diff --git a/heatitup-complete.cabal b/heatitup-complete.cabal
--- a/heatitup-complete.cabal
+++ b/heatitup-complete.cabal
@@ -1,5 +1,5 @@
 name:                heatitup-complete
-version:             0.5.4.1
+version:             0.5.5.0
 synopsis:            Find and annotate ITDs with assembly or read pair joining.
 description:         Find and annotate ITDs with assembly or read pair joining using suffix trees and characterize the exogenous segments within the spacer using heat diffusion.
 homepage:            http://github.com/GregorySchwartz/heatitup-complete#readme
diff --git a/src/Merge.hs b/src/Merge.hs
--- a/src/Merge.hs
+++ b/src/Merge.hs
@@ -23,6 +23,7 @@
 
 -- Cabal
 import Control.Lens
+import qualified Data.Fasta.Text as F
 import qualified Data.Text as T
 import qualified Data.Text.Read as T
 import Safe
@@ -101,8 +102,12 @@
         xs -> error ("Too many mate pairs (even after supplementary removal) for: " <> show xs)
   where
     posSeq xs = ( either error (Position . fst) . T.decimal $ xs !! 3
-                , Sequence $ xs !! 9
+                , Sequence . revComplCheck (BamRow xs) $ xs !! 9
                 )
+    revComplCheck row fSeq =
+      if checkSamFlag 16 row
+        then (F.fastaSeq . F.revCompl $ F.FastaSequence "" fSeq)
+        else fSeq
     valid x = not (checkSamFlag 2048 x) && not (checkSamFlag 256 x)  -- Make sure not supplementary nor not primary
 
 -- | Merge all mate pairs. Assumes that the lines are sorted by mate pair already