diff --git a/bwamem_pair.c b/bwamem_pair.c
index 6316f6a..51a844b 100644
--- a/bwamem_pair.c
+++ b/bwamem_pair.c
@@ -305,6 +305,12 @@ no_pairing:
 			h[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, &a[i].a[0]);
 		else h[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, 0);
 	}
+	if (h[0].rid == h[1].rid && h[0].rid >= 0) { // if the top hits from the two ends constitute a proper pair, flag it.
+		int64_t dist;
+		int d;
+		d = mem_infer_dir(bns->l_pac, a[0].a[0].rb, a[1].a[0].rb, &dist);
+		if (!pes[d].failed && dist >= pes[d].low && dist <= pes[d].high) extra_flag |= 2;
+	}
 	mem_reg2sam_se(opt, bns, pac, &s[0], &a[0], 0x41|extra_flag, &h[1]);
 	mem_reg2sam_se(opt, bns, pac, &s[1], &a[1], 0x81|extra_flag, &h[0]);
 	free(h[0].cigar); free(h[1].cigar);
diff --git a/main.c b/main.c
index c6d6e29..26e6661 100644
--- a/main.c
+++ b/main.c
@@ -3,7 +3,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.2-r360-beta"
+#define PACKAGE_VERSION "0.7.2-r361-beta"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);