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High Frequency Haplogroups: Calculation Criteria

For full-length (FL) or control region (CR) sequences, the following conditions are applied.
  • Screening is performed only for variants found in Mitomap's sequence database at a frequency of 0.5% or higher overall. Currently this requires a count of ~250 FL sequences that contain a specific variant.

  • Haplogroups are reported where a qualifying variant is found at 50% or higher in Mitomap's current set of GenBank sequences respectively.

    • A link to distribution details will be provided ONLY when this high frequency condition is met by one or more haplogroups in the sequence set.

    • The levels of phylogeny that qualify with a 50% or higher variant frequency will be reported as top level haplogroups (A-Z, HV, L0-L6) or as branches at either the letter-number level (e.g., B2) or letter-number-letter level (e.g., B2a).

    • All frequencies for haplogroups and branches include all sequences in the sub-branches and groups. For example, "J1" includes everything beginning with "J1"; "H6a" includes everything beginning with "H6a", etc.

  • Haplogroups must contain a minimum of 10 sequences to be considered; thus at 50% there would be at least 5 variant-containing sequences at a minimum threshold of 50%

Reminder: all sequences and haplogroups containing ANY given variant may be found throughout Mitomap and Mitomaster by clicking on that variant's GB sequence count link. The column headers in the resulting table are fully sortable, making it easier to pull out data of interest.
Topic revision: r9 - 21 Aug 2019, UnknownUser

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