High Frequency Haplogroup (HFHG) Flags: Calculation Criteria

For full-length (FL) or control region (CR) sequences, the following conditions are applied to flag variants that are found in specific haplogroups at high frequency.
  • Haplogroups are reported where a qualifying variant is found at 50% or higher in Mitomap's current sets of GenBank sequences. A link to HFHG distribution details will be provided ONLY when this 50% frequency 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.

    • Only haplogroups containing a minimum of 10 sequences are displayed; thus at 50% there would be at least 5 variant-containing sequences at a minimum threshold of 50%

  • The above screening is further filtered to display only those variants found in Mitomap's sequence database at a frequency of 0.2% or higher overall. Currently this requires a count of ~100 FL sequences that contain a specific variant. [This filter modifed March 2020].

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.

Variants satisfying the above filters in our current Full Length sequence set are listed here: https://mitomap.org/genbank_haplolist.html

This topic: MITOMAP > HiFreqHGcalc
Topic revision: 06 Mar 2020, UnknownUser
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