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THIS PAGE IS STILL BEING UPDATED TO THE NEW MITOMASTER SOFTWARE - SHOULD WORK PROPERLY SOON

AlleledelA16059 - delA at position 16059

Nucleotide Difference: %DATABASE_SQL{description="mitouser" sql="SELECT refseq(16059,16059)" format="$residue"}% to delA

Due to historical precedent mtDNA variants are typically reported with respect to the %REFSEQ%.

Affected Loci

Transcript Translation
Locus Position Ref Nuc. Nuc. Position Ref Codon Codon AA Change Conservation Structure
COI 873 U C 291 CAU CAC silent 1.00
D-Loop Non-coding Locus

  • Generate the table above with a pgplsql function in the database. This will be a very specialized query that produces a particular table of results. Probably easiest to union several queries, each for a different category of locus.
  • Make the conservation value a link to the multiple sequence alignment
  • Non-coding loci will have a 'non-coding' value in the table above
  • tRNA and rRNA loci will have '--' under the translation section

Prevalence

Seqs Containing Allele:  
(# of seqs having this allele / total # seqs in the database)

  • Would be nice to break this figure down by haplogroup

NuMT (pseudogene) Analysis

Spanning NuMTs:
Corroborating NuMTs:

  • Spanning NuMTs span this position when pairwise aligned with the reference sequence.
  • Corroborating NuMTs both span this position and match the nucleotide when aligned.
  • Spanning NuMTs can be used as a very rough indicator of the possibility that this allele may in fact be a sequencing artifact.
  • Due to the ambiguity of sequence alignments, corroborating NuMT information should be used with extreme caution.
  • The exact frequency of sequencing artifacts due to NuMT regions is not known, but is thought to be very low.

References

  • Revise the reference searching.
  • Literature references have been compiled by the MITOMAP curator.

Topic revision: r1 - 12 Feb 2016, MartyBrandon
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