Genomic Interval Changes

New positions for the 1Mb interval maps


So far, CNV histograms and .pgxseg segment and matrix files used a 1Mb genome binning, based on the consecutive assignment of 1Mb intervals from 1pter -> Yqter. This resulted in 3102 intervals, with the last interval of each chromosome being smaller.

On 2022-02-11 we have changed the procedure. Now, the last interval of the short arm of any chromosome is terminated at the centromere, leading to

  • a (potentially) shortened "last p" interval
  • a shift of most interval positions
  • a changed interval number from 3102 to 3106

Also, since a few qter intervals were very small we now use a padding factor (currently 100000 bases) to determine if the last band would be smaller - in which case it is discarded and the previous interval extended to cover up to the telomere. This applies to chromosomes 6 and X, where the last intervals become now slightly larger than 1Mb:

  • X:155000000-156040895, size 1040895
  • 6:169800000-170805979, size 1005979

Since many CNVs have natural breakpoints at chromosomal centromeres the new interval mapping should provide a better representation of genomic events. Also, such a mapping facilitates the calculation of e.g. arm specific CNV fractions which are sometimes used as statistical indicators.

More information can be found on the related news page and in the technical notes.