diff --git a/bwa.1 b/bwa.1
index 198c2ab..45b9921 100644
--- a/bwa.1
+++ b/bwa.1
@@ -93,6 +93,8 @@ genome.
 .IR gapOpenPen ]
 .RB [ -E
 .IR gapExtPen ]
+.RB [ -L
+.IR clipPen ]
 .RB [ -U
 .IR unpairPen ]
 .RB [ -R
@@ -190,6 +192,13 @@ Gap extension penalty. A gap of length k costs O + k*E (i.e.
 .B -O
 is for opening a zero-length gap). [1]
 .TP
+.BI -L \ INT
+Clipping penalty. When performing SW extension, BWA-MEM keeps track of the best
+score reaching the end of query. If this score is larger than the best SW score
+minus the clipping penalty, clipping will not be applied. Note that in this
+case, the SAM AS tag reports the best SW score; clipping penalty is not
+deducted. [5]
+.TP
 .BI -U \ INT
 Penalty for an unpaired read pair. BWA-MEM scores an unpaired read pair as
 .RI scoreRead1+scoreRead2- INT
diff --git a/bwamem.c b/bwamem.c
index 86b3e7a..f5173d3 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -42,8 +42,10 @@ mem_opt_t *mem_opt_init()
 {
 	mem_opt_t *o;
 	o = calloc(1, sizeof(mem_opt_t));
-	o->a = 1; o->b = 4; o->q = 6; o->r = 1; o->w = 100;
 	o->flag = 0;
+	o->a = 1; o->b = 4; o->q = 6; o->r = 1; o->w = 100;
+	o->pen_unpaired = 9;
+	o->pen_clip = 5;
 	o->min_seed_len = 19;
 	o->split_width = 10;
 	o->max_occ = 10000;
@@ -54,7 +56,6 @@ mem_opt_t *mem_opt_init()
 	o->split_factor = 1.5;
 	o->chunk_size = 10000000;
 	o->n_threads = 1;
-	o->pen_unpaired = 9;
 	o->max_matesw = 100;
 	mem_fill_scmat(o->a, o->b, o->mat);
 	return o;
@@ -487,23 +488,27 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
 
 		if (s->qbeg) { // left extension
 			uint8_t *rs, *qs;
-			int qle, tle;
+			int qle, tle, gtle, gscore;
 			qs = malloc(s->qbeg);
 			for (i = 0; i < s->qbeg; ++i) qs[i] = query[s->qbeg - 1 - i];
 			tmp = s->rbeg - rmax[0];
 			rs = malloc(tmp);
 			for (i = 0; i < tmp; ++i) rs[i] = rseq[tmp - 1 - i];
-			a->score = ksw_extend(s->qbeg, qs, tmp, rs, 5, opt->mat, opt->q, opt->r, opt->w, s->len * opt->a, &qle, &tle);
-			a->qb = s->qbeg - qle; a->rb = s->rbeg - tle;
+			a->score = ksw_extend(s->qbeg, qs, tmp, rs, 5, opt->mat, opt->q, opt->r, opt->w, s->len * opt->a, &qle, &tle, &gtle, &gscore);
+			// check whether we prefer to reach the end of the query
+			if (gscore <= 0 || gscore <= a->score - opt->pen_clip) a->qb = s->qbeg - qle, a->rb = s->rbeg - tle; // local hits
+			else a->qb = 0, a->rb = s->rbeg - gtle; // reach the end
 			free(qs); free(rs);
 		} else a->score = s->len * opt->a, a->qb = 0, a->rb = s->rbeg;
 
 		if (s->qbeg + s->len != l_query) { // right extension
-			int qle, tle, qe, re;
+			int qle, tle, qe, re, gtle, gscore;
 			qe = s->qbeg + s->len;
 			re = s->rbeg + s->len - rmax[0];
-			a->score = ksw_extend(l_query - qe, query + qe, rmax[1] - rmax[0] - re, rseq + re, 5, opt->mat, opt->q, opt->r, opt->w, a->score, &qle, &tle);
-			a->qe = qe + qle; a->re = rmax[0] + re + tle;
+			a->score = ksw_extend(l_query - qe, query + qe, rmax[1] - rmax[0] - re, rseq + re, 5, opt->mat, opt->q, opt->r, opt->w, a->score, &qle, &tle, &gtle, &gscore);
+			// similar to the above
+			if (gscore <= 0 || gscore <= a->score - opt->pen_clip) a->qe = qe + qle, a->re = rmax[0] + re + tle;
+			else a->qe = l_query, a->re = rmax[0] + re + gtle;
 		} else a->qe = l_query, a->re = s->rbeg + s->len;
 		if (bwa_verbose >= 4) printf("[%d] score=%d\t[%d,%d) <=> [%ld,%ld)\n", k, a->score, a->qb, a->qe, (long)a->rb, (long)a->re);
 
diff --git a/bwamem.h b/bwamem.h
index 8a7c7b8..5c63402 100644
--- a/bwamem.h
+++ b/bwamem.h
@@ -19,7 +19,10 @@ typedef struct __smem_i smem_i;
 
 typedef struct {
 	int a, b, q, r;         // match score, mismatch penalty and gap open/extension penalty. A gap of size k costs q+k*r
+	int pen_unpaired;       // phred-scaled penalty for unpaired reads
+	int pen_clip;           // clipping penalty. This score is not deducted from the DP score.
 	int w;                  // band width
+
 	int flag;               // see MEM_F_* macros
 	int min_seed_len;       // minimum seed length
 	float split_factor;     // split into a seed if MEM is longer than min_seed_len*split_factor
@@ -30,7 +33,6 @@ typedef struct {
 	int chunk_size;         // process chunk_size-bp sequences in a batch
 	float mask_level;       // regard a hit as redundant if the overlap with another better hit is over mask_level times the min length of the two hits
 	float chain_drop_ratio; // drop a chain if its seed coverage is below chain_drop_ratio times the seed coverage of a better chain overlapping with the small chain
-	int pen_unpaired;       // phred-scaled penalty for unpaired reads
 	int max_ins;            // when estimating insert size distribution, skip pairs with insert longer than this value
 	int max_matesw;         // perform maximally max_matesw rounds of mate-SW for each end
 	int8_t mat[25];         // scoring matrix; mat[0] == 0 if unset
diff --git a/fastmap.c b/fastmap.c
index b2d5f39..56cfb01 100644
--- a/fastmap.c
+++ b/fastmap.c
@@ -26,13 +26,14 @@ int main_mem(int argc, char *argv[])
 	void *ko = 0, *ko2 = 0;
 
 	opt = mem_opt_init();
-	while ((c = getopt(argc, argv, "paMCPHk:c:v:s:r:t:R:A:B:O:E:U:w:")) >= 0) {
+	while ((c = getopt(argc, argv, "paMCPHk:c:v:s:r:t:R:A:B:O:E:U:w:L:")) >= 0) {
 		if (c == 'k') opt->min_seed_len = atoi(optarg);
 		else if (c == 'w') opt->w = atoi(optarg);
 		else if (c == 'A') opt->a = atoi(optarg);
 		else if (c == 'B') opt->b = atoi(optarg);
 		else if (c == 'O') opt->q = atoi(optarg);
 		else if (c == 'E') opt->r = atoi(optarg);
+		else if (c == 'L') opt->pen_clip = atoi(optarg);
 		else if (c == 'U') opt->pen_unpaired = atoi(optarg);
 		else if (c == 't') opt->n_threads = atoi(optarg), opt->n_threads = opt->n_threads > 1? opt->n_threads : 1;
 		else if (c == 'P') opt->flag |= MEM_F_NOPAIRING;
@@ -64,6 +65,7 @@ int main_mem(int argc, char *argv[])
 		fprintf(stderr, "       -B INT     penalty for a mismatch [%d]\n", opt->b);
 		fprintf(stderr, "       -O INT     gap open penalty [%d]\n", opt->q);
 		fprintf(stderr, "       -E INT     gap extension penalty; a gap of size k cost {-O} + {-E}*k [%d]\n", opt->r);
+		fprintf(stderr, "       -L INT     penalty for clipping [%d]\n", opt->pen_clip);
 		fprintf(stderr, "       -U INT     penalty for an unpaired read pair [%d]\n", opt->pen_unpaired);
 		fprintf(stderr, "\nInput/output options:\n\n");
 		fprintf(stderr, "       -p         first query file consists of interleaved paired-end sequences\n");
diff --git a/ksw.c b/ksw.c
index 4cbcb32..b97fed5 100644
--- a/ksw.c
+++ b/ksw.c
@@ -359,11 +359,11 @@ typedef struct {
 	int32_t h, e;
 } eh_t;
 
-int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int h0, int *_qle, int *_tle)
+int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int h0, int *_qle, int *_tle, int *_gtle, int *_gscore)
 {
 	eh_t *eh; // score array
 	int8_t *qp; // query profile
-	int i, j, k, gapoe = gapo + gape, beg, end, max, max_i, max_j, max_gap;
+	int i, j, k, gapoe = gapo + gape, beg, end, max, max_i, max_j, max_gap, max_ie, gscore;
 	if (h0 < 0) h0 = 0;
 	// allocate memory
 	qp = malloc(qlen * m);
@@ -385,7 +385,7 @@ int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target,
 	max_gap = max_gap > 1? max_gap : 1;
 	w = w < max_gap? w : max_gap;
 	// DP loop
-	max = h0, max_i = max_j = -1;
+	max = h0, max_i = max_j = -1; max_ie = -1, gscore = -1;
 	beg = 0, end = qlen;
 	for (i = 0; LIKELY(i < tlen); ++i) {
 		int f = 0, h1, m = 0, mj = -1;
@@ -421,6 +421,10 @@ int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target,
 			f = f > h? f : h;   // computed F(i,j+1)
 		}
 		eh[end].h = h1; eh[end].e = 0;
+		if (j == qlen) {
+			max_ie = gscore > h1? max_ie : i;
+			gscore = gscore > h1? gscore : h1;
+		}
 		if (m == 0) break;
 		if (m > max) max = m, max_i = i, max_j = mj;
 		// update beg and end for the next round
@@ -433,6 +437,8 @@ int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target,
 	free(eh); free(qp);
 	if (_qle) *_qle = max_j + 1;
 	if (_tle) *_tle = max_i + 1;
+	if (_gtle) *_gtle = max_ie + 1;
+	if (_gscore) *_gscore = gscore;
 	return max;
 }
 
diff --git a/ksw.h b/ksw.h
index 5162dc0..40216d9 100644
--- a/ksw.h
+++ b/ksw.h
@@ -62,7 +62,7 @@ extern "C" {
 	 */
 	kswr_t ksw_align(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int xtra, kswq_t **qry);
 
-	int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int h0, int *_qle, int *_tle);
+	int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int h0, int *_qle, int *_tle, int *_gtle, int *_gscore);
 	int ksw_global(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int *_n_cigar, uint32_t **_cigar);
 
 #ifdef __cplusplus
diff --git a/main.c b/main.c
index da1d5dc..0590e63 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.6.2-r303-beta"
+#define PACKAGE_VERSION "0.6.2-r306-beta"
 #endif
 
 static int usage()