diff --git a/bwa-postalt.js b/bwa-postalt.js
index 96cc6ab..e321c07 100644
--- a/bwa-postalt.js
+++ b/bwa-postalt.js
@@ -479,6 +479,7 @@ function bwa_postalt(args)
 			if (hits[i].g != reported_g || i == reported_i) continue;
 			if (idx_alt[hits[i].ctg] == null) continue;
 			var s = [t[0], 0, hits[i].ctg, hits[i].start+1, mapQ, hits[i].cigar, t[6], t[7], t[8]];
+			if (t[6] == '=' && s[2] != t[2]) s[6] = t[2];
 			// print sequence/quality and set the rev flag
 			if (hits[i].rev == hits[reported_i].rev) {
 				s.push(t[9], t[10]);