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  • 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:
    Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


    Any help shall be appreciated.
    Bioinformaticscally calm

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