diff --git a/misc-scripts/surgery/SeqStoreConverter/PanTroglodytes.pm b/misc-scripts/surgery/SeqStoreConverter/PanTroglodytes.pm
index 4e3b02d211b6b92259fe1f059e2f8d40214302cf..910aa16fb527e36540b2e92ac3f7a0284419d3dd 100644
--- a/misc-scripts/surgery/SeqStoreConverter/PanTroglodytes.pm
+++ b/misc-scripts/surgery/SeqStoreConverter/PanTroglodytes.pm
@@ -37,7 +37,7 @@ sub create_coord_systems {
             qtl_feature           => 'scaffold',
             misc_feature          => 'scaffold',
             prediction_transcript => 'contig',
-            karyotype             => 'chromosome');
+            karyotype             => 'scaffold');
 
   $self->debug("Building coord_system table");