Step 1: Access a Query system.

Step 2: Input the mtDNA sequence.

mtDNA sequence data are entered as differences to the revised Cambridge Reference Sequence (rCRS). When a difference between a sequence data and the rCRS is observed, only the site (which is a designated number) and the nucleotide differing from the reference standard are recorded (e.g., 73G). Insertions are recorded by first noting the site immediately 5' to the insertion followed by a decimal point and a '1' (for the first insertion), a '2' (if there is a second insertion), and so on, and then by the nucleotide that is inserted (e.g., 315.1C). Deletions are recorded by listing the missing site followed by a 'd' (i.e., 249d) (Carracedo A et al. Forensic Sci Int. 2000;110(2):79-85). At confirmed heteroplasmic sites, IUPAC codes for base calling can be applied. For convenience's sake, the transition mutation can be recorded by listing only the site omitting the indication of the nucleotide difference, but the transversion mutation should be recorded with the nucleotide differing from the reference standard in all cases (e.g., 73 vs. 73C).

Input sequence example 1:

Input sequence example 2:

Step 3: Select the region to be analyzed.

Step 4: Select the target group from the mtDNAmanager database.

Step 5: Select an option to search sequence.

a. Retrieve sequences which include the queried nucleotide polymorphisms:

b. Retrieve sequences which show a match with the queried sequence data:

Users can select options concerning heteroplasmic insertions and mismatch.

Step 6: Click the button "Search". The results from mtDNAmanager will be presented.

Step 7: Click the button "Frequency Estimates". The match probabilities in all of the population groups of mtDNAmanager database will be presented.

Haplogroup estimation: The result for the submitted mtDNA sequence data is presented.

Search result: Match probability and retrieved sequences are presented with the estimated haplogroup-affiliation.

Worldwide frequency: The match probability in all of the population groups of mtDNAmanager database is presented in a new pop-up window.