diff --git a/packages/core/pluggableElementTypes/renderers/BoxRendererType.ts b/packages/core/pluggableElementTypes/renderers/BoxRendererType.ts
index a970827b52..47ceb7468f 100644
--- a/packages/core/pluggableElementTypes/renderers/BoxRendererType.ts
+++ b/packages/core/pluggableElementTypes/renderers/BoxRendererType.ts
@@ -189,16 +189,16 @@ export default class BoxRendererType extends FeatureRendererType {
       args,
     ) as ResultsSerialized
 
-    return {
-      ...serialized,
-      layout: results.layout.serializeRegion(
-        this.getExpandedRegion(args.regions[0]!, args),
-      ),
-      maxHeightReached: serialized.layout.maxHeightReached,
-      features: serialized.features.filter(
-        f => !!serialized.layout.rectangles[f.uniqueId],
-      ),
-    }
+    const region = args.regions[0]!
+    serialized.layout = results.layout.serializeRegion(
+      this.getExpandedRegion(region, args),
+    )
+    serialized.features = serialized.features.filter(f => {
+      return Boolean(serialized.layout.rectangles[f.uniqueId])
+    })
+
+    serialized.maxHeightReached = serialized.layout.maxHeightReached
+    return serialized
   }
 
   /**
diff --git a/packages/core/pluggableElementTypes/renderers/ServerSideRendererType.tsx b/packages/core/pluggableElementTypes/renderers/ServerSideRendererType.tsx
index f436d1b9a1..6ce8897b15 100644
--- a/packages/core/pluggableElementTypes/renderers/ServerSideRendererType.tsx
+++ b/packages/core/pluggableElementTypes/renderers/ServerSideRendererType.tsx
@@ -87,26 +87,34 @@ export default class ServerSideRenderer extends RendererType {
    * @param results - the results of the render
    * @param args - the arguments passed to render
    */
-  deserializeResultsInClient(res: ResultsSerialized, args: RenderArgs) {
-    // if we are rendering svg, we skip hydration and check if rendere support
-    // SVG (e.g. this.supportsSVG) and then return just the HTML if so
-    return args.exportSVG
-      ? {
-          ...res,
-          html: this.supportsSVG
-            ? res.html
-            : '<text y="12" fill="black">SVG export not supported for this track</text>',
-        }
-      : {
-          ...res,
-          reactElement: (
-            <ServerSideRenderedContent
-              {...args}
-              {...res}
-              RenderingComponent={this.ReactComponent}
-            />
-          ),
-        }
+  deserializeResultsInClient(
+    res: ResultsSerialized,
+    args: RenderArgs,
+  ): ResultsDeserialized {
+    // if we are rendering svg, we skip hydration
+    if (args.exportSVG) {
+      // only return the res if the renderer explicitly has
+      // this.supportsSVG support to avoid garbage being rendered in SVG
+      // document
+      return {
+        ...res,
+        html: this.supportsSVG
+          ? res.html
+          : '<text y="12" fill="black">SVG export not supported for this track</text>',
+      }
+    }
+
+    // get res using ServerSideRenderedContent
+    return {
+      ...res,
+      reactElement: (
+        <ServerSideRenderedContent
+          {...args}
+          {...res}
+          RenderingComponent={this.ReactComponent}
+        />
+      ),
+    }
   }
 
   /**
@@ -115,17 +123,18 @@ export default class ServerSideRenderer extends RendererType {
    *
    * @param args - the converted arguments to modify
    */
-  deserializeArgsInWorker(args: RenderArgsSerialized) {
-    console.log('deserializeArgsInWorker', { args })
-    return {
-      ...args,
-      config: this.configSchema.create(args.config || {}, {
-        pluginManager: this.pluginManager,
-      }),
-      filters: args.filters
-        ? new SerializableFilterChain({ filters: args.filters })
-        : undefined,
-    }
+  deserializeArgsInWorker(args: RenderArgsSerialized): RenderArgsDeserialized {
+    const deserialized = { ...args } as unknown as RenderArgsDeserialized
+    deserialized.config = this.configSchema.create(args.config || {}, {
+      pluginManager: this.pluginManager,
+    })
+    deserialized.filters = args.filters
+      ? new SerializableFilterChain({
+          filters: args.filters,
+        })
+      : undefined
+
+    return deserialized
   }
 
   /**
@@ -206,4 +215,4 @@ export default class ServerSideRenderer extends RendererType {
   }
 }
 
-export type { RenderResults } from './RendererType'
+export { type RenderResults } from './RendererType'
diff --git a/plugins/breakpoint-split-view/src/BreakpointAlignmentsFeatureDetail/BreakpointAlignmentsFeatureDetail.tsx b/plugins/breakpoint-split-view/src/BreakpointAlignmentsFeatureDetail/BreakpointAlignmentsFeatureDetail.tsx
index e502e5c21c..dee96293b6 100644
--- a/plugins/breakpoint-split-view/src/BreakpointAlignmentsFeatureDetail/BreakpointAlignmentsFeatureDetail.tsx
+++ b/plugins/breakpoint-split-view/src/BreakpointAlignmentsFeatureDetail/BreakpointAlignmentsFeatureDetail.tsx
@@ -6,15 +6,22 @@ import {
 } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'
 import { Paper } from '@mui/material'
 import { observer } from 'mobx-react'
+import { SimpleFeatureSerialized } from '@jbrowse/core/util'
 
 const BreakpointAlignmentsFeatureDetail = observer(function ({
   model,
 }: {
-  model: { featureData: Record<string, unknown> }
+  model: {
+    featureData: {
+      feature1: SimpleFeatureSerialized
+      feature2: SimpleFeatureSerialized
+    }
+  }
 }) {
-  const { feature1, feature2 } = JSON.parse(JSON.stringify(model.featureData))
+  const { featureData } = model
+  const { feature1, feature2 } = structuredClone(featureData)
   return (
-    <Paper data-testid="alignment-side-drawer">
+    <Paper>
       <BaseCoreDetails title="Feature 1" feature={feature1} />
       <BaseCoreDetails title="Feature 2" feature={feature2} />
       <BaseAttributes title="Feature 1 attributes" feature={feature1} />
diff --git a/plugins/linear-comparative-view/src/SyntenyFeatureDetail/SyntenyFeatureDetail.tsx b/plugins/linear-comparative-view/src/SyntenyFeatureDetail/SyntenyFeatureDetail.tsx
index 83b74a0ba7..f05e47a462 100644
--- a/plugins/linear-comparative-view/src/SyntenyFeatureDetail/SyntenyFeatureDetail.tsx
+++ b/plugins/linear-comparative-view/src/SyntenyFeatureDetail/SyntenyFeatureDetail.tsx
@@ -114,7 +114,7 @@ const SyntenyFeatureDetail = observer(function ({
   model: SyntenyFeatureDetailModel
 }) {
   return (
-    <Paper data-testid="alignment-side-drawer">
+    <Paper>
       <BaseFeatureDetail title="Feature" model={model} />
       <BaseCard title="Link to view">
         <CustomLinker model={model} />
diff --git a/plugins/variants/src/MultiLinearVariantDisplay/model.ts b/plugins/variants/src/MultiLinearVariantDisplay/model.ts
index 21905b76aa..1bf5d02bd9 100644
--- a/plugins/variants/src/MultiLinearVariantDisplay/model.ts
+++ b/plugins/variants/src/MultiLinearVariantDisplay/model.ts
@@ -22,9 +22,7 @@ import type { Instance } from 'mobx-state-tree'
 // lazies
 const Tooltip = lazy(() => import('../shared/Tooltip'))
 const SetColorDialog = lazy(() => import('../shared/SetColorDialog'))
-const HierarchicalClusterDialog = lazy(
-  () => import('../shared/HierarchicalClusterDialog'),
-)
+const ClusterDialog = lazy(() => import('../shared/ClusterDialog'))
 
 // using a map because it preserves order
 const rendererTypes = new Map([['multivariant', 'MultiVariantRenderer']])
@@ -263,7 +261,7 @@ export function stateModelFactory(
               label: 'Cluster by genotype',
               onClick: () => {
                 getSession(self).queueDialog(handleClose => [
-                  HierarchicalClusterDialog,
+                  ClusterDialog,
                   {
                     model: self,
                     handleClose,
diff --git a/plugins/variants/src/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.tsx b/plugins/variants/src/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.tsx
index 94b11871b6..6d4f95d288 100644
--- a/plugins/variants/src/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.tsx
+++ b/plugins/variants/src/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.tsx
@@ -15,6 +15,7 @@ import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 const useStyles = makeStyles()({
   cursor: {
     pointerEvents: 'none',
+    zIndex: 1000,
   },
 })
 
diff --git a/plugins/variants/src/MultiLinearVariantMatrixDisplay/model.ts b/plugins/variants/src/MultiLinearVariantMatrixDisplay/model.ts
index 5fd03bcc20..187b9fc452 100644
--- a/plugins/variants/src/MultiLinearVariantMatrixDisplay/model.ts
+++ b/plugins/variants/src/MultiLinearVariantMatrixDisplay/model.ts
@@ -19,9 +19,7 @@ import type { Instance } from 'mobx-state-tree'
 // lazies
 const SetColorDialog = lazy(() => import('../shared/SetColorDialog'))
 const MAFFilterDialog = lazy(() => import('../shared/MAFFilterDialog'))
-const HierarchicalClusterDialog = lazy(
-  () => import('../shared/HierarchicalClusterDialog'),
-)
+const ClusterDialog = lazy(() => import('../shared/ClusterDialog'))
 
 /**
  * #stateModel LinearVariantMatrixDisplay
@@ -176,7 +174,7 @@ export default function stateModelFactory(
               label: 'Cluster by genotype',
               onClick: () => {
                 getSession(self).queueDialog(handleClose => [
-                  HierarchicalClusterDialog,
+                  ClusterDialog,
                   {
                     model: self,
                     handleClose,
@@ -252,6 +250,21 @@ export default function stateModelFactory(
               }
             }
           })()
+
+          // eslint-disable-next-line @typescript-eslint/no-floating-promises
+          ;(async () => {
+            try {
+              const { getMultiVariantSourcesAutorun } = await import(
+                '../getMultiVariantSourcesAutorun'
+              )
+              getMultiVariantSourcesAutorun(self)
+            } catch (e) {
+              if (isAlive(self)) {
+                console.error(e)
+                getSession(self).notifyError(`${e}`, e)
+              }
+            }
+          })()
         },
 
         /**
diff --git a/plugins/variants/src/MultiLinearVariantMatrixRenderer/components/LinearVariantMatrixRendering.tsx b/plugins/variants/src/MultiLinearVariantMatrixRenderer/components/LinearVariantMatrixRendering.tsx
index ee24e51dfa..d29ee1ef00 100644
--- a/plugins/variants/src/MultiLinearVariantMatrixRenderer/components/LinearVariantMatrixRendering.tsx
+++ b/plugins/variants/src/MultiLinearVariantMatrixRenderer/components/LinearVariantMatrixRendering.tsx
@@ -17,11 +17,11 @@ const LinearVariantMatrixRendering = observer(function (props: {
   regions: Region[]
   bpPerPx: number
   simplifiedFeatures: Feature[]
-  exportSVG: boolean
   onMouseMove?: (event: React.MouseEvent, featureId?: string) => void
 }) {
-  const { exportSVG, simplifiedFeatures, displayModel, width, height } = props
-  const [renderLines, setRenderLines] = useState(exportSVG)
+  const { simplifiedFeatures, displayModel, width, height } = props
+  console.log('Rendering', props.regions)
+  const [renderLines, setRenderLines] = useState(false)
   useEffect(() => {
     setRenderLines(true)
   }, [])
diff --git a/plugins/variants/src/VariantRPC/MultiVariantGetHierarchicalMatrix.ts b/plugins/variants/src/VariantRPC/MultiVariantGetGenotypeMatrix.ts
similarity index 96%
rename from plugins/variants/src/VariantRPC/MultiVariantGetHierarchicalMatrix.ts
rename to plugins/variants/src/VariantRPC/MultiVariantGetGenotypeMatrix.ts
index be0a2a51b1..d0f2ff6e01 100644
--- a/plugins/variants/src/VariantRPC/MultiVariantGetHierarchicalMatrix.ts
+++ b/plugins/variants/src/VariantRPC/MultiVariantGetGenotypeMatrix.ts
@@ -9,8 +9,8 @@ import type { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAda
 import type { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods'
 import type { Feature, Region } from '@jbrowse/core/util'
 
-export class MultiVariantGetHierarchicalMatrix extends RpcMethodType {
-  name = 'MultiVariantGetHierarchicalMatrix'
+export class MultiVariantGetGenotypeMatrix extends RpcMethodType {
+  name = 'MultiVariantGetGenotypeMatrix'
 
   async deserializeArguments(args: any, rpcDriverClassName: string) {
     const l = await super.deserializeArguments(args, rpcDriverClassName)
diff --git a/plugins/variants/src/VariantRPC/MultiVariantGetSimplifiedFeatures.ts b/plugins/variants/src/VariantRPC/MultiVariantGetSimplifiedFeatures.ts
new file mode 100644
index 0000000000..50d43c8c55
--- /dev/null
+++ b/plugins/variants/src/VariantRPC/MultiVariantGetSimplifiedFeatures.ts
@@ -0,0 +1,76 @@
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType'
+import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'
+import { renameRegionsIfNeeded } from '@jbrowse/core/util'
+
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration'
+import type { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods'
+import type { Region } from '@jbrowse/core/util'
+import { toArray } from 'rxjs'
+
+export class MultiVariantGetSimplifiedFeatures extends RpcMethodType {
+  name = 'MultiVariantGetSimplifiedFeatures'
+
+  async deserializeArguments(args: any, rpcDriverClassName: string) {
+    const l = await super.deserializeArguments(args, rpcDriverClassName)
+    return {
+      ...l,
+      filters: args.filters
+        ? new SerializableFilterChain({
+            filters: args.filters,
+          })
+        : undefined,
+    }
+  }
+
+  async serializeArguments(
+    args: RenderArgs & {
+      stopToken?: string
+      statusCallback?: (arg: string) => void
+    },
+    rpcDriverClassName: string,
+  ) {
+    const pm = this.pluginManager
+    const assemblyManager = pm.rootModel?.session?.assemblyManager
+    if (!assemblyManager) {
+      return args
+    }
+
+    const renamedArgs = await renameRegionsIfNeeded(assemblyManager, {
+      ...args,
+      filters: args.filters?.toJSON().filters,
+    })
+
+    return super.serializeArguments(renamedArgs, rpcDriverClassName)
+  }
+
+  async execute(
+    args: {
+      adapterConfig: AnyConfigurationModel
+      stopToken?: string
+      sessionId: string
+      headers?: Record<string, string>
+      regions: Region[]
+      bpPerPx: number
+    },
+    rpcDriverClassName: string,
+  ) {
+    const pm = this.pluginManager
+    const deserializedArgs = await this.deserializeArguments(
+      args,
+      rpcDriverClassName,
+    )
+    const { regions, adapterConfig, sessionId } = deserializedArgs
+    const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig)
+
+    // @ts-expect-error
+    const feats = await firstValuFrom(
+      dataAdapter.getFeatures(regions, deserializedArgs).pipe(toArray()),
+    )
+    return feats.map(f => ({
+      start: f.get('start'),
+      end: f.get('end'),
+      refName: f.get('refName'),
+    }))
+  }
+}
diff --git a/plugins/variants/src/getMultiVariantSourcesAutorun.ts b/plugins/variants/src/getMultiVariantSourcesAutorun.ts
index 65276e67be..7c660a2f1f 100644
--- a/plugins/variants/src/getMultiVariantSourcesAutorun.ts
+++ b/plugins/variants/src/getMultiVariantSourcesAutorun.ts
@@ -42,7 +42,41 @@ export function getMultiVariantSourcesAutorun(self: {
           sessionId,
           'MultiVariantGetSources',
           {
-            regions: view.staticBlocks.contentBlocks,
+            regions: view.dynamicBlocks.contentBlocks,
+            sessionId,
+            adapterConfig,
+          },
+        )) as Source[]
+        if (isAlive(self)) {
+          self.setSources(sources)
+        }
+      } catch (e) {
+        if (!isAbortException(e) && isAlive(self)) {
+          console.error(e)
+          getSession(self).notifyError(`${e}`, e)
+        }
+      }
+    }),
+  )
+
+  addDisposer(
+    self,
+    autorun(async () => {
+      try {
+        const view = getContainingView(self) as LinearGenomeViewModel
+        if (!view.initialized) {
+          return
+        }
+        const { rpcManager } = getSession(self)
+        const { adapterConfig } = self
+        const token = createStopToken()
+        self.setSourcesLoading(token)
+        const sessionId = getRpcSessionId(self)
+        const sources = (await rpcManager.call(
+          sessionId,
+          'MultiVariantGetSimplifiedFeatures',
+          {
+            regions: view.dynamicBlocks.contentBlocks,
             sessionId,
             adapterConfig,
           },
diff --git a/plugins/variants/src/index.ts b/plugins/variants/src/index.ts
index e2295dd3cd..b01eecb32f 100644
--- a/plugins/variants/src/index.ts
+++ b/plugins/variants/src/index.ts
@@ -8,8 +8,9 @@ import LinearVariantMatrixRendererF from './MultiLinearVariantMatrixRenderer'
 import MultiVariantRendererF from './MultiLinearVariantRenderer'
 import StructuralVariantChordRendererF from './StructuralVariantChordRenderer'
 import VariantFeatureWidgetF from './VariantFeatureWidget'
-import { MultiVariantGetHierarchicalMatrix } from './VariantRPC/MultiVariantGetHierarchicalMatrix'
+import { MultiVariantGetGenotypeMatrix } from './VariantRPC/MultiVariantGetGenotypeMatrix'
 import { MultiVariantGetSources } from './VariantRPC/MultiVariantGetSources'
+import { MultiVariantGetSimplifiedFeatures } from './VariantRPC/MultiVariantGetSimplifiedFeatures'
 import VariantTrackF from './VariantTrack'
 import VcfAdapterF from './VcfAdapter'
 import VcfTabixAdapterF from './VcfTabixAdapter'
@@ -36,7 +37,10 @@ export default class VariantsPlugin extends Plugin {
 
     pluginManager.addRpcMethod(() => new MultiVariantGetSources(pluginManager))
     pluginManager.addRpcMethod(
-      () => new MultiVariantGetHierarchicalMatrix(pluginManager),
+      () => new MultiVariantGetGenotypeMatrix(pluginManager),
+    )
+    pluginManager.addRpcMethod(
+      () => new MultiVariantGetSimplifiedFeatures(pluginManager),
     )
   }
 }
diff --git a/plugins/variants/src/shared/HierarchicalClusterDialog.tsx b/plugins/variants/src/shared/ClusterDialog.tsx
similarity index 99%
rename from plugins/variants/src/shared/HierarchicalClusterDialog.tsx
rename to plugins/variants/src/shared/ClusterDialog.tsx
index daf763c046..3c0f4102ec 100644
--- a/plugins/variants/src/shared/HierarchicalClusterDialog.tsx
+++ b/plugins/variants/src/shared/ClusterDialog.tsx
@@ -68,7 +68,7 @@ export default function HierarchicalCluster({
         const sessionId = getRpcSessionId(model)
         const ret = (await rpcManager.call(
           sessionId,
-          'MultiVariantGetHierarchicalMatrix',
+          'MultiVariantGetGenotypeMatrix',
           {
             regions: view.dynamicBlocks.contentBlocks,
             sources,
diff --git a/yarn.lock b/yarn.lock
index 7f0059b2a0..f90a5798ad 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -139,9 +139,9 @@
     tslib "^2.6.2"
 
 "@aws-sdk/client-s3@^3.701.0":
-  version "3.705.0"
-  resolved "https://registry.yarnpkg.com/@aws-sdk/client-s3/-/client-s3-3.705.0.tgz#7a4a4784bd5b3ca3187ff876b771eaf0cbde1c42"
-  integrity sha512-Fm0Cbc4zr0yG0DnNycz7ywlL5tQFdLSb7xCIPfzrxJb3YQiTXWxH5eu61SSsP/Z6RBNRolmRPvst/iNgX0fWvA==
+  version "3.703.0"
+  resolved "https://registry.yarnpkg.com/@aws-sdk/client-s3/-/client-s3-3.703.0.tgz#5ca20c606e13ca751ef972c82bb8ef27095db083"
+  integrity sha512-4TSrIamzASTeRPKXrTLcEwo+viPTuOSGcbXh4HC1R0m/rXwK0BHJ4btJ0Q34nZNF+WzvM+FiemXVjNc8qTAxog==
   dependencies:
     "@aws-crypto/sha1-browser" "5.2.0"
     "@aws-crypto/sha256-browser" "5.2.0"
@@ -8074,9 +8074,9 @@ dotenv-expand@^11.0.3, dotenv-expand@^11.0.6, dotenv-expand@~11.0.6:
     dotenv "^16.4.5"
 
 dotenv@^16.3.1, dotenv@^16.4.5, dotenv@~16.4.5:
-  version "16.4.7"
-  resolved "https://registry.yarnpkg.com/dotenv/-/dotenv-16.4.7.tgz#0e20c5b82950140aa99be360a8a5f52335f53c26"
-  integrity sha512-47qPchRCykZC03FhkYAhrvwU4xDBFIj1QPqaarj6mdM/hgUzfPHcpkHJOn3mJAufFeeAxAzeGsr5X0M4k6fLZQ==
+  version "16.4.6"
+  resolved "https://registry.yarnpkg.com/dotenv/-/dotenv-16.4.6.tgz#fc88e8a664087abf3e19d61e21f7feee1849bbb1"
+  integrity sha512-JhcR/+KIjkkjiU8yEpaB/USlzVi3i5whwOjpIRNGi9svKEXZSe+Qp6IWAjFjv+2GViAoDRCUv/QLNziQxsLqDg==
 
 duplexer@^0.1.1, duplexer@^0.1.2:
   version "0.1.2"
@@ -16370,9 +16370,9 @@ whatwg-url@^11.0.0:
     webidl-conversions "^7.0.0"
 
 whatwg-url@^14.0.0:
-  version "14.1.0"
-  resolved "https://registry.yarnpkg.com/whatwg-url/-/whatwg-url-14.1.0.tgz#fffebec86cc8e6c2a657e50dc606207b870f0ab3"
-  integrity sha512-jlf/foYIKywAt3x/XWKZ/3rz8OSJPiWktjmk891alJUEjiVxKX9LEO92qH3hv4aJ0mN3MWPvGMCy8jQi95xK4w==
+  version "14.0.0"
+  resolved "https://registry.yarnpkg.com/whatwg-url/-/whatwg-url-14.0.0.tgz#00baaa7fd198744910c4b1ef68378f2200e4ceb6"
+  integrity sha512-1lfMEm2IEr7RIV+f4lUNPOqfFL+pO+Xw3fJSqmjX9AbXcXcYOkCe1P6+9VBZB6n94af16NfZf+sSk0JCBZC9aw==
   dependencies:
     tr46 "^5.0.0"
     webidl-conversions "^7.0.0"