diff --git a/main.c b/main.c
index 17dacc6..b2362f5 100644
--- a/main.c
+++ b/main.c
@@ -69,7 +69,7 @@ static ko_longopt_t long_options[] = {
 	{ "sam-hit-only",   ko_no_argument,       342 },
 	{ "chain-gap-scale",ko_required_argument, 343 },
 	{ "alt",            ko_required_argument, 344 },
-	{ "alt-diff",       ko_required_argument, 345 },
+	{ "alt-drop",       ko_required_argument, 345 },
 	{ "help",           ko_no_argument,       'h' },
 	{ "max-intron-len", ko_required_argument, 'G' },
 	{ "version",        ko_no_argument,       'V' },
@@ -216,7 +216,7 @@ int main(int argc, char *argv[])
 		else if (c == 342) opt.flag |= MM_F_SAM_HIT_ONLY; // --sam-hit-only
 		else if (c == 343) opt.chain_gap_scale = atof(o.arg); // --chain-gap-scale
 		else if (c == 344) alt_list = o.arg; // --alt
-		else if (c == 345) opt.alt_diff_frac = atof(o.arg); // --alt-diff
+		else if (c == 345) opt.alt_drop = atof(o.arg); // --alt-drop
 		else if (c == 314) { // --frag
 			yes_or_no(&opt, MM_F_FRAG_MODE, o.longidx, o.arg, 1);
 		} else if (c == 315) { // --secondary
diff --git a/map.c b/map.c
index 80a2a3a..01d323c 100644
--- a/map.c
+++ b/map.c
@@ -249,7 +249,7 @@ static mm128_t *collect_seed_hits(void *km, const mm_mapopt_t *opt, int max_occ,
 static void chain_post(const mm_mapopt_t *opt, int max_chain_gap_ref, const mm_idx_t *mi, void *km, int qlen, int n_segs, const int *qlens, int *n_regs, mm_reg1_t *regs, mm128_t *a)
 {
 	if (!(opt->flag & MM_F_ALL_CHAINS)) { // don't choose primary mapping(s)
-		mm_set_parent(km, opt->mask_level, *n_regs, regs, opt->a * 2 + opt->b, opt->flag&MM_F_HARD_MLEVEL, opt->alt_diff_frac);
+		mm_set_parent(km, opt->mask_level, *n_regs, regs, opt->a * 2 + opt->b, opt->flag&MM_F_HARD_MLEVEL, opt->alt_drop);
 		if (n_segs <= 1) mm_select_sub(km, opt->pri_ratio, mi->k*2, opt->best_n, n_regs, regs);
 		else mm_select_sub_multi(km, opt->pri_ratio, 0.2f, 0.7f, max_chain_gap_ref, mi->k*2, opt->best_n, n_segs, qlens, n_regs, regs);
 		if (!(opt->flag & (MM_F_SPLICE|MM_F_SR|MM_F_NO_LJOIN))) // long join not working well without primary chains
@@ -262,7 +262,7 @@ static mm_reg1_t *align_regs(const mm_mapopt_t *opt, const mm_idx_t *mi, void *k
 	if (!(opt->flag & MM_F_CIGAR)) return regs;
 	regs = mm_align_skeleton(km, opt, mi, qlen, seq, n_regs, regs, a); // this calls mm_filter_regs()
 	if (!(opt->flag & MM_F_ALL_CHAINS)) { // don't choose primary mapping(s)
-		mm_set_parent(km, opt->mask_level, *n_regs, regs, opt->a * 2 + opt->b, opt->flag&MM_F_HARD_MLEVEL, opt->alt_diff_frac);
+		mm_set_parent(km, opt->mask_level, *n_regs, regs, opt->a * 2 + opt->b, opt->flag&MM_F_HARD_MLEVEL, opt->alt_drop);
 		mm_select_sub(km, opt->pri_ratio, mi->k*2, opt->best_n, n_regs, regs);
 		mm_set_sam_pri(*n_regs, regs);
 	}
@@ -344,7 +344,7 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
 	regs0 = mm_gen_regs(b->km, hash, qlen_sum, n_regs0, u, a);
 	if (mi->n_alt) {
 		mm_mark_alt(mi, n_regs0, regs0);
-		mm_hit_sort(b->km, &n_regs0, regs0, opt->alt_diff_frac); // this step can be merged into mm_gen_regs(); will do if this shows up in profile
+		mm_hit_sort(b->km, &n_regs0, regs0, opt->alt_drop); // this step can be merged into mm_gen_regs(); will do if this shows up in profile
 	}
 
 	if (mm_dbg_flag & MM_DBG_PRINT_SEED)
@@ -365,7 +365,7 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
 		seg = mm_seg_gen(b->km, hash, n_segs, qlens, n_regs0, regs0, n_regs, regs, a); // split fragment chain to separate segment chains
 		free(regs0);
 		for (i = 0; i < n_segs; ++i) {
-			mm_set_parent(b->km, opt->mask_level, n_regs[i], regs[i], opt->a * 2 + opt->b, opt->flag&MM_F_HARD_MLEVEL, opt->alt_diff_frac); // update mm_reg1_t::parent
+			mm_set_parent(b->km, opt->mask_level, n_regs[i], regs[i], opt->a * 2 + opt->b, opt->flag&MM_F_HARD_MLEVEL, opt->alt_drop); // update mm_reg1_t::parent
 			regs[i] = align_regs(opt, mi, b->km, qlens[i], seqs[i], &n_regs[i], regs[i], seg[i].a);
 			mm_set_mapq(b->km, n_regs[i], regs[i], opt->min_chain_score, opt->a, rep_len, is_sr);
 		}
@@ -508,8 +508,8 @@ static void merge_hits(step_t *s)
 					}
 				}
 			}
-			mm_hit_sort(km, &s->n_reg[k], s->reg[k], opt->alt_diff_frac);
-			mm_set_parent(km, opt->mask_level, s->n_reg[k], s->reg[k], opt->a * 2 + opt->b, opt->flag&MM_F_HARD_MLEVEL, opt->alt_diff_frac);
+			mm_hit_sort(km, &s->n_reg[k], s->reg[k], opt->alt_drop);
+			mm_set_parent(km, opt->mask_level, s->n_reg[k], s->reg[k], opt->a * 2 + opt->b, opt->flag&MM_F_HARD_MLEVEL, opt->alt_drop);
 			if (!(opt->flag & MM_F_ALL_CHAINS)) {
 				mm_select_sub(km, opt->pri_ratio, s->p->mi->k*2, opt->best_n, &s->n_reg[k], s->reg[k]);
 				mm_set_sam_pri(s->n_reg[k], s->reg[k]);
diff --git a/minimap.h b/minimap.h
index eb236ae..251879b 100644
--- a/minimap.h
+++ b/minimap.h
@@ -129,7 +129,7 @@ typedef struct {
 	int min_join_flank_sc;
 	float min_join_flank_ratio;
 
-	float alt_diff_frac;
+	float alt_drop;
 
 	int a, b, q, e, q2, e2; // matching score, mismatch, gap-open and gap-ext penalties
 	int sc_ambi; // score when one or both bases are "N"
diff --git a/minimap2.1 b/minimap2.1
index a45cbed..88d895c 100644
--- a/minimap2.1
+++ b/minimap2.1
@@ -124,6 +124,11 @@ will be effectively overridden by the options stored in the index file.
 .TP
 .BI --alt \ FILE
 List of ALT contigs [null]
+.TP
+.BI --alt-drop \ FLOAT
+Drop ALT hits by
+.I FLOAT
+fraction when ranking and computing mapping quality [0.15]
 .SS Mapping options
 .TP 10
 .BI -f \ FLOAT | INT1 [, INT2 ]
diff --git a/python/cmappy.pxd b/python/cmappy.pxd
index c8efb07..72a19d7 100644
--- a/python/cmappy.pxd
+++ b/python/cmappy.pxd
@@ -27,7 +27,7 @@ cdef extern from "minimap.h":
 		int max_join_long, max_join_short
 		int min_join_flank_sc
 		float min_join_flank_ratio
-		float alt_diff_frac
+		float alt_drop
 		int a, b, q, e, q2, e2
 		int sc_ambi
 		int noncan