Track order for non-aneuploidy analyses

Note: In the GRCh38 genome reference, there exist alternate loci which are not part of the 1-22, X,Y chromosome contigs, and so are not annotated by the software (by design), for example chr22_K1270879v1_alt. Ion Reporter™ Software does, however, annotate the GSTT1 gene which is also located on an alternate loci.

After the Whole Genome View of each non-aneuploidy analysis, the various data tracks are loaded in this order by default:

  1. Selected chromosome ideogram

  2. Copy Number segment (.seg) file

  3. .vcf file

  4. .bam track for each sample

  5. genome reference track

  6. design .bed files and hotspot files

  7. annotation tracks (COSMIC, ClinVar, and preferred transcript annotation tracks)