diff --git a/tool_data_table_conf.xml.sample b/tool_data_table_conf.xml.sample
index 21709578c3d..f7fb377f1af 100644
--- a/tool_data_table_conf.xml.sample
+++ b/tool_data_table_conf.xml.sample
@@ -1,6 +1,17 @@
 <tables>
+    <!-- Locations of MAF files that have been indexed with bx-python -->    
     <table name="indexed_maf_files">
-        <column_names>name, value, dbkey, species</column_names>
-        <file name="tool-data/maf_index.loc" />
+        <columns>name, value, dbkey, species</columns>
+        <file path="tool-data/maf_index.loc" />
+    </table>
+    <!-- Locations of indexes in the BWA mapper format -->
+    <table name="bwa_indexes">
+        <columns>name, value</columns>
+        <file path="tool-data/bwa_index.loc" />
+    </table>
+    <!-- Locations of indexes in the Bowtie mapper format -->
+    <table name="bowtie_indexes">
+        <columns>name, value</columns>
+        <file path="tool-data/bowtie_indices.loc" />
     </table>
 </tables>