diff --git a/bwamem.c b/bwamem.c
index 7a6d175..766227d 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -670,9 +670,13 @@ void bwa_hit2sam(kstring_t *str, const int8_t mat[25], int q, int r, int w, cons
 		if (mid == rid) {
 			int64_t p0 = p->rb < bns->l_pac? p->rb : (bns->l_pac<<1) - 1 - p->rb;
 			int64_t p1 = m->rb < bns->l_pac? m->rb : (bns->l_pac<<1) - 1 - m->rb;
-			kputw(p0 - p1 + (p0 > p1? 1 : -1), str);
+			kputw(p0 - p1 + (p0 > p1? 1 : p0 < p1? -1 : 0), str);
 		} else kputw(0, str);
 		kputc('\t', str);
+	} else if (m && is_mapped(p)) { // then copy the position
+		kputsn("\t=\t", 3, str);
+		kputuw(pos - bns->anns[rid].offset + 1, str);
+		kputsn("\t0\t", 3, str);
 	} else kputsn("\t*\t0\t0\t", 7, str);
 	if (p->flag&0x100) { // for secondary alignments, don't write SEQ and QUAL
 		kputsn("*\t*", 3, str);
@@ -760,7 +764,12 @@ void mem_sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, b
 			else if (h.qual > mapq0) h.qual = mapq0;
 			bwa_hit2sam(&str, opt->mat, opt->q, opt->r, p->w, bns, pac, s, &h, opt->flag&MEM_F_HARDCLIP, m);
 		}
-	} else bwa_hit2sam(&str, opt->mat, opt->q, opt->r, opt->w, bns, pac, s, 0, opt->flag&MEM_F_HARDCLIP, m);
+	} else {
+		bwahit_t h;
+		memset(&h, 0, sizeof(bwahit_t));
+		h.rb = h.re = -1; h.flag = extra_flag;
+		bwa_hit2sam(&str, opt->mat, opt->q, opt->r, opt->w, bns, pac, s, &h, opt->flag&MEM_F_HARDCLIP, m);
+	}
 	s->sam = str.s;
 }
 
diff --git a/bwamem_pair.c b/bwamem_pair.c
index 49e9ad2..bbbbe02 100644
--- a/bwamem_pair.c
+++ b/bwamem_pair.c
@@ -306,7 +306,11 @@ no_pairing:
 		if (a[i].n && a[i].a[0].score >= opt->T) {
 			mem_alnreg2hit(&a[i].a[0], &h[i]);
 			bwa_fix_xref(opt->mat, opt->q, opt->r, opt->w, bns, pac, (uint8_t*)s[i].seq, &h[i].qb, &h[i].qe, &h[i].rb, &h[i].re);
-		} else h[i].rb = h[i].re = -1;
+		} else {
+			memset(&h[i], 0, sizeof(bwahit_t));
+			h[i].rb = h[i].re = -1;
+			h[i].flag = 1<<(6+i) | 1;
+		}
 	}
 	mem_sam_se(opt, bns, pac, &s[0], &a[0], 0x41, &h[1]);
 	mem_sam_se(opt, bns, pac, &s[1], &a[1], 0x81, &h[0]);
diff --git a/main.c b/main.c
index 4240ac7..1304a35 100644
--- a/main.c
+++ b/main.c
@@ -3,7 +3,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.0-r342-beta"
+#define PACKAGE_VERSION "0.7.0-r343-beta"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);