  
  	bool fromAlignTogether;                     // Was this alignment created by aligning both reads together, rather than from some combination of single-end aligners?
  	bool alignedAsPair;                         // Were the reads aligned as a pair, or separately?
-@@ -90,4 +147,4 @@ struct PairedAlignmentResult {
+@@ -90,4 +151,4 @@ struct PairedAlignmentResult {
  
      static int compareByContigAndScore(const void *first, const void *second);      // qsort()-style compare routine
      static int compareByScore(const void *first, const void *second);               // qsort()-style compare routine

+	unsigned secondBestScorePair;
+	double probabilityOfAllCandidates;
+	double probabilityOfBestCandidate;
+	unsigned popularSeedsSkipped;
+	unsigned popularSeedsSkippedPair;
+	_int64 countOfHashTableLookups;

 
     static int compareByContigAndScore(const void *first, const void *second);      // qsort()-style compare routine
     static int compareByScore(const void *first, const void *second);               // qsort()-style compare routine
@@ -81,6 +140,8 @@ struct PairedAlignmentResult {
 	int score[NUM_READS_PER_PAIR];              // score of each end if matched
 
 	int mapq[NUM_READS_PER_PAIR];               // mapping quality of each end, encoded like a Phred score (but as an integer, not ASCII Phred + 33).
