diff --git a/bwameth.py b/bwameth.py
index 0cdf47e..699e9a9 100755
--- a/bwameth.py
+++ b/bwameth.py
@@ -380,7 +380,7 @@ def handle_reads(alns, set_as_failed):
 
         # first letter of chrom is 'f' or 'r'
         direction = aln.chrom[0]
-        aln.chrom = aln.chrom.lstrip('fr')
+        aln.chrom = aln.chrom[1:]
 
         if not aln.is_mapped():
             aln.seq = orig_seq