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This section displays a phylogeny analysis of the accessions. |
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\ No newline at end of file |
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This section displays a phylogeny analysis of the accessions.
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To create this tree,separate variation files from the different origins were filtered on coding regions (exons, i.e. CDS and UTR) using GATK 4.1.7.0 VariantFiltration, then merged to create one file using bcftools 1.9 merge.
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Then variants were filtered again based on certain criteria. Were removed from file variants with :
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- QD (QualByDepth) < 2.0
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- FS (FisherStrand) > 60.0
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- SOR (StrandOddsRatio) > 3.0
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- MQ (RMSMappingQuality) < 40.0
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For further information on criteria, take a look on the page below :
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https://gatk.broadinstitute.org/hc/en-us/articles/360035890471-Hard-filtering-germline-short-variants
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The phylogenic tree was generated using SNPhylo.20181005, with a bootstrap confidence value of 100, and using Pathenocissus as outgroup. |
