Chimeric reads

Chimeric reads, also called split reads, are sequence reads that are split into two or more portions, where each portion aligns to a different region of the genome. The sequence for each split read will be annotated as "clipped" relative to the original read sequence. In the BAM format one of alignments will be designated "primary", the remaining are designated "supplementary". Both primary and supplementary alignments will optional contain an "SA" tag describing their relationship to the original read sequence. The features described on this page rely on this tag and are not available if the tag is absent.

Screenshot illustrating chimeric reads with alignments to multiple chromosomes. Display conventions are described in detail below.

Screenshot 2023-10-23 at 1 19 46 AM

Connection indicator#

Clipping indicator#

Between chromosome connections#

Within chromosome connections#

Supplementary alignment diagram#

New display to make viewing and navigating complex alignments easier.

Easier to see visually:

Screenshot 2023-10-23 at 1 40 38 AM

Access the new supplementary reads diagram by right-clicking on a read and selecting Supplementary Reads Diagram from the menu.


Shows the same reads in two different views simultaneously to help understand how the read is connected and aligned.

  1. Alignment Order: Shows the linked reads laid out according to how they were aligned. Its scaled so each chromosome is given equal space but within a chromome reads are size proportionally to how much space on the reference they align to.
  2. Read Order: The same reads laid out according to how they were read from the original molecule.
    The reads in this view are scaled proportionally to the number of bases in the read.
  3. Highlighted read: Mousing over a read will highlight the same read in both views and display, arcs indicate the connection to the next/previous read according to the read order. The arrow indicate forward/reverse strand.
  4. Selected Read Coordinates: shows the aligned coordinates of the highlighted read.


You can use it to jump around to the relevant reads.

Overlapping reads are displayed in the alignment view#

Reads which overlap are shown in the relevant proportion and position to one another. Screenshot 2023-10-21 at 10 18 00 PM

Other features#

Group by: chimeric#

To group all the reads with SA tags, right-click in the alignment track and select Group by > chimeric.

Sort by: clip length#

To sort the reads by clip length, right-click in the alignment track and select Sort by > left clip or Sort by > right clip

New navigation features#

Improved display in tooltips for long reads / SA tags#