diff --git a/hit.c b/hit.c
index 477dedb..ba6bb76 100644
--- a/hit.c
+++ b/hit.c
@@ -290,16 +290,18 @@ void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs_, mm_r
 
 void mm_set_mapq(int n_regs, mm_reg1_t *regs, int min_chain_sc)
 {
+	static const float q_coef = 30.0f;
 	int i;
 	for (i = 0; i < n_regs; ++i) {
 		mm_reg1_t *r = &regs[i];
 		if (r->parent == r->id) {
 			int mapq, subsc;
+			float pen_cm = r->cnt >= 10? 1.0f : 0.1f * r->cnt;
 			subsc = r->subsc > min_chain_sc? r->subsc : min_chain_sc;
 			if (r->p && r->p->dp_max2 > 0 && r->p->dp_max > 0) {
 				float identity = (float)(r->p->blen - r->p->n_diff - r->p->n_ambi) / (r->p->blen - r->p->n_ambi);
-				mapq = (int)(identity * 30.0 * (1. - (float)r->p->dp_max2 * subsc / r->p->dp_max / r->score) * logf(r->score));
-			} else mapq = (int)(30.0 * (1. - (float)subsc / r->score) * logf(r->score));
+				mapq = (int)(identity * pen_cm * q_coef * (1. - (float)r->p->dp_max2 * subsc / r->p->dp_max / r->score) * logf(r->score));
+			} else mapq = (int)(pen_cm * q_coef * (1. - (float)subsc / r->score) * logf(r->score));
 			mapq = mapq > 0? mapq : 0;
 			r->mapq = mapq < 60? mapq : 60;
 		} else r->mapq = 0;
diff --git a/main.c b/main.c
index 175d085..00cd5d5 100644
--- a/main.c
+++ b/main.c
@@ -8,7 +8,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0-r205-dirty"
+#define MM_VERSION "2.0-r206-dirty"
 
 void liftrlimit()
 {