The sequence in question is an approximately 2.2 Mb RS1 SMRT cell=4 Neisseria genome that i would like to seek your guidance on.
I used my assembly of this organism (which is the first single contig sequence of its strain's kind) as a reference for SNP calling using the breseq pipeline.
1) Every one of my results has an identical "unassigned missing coverage evidence" section. This consists of 2 sections at either end of the genome.
2) A graph displaying coverage over the course of the genome shows an average of 500x but two small negative spikes of quality at either end of the genome
3) I annotated my assembly using prokka and visualised the .gbk on artemis.
These two regions share 100% complemented homology
i.e. with numbers representing put. ORFS
1,2,3,4-high coverage genome-4,3,2,1
in 13000/16000 base pairs (these are annotated with the same hypothetical proteins and tbpB (transferrin binding protein) variants
Based off this body of evidence, am i justified in trimming this sequence off my final assembly which i will publish?
P.s.
I wanted to give the community all of my annotation files as well, is there a resource to this via refseq or should I privately host them somewhere?
I used my assembly of this organism (which is the first single contig sequence of its strain's kind) as a reference for SNP calling using the breseq pipeline.
1) Every one of my results has an identical "unassigned missing coverage evidence" section. This consists of 2 sections at either end of the genome.
2) A graph displaying coverage over the course of the genome shows an average of 500x but two small negative spikes of quality at either end of the genome
3) I annotated my assembly using prokka and visualised the .gbk on artemis.
These two regions share 100% complemented homology
i.e. with numbers representing put. ORFS
1,2,3,4-high coverage genome-4,3,2,1
in 13000/16000 base pairs (these are annotated with the same hypothetical proteins and tbpB (transferrin binding protein) variants
Based off this body of evidence, am i justified in trimming this sequence off my final assembly which i will publish?
P.s.
I wanted to give the community all of my annotation files as well, is there a resource to this via refseq or should I privately host them somewhere?
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