Reads track¶
Detailed and summary views¶
The reads track changes with zoom level.
When zoomed in, seqhiker shows individual reads.
When zoomed further out, it switches to summary representations such as coverage and strand summaries.
Read views¶
The reads track supports multiple view modes:
stack
strand stack
paired
fragment
These can be changed in the read-track settings.
BAM display¶
At close zoom, the reads track can show:
individual read rectangles
SNP markers and nucleotide letters
deletions
optional soft-clipped overhangs
optional pileup logo
Pileup logo¶
When enabled at base-level zoom, the pileup logo summarizes the visible read pileup per genomic position.
In most read views, it is drawn as a band inside the reads track
In strand stack mode, separate logos are shown for forward and reverse strands
Soft-clipped bases¶
When enabled, soft-clipped read ends are shown as overhang blocks beyond the aligned read body.
At high enough zoom, the clipped bases themselves are drawn as letters.
Read details¶
Double-click a read to inspect it in the right-hand panel.
For paired reads, the panel can also expose mate-jump actions when mate coordinates are available.