This example run is a semi-automated run of Haplotracker that requires only mouse-clicking throughout the run. A complete mitochondrial genome DNA sequence (GenBank accession number, JQ245759) was chosen as an example. We assumed that the sample was degraded. Its three short fragments of sequences in control region (hypervariable regions 1, 2, and 3) were first used for tracking its HG. The server searches the closest-ranked haplogroups in the ‘PhyloTree Build 17’ definitions and our scoring system. HG 'W9' was ranked top with this example. The HG should be verified because it was tracked only based on the partial sequences, not the complete genome sequence. Additional and differential variants for the HG 'W9' should be tracked. We recommend users first to narrow down the HGs to reduce the number of tests because there are many HGs to test and presumably there may not be a sufficient amount of DNA samples to try many times to get sequences by such as PCR and sequencing (we assumed that the sample DNA was degraded). This is done by clicking buttons for narrowing options. The sever narrows the HGs in Rank group 1 by integrating the HGs to the most recent common ancestors (MRCAs). Then, HGs that have ranking scores (>0) are chosen first and are tested to search their differential variants. In this example run, there were found three possible differential variants for HG 'W9' and 'W5' (variant 14097 for W9; 6528 and 15775 for W5). The variant 14097 is W9-specific and 15775, W5-specific. Two DNA fragment sequences across the variant positions (14097 and 15775) in coding region are added to the previous round sequences to re-track HG(s). As a result, The HG of this sample was confirmed as 'W9' based on the following results: (1) The sample has the coding region variant 14097 that is W9-specific. (2) HG 'W9' is ranked top. (3) There is only HG 'W9' in Rank group 1. An example run is finished.
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