MITOMAP Disease Mutations
This data track contains disease-annotated mutations (variants) in the
complete mtDNA. The item colors correspond to the variant type:
coding/control vs.
rRNA/tRNA.
For both tracks, item names correspond to the variant nucleotide change, and mousing over features displays all available metadata for MITOMAP. Linkouts to the specific MITOMAP datasets are available from the item description pages, however, you must input the variant on MITOMAP.
--All source data can be found on the -MITOMAP site. -
-The MITOMAP data on the UCSC Genome Browser can be explored interactively with the -Table Browser or the -Data Integrator. -For automated download and analysis, the genome annotation is stored at UCSC in bigBed -files that can be downloaded from the respective file, e.g. -MITOMAP Variants, on our download server. -The data may also be explored interactively using our -REST API.
+Abbreviations and Definitions +
-The file for this track may also be locally explored using our tools bigBedToBed
-which can be compiled from the source code or downloaded as a precompiled
-binary for your system. Instructions for downloading source code and binaries can be found
-here.
-The tools can also be used to obtain features confined to a given range, e.g.,
-
-bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/$db/bbi/mitoMapVars.bb stdout
Nucleotide changes are indicated as L-strand substitutions.
+Variant Classification:
+Disease Associations:
+Mutation Terminology:
+Mutation Status Definitions:
++MITOMAP collected the sequences from GenBank, aligned them to the rCRS using BLASTn, and +haplotyped them with Haplogrep via the Mitomaster web service.
+The data were originally downloaded from the MITOMAP resource. For the Control and Coding Variants track, the following datasets were combined:
And for the Disease Mutations track, the following two were combined:These tracks have since been updated to automatically fetch files from the MitoMap server. For all the details on how the data are processed and combined, see the MITOMAP makedoc.
++All source data can be found on the +MITOMAP site. +
+The MITOMAP data on the UCSC Genome Browser can be explored interactively with the +Table Browser or the +Data Integrator. +For automated download and analysis, the genome annotation is stored at UCSC in bigBed +files that can be downloaded from the respective file, e.g. +MITOMAP Variants, on our download server. +The data may also be explored interactively using our +REST API.
+ +
+The file for this track may also be locally explored using our tools bigBedToBed
+which can be compiled from the source code or downloaded as a precompiled
+binary for your system. Instructions for downloading source code and binaries can be found
+here.
+The tools can also be used to obtain features confined to a given range, e.g.,
+
+bigBedToBed -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/$db/bbi/mitoMapVars.bb stdout
Thanks to Shiping Zhang and the entire MITOMAP resource for making these annotations available.
-MITOMAP: A Human Mitochondrial Genome Database. http://www.mitomap.org, 2023 -
--Lott, M.T., Leipzig, J.N., Derbeneva, O., Xie, H.M., Chalkia, D., Sarmady, M., Procaccio, V., -and Wallace, D.C. 2013. mtDNA variation and analysis using MITOMAP and MITOMASTER. Current -Protocols in Bioinformatics 1(123):1.23.1-26. PMID: 25489354 URL: http://www.mitomap.org
+Lott MT, Leipzig JN, Derbeneva O, Xie HM, Chalkia D, Sarmady M, Procaccio V, Wallace DC. mtDNA Variation and Analysis +Using Mitomap and Mitomaster. Curr Protoc Bioinformatics. 2013Dec;44(123):1.23.1-26. +PMID: 25489354; PMC: PMC4257604