diff --git a/format.c b/format.c
index a84c735..fd51c00 100644
--- a/format.c
+++ b/format.c
@@ -72,8 +72,10 @@ static void write_cs(void *km, kstring_t *s, const mm_idx_t *mi, const mm_bseq1_
 		for (i = r->qs; i < r->qe; ++i)
 			qseq[i - r->qs] = seq_nt4_table[(uint8_t)t->seq[i]];
 	} else {
-		for (i = r->qs; i < r->qe; ++i)
-			qseq[r->qe - i - 1] = seq_nt4_table[(uint8_t)t->seq[i]];
+		for (i = r->qs; i < r->qe; ++i) {
+			uint8_t c = seq_nt4_table[(uint8_t)t->seq[i]];
+			qseq[r->qe - i - 1] = c >= 4? 4 : 3 - c;
+		}
 	}
 	for (i = q_off = t_off = 0; i < r->p->n_cigar; ++i) {
 		int j, op = r->p->cigar[i]&0xf, len = r->p->cigar[i]>>4;
diff --git a/main.c b/main.c
index f40c00a..7244265 100644
--- a/main.c
+++ b/main.c
@@ -8,7 +8,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0rc1-r237-dirty"
+#define MM_VERSION "2.0rc1-r238-dirty"
 
 void liftrlimit()
 {