diff --git a/bwape.c b/bwape.c
index 7dc3d74..08490e7 100644
--- a/bwape.c
+++ b/bwape.c
@@ -296,7 +296,7 @@ int bwa_cal_pac_pos_pe(const bntseq_t *bns, const char *prefix, bwt_t *const _bw
 				int strand;
 				int max_diff = gopt->fnr > 0.0? bwa_cal_maxdiff(p[j]->len, BWA_AVG_ERR, gopt->fnr) : gopt->max_diff;
 				p[j]->seQ = p[j]->mapQ = bwa_approx_mapQ(p[j], max_diff);
-				p[j]->pos = bwa_sa2pos(bns, bwt, p[j]->sa, p[j]->len, &strand);
+				p[j]->pos = bwa_sa2pos(bns, bwt, p[j]->sa, p[j]->len + p[j]->ref_shift, &strand);
 				p[j]->strand = strand;
 			}
 		}
@@ -345,7 +345,7 @@ int bwa_cal_pac_pos_pe(const bntseq_t *bns, const char *prefix, bwt_t *const _bw
 							z->a = (bwtint_t*)malloc(sizeof(bwtint_t) * z->n);
 							for (l = r->k; l <= r->l; ++l) {
 								int strand;
-								z->a[l - r->k] = bwa_sa2pos(bns, bwt, l, p[j]->len, &strand)<<1;
+								z->a[l - r->k] = bwa_sa2pos(bns, bwt, l, p[j]->len + p[j]->ref_shift, &strand)<<1;
 								z->a[l - r->k] |= strand;
 							}
 						}
@@ -357,7 +357,7 @@ int bwa_cal_pac_pos_pe(const bntseq_t *bns, const char *prefix, bwt_t *const _bw
 					} else { // then calculate on the fly
 						for (l = r->k; l <= r->l; ++l) {
 							int strand;
-							x.x = bwa_sa2pos(bns, bwt, l, p[j]->len, &strand);
+							x.x = bwa_sa2pos(bns, bwt, l, p[j]->len + p[j]->ref_shift, &strand);
 							x.y = k<<2 | strand<<1 | j;
 							kv_push(pair64_t, d->arr, x);
 						}
@@ -377,7 +377,7 @@ int bwa_cal_pac_pos_pe(const bntseq_t *bns, const char *prefix, bwt_t *const _bw
 					for (k = 0, n_multi = 0; k < p[j]->n_multi; ++k) {
 						int strand;
 						bwt_multi1_t *q = p[j]->multi + k;
-						q->pos = bwa_sa2pos(bns, bwt, q->pos, p[j]->len, &strand);
+						q->pos = bwa_sa2pos(bns, bwt, q->pos, p[j]->len + q->ref_shift, &strand);
 						q->strand = strand;
 						if (q->pos != p[j]->pos)
 							p[j]->multi[n_multi++] = *q;
diff --git a/bwase.c b/bwase.c
index 5bb8116..4c9e0fd 100644
--- a/bwase.c
+++ b/bwase.c
@@ -155,7 +155,7 @@ void bwa_cal_pac_pos(const bntseq_t *bns, const char *prefix, int n_seqs, bwa_se
 		bwa_cal_pac_pos_core(bns, bwt, p, max_mm, fnr);
 		for (j = n_multi = 0; j < p->n_multi; ++j) {
 			bwt_multi1_t *q = p->multi + j;
-			q->pos = bwa_sa2pos(bns, bwt, q->pos, p->len + p->ref_shift, &strand);
+			q->pos = bwa_sa2pos(bns, bwt, q->pos, p->len + q->ref_shift, &strand);
 			q->strand = strand;
 			if (q->pos != p->pos && q->pos != (bwtint_t)-1)
 				p->multi[n_multi++] = *q;
diff --git a/main.c b/main.c
index d243144..de50a70 100644
--- a/main.c
+++ b/main.c
@@ -3,7 +3,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.4-r397-beta"
+#define PACKAGE_VERSION "0.7.4-r401-beta"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);