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Ion Reporter™ Software 5.22 Help
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  1. Home
  2. Annotation sources
  3. Ion Reporter™ Software references
  • Introduction to Ion Reporter™ Software
  • Get started with Ion Reporter™ Software
  • Import and manage samples
  • Manage analysis workflows
  • Analyses
  • Analysis results
  • Detailed analysis metrics
  • Visualize analysis results with Ion Reporter™ Software
  • Create and view reports
  • Filters and filter chains
  • Annotation sources
    • Annotations available in Ion Reporter™ Software
    • Import a custom annotation source
    • Delete custom annotation sources
    • Change amino acid code
    • Variant identifiers for Oncomine™ panels
    • Preferred transcripts in default analysis workflows
    • Annotation sources and scores
    • Annotation versions and calculations
    • Codon differences in chromosome M
    • Effect of Ensembl and RefSeq sources on Polyphen and SIFT scores
    • Genetic Category Type variants
    • Grantham score
    • HGVS genomic codes
    • Ion Reporter™ Software references
      • Ambiguity codes for three positions on chromosome 3
      • Hard masked PAR regions in chromosome Y
      • Chromosome M
    • SIFT score
    • phyloP score
    • PolyPhen-2 score
    • phyloP
  • Administer Ion Reporter™ Software
  • Troubleshooting
  • Fusion analyses
  • Ion Reporter™ Software web services API
  • Programming guidelines for Ion Reporter™ Software plugins
  • Oncomine™ Variant Annotator plugin criteria
  • Documentation and support
  • Glossary
  • Legal

Ion Reporter™ Software references

  • hg19: This human reference is based on the GRCh37.p5 version of the human genome assembly. The GRCh37.p5 version is described at this web site: https://www.ncbi.nlm.nih.gov/grc/human/data?asm=GRCh37.p5.

  • GRCh38: This human reference is based on the GRCh38.p2 version of the human genome assembly. The GRCh38.p2 version is described at this web site: https://www.ncbi.nlm.nih.gov/grc/human/data?asm=GRCh38.p2.

  • Ambiguity codes for three positions on chromosome 3
  • Hard masked PAR regions in chromosome Y
  • Chromosome M

For Research Use Only. Not for use in diagnostic procedures.

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