diff --git a/cram/cram_encode.c b/cram/cram_encode.c
index 5d22db54de..3cad124ce1 100644
--- a/cram/cram_encode.c
+++ b/cram/cram_encode.c
@@ -1761,7 +1761,6 @@ static int cram_generate_reference(cram_container *c, cram_slice *s, int r1) {
     c->ref_start = ref_start+1;
     c->ref_end   = ref_end+1;
     c->ref_free  = 1;
-
     return 0;
 
  err:
@@ -1997,6 +1996,9 @@ int cram_encode_container(cram_fd *fd, cram_container *c) {
                 fd->no_ref_counter -= (fd->no_ref_counter > 0);
                 pthread_mutex_unlock(&fd->ref_lock);
             }
+
+            if (c->ref_end > fd->refs->ref_id[c->ref_id]->LN_length)
+                c->ref_end = fd->refs->ref_id[c->ref_id]->LN_length;
         }
 
         // Iterate through records creating the cram blocks for some
diff --git a/cram/cram_io.c b/cram/cram_io.c
index 7f7ffca49e..65d906fb54 100644
--- a/cram/cram_io.c
+++ b/cram/cram_io.c
@@ -2734,7 +2734,7 @@ int refs2id(refs_t *r, sam_hdr_t *hdr) {
  * Returns 0 on success
  *         -1 on failure
  */
-static int refs_from_header(cram_fd *fd) {
+ int refs_from_header(cram_fd *fd) {
     if (!fd)
         return -1;
 
@@ -2787,10 +2787,12 @@ static int refs_from_header(cram_fd *fd) {
 
         /* Initialise likely filename if known */
         if ((ty = sam_hrecs_find_type_id(h->hrecs, "SQ", "SN", h->hrecs->ref[i].name))) {
-            if ((tag = sam_hrecs_find_key(ty, "M5", NULL))) {
+            if ((tag = sam_hrecs_find_key(ty, "M5", NULL)))
                 r->ref_id[j]->fn = string_dup(r->pool, tag->str+3);
-                //fprintf(stderr, "Tagging @SQ %s / %s\n", r->ref_id[h]->name, r->ref_id[h]->fn);
-            }
+
+            if ((tag = sam_hrecs_find_key(ty, "LN", NULL)))
+                // LN tag used when constructing consensus reference
+                r->ref_id[j]->LN_length = strtoll(tag->str+3, NULL, 0);
         }
 
         k = kh_put(refs, r->h_meta, r->ref_id[j]->name, &n);
diff --git a/cram/cram_structs.h b/cram/cram_structs.h
index 9540b56180..49c2e81d55 100644
--- a/cram/cram_structs.h
+++ b/cram/cram_structs.h
@@ -671,7 +671,8 @@ struct cram_slice {
 typedef struct ref_entry {
     char *name;
     char *fn;
-    int64_t length;
+    int64_t length;        // if 0 this indicates we haven't loaded it yet
+    int64_t LN_length;     // @SQ LN length, used to trim consensus ref
     int64_t offset;
     int bases_per_line;
     int line_length;