diff --git a/bwamem_pair.c b/bwamem_pair.c
index 9325abe2..a85c28a6 100644
--- a/bwamem_pair.c
+++ b/bwamem_pair.c
@@ -334,12 +334,12 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
 		for (i = 0; i < 2; ++i) {
 			h[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, &a[i].a[z[i]]);
 			h[i].mapq = q_se[i];
-			h[i].flag |= 0x40 | extra_flag;
+			h[i].flag |= 0x40<<i | extra_flag;
 			h[i].XA = XA[i]? XA[i][z[i]] : 0;
 			aa[i][n_aa[i]++] = h[i];
 			if (n_pri[i] < a[i].n) { // the read has ALT hits
 				g[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, &a[i].a[n_pri[i]]);
-				g[i].flag |= 0x40 | extra_flag;
+				g[i].flag |= 0x40<<i | extra_flag;
 				g[i].XA = XA[i]? XA[i][n_pri[i]] : 0;
 				aa[i][n_aa[i]++] = g[i];
 			}
diff --git a/main.c b/main.c
index c34328ed..7a41b655 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.11-r1036-dirty"
+#define PACKAGE_VERSION "0.7.11-r1037-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);