diff --git a/hit.c b/hit.c
index d221ce6..dddba12 100644
--- a/hit.c
+++ b/hit.c
@@ -177,13 +177,14 @@ void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs) // keep mm_reg1_t::{id,
 	mm_set_sam_pri(n_regs, regs);
 }
 
-void mm_select_sub(void *km, float mask_level, float pri_ratio, int best_n, int *n_, mm_reg1_t *r)
+void mm_select_sub(void *km, float mask_level, float pri_ratio, int min_diff, int best_n, int *n_, mm_reg1_t *r)
 {
 	if (pri_ratio > 0.0f && *n_ > 0) {
 		int i, k, n = *n_, n_2nd = 0;
 		for (i = k = 0; i < n; ++i)
 			if (r[i].parent == i) r[k++] = r[i];
-			else if (r[i].score >= r[r[i].parent].score * pri_ratio && n_2nd++ < best_n) r[k++] = r[i];
+			else if ((r[i].score >= r[r[i].parent].score * pri_ratio || r[i].score + min_diff >= r[r[i].parent].score) && n_2nd++ < best_n)
+				r[k++] = r[i];
 			else if (r[i].p) free(r[i].p);
 		if (k != n) mm_sync_regs(km, k, r); // removing hits requires sync()
 		*n_ = k;
diff --git a/main.c b/main.c
index 9797c1b..2ee1a36 100644
--- a/main.c
+++ b/main.c
@@ -8,7 +8,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0-r202-dirty"
+#define MM_VERSION "2.0-r203-dirty"
 
 void liftrlimit()
 {
diff --git a/map.c b/map.c
index 81f7db8..cad4dd6 100644
--- a/map.c
+++ b/map.c
@@ -244,14 +244,14 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
 	*n_regs = n_u;
 	if (!(opt->flag & MM_F_AVA)) { // don't choose primary mapping(s) for read overlap
 		mm_set_parent(b->km, opt->mask_level, *n_regs, regs);
-		mm_select_sub(b->km, opt->mask_level, opt->pri_ratio, opt->best_n, n_regs, regs);
+		mm_select_sub(b->km, opt->mask_level, opt->pri_ratio, mi->k*2, opt->best_n, n_regs, regs);
 		mm_join_long(b->km, opt, qlen, n_regs, regs, a); // TODO: this can be applied to all-vs-all in principle
 	}
 	if (opt->flag & MM_F_CIGAR) {
 		regs = mm_align_skeleton(b->km, opt, mi, qlen, seq, n_regs, regs, a); // this calls mm_filter_regs()
 		if (!(opt->flag & MM_F_AVA)) {
 			mm_set_parent(b->km, opt->mask_level, *n_regs, regs);
-			mm_select_sub(b->km, opt->mask_level, opt->pri_ratio, opt->best_n, n_regs, regs);
+			mm_select_sub(b->km, opt->mask_level, opt->pri_ratio, mi->k*2, opt->best_n, n_regs, regs);
 			mm_set_sam_pri(*n_regs, regs);
 		}
 	}
diff --git a/mmpriv.h b/mmpriv.h
index 242c799..35ffa1c 100644
--- a/mmpriv.h
+++ b/mmpriv.h
@@ -45,7 +45,7 @@ void mm_split_reg(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *a);
 void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs);
 int mm_set_sam_pri(int n, mm_reg1_t *r);
 void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r);
-void mm_select_sub(void *km, float mask_level, float pri_ratio, int best_n, int *n_, mm_reg1_t *r);
+void mm_select_sub(void *km, float mask_level, float pri_ratio, int min_diff, int best_n, int *n_, mm_reg1_t *r);
 void mm_filter_regs(void *km, const mm_mapopt_t *opt, int *n_regs, mm_reg1_t *regs);
 void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs, mm_reg1_t *regs, mm128_t *a);
 void mm_hit_sort_by_dp(void *km, int *n_regs, mm_reg1_t *r);