diff --git a/format.c b/format.c
index 4b7df15..2425c05 100644
--- a/format.c
+++ b/format.c
@@ -203,7 +203,6 @@ static void write_cs(void *km, kstring_t *s, const mm_idx_t *mi, const mm_bseq1_
 static inline void write_tags(kstring_t *s, const mm_reg1_t *r)
 {
 	int type = r->inv? 'I' : r->id == r->parent? 'P' : 'S';
-	if (r->iden_flt) mm_sprintf_lite(s, "\tom:i:%d", r->mapq);
 	if (r->p) {
 		mm_sprintf_lite(s, "\tNM:i:%d\tms:i:%d\tAS:i:%d\tnn:i:%d", r->blen - r->mlen + r->p->n_ambi, r->p->dp_max, r->p->dp_score, r->p->n_ambi);
 		if (r->p->trans_strand == 1 || r->p->trans_strand == 2)
@@ -336,9 +335,8 @@ void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se
 			mm_sprintf_lite(s, "\t%s\t%d\t0\t*", mi->seq[this_rid].name, this_pos+1);
 		} else mm_sprintf_lite(s, "\t*\t0\t0\t*");
 	} else {
-		int mapq = !r->iden_flt? r->mapq : r->mapq < 3? r->mapq : 3;
 		this_rid = r->rid, this_pos = r->rs, this_rev = r->rev;
-		mm_sprintf_lite(s, "\t%s\t%d\t%d\t", mi->seq[r->rid].name, r->rs+1, mapq);
+		mm_sprintf_lite(s, "\t%s\t%d\t%d\t", mi->seq[r->rid].name, r->rs+1, r->mapq);
 		if ((opt_flag & MM_F_LONG_CIGAR) && r->p && r->p->n_cigar > max_bam_cigar_op - 2) {
 			int n_cigar = r->p->n_cigar;
 			if (r->qs != 0) ++n_cigar;
diff --git a/hit.c b/hit.c
index 75a8d93..c46c30f 100644
--- a/hit.c
+++ b/hit.c
@@ -76,7 +76,7 @@ mm_reg1_t *mm_gen_regs(void *km, uint32_t hash, int qlen, int n_u, uint64_t *u,
 		mm_reg1_t *ri = &r[i];
 		ri->id = i;
 		ri->parent = MM_PARENT_UNSET;
-		ri->score = z[i].x >> 32;
+		ri->score = ri->score0 = z[i].x >> 32;
 		ri->hash = (uint32_t)z[i].x;
 		ri->cnt = (int32_t)z[i].y;
 		ri->as = z[i].y >> 32;
@@ -425,14 +425,14 @@ void mm_set_mapq(int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, in
 			subsc = r->subsc > min_chain_sc? r->subsc : min_chain_sc;
 			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;
+				float x = (float)r->p->dp_max2 * subsc / r->p->dp_max / r->score0;
 				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 = mapq < mapq_alt? mapq : mapq_alt; // in case the long-read heuristic fails
 				}
 			} else {
-				float x = (float)subsc / r->score;
+				float x = (float)subsc / r->score0;
 				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));
diff --git a/main.c b/main.c
index ada48a6..6f01b1e 100644
--- a/main.c
+++ b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.4-r556-dirty"
+#define MM_VERSION "2.4-r557-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
diff --git a/minimap.h b/minimap.h
index 63e23d3..a7e375c 100644
--- a/minimap.h
+++ b/minimap.h
@@ -64,7 +64,7 @@ typedef struct {
 
 typedef struct {
 	int32_t id;                     // ID for internal uses (see also parent below)
-	uint32_t cnt:30, rev:1, seg_split:1; // number of minimizers; if on the reverse strand
+	uint32_t cnt:28, rev:1, seg_split:1, sam_pri:1, proper_frag:1; // number of minimizers; if on the reverse strand
 	uint32_t rid:31, inv:1;         // reference index; if this is an alignment from inversion rescue
 	int32_t score;                  // DP alignment score
 	int32_t qs, qe, rs, re;         // query start and end; reference start and end
@@ -72,7 +72,7 @@ typedef struct {
 	int32_t as;                     // offset in the a[] array (for internal uses only)
 	int32_t mlen, blen;             // seeded exact match length; seeded alignment block length
 	uint32_t mapq:8, split:2, n_sub:22; // mapQ; split pattern; number of suboptimal mappings
-	uint32_t sam_pri:1, proper_frag:1, iden_flt:1, pe_thru:1, dummy:28;
+	uint32_t pe_thru:1, score0:31;
 	uint32_t hash;
 	mm_extra_t *p;
 } mm_reg1_t;