+ Click and drag - the blue selection brush to highlight regions of + the genome. +
+ Click and drag - the edges of the selection brush to resize it. +
+ Hover - over a structural variant to see detailed information. +
+ Click - on a structural variant to inspect breakpoints in other + views. +
+ A structural variant (SV) may leave a footprint on the copy + number profile and may perturb genes. +
+ The black vertical line indicates region in focus. +
+ Click - on a structural variant to show its breakpoints in the + Read View. +
+ The positions of breakpoints are highlighted by dashed, vertical lines. +
+ Zoom in and out - on chromosomal regions by clicking the{' '} + + + + {' '} + and{' '} + + - + {' '} + buttons. +
+ Pan left and right - around the current region by clicking the{' '} + + ← + {' '} + and{' '} + + → + {' '} + buttons. +
Black stripes - indicate chromosome bands (cytobands) obtained from chromosome staining viewing under microscope.
Red Triangles - represent chromosome centromeres.
Circle with a dot - denotes bi-allelic gene loss.
Circle without a dot - denotes one mutation in gene.
Driver mutations are also annotated by name in the genome view.
Driver mutations need to be curated and pre-specified as part of Chromoscope configuration data specification.
Hover - over driver variants to see annotation details.
Arrows - represent genes.
Direction - denotes gene strand.
Thicker lines - represent Exons.
Zoom out - to see only selected genes sampling info.
Zoom in - to a smaller region to see all genes in that region.
Y-axis shows the distance (in kb) between adjacent point mutations, on a logarithmic scale.
At low magnification, only selected mutations are visible. More information on sampling here.
+ Zoom in - to reveal more point mutations. +
Hover - over a point mutation to see details.
Insertions are identified when the alternative allele is longer than the reference allele by the number of basepairs inserted.
Deletions are identified where the alternative allele is shorter by the number of basepairs that were deleted.
Orange lines - mark insertions.
Green lines - mark deletions.
When showing large chromosomal regions, Chromoscope selects 500 indels in each visible tile (see documentation on sampling).
Hover - on an insertion or deletion to see details.
Thick gray lines - represent copy number profiles.
Y-axis - represents the number of chromosome copies.
Copy number variants often coincide with structural variants.
+ Hover - over the copy number segment to see the number of copies of each chromosomal regions. +
Gains are declared in chromosomal regions where total number of copies exceeds 5.
Regions with gains are marked in blue on both Genome and Variant Views.
LOH is declared in regions where a chromosome copy from one of the parents was entirely lost (minor copy number of 0).
Regions with LOH are marked in coral in Variant View.
Regions with LOH are marked in coral in Genome View.
Arches - represent structural variants (SVs).
Colors - denote different types of SVs.
Click - on an SV to show its breakpoints in the read view.
Hover - over a SV to see more information about each event.
The sequencing coverage track quantifies the number of sequencing reads covering each position.
Black vertical dashed line - denotes the selected breakpoint (if selected).
Sequencing coverage is derived from the data on sequencing reads aligning to each position.
Black reads - (those parts of reads that were split) do not contribute to the coverage sum.
Colors - represent DNA base-pairs in human reference genome.
Gray rectangles - denote normally-mapping reads.
Black rectangles - denote split reads, used as evidence for structural variants.
Other read colors (e.g. green) denote aberrantly mapping reads, which are also used as evidence for structural variants (see more info).
Black vertical dashed line - denotes a SV breakpoint.
Hover - over a sequencing read to see more details.