diff --git a/format.c b/format.c
index 37355e1..56267f6 100644
--- a/format.c
+++ b/format.c
@@ -58,9 +58,9 @@ void mm_write_paf(kstring_t *s, const mm_idx_t *mi, bseq1_t *t, int which, mm_re
 {
 	s->l = 0;
 	mm_sprintf_lite(s, "%s\t%d\t%d\t%d\t%c\t%s\t%d\t%d\t%d", t->name, t->l_seq, r->qs, r->qe, "+-"[r->rev], mi->seq[r->rid].name, mi->seq[r->rid].len, r->rs, r->re);
-	if (r->p) mm_sprintf_lite(s, "\t%d\t%d\t255", r->p->blen - r->p->n_ambi - r->p->n_diff, r->p->blen);
-	else mm_sprintf_lite(s, "\t%d\t%d\t255", r->score, r->re - r->rs > r->qe - r->qs? r->re - r->rs : r->qe - r->qs);
-	mm_sprintf_lite(s, "\tcm:i:%d", r->cnt);
+	if (r->p) mm_sprintf_lite(s, "\t%d\t%d", r->p->blen - r->p->n_ambi - r->p->n_diff, r->p->blen);
+	else mm_sprintf_lite(s, "\t%d\t%d", r->score, r->re - r->rs > r->qe - r->qs? r->re - r->rs : r->qe - r->qs);
+	mm_sprintf_lite(s, "\t%d\tcm:i:%d", r->mapq, r->cnt);
 	if (r->p) mm_sprintf_lite(s, "\ts1:i:%d", r->score);
 	if (r->parent == which) mm_sprintf_lite(s, "\ts2:i:%d", r->subsc);
 	if (r->p) {
@@ -70,3 +70,50 @@ void mm_write_paf(kstring_t *s, const mm_idx_t *mi, bseq1_t *t, int which, mm_re
 			mm_sprintf_lite(s, "%d%c", r->p->cigar[k]>>4, "MID"[r->p->cigar[k]&0xf]);
 	}
 }
+
+static char comp_tab[] = {
+	  0,   1,	2,	 3,	  4,   5,	6,	 7,	  8,   9,  10,	11,	 12,  13,  14,	15,
+	 16,  17,  18,	19,	 20,  21,  22,	23,	 24,  25,  26,	27,	 28,  29,  30,	31,
+	 32,  33,  34,	35,	 36,  37,  38,	39,	 40,  41,  42,	43,	 44,  45,  46,	47,
+	 48,  49,  50,	51,	 52,  53,  54,	55,	 56,  57,  58,	59,	 60,  61,  62,	63,
+	 64, 'T', 'V', 'G', 'H', 'E', 'F', 'C', 'D', 'I', 'J', 'M', 'L', 'K', 'N', 'O',
+	'P', 'Q', 'Y', 'S', 'A', 'A', 'B', 'W', 'X', 'R', 'Z',	91,	 92,  93,  94,	95,
+	 64, 't', 'v', 'g', 'h', 'e', 'f', 'c', 'd', 'i', 'j', 'm', 'l', 'k', 'n', 'o',
+	'p', 'q', 'y', 's', 'a', 'a', 'b', 'w', 'x', 'r', 'z', 123, 124, 125, 126, 127
+};
+
+static void sam_write_sq(kstring_t *s, char *seq, int l, int rev, int comp)
+{
+	if (rev) {
+		int i;
+		str_enlarge(s, l);
+		for (i = 0; i < l; ++i) {
+			int c = seq[l - 1 - i];
+			s->s[s->l + i] = c < 128 && comp? comp_tab[c] : c;
+		}
+		s->l += l;
+	} else str_copy(s, seq, seq + l);
+}
+
+void mm_write_sam(kstring_t *s, const mm_idx_t *mi, bseq1_t *t, int which, mm_reg1_t *r)
+{
+	int flag = 0;
+	s->l = 0;
+	if (r->rev) flag |= 0x10;
+	if (r->parent != which) flag |= 0x80;
+	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;
+		if (clip_len) mm_sprintf_lite(s, "%dS", clip_len);
+		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, "%dS", clip_len);
+	} else mm_sprintf_lite(s, "*");
+	mm_sprintf_lite(s, "\t*\t0\t0\t");
+	sam_write_sq(s, t->seq, t->l_seq, r->rev, r->rev);
+	mm_sprintf_lite(s, "\t*\tcm:i:%d", r->cnt);
+	if (r->p) mm_sprintf_lite(s, "\ts1:i:%d", r->score);
+	if (r->parent == which) mm_sprintf_lite(s, "\ts2:i:%d", r->subsc);
+	if (r->p) mm_sprintf_lite(s, "\tNM:i:%d\tAS:i:%d\tnn:i:%d", r->p->n_diff, r->p->score, r->p->n_ambi);
+}
diff --git a/main.c b/main.c
index 9ef7119..6764255 100644
--- a/main.c
+++ b/main.c
@@ -54,7 +54,7 @@ int main(int argc, char *argv[])
 	mm_realtime0 = realtime();
 	mm_mapopt_init(&opt);
 
-	while ((c = getopt(argc, argv, "w:k:B:b:t:r:f:Vv:Ng:I:d:ST:s:Dx:Hp:m:z:")) >= 0) {
+	while ((c = getopt(argc, argv, "w:k:B:b:t:r:f:Vv:Ng:I:d:ST:s:Dx:Hp:m:z:F:")) >= 0) {
 		if (c == 'w') w = atoi(optarg);
 		else if (c == 'k') k = atoi(optarg);
 		else if (c == 'b') b = atoi(optarg);
@@ -85,6 +85,13 @@ int main(int argc, char *argv[])
 			else if (*p == 'K' || *p == 'k') x *= 1e3;
 			if (c == 'B') mini_batch_size = (uint64_t)(x + .499);
 			else batch_size = (uint64_t)(x + .499);
+		} else if (c == 'F') {
+			if (strcmp(optarg, "sam") == 0) opt.flag |= MM_F_OUT_SAM;
+			else if (strcmp(optarg, "paf") == 0) opt.flag &= ~MM_F_OUT_SAM;
+			else {
+				fprintf(stderr, "[E::%s] unknown output format '%s'\n", __func__, optarg);
+				return 0;
+			}
 		} else if (c == 'x') {
 			if (strcmp(optarg, "ava10k") == 0) {
 				opt.flag |= MM_F_AVA | MM_F_NO_SELF;
diff --git a/map.c b/map.c
index cad8a5c..037bc65 100644
--- a/map.c
+++ b/map.c
@@ -306,7 +306,6 @@ mm_reg1_t *mm_map(const mm_idx_t *mi, int l_seq, const char *seq, int *n_regs, m
 	if (opt->sdust_thres > 0)
 		mm_dust_minier(&b->mini, l_seq, seq, opt->sdust_thres, b->sdb);
 	regs = mm_map_frag(opt, mi, b, 0, b->mini.n, qname, l_seq, seq, n_regs);
-//	mm_select_sub(opt->mask_level, opt->pri_ratio, n_regs, regs, b->km);
 	return regs;
 }
 
@@ -368,7 +367,8 @@ 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];
-				mm_write_paf(&p->str, mi, t, j, r);
+				if (p->opt->flag & MM_F_OUT_SAM) mm_write_sam(&p->str, mi, t, j, r);
+				else mm_write_paf(&p->str, mi, t, j, r);
 				puts(p->str.s);
 				free(r->p);
 			}
@@ -389,7 +389,13 @@ int mm_map_file(const mm_idx_t *idx, const char *fn, const mm_mapopt_t *opt, int
 	if (pl.fp == 0) return -1;
 	pl.opt = opt, pl.mi = idx;
 	pl.n_threads = n_threads, pl.mini_batch_size = mini_batch_size;
+	if (opt->flag & MM_F_OUT_SAM) {
+		uint32_t i;
+		for (i = 0; i < idx->n_seq; ++i)
+			printf("@SQ\tID:%s\tLN:%d\n", idx->seq[i].name, idx->seq[i].len);
+	}
 	kt_pipeline(n_threads == 1? 1 : 2, worker_pipeline, &pl, 3);
+	free(pl.str.s);
 	bseq_close(pl.fp);
 	return 0;
 }
diff --git a/minimap.h b/minimap.h
index e9dafb1..ec54832 100644
--- a/minimap.h
+++ b/minimap.h
@@ -7,8 +7,9 @@
 
 #define MM_IDX_DEF_B    14
 
-#define MM_F_NO_SELF   0x2
-#define MM_F_AVA       0x8
+#define MM_F_NO_SELF   0x01
+#define MM_F_AVA       0x02
+#define MM_F_OUT_SAM   0x04
 
 #define MM_IDX_MAGIC   "MMI\2"
 
@@ -57,6 +58,7 @@ typedef struct {
 	int32_t qs, qe, rs, re;
 	int32_t parent, subsc;
 	int32_t as;
+	int32_t mapq, n_sub; // TODO: n_sub is not used for now
 	mm_extra_t *p;
 } mm_reg1_t;
 
diff --git a/mmpriv.h b/mmpriv.h
index 8527284..b74072b 100644
--- a/mmpriv.h
+++ b/mmpriv.h
@@ -28,6 +28,7 @@ void radix_sort_64(uint64_t *beg, uint64_t *end);
 uint32_t ks_ksmall_uint32_t(size_t n, uint32_t arr[], size_t kk);
 
 void mm_write_paf(kstring_t *s, const mm_idx_t *mi, bseq1_t *t, int which, mm_reg1_t *r);
+void mm_write_sam(kstring_t *s, const mm_idx_t *mi, bseq1_t *t, int which, mm_reg1_t *r);
 int mm_chain_dp(int max_dist, int bw, int max_skip, int min_sc, int n, mm128_t *a, uint64_t **_u, void *km);
 mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, const char *qstr, int *n_regs_, mm_reg1_t *regs, mm128_t *a);