
fix             TCGCCGTCCTGCTCGGCCAGATCTTCTTTC
                ***************************** 

In the example above ref and fix are identical except the first and last bases. My question is: why is this fix not reported as two independent nucletide insertion? It is possible that what I am looking at is a local misassembly?

Thanks

[lieven.sterck]

It might be that the "fix" is that pilon extended the contig with two bases: a C on either end of the contig.

(technically that would probably not indicated as 'insertion' but rather as 'extension' , I would think)

[andres.firrincieli]

Thank you for answering lieven.sterck

Those changes actually happen on a scaffold of several Mbp.

I will post the same question on https://github.com/broadinstitute/pilon in case someone has the same doubt.

It is not important, but for some odd reason it really bugs me