diff --git a/align.c b/align.c
index 73890da..68cd724 100644
--- a/align.c
+++ b/align.c
@@ -130,27 +130,21 @@ static void mm_update_extra(mm_reg1_t *r, const uint8_t *qseq, const uint8_t *qu
 		uint32_t op = p->cigar[k]&0xf, len = p->cigar[k]>>4;
 		if (op == 0) { // match/mismatch
 			int n_ambi = 0, n_diff = 0;
-			float n_diff2 = 0.0f;
 			for (l = 0; l < len; ++l) {
 				int cq = qseq[qoff + l], ct = tseq[toff + l];
 				if (ct > 3 || cq > 3) ++n_ambi;
-				else if (ct != cq) {
-					++n_diff;
-					n_diff2 += qual == 0 || qual[qoff + l] >= 20? 1.0f : .05f * qual[qoff + l];
-				}
+				else if (ct != cq) ++n_diff;
 				s += mat[ct * 5 + cq];
 				if (s < 0) s = 0;
 				else max = max > s? max : s;
 			}
 			r->blen += len - n_ambi, r->mlen += len - (n_ambi + n_diff), p->n_ambi += n_ambi;
-			p->n_diff2 += n_diff2, p->blen2 += len - n_ambi;
 			toff += len, qoff += len;
 		} else if (op == 1) { // insertion
 			int n_ambi = 0;
 			for (l = 0; l < len; ++l)
 				if (qseq[qoff + l] > 3) ++n_ambi;
 			r->blen += len - n_ambi, p->n_ambi += n_ambi;
-			p->n_diff2 += 1.0f, ++p->blen2;
 			s -= q + e * len;
 			if (s < 0) s = 0;
 			qoff += len;
@@ -159,7 +153,6 @@ static void mm_update_extra(mm_reg1_t *r, const uint8_t *qseq, const uint8_t *qu
 			for (l = 0; l < len; ++l)
 				if (tseq[toff + l] > 3) ++n_ambi;
 			r->blen += len - n_ambi, p->n_ambi += n_ambi;
-			p->n_diff2 += 1.0f, ++p->blen2;
 			s -= q + e * len;
 			if (s < 0) s = 0;
 			toff += len;
diff --git a/hit.c b/hit.c
index c5f84cd..4f62962 100644
--- a/hit.c
+++ b/hit.c
@@ -264,45 +264,6 @@ void mm_filter_regs(void *km, const mm_mapopt_t *opt, int *n_regs, mm_reg1_t *re
 	*n_regs = k;
 }
 
-void mm_filter_by_identity(void *km, int n_regs, mm_reg1_t *regs, float min_iden, int qlen, const char *qual) // TODO: make sure it is not beyond the ends of contigs
-{
-	int i, j, n_aux = 0, en, blen = 0;
-	uint64_t *aux;
-	float n_diff = 0.0f;
-	if (n_regs <= 0) return;
-	for (i = 0; i < n_regs; ++i)
-		if (regs[i].id == regs[i].parent && regs[i].pe_thru) // sequenced through the fragment; don't filter
-			return;
-	for (i = 0; i < n_regs; ++i)
-		if (regs[i].id == regs[i].parent)
-			++n_aux;
-	assert(n_aux >= 1);
-	aux = (uint64_t*)kmalloc(km, n_aux * 8);
-	for (i = 0, n_aux = 0; i < n_regs; ++i)
-		if (regs[i].id == regs[i].parent)
-			aux[n_aux++] = (uint64_t)regs[i].qs<<32 | i;
-	radix_sort_64(aux, aux + n_aux);
-	for (i = 0, en = 0; i < n_aux; ++i) {
-		mm_reg1_t *r = &regs[(int32_t)aux[i]];
-		if (r->qs > en) {
-			for (j = en; j < r->qs; ++j)
-				n_diff += qual == 0 || qual[j] >= 53? .25f : .05f * .25f * (qual[j] - 33);
-			blen += r->qs - en;
-		}
-		assert(r->p);
-		blen += r->p->blen2;
-		n_diff += r->p->n_diff2;
-		en = en > r->qe? en : r->qe;
-	}
-	for (j = en; j < qlen; ++j)
-		n_diff += qual == 0 || qual[j] >= 53? .25f : .05f * .25f * (qual[j] - 33);
-	blen += qlen - en;
-	kfree(km, aux);
-	if (1.0f - n_diff / blen < min_iden)
-		for (i = 0; i < n_regs; ++i)
-			regs[i].iden_flt = 1;
-}
-
 int mm_squeeze_a(void *km, int n_regs, mm_reg1_t *regs, mm128_t *a)
 { // squeeze out regions in a[] that are not referenced by regs[]
 	int i, as = 0;
diff --git a/main.c b/main.c
index 9feef04..f04310b 100644
--- a/main.c
+++ b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.3-r544-dirty"
+#define MM_VERSION "2.3-r545-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -67,7 +67,7 @@ static inline int64_t mm_parse_num(const char *str)
 
 int main(int argc, char *argv[])
 {
-	const char *opt_str = "2aSw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:i:LC:";
+	const char *opt_str = "2aSw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:LC:";
 	mm_mapopt_t opt;
 	mm_idxopt_t ipt;
 	int i, c, n_threads = 3, long_idx;
@@ -102,7 +102,6 @@ int main(int argc, char *argv[])
 		else if (c == 'g') opt.max_gap = (int)mm_parse_num(optarg);
 		else if (c == 'G') mm_mapopt_max_intron_len(&opt, (int)mm_parse_num(optarg));
 		else if (c == 'F') opt.max_frag_len = (int)mm_parse_num(optarg);
-		else if (c == 'i') opt.min_iden = atof(optarg);
 		else if (c == 'N') opt.best_n = atoi(optarg);
 		else if (c == 'p') opt.pri_ratio = atof(optarg);
 		else if (c == 'M') opt.mask_level = atof(optarg);
@@ -226,7 +225,6 @@ int main(int argc, char *argv[])
 		fprintf(fp_help, "    -z INT       Z-drop score [%d]\n", opt.zdrop);
 		fprintf(fp_help, "    -s INT       minimal peak DP alignment score [%d]\n", opt.min_dp_max);
 		fprintf(fp_help, "    -u CHAR      how to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG [n]\n");
-		fprintf(fp_help, "    -i FLOAT     min identity (mapQ reduced to 0 if below) [0]\n");
 		fprintf(fp_help, "  Input/Output:\n");
 		fprintf(fp_help, "    -a           output in the SAM format (PAF by default)\n");
 		fprintf(fp_help, "    -Q           don't output base quality in SAM\n");
diff --git a/map.c b/map.c
index eea9690..086f357 100644
--- a/map.c
+++ b/map.c
@@ -360,9 +360,6 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
 		if (n_segs == 2 && opt->pe_ori >= 0 && (opt->flag&MM_F_CIGAR))
 			mm_pair(b->km, max_chain_gap_ref, opt->pe_bonus, opt->a * 2 + opt->b, opt->a, qlens, n_regs, regs); // pairing
 	}
-	if (opt->min_iden > 0.0f)
-		for (i = 0; i < n_segs; ++i)
-			mm_filter_by_identity(b->km, n_regs[i], regs[i], opt->min_iden, qlens[i], quals[i]);
 
 	kfree(b->km, a);
 	kfree(b->km, u);
diff --git a/minimap.h b/minimap.h
index 17e411c..d5c22fd 100644
--- a/minimap.h
+++ b/minimap.h
@@ -59,8 +59,6 @@ typedef struct {
 	int32_t dp_score, dp_max, dp_max2;  // DP score; score of the max-scoring segment; score of the best alternate mappings
 	uint32_t n_ambi:30, trans_strand:2; // number of ambiguous bases; transcript strand: 0 for unknown, 1 for +, 2 for -
 	uint32_t n_cigar;                   // number of cigar operations in cigar[]
-	float n_diff2;
-	uint32_t blen2;
 	uint32_t cigar[];
 } mm_extra_t;
 
@@ -101,7 +99,6 @@ typedef struct {
 	float mask_level;
 	float pri_ratio;
 	int best_n;      // top best_n chains are subjected to DP alignment
-	float min_iden;
 
 	int max_join_long, max_join_short;
 	int min_join_flank_sc;
diff --git a/mmpriv.h b/mmpriv.h
index bbf54e5..e0b06c9 100644
--- a/mmpriv.h
+++ b/mmpriv.h
@@ -75,7 +75,6 @@ void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r, int sub_diff
 void mm_select_sub(void *km, float pri_ratio, int min_diff, int best_n, int *n_, mm_reg1_t *r);
 void mm_select_sub_multi(void *km, float pri_ratio, float pri1, float pri2, int max_gap_ref, int min_diff, int best_n, int n_segs, const int *qlens, int *n_, mm_reg1_t *r);
 void mm_filter_regs(void *km, const mm_mapopt_t *opt, int *n_regs, mm_reg1_t *regs);
-void mm_filter_by_identity(void *km, int n_regs, mm_reg1_t *regs, float min_iden, int qlen, const char *qual);
 void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs, mm_reg1_t *regs, mm128_t *a);
 void mm_hit_sort_by_dp(void *km, int *n_regs, mm_reg1_t *r);
 void mm_set_mapq(int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, int rep_len, int is_sr);