--- a
+++ b/singlecellmultiomics/statistic/mappingquality.py
@@ -0,0 +1,49 @@
+from .statistic import StatisticHistogram
+import singlecellmultiomics.pyutils as pyutils
+import collections
+import pandas as pd
+import matplotlib.pyplot as plt
+import seaborn as sns
+
+
+class MappingQualityHistogram(StatisticHistogram):
+    def __init__(self, args):
+        StatisticHistogram.__init__(self, args)
+        self.histogram = collections.Counter()
+
+    def processRead(self, R1,R2):
+
+        for read in [R1,R2]:
+            if read is None:
+                continue
+
+            self.histogram[read.mapping_quality] += 1
+
+    def __repr__(self):
+        return f'The average mapping quality is {pyutils.meanOfCounter(self.histogram)}, SD:{pyutils.varianceOfCounter(self.histogram)}'
+
+    def get_df(self):
+        return pd.DataFrame.from_dict({'mq': self.histogram})
+
+    def to_csv(self, path):
+        self.get_df().to_csv(path)
+
+    def plot(self, target_path, title=None):
+        df = self.get_df()  # ,'UnmappedReads']]
+
+        df['mq'].plot.bar(figsize=(10, 4))
+        ax = plt.gca()
+        ax.set_xlabel('Mapping quality')
+        ax.set_ylabel('Frequency (reads)')
+
+        if title is not None:
+            plt.title(title)
+        plt.tight_layout()
+        plt.savefig(target_path)
+
+        ax.set_yscale('log')
+        sns.despine()
+        plt.tight_layout()
+        plt.savefig(target_path.replace('.png', '.log.png'))
+
+        plt.close()