# SV visualization **TL;DR:** Triage structural variant (SV) candidates in the [SV inspector](https://jbrowse.org/jb2/docs/user_guides/sv_inspector_view), then open the [alignments](https://jbrowse.org/jb2/docs/user_guides/alignments_track) at each breakpoint for the read-level evidence. This page is what those read patterns mean: which color scheme lifts which pattern out of the pileup, what each SV type looks like in short and long reads, and which view to open once a breakpoint is found. The [alignments track guide](https://jbrowse.org/jb2/docs/user_guides/alignments_track) covers what each control does. End-to-end walkthroughs: [](https://jbrowse.org/jb2/docs/tutorials/sv_visualization_cgiab), [](https://jbrowse.org/jb2/docs/tutorials/cancer_sv), [](https://jbrowse.org/jb2/docs/tutorials/sv_multisamples). How the SAM format itself encodes SV evidence, in split alignments, the `SA` tag, pair orientation, `TLEN` and clipping, is in [Structural variants and the SAM format](https://cmdcolin.github.io/posts/2022-02-06-sv-sam/). ## Where the evidence is A structural variant leaves three kinds of mark in an alignments track: - **Coverage.** A deletion drops it between the breakpoints and a duplication raises it. An inversion or a translocation leaves it alone. - **Clipped reads.** A read crossing a breakpoint ends there, and its overhang is soft-clipped. The [insertion and clipping indicators](https://jbrowse.org/jb2/docs/user_guides/alignments_track#insertion-and-clipping-indicators) flag a cluster of them above the coverage row before you zoom to the pileup, and [Show soft clipping](https://jbrowse.org/jb2/docs/user_guides/alignments_track#soft-clipping) draws the clipped bases. - **Reads whose two halves land apart.** In a paired-end library that is a pair with an unexpected insert size or orientation. In a long-read library one read spans the breakpoint and splits into a primary and a supplementary alignment, joined by the `SA` tag.
The rest of this page takes the third kind in turn, paired-end reads then long reads, then the views that show both sides of a breakpoint at once. ## Paired-end reads ### Pair orientation **Color by → Pair orientation** colors each read by the strands its two mates aligned to. The colors follow [IGV's](https://igv.org/doc/desktop/#UserGuide/tracks/alignments/paired_end_alignments/) and assume a standard `fr` (Illumina) library. SOLiD-style orientations are not supported. | Color | Name | Value | Description | | --- | --- | --- | --- | | | LR (→ ←) | `#d3d3d3` | Normal proper pair | | | RL (← →) | `#0099bb` | Mates point away from each other | | | LL (→ →) | `#4d9a4d` | Both mates on the forward strand | | | RR (← ←) | `#5555bb` | Both mates on the reverse strand | | | Inter-chromosomal | `#af4d19` | Mate on another chromosome | | | Mate unmapped | `#000000` | Mate aligned nowhere | | | Split read (inverted) | `#9b30b0` | Supplementary segment on the opposite strand to its primary | Colored this way, an inversion is a green LL bundle and a navy RR bundle spanning the same stretch, with magenta split reads at the breakpoints, in a pileup that is otherwise grey.
The two bundles come from pairs that straddle a junction. An inversion turns a stretch of sequence around, and every read inside it with it, so a pair with one end inside the segment and one end outside has one end reversed and one not: both point the same way, forward-forward across the left junction and reverse-reverse across the right. The end inside the segment also maps to the mirrored position, which is why each bundle reaches across the segment. A pair wholly inside the segment, or wholly outside it, maps as an ordinary LR pair.
junction junction Sample Reference inverted segment LL pair RR pair LR pair
A pair sequenced across a junction of an inverted segment. The end that fell inside the segment maps to the mirrored position on the opposite strand, so the pair lands as LL on the left junction and RR on the right, and the two reach across the same segment. A pair wholly inside the segment maps as an ordinary LR pair.
The duplication half of an inverted duplication has no orientation signature. Where the second copy went is what the call's `INFO.CPX_INTERVALS` names, and no pair in the pileup states it. ### Insert size **Color by → Insert size** colors a read by how far apart its mates aligned: red for larger than expected, pink for smaller, light grey for normal. **Insert size (gradient)** shades continuously by the size of the deviation instead. Expected is a robust band around the typical insert.[^mad] | Color | Name | Value | Description | | --- | --- | --- | --- | | | Inter-chromosomal | `#af4d19` | Mate on another chromosome | | | Insert larger than expected | `#ff0000` | Deletion between the mates | | | Insert smaller than expected | `#f582c0` | Insertion between the mates | | | Mate unmapped | `#000000` | Mate aligned nowhere | **Insert size and orientation** combines both. A short insert paints pink whatever its orientation, an abnormal orientation wins over a normal insert, and a large insert with normal orientation paints red, the classic deletion. It is usually the most informative single setting for a first scan. ### Read arcs **Read connections → Show read arcs** draws a bezier between the ends of each pair, in the color of the scheme in force. Concordant pairs make short local arcs, so a deletion reads as a bundle of long red arcs standing on the same two breakpoints, and a mate on another chromosome draws as a vertical line at the breakpoint. Reads describing the same connection draw as one arc thickened by how many there are, so the arcs count the support as well as locate it. [](https://jbrowse.org/jb2/docs/tutorials/k562_fusions) counts a fusion's support that way.
Hover any arc for its classification. A read can have a grey LR fill and still carry a colored arc: the read itself crosses the breakpoint, splits into a primary and a strand-flipped supplementary alignment, and the arc joining those takes the magenta split-read color. That is evidence from one molecule rather than from a pair. ### SV channels Every scheme above paints one pileup, so an event's evidence arrives mixed into the rows around it. **Read connections → SV channels (pairs by orientation)** takes the same reads apart: each orientation class becomes its own band with its own coverage curve and its own arcs, the concordant pairs drop out, and the pileup goes away. Which band fills names the rearrangement, and a band that stays empty under a call is a call with no read-pair evidence behind it.
Deletion Tandem duplication Inversion LR → ← RL ← → LL → → RR ← ←
Which band each SV type fills. A deletion is ordinary-facing pairs that are too far apart, a tandem duplication lights the outward-pointing band, and an inversion lights the two same-strand bands, each holding one junction.
Clicking the row again restores the pileup, with the color scheme untouched. [](https://jbrowse.org/jb2/docs/tutorials/sv_multisamples) reads a complex 1000 Genomes call band by band. ### Read cloud [Read cloud](https://jbrowse.org/jb2/docs/user_guides/alignments_track#read-cloud) lays pairs out on the Y axis by the log distance between mates, so the insertion pairs lift clear of the background and how many reads span a breakpoint is countable. Chains with supplementary alignments are joined by an orange line, and **Edit filters** shows or hides proper pairs and singletons.
## Long reads ### Split reads A long read spans the whole event, so it carries what a short-read pair could only infer. At an inversion it splits into three alignments, the middle one on the opposite strand. With **View as pairs / link supplementary alignments** on, those segments chain onto one row: the inverted middle paints in the reverse-strand color between two forward-strand segments, and a magenta arc joins the two breakpoints. **Group by → Split read (SA tag)** puts the reads carrying a supplementary alignment in their own section. The two sections together are the genotype: a locus where some reads invert and the rest run through unbroken is one inverted copy and one uninverted, read off the pileup rather than from the caller's `GT`.
### One read against the reference Right-click any read for **Linear read vs ref** or **Dotplot of read vs ref**, which lay one read out against every locus it touches. On a read spanning a breakpoint, the order it visits those loci in is the structure of the rearrangement. See [one read against the reference](https://jbrowse.org/jb2/docs/user_guides/alignments_track#one-read-against-the-reference).
### Reconstructing a derivative allele Where several long reads cross the same junctions in the same order, **Launch → Reconstruct derivative allele...** groups them by route and draws the allele the chosen route describes. What it needs, how to judge its list and how far its recall reaches are in [](https://jbrowse.org/jb2/docs/user_guides/derivative_allele). ## Signatures by SV type | SV type | Read pairs | Coverage | Clipping and arcs | | ------------------ | ------------------------------------------ | -------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------- | | Deletion | red, insert larger than expected | drops between the breakpoints, halves for a heterozygote | clipped reads at both edges, unusually long arcs | | Insertion | pink, insert smaller than expected | unchanged | clipped reads at one site, a purple insertion indicator, mates unmapped once the insertion outruns the fragment | | Inversion | green LL and dark blue RR at the junctions | unchanged | clipped reads at both breakpoints, magenta split-read arcs | | Tandem duplication | teal RL | elevated over the duplicated segment | arcs pointing back upstream across the junction | | Translocation | rust, mate on another chromosome | unchanged | a cluster of rust reads at one end, arcs drawn as verticals at the view edge | Any one column has artifacts that produce it, and in segmental duplications and repeats all of them are common, so combine several before calling. Zoomed inside an inverted segment the interior reads look concordant, so the junctions are where to look. The clipped bases at an inversion breakpoint often carry the short homology the junction formed on. For a translocation, open the [breakpoint split view](#breakpoint-split-view) to see both ends at once. ## Breakpoint split view The breakpoint split view opens synchronized panels side by side, each centered on one breakpoint locus. Splines connect the reads that span the junction across the panels, and the variant call is drawn as a colored line with feet indicating directionality. The header bar accepts location searches in either panel.
Hovering a spline shades the reads it joins, every segment of the read in every panel it visits, and every other spline of the same read thickens alongside it. Untick **Show... → Allow clicking alignment squiggles** to turn the overlay back into a static picture. ### Launching it - **From the SV inspector**: click a feature in the circular overview, or the triangle dropdown on a table row. See the [SV inspector guide](https://jbrowse.org/jb2/docs/user_guides/sv_inspector_view). - **From variant feature details**: click a BND or TRA variant in a variant track. The feature details panel has a button to open the split view, which loads any open alignments tracks. - **From alignment feature details**: click a read with a supplementary alignment, for a split view centered on that read and its supplementary partner. - **From the circular genome view**: click a chord and use the "Open breakpoints in split view" link in its Breakends section.
### Multi-hop events A read with several supplementary alignments visits more than two loci, and the view grows a panel per locus. [](https://jbrowse.org/jb2/docs/tutorials/cancer_sv) follows one such chain across three chromosomes.
### Following a chain of breakends A BND record names one partner, so a launch from one record is two loci however many the rearrangement has. **Follow further breakends at each end** reaches the rest from the callset: at each end of the chain it looks for another junction leaving from within a kilobase of the same place, and takes it when there is exactly one, adding a panel per hop up to four. It is offered by the two launches that can read the callset, a variant track's right-click menu and a click on a chord drawn from that same file, and only for the stacked shape.
The walk treats two junctions leaving one locus as one molecule, which the caller does not assert, so it stops where that would be a guess: two open continuations at a locus, or a continuation leading back to a locus already on screen. To work from the reads themselves instead, use [Reconstruct derivative allele](https://jbrowse.org/jb2/docs/user_guides/derivative_allele), which ranks whole routes by how many molecules independently take each. ## Phasing heterozygous SVs For a heterozygous SV, the supporting reads all coming from one haplotype is strong evidence for the call. Where the BAM/CRAM has been haplotagged (WhatsHap, HiPhase), reads carry an `HP` tag, and sorting, coloring or [grouping](https://jbrowse.org/jb2/docs/user_guides/alignments_track#grouping-reads) by it from the track menu clusters each haplotype. Grouping goes furthest, giving each haplotype its own pileup section with untagged reads collected in their own, so unphased support stays visible. The [phased trio tutorial](https://jbrowse.org/jb2/docs/tutorials/analyze_trio) covers phased haplotypes end to end.
## Working with large SVs The pileup, read arcs and read cloud only render once the view is zoomed in far enough to load the reads, and a very large SV cannot be spanned in one pileup. For large or inter-chromosomal SVs: - Survey the region with a BigWig coverage track, or a [multi-quantitative track](https://jbrowse.org/jb2/docs/user_guides/multiquantitative_track) for tumor vs normal. It loads at any scale and makes copy-number changes visible at chromosome scale. - Load the call set as a variant track for a compact overview, where clicking a feature navigates to it. - Open the breakpoint split view for the breakpoint loci themselves. Each panel is a local window around one end, so the distance between them does not matter. - Use the SV inspector for whole-genome triage before drilling in.
## Whole-genome assembly comparison Where a de novo assembly of the sample is available, aligning it back to the reference with [minimap2](https://github.com/lh3/minimap2) and loading the PAF as a [synteny track](https://jbrowse.org/jb2/docs/tutorials/synteny_visualization) gives a chromosome-scale view of the rearrangements. Complex events appear as off-diagonal blocks in the [dotplot view](https://jbrowse.org/jb2/docs/user_guides/dotplot_view), and dragging over one launches a base-level [linear synteny view](https://jbrowse.org/jb2/docs/user_guides/linear_synteny_view) on the same alignment. The [C-GIAB tutorial](https://jbrowse.org/jb2/docs/tutorials/sv_visualization_cgiab) walks this through with the HG008 phased tumor assembly. ## Summary | Display / setting | How to enable | Best for | | ----------------------------- | ------------------------------- | -------------------------------------------------- | | Pileup (default) | Default lower panel | Base-level detail, individual reads | | Color by pair orientation | Color by in track menu | Abnormal orientation patterns (RL/LL/RR) | | Color by insert size | Color by in track menu | Insert size anomalies (pileup) | | Read arcs | Read connections in track menu | Overview of long-range connections | | SV channels | Read connections in track menu | One band per orientation class, with arcs | | Read cloud | Read connections in track menu | Counting discordant pairs, orientation per read | | Linear read vs ref | Right-click on any read | Complex alignment of a single long read | | Reconstruct derivative allele | Launch in the track menu | The route several long reads agree on | | Breakpoint split view | Feature details or SV inspector | Side-by-side inspection of both breakpoint loci | | Group by HP tag | Group by in track menu | Confirming heterozygous SVs on one haplotype | | Dotplot view | Launch from the Add menu | Chromosome-scale rearrangements (de novo assembly) | | Linear synteny view | Add menu or dotplot selection | Base-level alignment between two genomes | ## See also - [](https://jbrowse.org/jb2/docs/user_guides/alignments_track) - [](https://jbrowse.org/jb2/docs/user_guides/derivative_allele) - [SV inspector](https://jbrowse.org/jb2/docs/user_guides/sv_inspector_view) - [](https://jbrowse.org/jb2/docs/user_guides/circular_view) - [](https://jbrowse.org/jb2/docs/user_guides/variant_track) - [Alignments track configuration](https://jbrowse.org/jb2/docs/config_guides/alignments_track) - [Gallery: structural variant examples](https://jbrowse.org/jb2/gallery/#sv) [^mad]: The band is `median ± 3·1.4826·MAD` rather than `mean ± 3σ`, because the long right tail of large inserts inflates the standard deviation and pushes a `mean − 3σ` lower bound below zero, where no short insert is ever flagged.