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You are here: Foswiki>MITOMASTER Web>HumanAllele (12 Feb 2016, MartyBrandon)Edit Attach
THIS PAGE IS STILL BEING UPDATED TO THE NEW MITOMASTER SOFTWARE - SHOULD WORK PROPERLY SOON
(# of seqs having this allele / total # seqs in the database)
AlleleG16040 - G at position 16040
Nucleotide Difference: %DATABASE_SQL{description="mitouser" sql="SELECT refseq(16040,16040)" format="$residue"}% to G 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: |
- 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.
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Topic revision: r1 - 12 Feb 2016, MartyBrandon
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