Mitomaster Instructions

Mitomaster has been rebuilt on a new framework. Analysis is done on input mitochondrial DNA sequences. The current version (Beta 1) performs variant calling relative to the rCRS, haplogrouping based on Phylotree, and variant annotation based on Mitomap. We will continue to improve the Mitomaster tool by adding more features.

Input sequences can be either full mtDNAs or partial mtDNA sequences.

  • The minimum length of a sequence for variant listing is 100 nt.

  • Haplogroup prediction is accurate only for full mtDNA sequences. Use of HSV-I or HSV-II sequences does not guarantee correct haplogrouping. However, use of concatenated HSV-I and HSV-II sequences results in correct haplogrouping for most cases.


A Mitomaster run can be started by pasting a sequence to the textbox or choosing a fasta file of nucleotides and then clicking submit. The textbox recognizes only one sequence. For more than one sequence please upload a fasta file containing the sequences. (For fasta file format, see


A summary page is displayed after a successful submission. Please note that depending on server load, results may be deleted after 60 minutes. Use the download link on the summary page to download csv files.

The summary page for sequence or GenBank queries lists the following attributes:
  • Predicted Haplogroup: A top-level (letter-number-letter) haplogroup prediction as well as a full haplogroup predication for the sequence. A detailed report of haplogrouping will be available soon.
  • Total Variants: Number of variants in the query sequence when compared with the rCRS.
  • Variants: Lists locations and nucleotides for all differences detected in the query sequence compared to that found in the rCRS. For example, "A73G" indicates that at rCRS position 73, the rCRS nucleotide is "A" but the query sequece is "G".

Sequence Variants Details

This page reports the variants detected in the query sequence along with their annotations:
  • Query position: variant's position in rCRS (after alignment)
  • rCRS NT: reference nucleotide in the rCRS
  • Query NT: nucleotide observed in the query sequence
  • Mut Type (Mutation Type): type of nucleotide change
  • Locus: locus of the variant in the mtDNA
  • Tx Effect (Translation Effect): the type of amino acid change. If a variant is located in a non-coding region, this field will state "tRNA", "rRNA", or simply "non-coding" as appropriate.
  • GB Freq: The number of sequences containing this variant, and the percentage this represents, in our current set of GenBank sequences. For variants in the Control Region, a second number and percentage are listed as found in our set of shorter, Control-Region-only sequences.
  • Frequency in Haplogroup: This number shows the percentage of all sequences which contain the variant in the predicted high-level (letter-number-letter) haplogroup of the analyzed sequence.
  • Refs: "Refs" are references which have been added individually by the Mitomap team. "Unpub" gives links to variants submitted by users, but not found in published literature at the time of submittal. Other references may be found by examining the GB sequence listings found under "GB Freq". [Caution: variants with extremely large numbers of GB sequences will take an extremely long time to display the list and analyses of all of the sequences. We have to make this more efficient in the future.]
  • Conservation: if the variant is in a coding region, this number is the % of comparison species which have the reference allele.Click on the Species tab at the top of the Mitomaster page to select species for comparison. By default, all species listed on that page are included.
  • Patient Phenotype: Reported patient phenotype(s) from the literature. The fact that a patient has been reported with a particular variant does not, by itself, imply causality.


Your feedback will help us improve Mitomaster. Please contact Mitomaster development team at:


Mitomaster is developed at Children's Hospital of Philadelphia by the Bioinformatics Core (BiC) and the Center for Mitochondrial and Epigenomic Medicine.

Current Mitomaster Team

  • Shiping Zhang, PhD
  • Marie Lott
  • Vincent Procaccio, MD, PhD
  • Dimitra Chalkia, PhD
  • Doug Wallace, PhD

Mitomaster Alumni

  • Jeremy Leipzig, PhD (now at TileDB)

Topic revision: r7 - 16 Oct 2022, JeremyLeipzig

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