diff --git a/bwamem.c b/bwamem.c
index 71bf387..3fd008f 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -79,7 +79,6 @@ mem_opt_t *mem_opt_init()
 	o->min_chain_weight = 0;
 	o->max_chain_extend = 1<<30;
 	o->mapQ_coef_len = 50; o->mapQ_coef_fac = log(o->mapQ_coef_len);
-	o->min_pa_ratio = 0;
 	bwa_fill_scmat(o->a, o->b, o->mat);
 	return o;
 }
@@ -841,7 +840,7 @@ void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq
 	if (p->rid >= 0) { // with coordinate
 		kputs(bns->anns[p->rid].name, str); kputc('\t', str); // RNAME
 		kputl(p->pos + 1, str); kputc('\t', str); // POS
-		kputw(p->score < opt->min_pa_ratio * p->alt_sc? 0 : p->mapq, str); kputc('\t', str); // MAPQ
+		kputw(p->mapq, str); kputc('\t', str); // MAPQ
 		if (p->n_cigar) { // aligned
 			for (i = 0; i < p->n_cigar; ++i) {
 				int c = p->cigar[i]&0xf;
@@ -931,8 +930,6 @@ void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq
 		}
 		if (p->alt_sc > 0)
 			ksprintf(str, "\tpa:f:%.3f", (double)p->score / p->alt_sc);
-		if (p->score < opt->min_pa_ratio * p->alt_sc)
-			ksprintf(str, "\tom:i:%d", p->mapq);
 	}
 	if (p->XA) { kputsn("\tXA:Z:", 6, str); kputs(p->XA, str); }
 	if (s->comment) { kputc('\t', str); kputs(s->comment, str); }
diff --git a/bwamem.h b/bwamem.h
index ae53601..1746ab5 100644
--- a/bwamem.h
+++ b/bwamem.h
@@ -48,7 +48,6 @@ typedef struct {
 	float XA_drop_ratio;    // when counting hits for the XA tag, ignore alignments with score < XA_drop_ratio * max_score; only effective for the XA tag
 	float mask_level_redun;
 	float mapQ_coef_len;
-	float min_pa_ratio;
 	int mapQ_coef_fac;
 	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
diff --git a/fastmap.c b/fastmap.c
index ddf464a..18f3b0e 100644
--- a/fastmap.c
+++ b/fastmap.c
@@ -55,7 +55,7 @@ int main_mem(int argc, char *argv[])
 
 	opt = mem_opt_init();
 	memset(&opt0, 0, sizeof(mem_opt_t));
-	while ((c = getopt(argc, argv, "epaFMCSPHVYjk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:y:K:g:")) >= 0) {
+	while ((c = getopt(argc, argv, "epaFMCSPHVYjk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:y:K:")) >= 0) {
 		if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
 		else if (c == 'x') mode = optarg;
 		else if (c == 'w') opt->w = atoi(optarg), opt0.w = 1;
@@ -85,7 +85,6 @@ int main_mem(int argc, char *argv[])
 		else if (c == 'N') opt->max_chain_extend = atoi(optarg), opt0.max_chain_extend = 1;
 		else if (c == 'W') opt->min_chain_weight = atoi(optarg), opt0.min_chain_weight = 1;
 		else if (c == 'y') opt->max_mem_intv = atol(optarg), opt0.max_mem_intv = 1;
-		else if (c == 'g') opt->min_pa_ratio = atof(optarg), opt0.min_pa_ratio = 1;
 		else if (c == 'C') copy_comment = 1;
 		else if (c == 'K') fixed_chunk_size = atoi(optarg);
 		else if (c == 'h') {
@@ -172,7 +171,6 @@ int main_mem(int argc, char *argv[])
 		fprintf(stderr, "       -j            ignore ALT contigs\n");
 		fprintf(stderr, "\n");
 		fprintf(stderr, "       -v INT        verbose level: 1=error, 2=warning, 3=message, 4+=debugging [%d]\n", bwa_verbose);
-		fprintf(stderr, "       -g FLOAT      set mapQ to zero if the ratio of the primary-to-alt scores below FLOAT [%.3f]\n", opt->min_pa_ratio);
 		fprintf(stderr, "       -T INT        minimum score to output [%d]\n", opt->T);
 		fprintf(stderr, "       -h INT[,INT]  if there are <INT hits with score >80%% of the max score, output all in XA [%d,%d]\n", opt->max_XA_hits, opt->max_XA_hits_alt);
 		fprintf(stderr, "       -a            output all alignments for SE or unpaired PE\n");
diff --git a/main.c b/main.c
index e8fb688..12b0930 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.10-r930-dirty"
+#define PACKAGE_VERSION "0.7.10-r933-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);