THIS PAGE IS STILL BEING UPDATED TO THE NEW MITOMASTER SOFTWARE - SHOULD WORK PROPERLY SOON
AlleleinsATTCTCTGTTCTTTC16030 - insATTCTCTGTTCTTTC at position 16030
Nucleotide Difference: %DATABASE_SQL{description="mitouser" sql="SELECT refseq(16030,16030)" format="$residue"}% to insATTCTCTGTTCTTTC
Due to historical precedent mtDNA variants are typically reported with respect to the %REFSEQ%.
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.
This topic: MITOMASTER > HumanAllele
Topic revision: 12 Feb 2016, MartyBrandon