How to read Geneious variant call reports

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Geneious Reports

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 and 3′-UTR untranslated regions.

 

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: A single nucleotide substitution at a specific genomic locus.
  • SNP (Transition): a single nucleotide substitution of one purine for another purine (i.e. adenine for guanine, or vice-versa) or substitution of one pyrimidine for another pyrimidine (i.e. cytosine for thymine, or vice-versa).
  • SNP (Transversion): a single nucleotide substitution of one purine for a pyrimidine, or vice-versa (i.e. adenine for cytosine, or vice-versa; guanine for thymine, or vice-versa; adenine for thymine, or vice-versa; guanine for cytosine, or vice-versa).
  • Substitution: A change of two or more adjacent nucleotides relative to 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.