> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/illumina-trupath-genome/data-visualizations-and-analysis/visualize-data-in-platform-core/how-to-use-colocation-maps.md). # How to Use Colocation Maps This page provides a tutorial for understanding colocation plots and how structural variant events are represented along the map. ## Colocation Signatures for Structural Rearrangements {% @storylane/embed subdomain="illumina-informatics" url="" linkValue="gvn33adxbo8a" %} TruPath proximity-mapped reads retain long-range linkage from the original DNA molecule. When a rearrangement joins reference segments that were previously distant — or reverses their order — proximal templates that span the new junctions produce off-diagonal contact in the colocation map.

The instructions below pairs each event’s chromosome structure and proximal templates (left) with the matching signature in reference coordinates (right). Use it as a visual catalog when reviewing Genome Viewer, HiGlass, or static colocation plots. How to read the figure below: * Caption — Illustrative maps of rearranged chromosomes only (not to scale). Colored triangles mark junctions; segment ends are 1 (start) and 2 (end). Intensity runs low (yellow) to high (dark). * Left — Allele structure vs reference, with proximal templates (≈5–20 kbp) spanning each novel junction. * Right — The same event as a contact map in reference coordinates; off-diagonal triangles are the new junctions. * Triangle tip — Approximate breakpoint (\~2 kb). Confirm exact breakpoints in BAM and SV tracks.\ Corroborate — Use colocation for structure/orientation, CNV/coverage for dosage, and BAM/SV for base-level calls.

### a. Inversion

**What changed:** A middle segment (B) is reversed relative to the flanking segments (A and C). Order becomes A → inverted B → C. **Novel junctions** * A2–B2 — End of A joins the (now adjacent) end of inverted B * B1–C1 — Start of inverted B joins the start of C **What you see on the map:** Two off-diagonal triangles whose tips mark the inversion breakpoints — the classic bow-tie (or X) pattern. Small inversions sit close to the diagonal; larger ones pull the bow-tie farther off-diagonal. **Dosage:** A balanced inversion shows little or no copy-number change across the interval. Confirm on the CNV track. Unbalanced inversions can add loss or gain at the distal ends. *** ### b. Balanced translocation

**What changed:** Segments are exchanged between two chromosomes. In the schematic, Chr 1 (A–B) and Chr 2 (C–D) form reciprocal derivatives: der(1) = A–D and der(2) = C–B. **Novel junctions** * A2–D1 — End of A joins start of D * C2–B1 — End of C joins start of B **What you see on the map:** Two reciprocal off-diagonal signals with tips that point toward each other — one for each derivative junction. The contacts are inter-chromosomal when the partners are on different chromosomes. **Dosage:** No net copy-number change if the exchange is balanced. Confirm diploid dosage on CNV across both partners. An unbalanced translocation typically shows a single off-diagonal signal plus dosage change (one flank gained, the other lost). *** ### c. Ring chromosome

**What changed:** A retained interval (A–B–C) circularizes: the end of the interval joins its start. Distal arms (P and Q in the schematic) are lost. **Novel junctions** * C2–A1 — End of the retained region joins its start (wraparound contact) **What you see on the map:** Diagonal signal across the retained A–B–C region, with an off-diagonal triangle joining the last bins of the interval to the first. Lost flanks (P, Q) appear as gaps or absent signal. Look at the ends of the chromosome or retained segment — not mid-diagonal. **Dosage:** Unbalanced rings often show deletions at the breakpoints; check CNV at both ends of the retained region. *** ### d. Tandem duplication

**What changed:** Segment B is copied in place, producing A–B–B–C. **Novel junctions** * B2–B1 — End of the first copy of B joins the start of the second copy **What you see on the map:** Increased proximity within the duplicated interval (darker on-diagonal signal). The B2–B1 junction appears as an off-diagonal triangle; larger tandem duplications stretch into a triangular signal that loops back on itself. **Dosage:** Copy number is elevated across the duplicated segment — opposite of a deletion. Confirm gain on the CNV track. *** ### e. Deletion

**What changed:** Segment B is lost; flanks A and C are joined directly (A–C). Heterozygous: paler diagonal across B with flank-joining signal. Homozygous: clearer gap on the diagonal over B, with signal at the boundaries. **Novel junctions** * A2–C1 — End of A joins start of C **What you see on the map:** Reduced or missing diagonal signal across deleted segment B, plus an off-diagonal triangle at A2–C1 joining the two flanks. **Dosage:** Copy number is reduced across B. Confirm on CNV / coverage before trusting a faint off-diagonal alone. *** ### Quick Reference | Pattern | Junctions | Colocation signature | Typical dosage | | ---------------------- | --------------- | -------------------------------------- | ------------------------- | | Inversion | A2–B2 and B1–C1 | Bow-tie / two off-diagonal triangles | Unchanged if balanced | | Balanced translocation | A2–D1 and C2–B1 | Two reciprocal off-diagonal signals | Unchanged | | Ring chromosome | C2–A1 | Wraparound contact (end ↔ start) | Often loss at distal arms | | Tandem duplication | B2–B1 | Darker interval + loop-back triangle | Gain across B | | Deletion | A2–C1 | Pale/gap on B + flank-joining triangle | Loss across B | --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation by asking a question. Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters: ``` GET https://help.bioinsight.illumina.com/illumina-trupath-genome/data-visualizations-and-analysis/visualize-data-in-platform-core/how-to-use-colocation-maps.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.