Charity Output Column Descriptions

Mapback Header (MBH) columns:

  1. MBH:Build — genome build (eg, hg19, hg18, mm9, dm3)
  2. MBH:Gene — gene symbol
  3. MBH:Strand — coding strand
  4. MBH:Gene Annotation Issue — any transcription/translation issues noted in the Mapback table
  5. MBH:Transcript — transcript reference accession
  6. MBH:Protein — protein reference acccession
  7. MBH:Product — description of protein product
  8. MBH:Product Coverage — percentage of product overlaps by event segment in input file

Mapback Function (MBF) columns:

  1. MBF:CDS Mutation — short string in semi-standard nomenclature indicating the consequence of any variant sequence in the context of coding DNA sequence coordinates
  2. MBF:Mutation Type — pithy description of the type of mutation in semi-standard format (eg, Synonymous, Nonsense, etc.)
  3. MBF:Protein Mutation — short string in semi-standard nomencalture indicating the consequence of the any variant sequene in the context of protein coordinates

Mapback Codon (MBC) columns:

  1. MBC:Codon Number — codon or protein residue number, where the start Methionine is at position 1
  2. MBC:Amino Acid — single amino acid residue code
  3. MBC:Codon — codon triplet that codes for the amino acid
  4. MBC:CDS Coordinates — coding DNA sequence coordinates for the codon
  5. MBC:Genomic Coordinates — genomic (chromosomal) coordinates for the codon
  6. MBC:Coding Exon — coding exon number in which the codon resides
  7. MBC:Transcribed Exon — transcribed exon number in which the codon resides
  8. MBC:Gene Model Exon — global gene exon number (all transcribed exons merged and renumbered) in which the codon resides
  9. MBC:Variations — any annotated variations for the codon
  10. MBC:Sites — any annotated functional sites for the codon
  11. MBC:Regions — any annotated functional regions/domains for the codon
  12. MBC:COSMIC Mutations — any annotated somatic mutations from the Sanger COSMIC database

Charity Map Annotation (CMA) columns (naming depends on the particular map chosen):

  1. CMA:__MAP_NAME__ — the annotation string for any overlapping annotation
  2. CMA:__MAP_NAME__.event_overlap — percentage of event segment (in input file) overlapped by the annotation
  3. CMA:__MAP_NAME__.map_element_overlap — percentage of annotation segment (in map file) overlapped by the event

Note: multiple values in columns are delimited by “///”

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