diff --git a/hit.c b/hit.c
index ed013ac..c5f84cd 100644
--- a/hit.c
+++ b/hit.c
@@ -459,16 +459,14 @@ void mm_set_mapq(int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, in
 			if (r->p && r->p->dp_max2 > 0 && r->p->dp_max > 0) {
 				float identity = (float)r->mlen / r->blen;
 				float x = (float)r->p->dp_max2 * subsc / r->p->dp_max / r->score;
-				if (is_sr) {
-					mapq = (int)(identity * pen_cm * q_coef * (1.0f - x * x) * logf((float)r->p->dp_max / match_sc));
-				} else {
+				mapq = (int)(identity * pen_cm * q_coef * (1.0f - x * x) * logf((float)r->p->dp_max / match_sc));
+				if (!is_sr) {
 					int mapq_alt = (int)(6.02f * identity * identity * (r->p->dp_max - r->p->dp_max2) / match_sc + .499f); // BWA-MEM like mapQ, mostly for short reads
-					mapq = (int)(identity * pen_cm * q_coef * (1.0f - x) * logf(r->score)); // more for long reads
 					mapq = mapq < mapq_alt? mapq : mapq_alt; // in case the long-read heuristic fails
 				}
 			} else {
 				float x = (float)subsc / r->score;
-				if (is_sr && r->p) {
+				if (r->p) {
 					float identity = (float)r->mlen / r->blen;
 					mapq = (int)(identity * pen_cm * q_coef * (1.0f - x) * logf((float)r->p->dp_max / match_sc));
 				} else {
diff --git a/main.c b/main.c
index b919958..37583d5 100644
--- a/main.c
+++ b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.3-r542-dirty"
+#define MM_VERSION "2.3-r543-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>