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:
Selected chromosome ideogram
Copy Number segment (.seg) file
VCF file
BAM track for each sample.
Note: A maximum of 500
aligned reads are shown in each BAM track in Ion Reporter™ Genomic Viewer(IRGV). To see more than 500 aligned reads, use Integrative Genomics Viewer (IGV).
Genome reference track
Design BED files and hotspot files
Annotation tracks (COSMIC, ClinVar, and preferred transcript annotation tracks)
