diff --git a/bwamem.c b/bwamem.c
index 64c26fa..1699e97 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -880,11 +880,13 @@ void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq
 		for (i = 0; i < n; ++i)
 			if (i != which && !(list[i].flag&0x100)) break;
 		if (i < n) { // there are other primary hits; output them
+			int has_pri_alt = 0;
 			kputsn("\tSA:Z:", 6, str);
 			for (i = 0; i < n; ++i) {
 				const mem_aln_t *r = &list[i];
 				int k;
 				if (i == which || (list[i].flag&0x100)) continue; // proceed if: 1) different from the current; 2) not shadowed multi hit
+				if (list[i].is_alt) has_pri_alt = 1;
 				kputs(bns->anns[r->rid].name, str); kputc(',', str);
 				kputl(r->pos+1, str); kputc(',', str);
 				kputc("+-"[r->is_rev], str); kputc(',', str);
@@ -895,6 +897,7 @@ void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq
 				kputc(',', str); kputw(r->NM, str);
 				kputc(';', str);
 			}
+			if (has_pri_alt) kputsn("\tpa:A:Y", 7, str);
 		}
 	}
 	if (p->XA) { kputsn("\tXA:Z:", 6, str); kputs(p->XA, str); }
@@ -1094,6 +1097,7 @@ mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *
 	assert(a.rid == ar->rid);
 	a.pos = pos - bns->anns[a.rid].offset;
 	a.score = ar->score; a.sub = ar->sub > ar->csub? ar->sub : ar->csub;
+	a.is_alt = ar->is_alt;
 	free(query);
 	return a;
 }
diff --git a/bwamem.h b/bwamem.h
index 8b8ec0d..20e8d05 100644
--- a/bwamem.h
+++ b/bwamem.h
@@ -85,7 +85,7 @@ typedef struct { // This struct is only used for the convenience of API.
 	int64_t pos;     // forward strand 5'-end mapping position
 	int rid;         // reference sequence index in bntseq_t; <0 for unmapped
 	int flag;        // extra flag
-	uint32_t is_rev:1, mapq:8, NM:23; // is_rev: whether on the reverse strand; mapq: mapping quality; NM: edit distance
+	uint32_t is_rev:1, is_alt:1, mapq:8, NM:22; // is_rev: whether on the reverse strand; mapq: mapping quality; NM: edit distance
 	int n_cigar;     // number of CIGAR operations
 	uint32_t *cigar; // CIGAR in the BAM encoding: opLen<<4|op; op to integer mapping: MIDSH=>01234
 	char *XA;        // alternative mappings
diff --git a/main.c b/main.c
index 35e598b..ca71750 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.10-r845-dirty"
+#define PACKAGE_VERSION "0.7.10-r848-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);