diff --git a/hit.c b/hit.c
index e1bb3b9..4d98847 100644
--- a/hit.c
+++ b/hit.c
@@ -203,7 +203,7 @@ void mm_filter_regs(void *km, const mm_mapopt_t *opt, int *n_regs, mm_reg1_t *re
 	for (i = k = 0; i < *n_regs; ++i) {
 		mm_reg1_t *r = &regs[i];
 		int flt = 0;
-		if (!r->inv && r->cnt < opt->min_cnt) flt = 1;
+		if (!r->inv && !r->seg_split && r->cnt < opt->min_cnt) flt = 1;
 		if (r->p) {
 			if (r->p->blen - r->p->n_ambi - r->p->n_diff < opt->min_chain_score) flt = 1;
 			else if (r->p->dp_max < opt->min_dp_max) flt = 1;
@@ -342,6 +342,8 @@ mm_seg_t *mm_seg_gen(void *km, int n_segs, const int *qlens, int n_regs0, const
 	for (s = 0; s < n_segs; ++s) {
 		regs[s] = mm_gen_regs(km, qlens[s], seg[s].n_u, seg[s].u, seg[s].a);
 		n_regs[s] = seg[s].n_u;
+		for (i = 0; i < n_regs[s]; ++i)
+			regs[s][i].seg_split = 1;
 	}
 	return seg;
 }
diff --git a/main.c b/main.c
index 89b2c47..014c57b 100644
--- a/main.c
+++ b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.2-r442-dirty"
+#define MM_VERSION "2.2-r443-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
diff --git a/map.c b/map.c
index 1568675..10e5054 100644
--- a/map.c
+++ b/map.c
@@ -234,7 +234,7 @@ static void chain_post(const mm_mapopt_t *opt, const mm_idx_t *mi, void *km, int
 	if (!(opt->flag & MM_F_AVA)) { // don't choose primary mapping(s) for read overlap
 		mm_set_parent(km, opt->mask_level, *n_regs, regs, opt->a * 2 + opt->b);
 		if (n_segs <= 1) mm_select_sub(km, opt->pri_ratio, mi->k*2, opt->best_n, n_regs, regs);
-		else mm_select_sub_multi(km, opt->pri_ratio, 0.2f, 0.7f, opt->max_gap_ref, mi->k*2, opt->best_n, n_segs, qlens, n_regs, regs);
+		else mm_select_sub_multi(km, opt->pri_ratio, 0.2f, 0.7f, opt->max_gap_ref, mi->k*2, opt->best_n * n_segs, n_segs, qlens, n_regs, regs);
 		if (!(opt->flag & MM_F_SPLICE) && !(opt->flag & MM_F_SR))
 			mm_join_long(km, opt, qlen, n_regs, regs, a); // TODO: this can be applied to all-vs-all in principle
 	}
diff --git a/minimap.h b/minimap.h
index 742a4a7..4d7f393 100644
--- a/minimap.h
+++ b/minimap.h
@@ -61,7 +61,7 @@ typedef struct {
 
 typedef struct {
 	int32_t id;                     // ID for internal uses (see also parent below)
-	uint32_t cnt:31, rev:1;         // number of minimizers; if on the reverse strand
+	uint32_t cnt:30, rev:1, seg_split:1; // number of minimizers; if on the reverse strand
 	uint32_t rid:31, inv:1;         // reference index; if this is an alignment from inversion rescue
 	int32_t score;                  // DP alignment score
 	int32_t qs, qe, rs, re;         // query start and end; reference start and end