See this page in the users guide:  Personal Synonyms

...

Chromosome synonyms

Here is an example chromosome synonyms file:  chromosome.txt

KlingonChr1 Chr1
KlingonChr2 Chr2
KlingonChr3 Chr3
KlingonChr4 Chr4
KlingonChr5 Chr5

And I made Here is an example bed file, made by taking segments from the Athe A_thaliana_Jun_2009 gene annotations and replacing the chromosome names:  exBed.bed

KlingonChr5 550034 552647 AT5G02490.1 0 - 550295 552565 0 2 2009,296, 0,2317,
KlingonChr5 553744 556442 AT5G02500.1 0 - 554054 556334 0 2 2052,322, 0,2376,
KlingonChr5 553744 556442 AT5G02500.2 0 - 554054 556334 0 3 697,965,322, 0,1087,2376,
KlingonChr5 558284 559235 AT5G02502.1 0 - 558603 558711 0 2 427,94, 0,857,
KlingonChr5 560134 560860 AT5G02510.1 0 + 560134 560860 0 3 273,177,90, 0,356,636,

etc.

 I loaded my synonyms

As per the directions in Personal Synonyms, add this chromosome.txt file as a chromosome synonyms , and restarted IGB.  Now I expect that if I open exBed.bed in IGB, it will treat these entries as if they were unchanged, recognizing that KlingonChr5 is equivilent to Chr5.  But instead it is creating entire new chromosomes to display the KlingonChr annotations.  The (lack of) response is the same when I add the chromosome.txt file to the root of a quickload file.file.  Restart IGB.

Start IGB and choose the A_thaliana_Jun_2009 genome.  Load the exBed.bed file.  Use the "genome" load mode, the file only includes a scattering of annotations.

•  Observe that the annotations from exBed appear on the same chromosomes as the automatically loaded annotations.

...

If IGB creates new chromosomes labeled "KlingonChr1" etc, then the link between chromosome "KlingonChr5" and "Chr5" is not functioning.

Genome Version synonyms

TBD