Geneious Variant Call Reports

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We often use Geneious to generate SNP/indel variant call reports.  A truncated report is available here.  (The number of SNP’s/indels in a typical report can be quite large so we only show a few records in this example).

The column definitions in the report are as follows:

Name: This column is an artificial identifier generated by Geneious to be used as a reference for each record.

CDS: This column shows the name of the coding sequence for a particular gene.  It represents protein coding regions of the genome.  This region is typically flanked by 5′-UTR start codons and 3′-UTR stop codons.

Minimum, Maximum, Length: These columns indicate the start locus, end locus and length, respectively, of the CDS region.

Polymorphism Type: This column defines the type of polymorphism located in the respective CDS region.  Polymorphisms may be one of the following types:

  • SNP (Transition): a single nucleotide transition change from the reference sequence
  • SNP (Transversion): a single nucleotide transversion change from the reference sequence
  • SNP: At a single position, there are multiple variations from the reference sequence
  • Substitution: A change of 2 or more adjacent nucleotides from the reference sequence
  • Insertion: One or more nucleotides inserted relative to the reference sequence
  • Deletion: One or more nucleotides deleted relative to the reference sequence
  • Mixture: multiple variations from the reference sequence which are not all the same length

Codon Change: Indicates the change in codon (if any) caused by the respective polymorphism type.

Amino Acid Change: Indicates the change in protein amino acid(s) (if any) caused by the respective codon change.

Protein Effect: Indicates the potential change in protein structure and/or function caused by the respective change in amino acid.  Possible effects include:

  • None: No change in protein amino acid sequence.
  • Insertion: Insertion of new amino acid in protein amino acid sequence.
  • Substitution: Replacement of one amino acid by another in protein amino acid sequence.
  • Truncation: Early termination of protein amino acid sequence.  (Stop codon introduced in genome sequence).
  • Extension: Abnormal extension of protein amino acid sequence. (Stop codon lost in genome sequence).
  • Start codon loss: Truncation of protein amino acid sequence, or frameshift reading error, or no mRNA translation, depending on genomic sequence after the normal start codon location.
  • Frameshift: Codon reading error resulting in altered protein amino acid sequence.