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Old 04-04-2016, 09:35 AM   #1
bio_informatics
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Location: USA

Join Date: Nov 2013
Posts: 182
Default Mapping assembled genome back to reads: why SNPs?

Hi members,

I've paired end, Illumina, Klebsiella Pneumonia.
Read length 251, MiSeq run
Quality remains good until the read end.

Assembled genome's quality is reasonable checked with Quast.

When I map my reads back to assembled genome, and carry out SNP analysis, I find SNP within it.
I set coverage as 10 to call a base SNP.
I fail to understand why a reference has SNP when mapped against itself.

Is it something to do with SPAdes' correction?

Tool used for mapping, and VCF - bowtie, and GATK.
spades version: 3.5.0

Spades run on auto coverage settings, everything else default. Bowtie, and GATK default.

I found similar post at:
http://seqanswers.com/forums/showthread.php?t=41739

Any help shall be appreciated.
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