diff --git a/bwamem.c b/bwamem.c
index 6f36128..a7e7150 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -514,7 +514,8 @@ static void mem_mark_primary_se_core(const mem_opt_t *opt, int n, mem_alnreg_t *
 				int min_l = a[i].qe - a[i].qb < a[j].qe - a[j].qb? a[i].qe - a[i].qb : a[j].qe - a[j].qb;
 				if (e_min - b_max >= min_l * opt->mask_level) { // significant overlap
 					if (a[j].sub == 0) a[j].sub = a[i].score;
-					if (a[j].score - a[i].score <= tmp) ++a[j].sub_n;
+					if (a[j].score - a[i].score <= tmp && (a[j].is_alt || !a[i].is_alt))
+						++a[j].sub_n;
 					break;
 				}
 			}
diff --git a/main.c b/main.c
index 59c659e..a7ad841 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.10-r941-dirty"
+#define PACKAGE_VERSION "0.7.10-r942-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);