diff --git a/bseq.c b/bseq.c
index 3179fa1..16ead16 100644
--- a/bseq.c
+++ b/bseq.c
@@ -48,6 +48,7 @@ bseq1_t *bseq_read(bseq_file_t *fp, int chunk_size, int *n_)
 		s = &seqs[n];
 		s->name = strdup(ks->name.s);
 		s->seq = strdup(ks->seq.s);
+		s->qual = ks->qual.l? strdup(ks->qual.s) : 0;
 		s->l_seq = ks->seq.l;
 		size += seqs[n++].l_seq;
 		if (size >= chunk_size) break;
diff --git a/bseq.h b/bseq.h
index 0595d98..bb06766 100644
--- a/bseq.h
+++ b/bseq.h
@@ -8,7 +8,7 @@ typedef struct bseq_file_s bseq_file_t;
 
 typedef struct {
 	int l_seq, rid;
-	char *name, *seq;
+	char *name, *seq, *qual;
 } bseq1_t;
 
 bseq_file_t *bseq_open(const char *fn);
diff --git a/format.c b/format.c
index 092aaf4..7690baf 100644
--- a/format.c
+++ b/format.c
@@ -110,23 +110,40 @@ void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const bseq1_t *t, const mm_r
 {
 	int flag = 0;
 	s->l = 0;
-	if (r->rev) flag |= 0x10;
-	if (r->parent != r->id) flag |= 0x100;
-	else if (!r->sam_pri) flag |= 0x800;
-	mm_sprintf_lite(s, "%s\t%d\t%s\t%d\t%d\t", t->name, flag, mi->seq[r->rid].name, r->rs+1, r->mapq);
-	if (r->p) { // TODO: using hard clippings
-		uint32_t k, clip_len = r->rev? t->l_seq - r->qe : r->qs;
-		int clip_char = (flag&0x800)? 'H' : 'S';
-		if (clip_len) mm_sprintf_lite(s, "%d%c", clip_len, clip_char);
-		for (k = 0; k < r->p->n_cigar; ++k)
-			mm_sprintf_lite(s, "%d%c", r->p->cigar[k]>>4, "MID"[r->p->cigar[k]&0xf]);
-		clip_len = r->rev? r->qs : t->l_seq - r->qe;
-		if (clip_len) mm_sprintf_lite(s, "%d%c", clip_len, clip_char);
-	} else mm_sprintf_lite(s, "*");
-	mm_sprintf_lite(s, "\t*\t0\t0\t");
-	if ((flag & 0x900) == 0) sam_write_sq(s, t->seq, t->l_seq, r->rev, r->rev);
-	else if (flag & 0x100) mm_sprintf_lite(s, "*");
-	else sam_write_sq(s, t->seq + r->qs, r->qe - r->qs, r->rev, r->rev);
-	mm_sprintf_lite(s, "\t*"); // quality
-	write_tags(s, r);
+	if (r == 0) {
+		mm_sprintf_lite(s, "%s\t0\t*\t0\t0\t*\t*\t0\t0\t", t->name);
+		sam_write_sq(s, t->seq, t->l_seq, 0, 0);
+		mm_sprintf_lite(s, "\t");
+		if (t->qual) sam_write_sq(s, t->qual, t->l_seq, 0, 0);
+		else mm_sprintf_lite(s, "*");
+	} else {
+		if (r->rev) flag |= 0x10;
+		if (r->parent != r->id) flag |= 0x100;
+		else if (!r->sam_pri) flag |= 0x800;
+		mm_sprintf_lite(s, "%s\t%d\t%s\t%d\t%d\t", t->name, flag, mi->seq[r->rid].name, r->rs+1, r->mapq);
+		if (r->p) { // TODO: using hard clippings
+			uint32_t k, clip_len = r->rev? t->l_seq - r->qe : r->qs;
+			int clip_char = (flag&0x800)? 'H' : 'S';
+			if (clip_len) mm_sprintf_lite(s, "%d%c", clip_len, clip_char);
+			for (k = 0; k < r->p->n_cigar; ++k)
+				mm_sprintf_lite(s, "%d%c", r->p->cigar[k]>>4, "MID"[r->p->cigar[k]&0xf]);
+			clip_len = r->rev? r->qs : t->l_seq - r->qe;
+			if (clip_len) mm_sprintf_lite(s, "%d%c", clip_len, clip_char);
+		} else mm_sprintf_lite(s, "*");
+		mm_sprintf_lite(s, "\t*\t0\t0\t");
+		if ((flag & 0x900) == 0) {
+			sam_write_sq(s, t->seq, t->l_seq, r->rev, r->rev);
+			mm_sprintf_lite(s, "\t");
+			if (t->qual) sam_write_sq(s, t->qual, t->l_seq, r->rev, 0);
+			else mm_sprintf_lite(s, "*");
+		} else if (flag & 0x100) {
+			mm_sprintf_lite(s, "*\t*");
+		} else {
+			sam_write_sq(s, t->seq + r->qs, r->qe - r->qs, r->rev, r->rev);
+			mm_sprintf_lite(s, "\t");
+			if (t->qual) sam_write_sq(s, t->qual + r->qs, r->qe - r->qs, r->rev, 0);
+			else mm_sprintf_lite(s, "*");
+		}
+		write_tags(s, r);
+	}
 }
diff --git a/main.c b/main.c
index 24b9e34..d24c952 100644
--- a/main.c
+++ b/main.c
@@ -10,7 +10,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0-r120-pre"
+#define MM_VERSION "2.0-r121-pre"
 
 void liftrlimit()
 {
diff --git a/map.c b/map.c
index c725ba8..1ec5fec 100644
--- a/map.c
+++ b/map.c
@@ -321,12 +321,15 @@ static void *worker_pipeline(void *shared, int step, void *in)
 			bseq1_t *t = &s->seq[i];
 			for (j = 0; j < s->n_reg[i]; ++j) {
 				mm_reg1_t *r = &s->reg[i][j];
-				if (r->cnt == 0) continue;
 				if (p->opt->flag & MM_F_OUT_SAM) mm_write_sam(&p->str, mi, t, r);
 				else mm_write_paf(&p->str, mi, t, r);
 				puts(p->str.s);
 				free(r->p);
 			}
+			if (s->n_reg[i] == 0 && (p->opt->flag & MM_F_OUT_SAM)) {
+				mm_write_sam(&p->str, 0, t, 0);
+				puts(p->str.s);
+			}
 			free(s->reg[i]);
 			free(s->seq[i].seq); free(s->seq[i].name);
 		}