diff --git a/src/assembler/assembleresult.cpp b/src/assembler/assembleresult.cpp
index 078741d4..18435e2a 100644
--- a/src/assembler/assembleresult.cpp
+++ b/src/assembler/assembleresult.cpp
@@ -66,7 +66,8 @@ inline char* getRevFragment(const char* fragment, size_t fragLen, NucleotideMatr
     char *fragmentRev = new char[fragLen];
     for (int pos = fragLen - 1; pos > -1; pos--) {
         int res = nuclMatrix->aa2int[static_cast<int>(fragment[pos])];
-        fragmentRev[(fragLen - 1) - pos] = nuclMatrix->int2aa[nuclMatrix->reverseResidue(res)];
+        char revRes = nuclMatrix->int2aa[nuclMatrix->reverseResidue(res)];
+        fragmentRev[(fragLen - 1) - pos] = (revRes == 'X')? 'N' : revRes;
     }
     return fragmentRev;
 }
@@ -133,8 +134,8 @@ int doassembly(LocalParameters &par) {
                 NucleotideMatrix *nuclMatrix = (NucleotideMatrix *) subMat;
                 for (int pos = querySeqLen - 1; pos > -1; pos--) {
                     int res = subMat->aa2int[static_cast<int>(querySeq[pos])];
-                    res = (res == 'X')? 'N' : res;
-                    queryRevSeq[(querySeqLen - 1) - pos] = subMat->int2aa[nuclMatrix->reverseResidue(res)];
+                    char revRes = subMat->int2aa[nuclMatrix->reverseResidue(res)];
+                    queryRevSeq[(querySeqLen - 1) - pos] = (revRes == 'X')? 'N' : revRes;
                 }
                 queryRev = std::string(queryRevSeq,querySeqLen);