diff --git a/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.ts b/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.ts
index 4fbb87aace..47d97bdcbe 100644
--- a/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.ts
+++ b/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.ts
@@ -81,8 +81,9 @@ export default class PAFAdapter extends BaseFeatureDataAdapter {
     return ObservableCreate<Feature>(async observer => {
       const { assemblyName } = query
 
-      const idx = this.getAssemblyNames().indexOf(assemblyName)
-      const flip = idx === 1
+      const assemblyNames = this.getAssemblyNames()
+      const index = assemblyNames.indexOf(assemblyName)
+      const flip = index === 0
       const letter = flip ? 't' : 'q'
 
       await this.paf.getLines(letter + query.refName, query.start, query.end, {
@@ -117,7 +118,7 @@ export default class PAFAdapter extends BaseFeatureDataAdapter {
                 start: mateStart,
                 end: mateEnd,
                 refName: mateName,
-                assemblyName,
+                assemblyName: assemblyNames[+flip],
               },
             }),
           )
diff --git a/plugins/comparative-adapters/src/PAFAdapter/util.test.ts b/plugins/comparative-adapters/src/util.test.ts
similarity index 100%
rename from plugins/comparative-adapters/src/PAFAdapter/util.test.ts
rename to plugins/comparative-adapters/src/util.test.ts