diff --git a/db_schema_patches/3_to_4.sql b/db_schema_patches/3_to_4.sql
new file mode 100644
index 0000000..db2a69b
--- /dev/null
+++ b/db_schema_patches/3_to_4.sql
@@ -0,0 +1,10 @@
+# Updates schema from version 3 to version 4
+ALTER TABLE QC ADD samtools_positions_with_depth_of_0 INT UNSIGNED,
+	samtools_positions_with_depth_atleast_2 INT UNSIGNED,
+	samtools_positions_with_depth_atleast_5 INT UNSIGNED,
+	samtools_positions_with_depth_atleast_10 INT UNSIGNED,
+	samtools_positions_with_depth_atleast_20 INT UNSIGNED,
+	samtools_positions_with_depth_atleast_100 INT UNSIGNED;
+
+UPDATE Version SET version=4 WHERE version=3;
+
diff --git a/python/clockwork/db.py b/python/clockwork/db.py
index 3a89ba1..7da5201 100644
--- a/python/clockwork/db.py
+++ b/python/clockwork/db.py
@@ -5,6 +5,7 @@
 import re
 import sys
 import tempfile
+import shutil
 from operator import itemgetter
 from clockwork import (
     db_connection,
@@ -558,7 +559,9 @@ def make_qc_jobs_tsv(
                 output_dir = iso_dir.pipeline_dir(
                     row["sequence_replicate_number"], "qc", pipeline_version
                 )
-                assert not os.path.exists(output_dir)
+                if os.path.exists(output_dir):
+                    print("Warning:", output_dir, "already exists. Removing.", file=sys.stderr)
+                    shutil.rmtree(output_dir)
                 try:
                     os.makedirs(output_dir)
                 except:
@@ -1163,6 +1166,10 @@ def _update_qc_stats(self, seqrep_id, pipeline_version, pipeline_root):
         samtools_stats = samtools_qc.SamtoolsQc.stats_from_report(
             os.path.join(qc_dir, "samtools_qc", "samtools_qc.stats")
         )
+        depth_stats = samtools_qc.SamtoolsQc.depth_stats(
+             os.path.join(qc_dir, "samtools_qc", "samtools_qc.depths")
+        )
+
         fastqc_stats = fastqc.Fastqc.gather_all_stats(os.path.join(qc_dir, "fastqc"))
         assert len(fastqc_stats) == 2
         new_row = {"seqrep_id": seqrep_id, "pipeline_version": pipeline_version}
@@ -1196,6 +1203,13 @@ def _update_qc_stats(self, seqrep_id, pipeline_version, pipeline_root):
         new_row["het_snp_positions"] = het_stats["Positions_used"]
         new_row["het_snp_total_snps"] = het_stats["Total_SNPs"]
         new_row["het_snp_het_calls"] = het_stats["Het_SNPs"]
+        new_row["samtools_positions_with_depth_of_0"] = depth_stats["eq_0"]
+        new_row["samtools_positions_with_depth_atleast_2"] = depth_stats["atleast_2"]
+        new_row["samtools_positions_with_depth_atleast_5"] = depth_stats["atleast_5"]
+        new_row["samtools_positions_with_depth_atleast_10"] = depth_stats["atleast_10"]
+        new_row["samtools_positions_with_depth_atleast_20"] = depth_stats["atleast_20"]
+        new_row["samtools_positions_with_depth_atleast_100"] = depth_stats["atleast_100"]
+
 
         self.add_row_to_table("QC", new_row)
 
diff --git a/python/clockwork/db_schema.py b/python/clockwork/db_schema.py
index 9407415..827f7a5 100644
--- a/python/clockwork/db_schema.py
+++ b/python/clockwork/db_schema.py
@@ -1,4 +1,4 @@
-version = 3
+version = 4
 
 tables = {
     "Isolate": [
@@ -67,7 +67,13 @@
         ("het_snp_positions", "integer unsigned"),
         ("het_snp_total_snps", "integer unsigned"),
         ("het_snp_het_calls", "integer unsigned"),
-    ],
+        ("samtools_positions_with_depth_of_0", "integer unsigned"),
+        ("samtools_positions_with_depth_atleast_2", "integer unsigned"),
+        ("samtools_positions_with_depth_atleast_5", "integer unsigned"),
+        ("samtools_positions_with_depth_atleast_10", "integer unsigned"),
+        ("samtools_positions_with_depth_atleast_20", "integer unsigned"),
+        ("samtools_positions_with_depth_atleast_100", "integer unsigned"),
+ ],
     "Read_counts": [
         ("seqrep_id", "integer"),
         ("original_total", "integer unsigned"),
diff --git a/python/clockwork/samtools_qc.py b/python/clockwork/samtools_qc.py
index 0c4bf19..71f2ccc 100644
--- a/python/clockwork/samtools_qc.py
+++ b/python/clockwork/samtools_qc.py
@@ -21,6 +21,41 @@ def __init__(self, ref_fasta, reads1, reads2, outdir):
     def _map_reads(cls, ref_fasta, reads1, reads2, outfile):
         read_map.map_reads(ref_fasta, reads1, reads2, outfile, markdup=True)
 
+    @classmethod
+    def _make_depth_stats(cls, samfile, outprefix):
+        depth_file = outprefix + ".depths"
+        cmd = " ".join(["samtools depth", "-a", samfile, ">", depth_file])
+        utils.syscall(cmd)
+
+    @classmethod
+    def depth_stats(cls, filename):
+        depths = {
+            "eq_0": 0,
+            "atleast_2": 0,
+            "atleast_5": 0,
+            "atleast_10": 0,
+            "atleast_20": 0,
+            "atleast_100": 0,
+        }
+
+        with open(filename) as f:
+            for line in f:
+                _, _, depth = line.rstrip().split("\t")
+                depth = int(depth)
+                if depth == 0:
+                    depths["eq_0"] += 1
+                if depth >= 2:
+                    depths["atleast_2"] += 1
+                if depth >= 5:
+                    depths["atleast_5"] += 1
+                if depth >= 10:
+                    depths["atleast_10"] += 1
+                if depth >= 20:
+                    depths["atleast_20"] += 1
+                if depth >= 100:
+                    depths["atleast_100"] += 1
+        return depths
+
     @classmethod
     def _make_stats_and_plots(cls, samfile, ref_fasta, outprefix):
         stats_file = outprefix + ".stats"
@@ -101,6 +136,7 @@ def run(self):
         outprefix = os.path.join(self.outdir, "samtools_qc")
         samfile = os.path.join(self.outdir, "tmp.sam")
         SamtoolsQc._map_reads(self.ref_fasta, self.reads1, self.reads2, samfile)
+        SamtoolsQc._make_depth_stats(samfile, outprefix)
         SamtoolsQc._make_stats_and_plots(samfile, self.ref_fasta, outprefix)
         hsc = het_snp_caller.HetSnpCaller(
             samfile, self.ref_fasta, os.path.join(self.outdir, "het_snps")
diff --git a/python/clockwork/tests/data/db/update_qc_stats_pipeline_root/00/00/00/01/2/Pipelines/3/qc/1.0.0/samtools_qc/samtools_qc.depths b/python/clockwork/tests/data/db/update_qc_stats_pipeline_root/00/00/00/01/2/Pipelines/3/qc/1.0.0/samtools_qc/samtools_qc.depths
new file mode 100644
index 0000000..befaed6
--- /dev/null
+++ b/python/clockwork/tests/data/db/update_qc_stats_pipeline_root/00/00/00/01/2/Pipelines/3/qc/1.0.0/samtools_qc/samtools_qc.depths
@@ -0,0 +1,10 @@
+1	1	0
+1	2	1
+1	3	2
+1	4	3
+1	5	5
+1	6	7
+1	7	8
+1	8	0
+1	9	11
+1	10	110
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diff --git a/python/clockwork/tests/data/nextflow_qc/Reads/reads.1.1.fq.gz b/python/clockwork/tests/data/nextflow_qc/Reads/reads.1.1.fq.gz
index 90f11ba..5b068ee 100644
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diff --git a/python/clockwork/tests/data/nextflow_qc/Reads/reads.1.2.fq.gz b/python/clockwork/tests/data/nextflow_qc/Reads/reads.1.2.fq.gz
index 41d8349..0085a8b 100644
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diff --git a/python/clockwork/tests/data/nextflow_qc/mysql.dump b/python/clockwork/tests/data/nextflow_qc/mysql.dump
index 94165f1..234e46a 100644
--- a/python/clockwork/tests/data/nextflow_qc/mysql.dump
+++ b/python/clockwork/tests/data/nextflow_qc/mysql.dump
@@ -1,8 +1,8 @@
--- MySQL dump 10.13  Distrib 5.7.19, for Linux (x86_64)
+-- MySQL dump 10.13  Distrib 5.7.32, for Linux (x86_64)
 --
 -- Host: localhost    Database: test_db
 -- ------------------------------------------------------
--- Server version	5.7.19-0ubuntu0.17.04.1
+-- Server version	5.7.32-0ubuntu0.18.04.1
 
 /*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
 /*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
@@ -66,7 +66,7 @@ CREATE TABLE `Pipeline` (
 
 LOCK TABLES `Pipeline` WRITE;
 /*!40000 ALTER TABLE `Pipeline` DISABLE KEYS */;
-INSERT INTO `Pipeline` VALUES (1,1,NULL,'0.0.1','remove_contam',1,1),(2,2,NULL,'0.0.1','remove_contam',1,1),(3,3,NULL,'0.0.1','remove_contam',1,1),(4,4,NULL,'0.0.1','remove_contam',1,1);
+INSERT INTO `Pipeline` VALUES (1,1,NULL,'0.9.0','remove_contam',1,1),(2,2,NULL,'0.9.0','remove_contam',1,1),(3,3,NULL,'0.9.0','remove_contam',1,1),(4,4,NULL,'0.9.0','remove_contam',1,1);
 /*!40000 ALTER TABLE `Pipeline` ENABLE KEYS */;
 UNLOCK TABLES;
 
@@ -84,8 +84,8 @@ CREATE TABLE `QC` (
   `fastqc1_adapter_content` text,
   `fastqc1_basic_statistics` text,
   `fastqc1_kmer_content` text,
-  `fastqc1_max_sequence_length` int(11) DEFAULT NULL,
-  `fastqc1_min_sequence_length` int(11) DEFAULT NULL,
+  `fastqc1_max_sequence_length` int(10) unsigned DEFAULT NULL,
+  `fastqc1_min_sequence_length` int(10) unsigned DEFAULT NULL,
   `fastqc1_overrepresented_sequences` text,
   `fastqc1_per_base_n_content` text,
   `fastqc1_per_base_sequence_content` text,
@@ -94,14 +94,14 @@ CREATE TABLE `QC` (
   `fastqc1_per_sequence_quality_scores` text,
   `fastqc1_sequence_duplication_levels` text,
   `fastqc1_sequence_length_distribution` text,
-  `fastqc1_sequences_flagged_as_poor_quality` int(11) DEFAULT NULL,
-  `fastqc1_total_sequences` int(11) DEFAULT NULL,
+  `fastqc1_sequences_flagged_as_poor_quality` int(10) unsigned DEFAULT NULL,
+  `fastqc1_total_sequences` int(10) unsigned DEFAULT NULL,
   `fastqc2_gc` float DEFAULT NULL,
   `fastqc2_adapter_content` text,
   `fastqc2_basic_statistics` text,
   `fastqc2_kmer_content` text,
-  `fastqc2_max_sequence_length` int(11) DEFAULT NULL,
-  `fastqc2_min_sequence_length` int(11) DEFAULT NULL,
+  `fastqc2_max_sequence_length` int(10) unsigned DEFAULT NULL,
+  `fastqc2_min_sequence_length` int(10) unsigned DEFAULT NULL,
   `fastqc2_overrepresented_sequences` text,
   `fastqc2_per_base_n_content` text,
   `fastqc2_per_base_sequence_content` text,
@@ -110,23 +110,29 @@ CREATE TABLE `QC` (
   `fastqc2_per_sequence_quality_scores` text,
   `fastqc2_sequence_duplication_levels` text,
   `fastqc2_sequence_length_distribution` text,
-  `fastqc2_sequences_flagged_as_poor_quality` int(11) DEFAULT NULL,
-  `fastqc2_total_sequences` int(11) DEFAULT NULL,
-  `samtools_raw_total_sequences` int(11) DEFAULT NULL,
-  `samtools_reads_mapped` int(11) DEFAULT NULL,
-  `samtools_reads_duplicated` int(11) DEFAULT NULL,
-  `samtools_bases_mapped_cigar` int(11) DEFAULT NULL,
-  `samtools_bases_trimmed` int(11) DEFAULT NULL,
+  `fastqc2_sequences_flagged_as_poor_quality` int(10) unsigned DEFAULT NULL,
+  `fastqc2_total_sequences` int(10) unsigned DEFAULT NULL,
+  `samtools_raw_total_sequences` int(10) unsigned DEFAULT NULL,
+  `samtools_reads_mapped` int(10) unsigned DEFAULT NULL,
+  `samtools_reads_duplicated` int(10) unsigned DEFAULT NULL,
+  `samtools_bases_mapped_cigar` bigint(20) unsigned DEFAULT NULL,
+  `samtools_bases_trimmed` bigint(20) unsigned DEFAULT NULL,
   `samtools_error_rate` float DEFAULT NULL,
   `samtools_average_quality` float DEFAULT NULL,
   `samtools_insert_size_average` float DEFAULT NULL,
   `samtools_insert_size_standard_deviation` float DEFAULT NULL,
-  `samtools_inward_oriented_pairs` int(11) DEFAULT NULL,
-  `samtools_outward_oriented_pairs` int(11) DEFAULT NULL,
-  `samtools_pairs_with_other_orientation` int(11) DEFAULT NULL,
-  `het_snp_positions` int(11) DEFAULT NULL,
-  `het_snp_total_snps` int(11) DEFAULT NULL,
-  `het_snp_het_calls` int(11) DEFAULT NULL
+  `samtools_inward_oriented_pairs` int(10) unsigned DEFAULT NULL,
+  `samtools_outward_oriented_pairs` int(10) unsigned DEFAULT NULL,
+  `samtools_pairs_with_other_orientation` int(10) unsigned DEFAULT NULL,
+  `het_snp_positions` int(10) unsigned DEFAULT NULL,
+  `het_snp_total_snps` int(10) unsigned DEFAULT NULL,
+  `het_snp_het_calls` int(10) unsigned DEFAULT NULL,
+  `samtools_positions_with_depth_of_0` int(10) unsigned DEFAULT NULL,
+  `samtools_positions_with_depth_atleast_2` int(10) unsigned DEFAULT NULL,
+  `samtools_positions_with_depth_atleast_5` int(10) unsigned DEFAULT NULL,
+  `samtools_positions_with_depth_atleast_10` int(10) unsigned DEFAULT NULL,
+  `samtools_positions_with_depth_atleast_20` int(10) unsigned DEFAULT NULL,
+  `samtools_positions_with_depth_atleast_100` int(10) unsigned DEFAULT NULL
 ) ENGINE=InnoDB DEFAULT CHARSET=latin1;
 /*!40101 SET character_set_client = @saved_cs_client */;
 
@@ -148,11 +154,11 @@ DROP TABLE IF EXISTS `Read_counts`;
 /*!40101 SET character_set_client = utf8 */;
 CREATE TABLE `Read_counts` (
   `seqrep_id` int(11) DEFAULT NULL,
-  `original_total` int(11) DEFAULT NULL,
-  `contamination` int(11) DEFAULT NULL,
-  `not_contamination` int(11) DEFAULT NULL,
-  `unmapped` int(11) DEFAULT NULL,
-  `total_after_remove_contam` int(11) DEFAULT NULL
+  `original_total` int(10) unsigned DEFAULT NULL,
+  `contamination` int(10) unsigned DEFAULT NULL,
+  `not_contamination` int(10) unsigned DEFAULT NULL,
+  `unmapped` int(10) unsigned DEFAULT NULL,
+  `total_after_remove_contam` int(10) unsigned DEFAULT NULL
 ) ENGINE=InnoDB DEFAULT CHARSET=latin1;
 /*!40101 SET character_set_client = @saved_cs_client */;
 
@@ -162,7 +168,7 @@ CREATE TABLE `Read_counts` (
 
 LOCK TABLES `Read_counts` WRITE;
 /*!40000 ALTER TABLE `Read_counts` DISABLE KEYS */;
-INSERT INTO `Read_counts` VALUES (1,156,12,132,12,144),(2,156,12,132,12,144),(3,156,12,132,12,144),(4,156,12,132,12,144);
+INSERT INTO `Read_counts` VALUES (2,156,12,132,12,144),(4,156,12,132,12,144),(1,156,12,132,12,144),(3,156,12,132,12,144);
 /*!40000 ALTER TABLE `Read_counts` ENABLE KEYS */;
 UNLOCK TABLES;
 
@@ -230,7 +236,7 @@ DROP TABLE IF EXISTS `Seqrep`;
 CREATE TABLE `Seqrep` (
   `seqrep_id` int(11) NOT NULL AUTO_INCREMENT,
   `isolate_id` int(11) DEFAULT NULL,
-  `sequence_replicate_number` int(11) DEFAULT NULL,
+  `sequence_replicate_number` bigint(20) unsigned DEFAULT NULL,
   `original_reads_file_1_md5` text,
   `original_reads_file_2_md5` text,
   `remove_contam_reads_file_1_md5` text,
@@ -252,7 +258,7 @@ CREATE TABLE `Seqrep` (
 
 LOCK TABLES `Seqrep` WRITE;
 /*!40000 ALTER TABLE `Seqrep` DISABLE KEYS */;
-INSERT INTO `Seqrep` VALUES (1,1,43,'a3b22e537be7e1fc03c29df820f65b06','1676bdb60c23159fbaccc6975aed86c4','d9ea5077779c50c82bb9852fe5582cc0','5a1ef78ffdf7a4071a2b91d7c7dde8d5',0,1,'2017-12-25',0,'Illumina HiSeq 2000',NULL,0),(2,2,45,'b08620e2b9231ee66ae56f926d97f097','808911bb28af5c5674bda3b7c71e3a75','0da67fe9d1f3b4313304c87c4dbc635f','4f20723c34220b96995550b0e627cc1f',0,1,'2017-12-25',0,'Illumina HiSeq 2000',NULL,0),(3,3,47,'9981927389818aa1b57d6285ff490d23','5ffb53b040c7491807f963c3a94ad8fb','8e59250c494f103450c55f373a28ed96','e0c29c85b29af66dd810c5b0e741d0b7',0,1,'2017-12-25',0,'Illumina HiSeq 2000',NULL,0),(4,4,49,'9306e04decb6b721daf0ea765d860c3a','fb0f64bf6f7ff2b05d1fb521634b41b4','164f99ffb7f4416b2c60d7491019d65e','fd7a1fdfe55bcc47ffc5cfa0a655b52f',0,1,'2017-12-25',0,'Illumina HiSeq 2000',NULL,0);
+INSERT INTO `Seqrep` VALUES (1,1,43,'25c461ececa0271428a283c534497417','ece4028afddf2365477e130d84748c56','2096a6996aef36c5c75c0a9dba3ed3a4','e77815e19d1f81db41888900039cb1b1',0,1,'2017-12-25',0,'Illumina HiSeq 2000',NULL,0),(2,2,45,'e52a403846ab49eeb5cb9573822e1d92','3eef5d5e74295f7951526e23c7de656a','a4b21345c9ee84baeb4ce3b94aa478ca','3dc2b9875ddbf95de24990aa916492e4',0,1,'2017-12-25',0,'Illumina HiSeq 2000',NULL,0),(3,3,47,'bba6cc17819a133c18e8f0c0e099a55e','e72c48a02f49ee98a45682b6e4dfac56','f35b1d902a4fcfd475b4e3e325942683','a00056bcca5a6c99a4448a2354f6245c',0,1,'2017-12-25',0,'Illumina HiSeq 2000',NULL,0),(4,4,49,'866e1700d3c7e0d8c37edf8bb8399ffe','58ea111df4310f356460023a5483229f','e615dc85493f66a33594f8ff22292aa7','a69ad444c1b84271101f460c63e43e2b',0,1,'2017-12-25',0,'Illumina HiSeq 2000',NULL,0);
 /*!40000 ALTER TABLE `Seqrep` ENABLE KEYS */;
 UNLOCK TABLES;
 
@@ -274,7 +280,7 @@ CREATE TABLE `Version` (
 
 LOCK TABLES `Version` WRITE;
 /*!40000 ALTER TABLE `Version` DISABLE KEYS */;
-INSERT INTO `Version` VALUES (1);
+INSERT INTO `Version` VALUES (4);
 /*!40000 ALTER TABLE `Version` ENABLE KEYS */;
 UNLOCK TABLES;
 /*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */;
@@ -287,4 +293,4 @@ UNLOCK TABLES;
 /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
 /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
 
--- Dump completed on 2017-10-13 16:08:54
+-- Dump completed on 2020-11-13 14:09:42
diff --git a/python/clockwork/tests/data/samtools_qc/sam b/python/clockwork/tests/data/samtools_qc/depth_stats.sorted.sam
similarity index 99%
rename from python/clockwork/tests/data/samtools_qc/sam
rename to python/clockwork/tests/data/samtools_qc/depth_stats.sorted.sam
index ed3742a..f8e23f6 100644
--- a/python/clockwork/tests/data/samtools_qc/sam
+++ b/python/clockwork/tests/data/samtools_qc/depth_stats.sorted.sam
@@ -1,54 +1,56 @@
+@HD	VN:1.6	SO:coordinate
 @SQ	SN:1	LN:2000
 @PG	ID:bwa	PN:bwa	VN:0.7.12-r1039	CL:bwa mem samtools_qc.ref.fa samtools_qc.reads.1.fq samtools_qc.reads.2.fq
-1-52	83	1	899	60	75M	=	774	-200	CTGGGATGAATGCGCCGCAAGTAGCAGGTCCCGGCGTGGATACCTGATAGATGGTGACTAGCATGTACAAGTAAC	@D5DHDJHCEHH9IJ@IJJI3GGJJJIJIJDJJIH1?H8IGJJJ):G:JHFFJJ@JFJJJ8JFHH.HF<DFFCCB	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
-1-52	163	1	774	60	75M	=	899	200	CCGATACATACTGGTTTCTCTCCAGTGGAGGTCTTGGTTGCCTCTAGTTTCTACGATATACTCATGGTAGTGTAA	@@CD;F,F?HHHFJIHJGII32JJ+GIIH?JJHI)HA.GDGF3IBIB3(IG5IHJJJGDDH754G7FH<,4ED<D	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
-1-50	83	1	1861	60	75M	=	1737	-199	GGGCGGCAATGCTGAGGCCCTCTGTTCAATGAAACCCGTACTATATCTTATGATGACAATGAAATAGTCCTGTTT	DEC)H8FJDJGA)EH5&JJ7ABJ8IJH&JFIGJFGJJIFAJDIJHJCJIJE@I<IJJCHHIG=HHHHFF=FFCCC	NM:i:2	MD:Z:3A23C47	AS:i:66	XS:i:0
-1-50	163	1	1737	60	75M	=	1861	199	TCTCTTACCGTGGCTGGGTCCGGCGGCTGTGGGATTGCGAGAGTGTCCGGCACCACCCATGTACACTTTCGGGAA	C1@FF?FFHHH)HI+JCHJH@JJ:IJJIEI9DIGCBHJJGJHGI=GGDJGG,DG=JD,GGIGIDJJFDIDIFICC	NM:i:2	MD:Z:11T45A17	AS:i:65	XS:i:0
-1-48	99	1	1237	60	75M	=	1370	208	TGGAGAGTTAAGGAATTATCGTCATAGACACTTCGGGTTGAGAGATGGCGACGGTCAGTGCATGAGGCCGTCCAC	B@CDFFFF3HHB)JBIJE7EGEJCJIJJGFJJJIDGHI.IDJIDJJJIJJJE1IGJBGIGIHEEDGIIDICEH(H	NM:i:1	MD:Z:73C1	AS:i:73	XS:i:0
-1-48	147	1	1370	60	75M	=	1237	-208	GCAGAGCCAGTCTTAAAGCCTAGCGAACTTAATACCGTAGCTCAGAATTATGGAGAGCAGCAGGCTTCCATAGCA	D(DFAFIJEI@EIJ@5FI@JC>I=J>JIBJJIIIJE?:I0)CEIIHJIH1)>BIFGJJJIE<HHHHH@=FFDCCC	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
-1-46	99	1	1421	60	75M	=	1549	203	GGAGAGCAGCAGGCTTCCATAGCACAGGTTGACGGAGGAGTTTTGCTTGGATATCGGATGGGTTCTGTAGTGAAT	?:CDFFDDH;HHHHJGGJJJJJG?J1JI-2JE>IGJFIE?J;IJGE4JJJGIHIJGII(IJIJJDDIG:=HH@CD	NM:i:1	MD:Z:58A16	AS:i:70	XS:i:0
-1-46	147	1	1549	60	75M	=	1421	-203	CACCCTAGGTCAAGTTTTACGATTGCCCTAACGCCGCGGAGCGCGACCCGAAAAGCTATGGTCTGTAACTTTTCG	CDBDEFH;BHHBGJJJJDJDJJIGB?JH0GIJJIIGG*GJ@JFI?I0HFJIHIIJJ?GJ@I0FHFH;FFFFFCCB	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
-1-44	99	1	735	60	75M	=	864	204	TATGTGGACGTTGTATAGGGATATTACGTTACGCGTTAACCGATACATACTGGTTTCTCTCCAGTGGAGCTCTTG	CBCFFF@D?H)>HJ;IIJIJJGIIH<HIIJJ@DIJJ93AAIBDE?EJIDDFBIJI'J<HFJDG0JEJ2E/@B@DD	NM:i:1	MD:Z:69G5	AS:i:70	XS:i:0
-1-44	147	1	864	60	75M	=	735	-204	GGTCCTCCCATCTCCTGTGATGCATGGTGTGCTTTCTGGGATGAATGCGCCGCAAGTAGCAGGTCCCGGCGTGGA	BEF+<J'H>AHFI;JDJ?CDJEJGF>GIJEICHI*FJJ?IGIIHCJ<IGJGCJJ@JFAJJJ+DDHFDDDF+F@C@	NM:i:1	MD:Z:34A40	AS:i:70	XS:i:0
-1-42	99	1	1355	60	75M	=	1473	193	TCTACTGATATGCTAGCAGAGCCAGTCTTAAAGCATAGCGAACTTAATACCGTAGCTCAGAATTATGGAGAGCAG	B?C=FD?AHHH<CIIJGJJJIJEBJFCHH?JJEH(<J<DDHJEIIJEJGCIJ>J7';BEFD?EFGDGDEIE.HHE	NM:i:1	MD:Z:34C40	AS:i:70	XS:i:0
-1-42	147	1	1473	60	75M	=	1355	-193	ATCGGAAGGGTTCTGTAGTGAATGCACTACACGGTACTGGTACGTGGCAACTTAGGTCGTCACATCTAGGAGTCC	C(JFCF@(EF.CJD5JHH8HJDGJD3F@8GHHIDHECIJDIJBCJIJ1IJJJJHIEJJIIJG+F8HFF:D:D#C@	NM:i:1	MD:Z:72G2	AS:i:72	XS:i:0
-1-40	83	1	1547	60	75M	=	1434	-188	CGCACCCTAGGTCAAGTTTTACGATTGCCCTAACGCCGCGGAGCGCGACCCGAAAAGCTATGGTCTGTAACTTTT	>EDGJJF=GD77J7EDGJDIJJHJHJDGGIIGII@JFF8IG)IIII*J>HAJIII@IIJJ+CFHFHHFF:FFB?B	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
-1-40	163	1	1434	60	75M	=	1547	188	CTTCCATAGCACAGGTTGACGGAGGAGTTTTGCTTGGATATCGGAAGGGTTCTGTAGTGAATGCACTACACGGTA	@@CFFFAFH?DHG?8JIAJIE<FGJFGIJJI=GEJ0IJHIJI@GJBBEFJIG*BJJGCDDCJEGC?GJ0>E+HFD	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
-1-38	99	1	680	60	75M	=	801	196	CCCACATTTGACGGTACGCTACCGCAAAGGTATGTGTTAATGGAACAGACTTGCCTATGTGGACGTTGTATAGGG	@CCFFFFF?HHHHAIIEJGAJJJHFIH>EJGIIGGG<AJBJGIIIB;IJGJIFH.H(FIBD2IJD=@DB=E/DBE	NM:i:2	MD:Z:27C26T20	AS:i:65	XS:i:0
-1-38	147	1	801	60	75M	=	680	-196	GAGGTCTTGGTTGCCTCTAGTTTCTACGATATACTCATGGTAGTGTAACGCATAATCGAAGAGGGTCCTCCCATC	9HD?EDEEE;:IDJHGFJIIDH*FEI;HF?IJC)I*JGGIIDEJHJJJHDIJ8HGJFJJIJIFDCDHAFDFFC@;	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
-1-36	83	1	354	60	75M	=	230	-199	CGAATGGTATCGATACGTAGGAGGTGTGCCTTCGTAGGCTGTTTCTCAGGACGCCCAACTATTCTTTCCAATCCT	B9F8HGADIGJCDIEJJJDIJHIJG;IHJIJCD-JHJIGIFBJHJIIB)JJJ@JFJCJJJIJGHCF?DDDFF@@C	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
+@PG	ID:samtools	PN:samtools	PP:bwa	VN:1.10	CL:samtools sort -O sam sam
+1-22	99	1	127	60	75M	=	249	197	GGCACAATACCTCGTCCGTGTTACCAGACCAAACAAGACGTCCTCTTCAATGTTTAAATGACCCTCTCGTCATAC	@C@FFFFDBGH3G@JJG?)BJJJHHHIJEI9IHGJFDGIGJ@G>D/JI?JIJIID:JJIBGIIJ@IBD?IGI-;,	NM:i:1	MD:Z:74A0	AS:i:74	XS:i:0
+1-16	163	1	190	60	75M	=	311	196	CTCTCGTCATAAAACCTTTCTACTATGTGTTCCGCAACAATCAACAACTACAATGGCGCGTCGTGAATAACGCGA	<;@FFAF+DH:HHFHH?IJJ?CJJI<FGJJ*JJHHFI#FJHGIDI9IIHIGHIFHGGJJDFJDDCIGJHJFCCDD	NM:i:1	MD:Z:37G37	AS:i:70	XS:i:0
 1-36	163	1	230	60	75M	=	354	199	TCAACAACTACAATGGCGCGTCGTGAATAACGCGACGGCTGAGACGAACGGCGCGTGAATGAAGCGCTTAAACAG	BC@:FDFD?:DHGAJGIIJJIGJJIHJICJ&JIEJ0IFGIFIHIIB5DII>B;J8IDJEGHDC@H4BCDFJGBDD	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
-1-34	83	1	396	60	75M	=	267	-204	TTCTCAGGACGCCCAACTATTCTTTCCAATCCTACATCTGTTTCTTGCGTCGTAGCGGGACCCTCCACTGTTACT	DECJJBHHIJDE?H;FDGEJJGBJIDJ9JIJII>ADGJGGJIGJGI<HIJJ.JJJIIEGGJJHHHFH*BF;=@CC	NM:i:1	MD:Z:67T7	AS:i:70	XS:i:0
-1-34	163	1	267	60	75M	=	396	204	GCTGAGACGAACGGCGCGTGAATGAAGCGCTTAAACAGCTCAGGAGCCAGTCCCCTACGTCGCATATCCTGGCCA	=@@DDFF8HFHHHH)BIJGJ3FJJ<>J9HHIIJJJ3II<GJ)9IG9JJJ=IIFIIGJFHDJ@JI>IIHEJ>DIB?	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
 1-32	99	1	248	60	75M	=	372	199	CGTCGTGAATAACGCGACGGCTGAGACGAACGGCGCGTGAATGAAGCGCTTAAACAGCTCAGGAGCCAGTCGCCT	C?CFFFF=FHH>HFIIIEJHJJJEHBHCIIIFIDAHJIH9?.AJDIDJJADHJ;ICC@EJHJ;D>BHJIB4'B@F	NM:i:1	MD:Z:71C3	AS:i:71	XS:i:0
+1-22	147	1	249	60	75M	=	127	-197	GTCGTGAATAACGCGACGGCTGAGACGAACGGCGCGTGAATGAAGCGCTTAAACAGCTCAGGAGCCAGTCCCCTA	CBI,DGJD)J:GHJE@HGJFIJ<GG)JIIGIEJA>*IJEGFE@HEJCCJAF9E<IJFHJHIHDHHDHDF+DF+?@	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
+1-34	163	1	267	60	75M	=	396	204	GCTGAGACGAACGGCGCGTGAATGAAGCGCTTAAACAGCTCAGGAGCCAGTCCCCTACGTCGCATATCCTGGCCA	=@@DDFF8HFHHHH)BIJGJ3FJJ<>J9HHIIJJJ3II<GJ)9IG9JJJ=IIFIIGJFHDJ@JI>IIHEJ>DIB?	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
+1-16	83	1	311	60	75M	=	190	-196	AGCCAGTCCCCTACGTCGCATATCCTGGCCACTGGAGGTGAAGCGAATGGTATCGATACGTAGGAGGTGTGCCTT	EDFEDDDHHAGIF9JHFBCI-J=H0IGGIIF4(G@IIE=JIIJJIIHJCFIIJIBJJJ-JJJHFHHHFFFFFC@@	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
+1-4	99	1	336	60	75M	=	458	197	TGGCCACTGGAGGTGAAGCGAATGGTATCGATACGTAGGAGGTGTGCCTTCGTAGGCTGTTTCTCAGGACGCCCA	B@CFFFDAHGHFHI<HJJIICII2HJJJIGJCIIJ@B?DIHBJJIJEHIJ9IGIIJGHG=JDCEI@F)CIEG.DE	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
+1-36	83	1	354	60	75M	=	230	-199	CGAATGGTATCGATACGTAGGAGGTGTGCCTTCGTAGGCTGTTTCTCAGGACGCCCAACTATTCTTTCCAATCCT	B9F8HGADIGJCDIEJJJDIJHIJG;IHJIJCD-JHJIGIFBJHJIIB)JJJ@JFJCJJJIJGHCF?DDDFF@@C	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
 1-32	147	1	372	60	75M	=	248	-199	AGGAGGTGTGCCTTCGTAGGCTGTTTCTCAGGACGCCCAACTATTCTTTCCAATCCTACATCTGTTTCTTGCGTC	DADBF<;DJHCJ7DJJGIBFJJDIH*4H0EHAHF?CDG?JIJ:DJBI?JG?J3EJGJJJJJF1F?H?DFDFF1CB	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
-1-30	83	1	1359	60	75M	=	1241	-193	CTGATATGCTAGCAGAGCCAGTCTTAAAGCCTAGCGAACTTAATACCGTAGCTCAGAATTATGGAGAGCAGCAGG	HC5JE@CDDJ>IHDE.DJC=8JJ@JHGI?HJJJJIBIGEIFJGIJIJEJIGJJGJCHJJFJAFHCFH66FDFCCC	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
-1-30	163	1	1241	60	75M	=	1359	193	GAGTTAAGGAATTATCGTCATAGACACTTCGGGTTGAGAGATGGCGACGGTCAGTGCATGAGGCCGTCCCCAGAA	7C1FDFFFGFHHHHJIJEGIHFAJIGHIGJHHIHC):JGH<J.IFJFB?IHGJJFHDJ;IHHAD9DD@@HFCHF)	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
+1-34	83	1	396	60	75M	=	267	-204	TTCTCAGGACGCCCAACTATTCTTTCCAATCCTACATCTGTTTCTTGCGTCGTAGCGGGACCCTCCACTGTTACT	DECJJBHHIJDE?H;FDGEJJGBJIDJ9JIJII>ADGJGGJIGJGI<HIJJ.JJJIIEGGJJHHHFH*BF;=@CC	NM:i:1	MD:Z:67T7	AS:i:70	XS:i:0
+1-4	147	1	458	60	75M	=	336	-197	CTCCATTGTTACTTATTAGGTTCTCGTTATGTCTCATAATCTCAGTGCTGGTGTGATAAGCAAACCACCCAACTG	HECDCFDBDDEJHGEJHE)FJ<JI5J(IJJIFDIJ;C.JHJJHIJ1JDIJHJ+<JHJ+JIJ9GCHHFFDF#BC@B	NM:i:1	MD:Z:70T4	AS:i:70	XS:i:0
+1-8	99	1	463	60	75M	=	586	198	TTGTTACTTATTAGGTTCTCGTTATGTCTCATAATCTCAGTGCTGGTGTGATAAGCAAACCACCCTACTGGCACG	CBCFFFFF?HHHHJ(?JJFJHGH8IHDFFJJDHH:JGIHHG5BJ'B)J5DIGHJG<EIDHH8J8FJJJDDDHDEF	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
 1-28	99	1	534	60	75M	=	655	196	CACGAAGTTCACAGAAGTGAGATTATTTCTCGTTTGGCAGTCTTGATGCGCGGGGGACACTTCTTTAAGCTCGGT	C=CAFFFFH:FHGJJJ@IIJAI:86J)JJD>IGIJIGHFJHIGJHEHIJ)EJIF-IE.E?BFIF:FAE3ECD<GD	NM:i:2	MD:Z:26G22T25	AS:i:65	XS:i:0
+1-8	147	1	586	60	75M	=	463	-198	GGGGACACTTCTTTAAGCTCGGTGTGGTGGGCCCGACCCTGGACGCGCGACGAAGCTAAGTTTGCAGTAATTAAC	)D@GDDI;FJD)-HEGHHGGGJ<IGC<GE)CD#IJFJJJHJJIHJJ1CAIGIDJJFJ?C4+IGHHHHD*0FDCC@	NM:i:1	MD:Z:32A42	AS:i:70	XS:i:0
 1-28	147	1	655	60	75M	=	534	-196	ATTAACCGACATCTTTGTGAACCGACCCACATTTGACGGTACGCTACCGCAACGGTATGTGTTAATGGAACAGAC	HCIBDJJJJH.JJ7JH,JJGI@GI8GID=GJIJJDHJEJ,IJ9G+JJIBI*J:JFJGCFIJ,FFHHHFFFFDC<B	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
-1-26	99	1	1031	60	75M	=	1156	200	ACTAATTGATCAGTAATTTATTAAGCACGGTGTTAACTTCTGTTTAGTGGGCTAAAATAGCAGATGTAGGGACCT	?@CFDFAFFFHGHJJ2IHJGHJ?AJJ<HJJI@);.DJA?BG.I<)G?HJ(JAJJDIIE;H=GH=HHDEJDFBDBC	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
-1-26	147	1	1156	60	75M	=	1031	-200	AGTGACTAACGCCGGGAATTCCTCGATATATAGTTTGATAGCTGATACTTATGGCGCAACGGCCACGCCCACTTT	+CEDEFDJFJIAD=DJJBJDFFIDDDJJHJEHI(?I0GBGIIJI@?JJJHH:JIIIJJI)EGGAHHGFFFF+BCB	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
+1-20	163	1	662	60	75M	=	783	196	GACATCTTTGTGAACCGACCCACATTTGACGGTACGCTACCGCAACGGTATGTGTTAATGGAACAGACTTGCTTA	BB@DFFFEHH??HFHJIIJIH<3ID<HJIFG<JJEII8JBH/DHDICJDJDHJGDBHIJ>(CCJ5FDHFDI?D@F	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
+1-10	99	1	662	60	75M	=	785	198	GACATCTTTGTGAACCGACCCACATTTGACGGTACGCTACCGCAACGGTATGTGTTAATGGAACAGACTTGCTTA	CCCDFFFDFHHDDJH+IJJEJIG9HJJCIJIHIEIGIEIJCC?GJHGHBDI5J(=BJJEFHJJC=FGHICG6DHD	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
+1-38	99	1	680	60	75M	=	801	196	CCCACATTTGACGGTACGCTACCGCAAAGGTATGTGTTAATGGAACAGACTTGCCTATGTGGACGTTGTATAGGG	@CCFFFFF?HHHHAIIEJGAJJJHFIH>EJGIIGGG<AJBJGIIIB;IJGJIFH.H(FIBD2IJD=@DB=E/DBE	NM:i:2	MD:Z:27C26T20	AS:i:65	XS:i:0
+1-44	99	1	735	60	75M	=	864	204	TATGTGGACGTTGTATAGGGATATTACGTTACGCGTTAACCGATACATACTGGTTTCTCTCCAGTGGAGCTCTTG	CBCFFF@D?H)>HJ;IIJIJJGIIH<HIIJJ@DIJJ93AAIBDE?EJIDDFBIJI'J<HFJDG0JEJ2E/@B@DD	NM:i:1	MD:Z:69G5	AS:i:70	XS:i:0
+1-52	163	1	774	60	75M	=	899	200	CCGATACATACTGGTTTCTCTCCAGTGGAGGTCTTGGTTGCCTCTAGTTTCTACGATATACTCATGGTAGTGTAA	@@CD;F,F?HHHFJIHJGII32JJ+GIIH?JJHI)HA.GDGF3IBIB3(IG5IHJJJGDDH754G7FH<,4ED<D	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
+1-20	83	1	783	60	75M	=	662	-196	ACTGGTTTCTCTCCAGTGGAGGTCTTGGTTGCCTCTAGTTTCTACGATATACTCATGGTAGTGTAACGCATACTC	EHDDH,;;DDJ/J<CID?GHIIIIIGAIJI3BJGGJIICGHJJEJBEJIJJ(AHIJIIIJJJHDHHHDDFFD(C1	NM:i:1	MD:Z:72A2	AS:i:72	XS:i:0
+1-10	147	1	785	60	75M	=	662	-198	TGGTTTCTCTCCAGTGGAGGTCTTGGTTGCCTCTAGTTTCTACGATATACTCATGGTAGTGTAACGAATAATCGA	BEIJ>DAIF@FFIFJEEJFIIJ?BHGIDG;;EGHIEJ*E=G9HG@?JIDHIHBJII3ID?IIHDHH#FFDFFC@@	NM:i:1	MD:Z:66C8	AS:i:70	XS:i:0
+1-38	147	1	801	60	75M	=	680	-196	GAGGTCTTGGTTGCCTCTAGTTTCTACGATATACTCATGGTAGTGTAACGCATAATCGAAGAGGGTCCTCCCATC	9HD?EDEEE;:IDJHGFJIIDH*FEI;HF?IJC)I*JGGIIDEJHJJJHDIJ8HGJFJJIJIFDCDHAFDFFC@;	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
+1-44	147	1	864	60	75M	=	735	-204	GGTCCTCCCATCTCCTGTGATGCATGGTGTGCTTTCTGGGATGAATGCGCCGCAAGTAGCAGGTCCCGGCGTGGA	BEF+<J'H>AHFI;JDJ?CDJEJGF>GIJEICHI*FJJ?IGIIHCJ<IGJGCJJ@JFAJJJ+DDHFDDDF+F@C@	NM:i:1	MD:Z:34A40	AS:i:70	XS:i:0
 1-24	99	1	887	60	75M	=	1016	204	ATGGTGTGCTTACTGGGATGAATGCGCCGCAAGTAGCAGGTCCCGGCGTGGATACCTGATAGATGGTGACTAGCA	C@=FFDFFHHGBGJJIIIJICJEIJJ?DIJHCAIIJJFGIJJIEGHJJJIE>DHH@FIDJGI;HDGG;J+FIFC?	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
+1-52	83	1	899	60	75M	=	774	-200	CTGGGATGAATGCGCCGCAAGTAGCAGGTCCCGGCGTGGATACCTGATAGATGGTGACTAGCATGTACAAGTAAC	@D5DHDJHCEHH9IJ@IJJI3GGJJJIJIJDJJIH1?H8IGJJJ):G:JHFFJJ@JFJJJ8JFHH.HF<DFFCCB	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
+1-14	163	1	949	60	75M	=	1069	195	ATGGTGACTAGCATGTACAAGTAACCTTGTCTATTGAGCTTCGAGGATGCATACAAGCCCACCCGCAGCCGCAAC	B@CBFFFFD:HHH<F@JJI=JJCHJBC@I:JDGGG?GJIIJDEJEHJCGGCCBHJJIJ3E)JHDB(EFJB@IDDF	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
 1-24	147	1	1016	60	75M	=	887	-204	GCCGCAACAGCGACGACTAATTGATCAGTAATTTATTAAGCACGGTGTTAACTTCTGTTTAGTGGGCTAAAATAG	=DE@FFFJBJ;IGJ?DIFBJJJIBGII.BEBJJJIIGIJGFBIECJ9JGG3JF<IIHGJGIFFAHHHFEFF4CC?	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
-1-22	99	1	127	60	75M	=	249	197	GGCACAATACCTCGTCCGTGTTACCAGACCAAACAAGACGTCCTCTTCAATGTTTAAATGACCCTCTCGTCATAC	@C@FFFFDBGH3G@JJG?)BJJJHHHIJEI9IHGJFDGIGJ@G>D/JI?JIJIID:JJIBGIIJ@IBD?IGI-;,	NM:i:1	MD:Z:74A0	AS:i:74	XS:i:0
-1-22	147	1	249	60	75M	=	127	-197	GTCGTGAATAACGCGACGGCTGAGACGAACGGCGCGTGAATGAAGCGCTTAAACAGCTCAGGAGCCAGTCCCCTA	CBI,DGJD)J:GHJE@HGJFIJ<GG)JIIGIEJA>*IJEGFE@HEJCCJAF9E<IJFHJHIHDHHDHDF+DF+?@	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
-1-20	83	1	783	60	75M	=	662	-196	ACTGGTTTCTCTCCAGTGGAGGTCTTGGTTGCCTCTAGTTTCTACGATATACTCATGGTAGTGTAACGCATACTC	EHDDH,;;DDJ/J<CID?GHIIIIIGAIJI3BJGGJIICGHJJEJBEJIJJ(AHIJIIIJJJHDHHHDDFFD(C1	NM:i:1	MD:Z:72A2	AS:i:72	XS:i:0
-1-20	163	1	662	60	75M	=	783	196	GACATCTTTGTGAACCGACCCACATTTGACGGTACGCTACCGCAACGGTATGTGTTAATGGAACAGACTTGCTTA	BB@DFFFEHH??HFHJIIJIH<3ID<HJIFG<JJEII8JBH/DHDICJDJDHJGDBHIJ>(CCJ5FDHFDI?D@F	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
-1-18	83	1	1458	60	75M	=	1333	-200	GAGTTTTGCTTGGATATCGGAAGGGTTCTGTAGTGAATGCACTACACGGTACTGGTACGTGGCAACTTAGGTCGT	D>GB;)HE9EA.?FIJJGF.DDEEJI)JGE(B6JIIJCG3GJECIGIJF?JJHJGAGJJEGFHHHGDFFFFD@CB	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
-1-18	163	1	1333	60	75M	=	1458	200	GTCGTTGTTCCCGATGAAGACGTCTACTGATATGCTAGCAGAGCCAGTCTTAAAGCCTAGCGAACTTAATTCCGT	C@CFFFFFHH?HFIJGHGIII+ICJIF8GHIDJGJGJHEIGGII'H(GJGIGGGID8JDGEJIDDGIB89(DDE@	NM:i:1	MD:Z:70A4	AS:i:70	XS:i:0
-1-16	83	1	311	60	75M	=	190	-196	AGCCAGTCCCCTACGTCGCATATCCTGGCCACTGGAGGTGAAGCGAATGGTATCGATACGTAGGAGGTGTGCCTT	EDFEDDDHHAGIF9JHFBCI-J=H0IGGIIF4(G@IIE=JIIJJIIHJCFIIJIBJJJ-JJJHFHHHFFFFFC@@	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
-1-16	163	1	190	60	75M	=	311	196	CTCTCGTCATAAAACCTTTCTACTATGTGTTCCGCAACAATCAACAACTACAATGGCGCGTCGTGAATAACGCGA	<;@FFAF+DH:HHFHH?IJJ?CJJI<FGJJ*JJHHFI#FJHGIDI9IIHIGHIFHGGJJDFJDDCIGJHJFCCDD	NM:i:1	MD:Z:37G37	AS:i:70	XS:i:0
+1-26	99	1	1031	60	75M	=	1156	200	ACTAATTGATCAGTAATTTATTAAGCACGGTGTTAACTTCTGTTTAGTGGGCTAAAATAGCAGATGTAGGGACCT	?@CFDFAFFFHGHJJ2IHJGHJ?AJJ<HJJI@);.DJA?BG.I<)G?HJ(JAJJDIIE;H=GH=HHDEJDFBDBC	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
 1-14	83	1	1069	60	75M	=	949	-195	TCTGTTTAGTGGGCTAAAATAGCAGATGTAGGGACCTCAGGAGCTAGACGGGGACCTACAACTTTGCGGGAACCA	DHDDFJJF5@)@DGIAGHJGJHEJEDHI8G(BCHG8JJIJJHGD)FG<IGCAF<HJDAJJCIHCHHH2(BFFB<C	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
-1-14	163	1	949	60	75M	=	1069	195	ATGGTGACTAGCATGTACAAGTAACCTTGTCTATTGAGCTTCGAGGATGCATACAAGCCCACCCGCAGCCGCAAC	B@CBFFFFD:HHH<F@JJI=JJCHJBC@I:JDGGG?GJIIJDEJEHJCGGCCBHJJIJ3E)JHDB(EFJB@IDDF	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
-1-12	83	1	1286	60	75M	=	1158	-203	GACGGTCAGTGCATGAGGCCGTCCCCAGAAGCTCCCCTATGCTGTCCGTCGTTGTTCCCGATGAAGACGTCTACT	FF(9JFE?F8D7;FAJ6HHHIJIJII=J3GBJJGIJ1HJIJJJFHIEIJIJJH)JJIJJGIJD+F>HFFFFFB@:	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
+1-26	147	1	1156	60	75M	=	1031	-200	AGTGACTAACGCCGGGAATTCCTCGATATATAGTTTGATAGCTGATACTTATGGCGCAACGGCCACGCCCACTTT	+CEDEFDJFJIAD=DJJBJDFFIDDDJJHJEHI(?I0GBGIIJI@?JJJHH:JIIIJJI)EGGAHHGFFFF+BCB	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
 1-12	163	1	1158	60	75M	=	1286	203	TGACTAACGCCGGGAATTCCTCGATATATAGTTTGATAGCTGATACTTATGGCGCAACGGCCACGCCCACTTTGG	??C=DFFBDHHHFHJ?IFEJIGGJJJJJJIJBIIEJCJ?GI(?JGJJ2AAHIG9HF4ED.J>BHIEF4DHD)FEH	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
-1-10	99	1	662	60	75M	=	785	198	GACATCTTTGTGAACCGACCCACATTTGACGGTACGCTACCGCAACGGTATGTGTTAATGGAACAGACTTGCTTA	CCCDFFFDFHHDDJH+IJJEJIG9HJJCIJIHIEIGIEIJCC?GJHGHBDI5J(=BJJEFHJJC=FGHICG6DHD	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
-1-10	147	1	785	60	75M	=	662	-198	TGGTTTCTCTCCAGTGGAGGTCTTGGTTGCCTCTAGTTTCTACGATATACTCATGGTAGTGTAACGAATAATCGA	BEIJ>DAIF@FFIFJEEJFIIJ?BHGIDG;;EGHIEJ*E=G9HG@?JIDHIHBJII3ID?IIHDHH#FFDFFC@@	NM:i:1	MD:Z:66C8	AS:i:70	XS:i:0
-1-8	99	1	463	60	75M	=	586	198	TTGTTACTTATTAGGTTCTCGTTATGTCTCATAATCTCAGTGCTGGTGTGATAAGCAAACCACCCTACTGGCACG	CBCFFFFF?HHHHJ(?JJFJHGH8IHDFFJJDHH:JGIHHG5BJ'B)J5DIGHJG<EIDHH8J8FJJJDDDHDEF	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
-1-8	147	1	586	60	75M	=	463	-198	GGGGACACTTCTTTAAGCTCGGTGTGGTGGGCCCGACCCTGGACGCGCGACGAAGCTAAGTTTGCAGTAATTAAC	)D@GDDI;FJD)-HEGHHGGGJ<IGC<GE)CD#IJFJJJHJJIHJJ1CAIGIDJJFJ?C4+IGHHHHD*0FDCC@	NM:i:1	MD:Z:32A42	AS:i:70	XS:i:0
-1-6	83	1	1880	60	75M	=	1760	-195	CTCTGTTCCATGAAACCCGTACTATATCTTATGATGACAATGAAATAGTCCTGTTTTACGACTCCAAGTTTCCTG	JDD=DJDID;)DF=FIB@FB8IBIJJGHJIIJJHIIIGJ1IJJJJGG(?J*HJFEI<JJ<JEDFHDHFFF@FCC@	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
-1-6	163	1	1760	60	75M	=	1880	195	CGGCTGTGGGATTGCGAGAGTGTCCGGCACCACCCATGTACACTTTCGGGAACACTCATTCGAAGAGGTTCTGCA	?1CFFFF@8FDFHGIIJICFIFJIJJ:JBIJGIJ)*II?I(EJJIGFG<HHHIGDI>FHDJFHFCHEJCFFCJE>	NM:i:1	MD:Z:34A40	AS:i:70	XS:i:0
-1-4	99	1	336	60	75M	=	458	197	TGGCCACTGGAGGTGAAGCGAATGGTATCGATACGTAGGAGGTGTGCCTTCGTAGGCTGTTTCTCAGGACGCCCA	B@CFFFDAHGHFHI<HJJIICII2HJJJIGJCIIJ@B?DIHBJJIJEHIJ9IGIIJGHG=JDCEI@F)CIEG.DE	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
-1-4	147	1	458	60	75M	=	336	-197	CTCCATTGTTACTTATTAGGTTCTCGTTATGTCTCATAATCTCAGTGCTGGTGTGATAAGCAAACCACCCAACTG	HECDCFDBDDEJHGEJHE)FJ<JI5J(IJJIFDIJ;C.JHJJHIJ1JDIJHJ+<JHJ+JIJ9GCHHFFDF#BC@B	NM:i:1	MD:Z:70T4	AS:i:70	XS:i:0
-1-2	83	1	1483	60	75M	=	1358	-200	TTCTGTAGTGAATGCACTACCCGGTACTGATACGTGGCAACTTAGGTCGTCACATCTAGGAGGCCGCACCCTAGG	@>CECECECB?IGD;5GHGD)IJDIJJH70IIJJEJD>GIIJIIJIIFIJGJJ+GGJJJIEJF3HDHFFFFDC?C	NM:i:2	MD:Z:20A8G45	AS:i:65	XS:i:0
+1-48	99	1	1237	60	75M	=	1370	208	TGGAGAGTTAAGGAATTATCGTCATAGACACTTCGGGTTGAGAGATGGCGACGGTCAGTGCATGAGGCCGTCCAC	B@CDFFFF3HHB)JBIJE7EGEJCJIJJGFJJJIDGHI.IDJIDJJJIJJJE1IGJBGIGIHEEDGIIDICEH(H	NM:i:1	MD:Z:73C1	AS:i:73	XS:i:0
+1-30	163	1	1241	60	75M	=	1359	193	GAGTTAAGGAATTATCGTCATAGACACTTCGGGTTGAGAGATGGCGACGGTCAGTGCATGAGGCCGTCCCCAGAA	7C1FDFFFGFHHHHJIJEGIHFAJIGHIGJHHIHC):JGH<J.IFJFB?IHGJJFHDJ;IHHAD9DD@@HFCHF)	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
+1-12	83	1	1286	60	75M	=	1158	-203	GACGGTCAGTGCATGAGGCCGTCCCCAGAAGCTCCCCTATGCTGTCCGTCGTTGTTCCCGATGAAGACGTCTACT	FF(9JFE?F8D7;FAJ6HHHIJIJII=J3GBJJGIJ1HJIJJJFHIEIJIJJH)JJIJJGIJD+F>HFFFFFB@:	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
+1-18	163	1	1333	60	75M	=	1458	200	GTCGTTGTTCCCGATGAAGACGTCTACTGATATGCTAGCAGAGCCAGTCTTAAAGCCTAGCGAACTTAATTCCGT	C@CFFFFFHH?HFIJGHGIII+ICJIF8GHIDJGJGJHEIGGII'H(GJGIGGGID8JDGEJIDDGIB89(DDE@	NM:i:1	MD:Z:70A4	AS:i:70	XS:i:0
+1-42	99	1	1355	60	75M	=	1473	193	TCTACTGATATGCTAGCAGAGCCAGTCTTAAAGCATAGCGAACTTAATACCGTAGCTCAGAATTATGGAGAGCAG	B?C=FD?AHHH<CIIJGJJJIJEBJFCHH?JJEH(<J<DDHJEIIJEJGCIJ>J7';BEFD?EFGDGDEIE.HHE	NM:i:1	MD:Z:34C40	AS:i:70	XS:i:0
 1-2	163	1	1358	60	75M	=	1483	200	ACTGATATGCTAGCAGAGCCAGTCTTAAAGCCTAGCGCACTTAATACCGTAGCTCAGAATTATGGAGAGCAGCAG	+@@FBDDFDHHHG<,IDH;#IGG@IJHFFIIFJJJ*:'HEJJJF.JJBCJ@ICHJJGFBJ7I7JGJJHID(HDG<	NM:i:1	MD:Z:37A37	AS:i:70	XS:i:0
+1-30	83	1	1359	60	75M	=	1241	-193	CTGATATGCTAGCAGAGCCAGTCTTAAAGCCTAGCGAACTTAATACCGTAGCTCAGAATTATGGAGAGCAGCAGG	HC5JE@CDDJ>IHDE.DJC=8JJ@JHGI?HJJJJIBIGEIFJGIJIJEJIGJJGJCHJJFJAFHCFH66FDFCCC	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
+1-48	147	1	1370	60	75M	=	1237	-208	GCAGAGCCAGTCTTAAAGCCTAGCGAACTTAATACCGTAGCTCAGAATTATGGAGAGCAGCAGGCTTCCATAGCA	D(DFAFIJEI@EIJ@5FI@JC>I=J>JIBJJIIIJE?:I0)CEIIHJIH1)>BIFGJJJIE<HHHHH@=FFDCCC	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
+1-46	99	1	1421	60	75M	=	1549	203	GGAGAGCAGCAGGCTTCCATAGCACAGGTTGACGGAGGAGTTTTGCTTGGATATCGGATGGGTTCTGTAGTGAAT	?:CDFFDDH;HHHHJGGJJJJJG?J1JI-2JE>IGJFIE?J;IJGE4JJJGIHIJGII(IJIJJDDIG:=HH@CD	NM:i:1	MD:Z:58A16	AS:i:70	XS:i:0
+1-40	163	1	1434	60	75M	=	1547	188	CTTCCATAGCACAGGTTGACGGAGGAGTTTTGCTTGGATATCGGAAGGGTTCTGTAGTGAATGCACTACACGGTA	@@CFFFAFH?DHG?8JIAJIE<FGJFGIJJI=GEJ0IJHIJI@GJBBEFJIG*BJJGCDDCJEGC?GJ0>E+HFD	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
+1-18	83	1	1458	60	75M	=	1333	-200	GAGTTTTGCTTGGATATCGGAAGGGTTCTGTAGTGAATGCACTACACGGTACTGGTACGTGGCAACTTAGGTCGT	D>GB;)HE9EA.?FIJJGF.DDEEJI)JGE(B6JIIJCG3GJECIGIJF?JJHJGAGJJEGFHHHGDFFFFD@CB	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
+1-42	147	1	1473	60	75M	=	1355	-193	ATCGGAAGGGTTCTGTAGTGAATGCACTACACGGTACTGGTACGTGGCAACTTAGGTCGTCACATCTAGGAGTCC	C(JFCF@(EF.CJD5JHH8HJDGJD3F@8GHHIDHECIJDIJBCJIJ1IJJJJHIEJJIIJG+F8HFF:D:D#C@	NM:i:1	MD:Z:72G2	AS:i:72	XS:i:0
+1-2	83	1	1483	60	75M	=	1358	-200	TTCTGTAGTGAATGCACTACCCGGTACTGATACGTGGCAACTTAGGTCGTCACATCTAGGAGGCCGCACCCTAGG	@>CECECECB?IGD;5GHGD)IJDIJJH70IIJJEJD>GIIJIIJIIFIJGJJ+GGJJJIEJF3HDHFFFFDC?C	NM:i:2	MD:Z:20A8G45	AS:i:65	XS:i:0
+1-40	83	1	1547	60	75M	=	1434	-188	CGCACCCTAGGTCAAGTTTTACGATTGCCCTAACGCCGCGGAGCGCGACCCGAAAAGCTATGGTCTGTAACTTTT	>EDGJJF=GD77J7EDGJDIJJHJHJDGGIIGII@JFF8IG)IIII*J>HAJIII@IIJJ+CFHFHHFF:FFB?B	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
+1-46	147	1	1549	60	75M	=	1421	-203	CACCCTAGGTCAAGTTTTACGATTGCCCTAACGCCGCGGAGCGCGACCCGAAAAGCTATGGTCTGTAACTTTTCG	CDBDEFH;BHHBGJJJJDJDJJIGB?JH0GIJJIIGG*GJ@JFI?I0HFJIHIIJJ?GJ@I0FHFH;FFFFFCCB	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
+1-50	163	1	1737	60	75M	=	1861	199	TCTCTTACCGTGGCTGGGTCCGGCGGCTGTGGGATTGCGAGAGTGTCCGGCACCACCCATGTACACTTTCGGGAA	C1@FF?FFHHH)HI+JCHJH@JJ:IJJIEI9DIGCBHJJGJHGI=GGDJGG,DG=JD,GGIGIDJJFDIDIFICC	NM:i:2	MD:Z:11T45A17	AS:i:65	XS:i:0
+1-6	163	1	1760	60	75M	=	1880	195	CGGCTGTGGGATTGCGAGAGTGTCCGGCACCACCCATGTACACTTTCGGGAACACTCATTCGAAGAGGTTCTGCA	?1CFFFF@8FDFHGIIJICFIFJIJJ:JBIJGIJ)*II?I(EJJIGFG<HHHIGDI>FHDJFHFCHEJCFFCJE>	NM:i:1	MD:Z:34A40	AS:i:70	XS:i:0
+1-50	83	1	1861	60	75M	=	1737	-199	GGGCGGCAATGCTGAGGCCCTCTGTTCAATGAAACCCGTACTATATCTTATGATGACAATGAAATAGTCCTGTTT	DEC)H8FJDJGA)EH5&JJ7ABJ8IJH&JFIGJFGJJIFAJDIJHJCJIJE@I<IJJCHHIG=HHHHFF=FFCCC	NM:i:2	MD:Z:3A23C47	AS:i:66	XS:i:0
+1-6	83	1	1880	60	75M	=	1760	-195	CTCTGTTCCATGAAACCCGTACTATATCTTATGATGACAATGAAATAGTCCTGTTTTACGACTCCAAGTTTCCTG	JDD=DJDID;)DF=FIB@FB8IBIJJGHJIIJJHIIIGJ1IJJJJGG(?J*HJFEI<JJ<JEDFHDHFFF@FCC@	NM:i:0	MD:Z:75	AS:i:75	XS:i:0
diff --git a/python/clockwork/tests/db_test.py b/python/clockwork/tests/db_test.py
index ab5faa7..0cc1e9c 100644
--- a/python/clockwork/tests/db_test.py
+++ b/python/clockwork/tests/db_test.py
@@ -2031,6 +2031,12 @@ def test_update_qc_stats(self):
                 "samtools_inward_oriented_pairs": 27,
                 "samtools_outward_oriented_pairs": 0,
                 "samtools_pairs_with_other_orientation": 0,
+                "samtools_positions_with_depth_of_0": 2,
+                "samtools_positions_with_depth_atleast_2": 7,
+                "samtools_positions_with_depth_atleast_5": 5,
+                "samtools_positions_with_depth_atleast_10": 2,
+                "samtools_positions_with_depth_atleast_20": 1,
+                "samtools_positions_with_depth_atleast_100": 1,
                 "samtools_raw_total_sequences": 54,
                 "samtools_reads_duplicated": 2,
                 "samtools_reads_mapped": 54,
diff --git a/python/clockwork/tests/nextflow_qc_test.py b/python/clockwork/tests/nextflow_qc_test.py
index 343baca..caa6cab 100644
--- a/python/clockwork/tests/nextflow_qc_test.py
+++ b/python/clockwork/tests/nextflow_qc_test.py
@@ -87,7 +87,7 @@ def test_nextflow_qc_using_database(self):
                 "isolate_id": 1,
                 "seqrep_id": 1,
                 "seqrep_pool": None,
-                "version": "0.0.1",
+                "version": "0.9.0",
                 "pipeline_name": "remove_contam",
                 "status": 1,
                 "reference_id": 1,
@@ -105,7 +105,7 @@ def test_nextflow_qc_using_database(self):
                 "isolate_id": 2,
                 "seqrep_id": 2,
                 "seqrep_pool": None,
-                "version": "0.0.1",
+                "version": "0.9.0",
                 "pipeline_name": "remove_contam",
                 "status": 1,
                 "reference_id": 1,
@@ -123,7 +123,7 @@ def test_nextflow_qc_using_database(self):
                 "isolate_id": 3,
                 "seqrep_id": 3,
                 "seqrep_pool": None,
-                "version": "0.0.1",
+                "version": "0.9.0",
                 "pipeline_name": "remove_contam",
                 "status": 1,
                 "reference_id": 1,
@@ -141,7 +141,7 @@ def test_nextflow_qc_using_database(self):
                 "isolate_id": 4,
                 "seqrep_id": 4,
                 "seqrep_pool": None,
-                "version": "0.0.1",
+                "version": "0.9.0",
                 "pipeline_name": "remove_contam",
                 "status": 1,
                 "reference_id": 1,
@@ -197,6 +197,12 @@ def test_nextflow_qc_using_database(self):
                 "samtools_inward_oriented_pairs": 66,
                 "samtools_outward_oriented_pairs": 0,
                 "samtools_pairs_with_other_orientation": 0,
+                "samtools_positions_with_depth_atleast_10": 562,
+                "samtools_positions_with_depth_atleast_100": 0,
+                "samtools_positions_with_depth_atleast_2": 968,
+                "samtools_positions_with_depth_atleast_20": 0,
+                "samtools_positions_with_depth_atleast_5": 876,
+                "samtools_positions_with_depth_of_0": 17,
                 "samtools_raw_total_sequences": 144,
                 "samtools_reads_duplicated": 4,
                 "samtools_reads_mapped": 132,
@@ -248,6 +254,12 @@ def test_nextflow_qc_using_database(self):
                 "samtools_inward_oriented_pairs": 66,
                 "samtools_outward_oriented_pairs": 0,
                 "samtools_pairs_with_other_orientation": 0,
+                "samtools_positions_with_depth_atleast_10": 547,
+                "samtools_positions_with_depth_atleast_100": 0,
+                "samtools_positions_with_depth_atleast_2": 955,
+                "samtools_positions_with_depth_atleast_20": 0,
+                "samtools_positions_with_depth_atleast_5": 902,
+                "samtools_positions_with_depth_of_0": 17,
                 "samtools_raw_total_sequences": 144,
                 "samtools_reads_duplicated": 0,
                 "samtools_reads_mapped": 132,
diff --git a/python/clockwork/tests/samtools_qc_test.py b/python/clockwork/tests/samtools_qc_test.py
index 50827e5..659f211 100644
--- a/python/clockwork/tests/samtools_qc_test.py
+++ b/python/clockwork/tests/samtools_qc_test.py
@@ -1,4 +1,5 @@
 import unittest
+import subprocess
 import shutil
 import os
 from clockwork import samtools_qc
@@ -31,8 +32,9 @@ def test_map_reads(self):
     def test_make_stats_and_plots(self):
         """test _make_stats_and_plots"""
         ref_fasta = os.path.join(data_dir, "ref.fa")
-        sam_file = os.path.join(data_dir, "sam")
+        sam_file = os.path.join(data_dir, "depth_stats.sorted.sam")
         tmp_dir = "tmp.samtools_qc.make_stats_and_plots"
+        subprocess.check_output(f"rm -rf {tmp_dir}", shell=True)
         os.mkdir(tmp_dir)
         outprefix = os.path.join(tmp_dir, "test")
         samtools_qc.SamtoolsQc._make_stats_and_plots(sam_file, ref_fasta, outprefix)
@@ -55,6 +57,24 @@ def test_make_stats_and_plots(self):
         self.assertEqual(expected_files, got_files)
         shutil.rmtree(tmp_dir)
 
+    def test_make_depth_stats(self):
+        """test _make_depth_stats"""
+        sam_file = os.path.join(data_dir, "depth_stats.sorted.sam")
+        tmp_dir = "tmp.samtools_qc.make_depth_stats"
+        subprocess.check_output(f"rm -rf {tmp_dir}", shell=True)
+        os.mkdir(tmp_dir)
+        outprefix = os.path.join(tmp_dir, "test")
+        samtools_qc.SamtoolsQc._make_depth_stats(sam_file, outprefix)
+
+        expected_files = [
+            "test.depths",
+        ]
+        expected_files.sort()
+
+        got_files = sorted(list(os.listdir(tmp_dir)))
+        self.assertEqual(expected_files, got_files)
+        shutil.rmtree(tmp_dir)
+
     def test_stats_from_report(self):
         """test stats_from_report"""
         stats_file = os.path.join(data_dir, "stats_from_report.txt")
@@ -96,6 +116,7 @@ def test_run(self):
         reads2 = os.path.join(data_dir, "reads.2.fq")
         ref_fasta = os.path.join(data_dir, "ref.fa")
         tmp_dir = "tmp.test.samtools_qc.run"
+        subprocess.check_output(f"rm -rf {tmp_dir}", shell=True)
         samqc = samtools_qc.SamtoolsQc(ref_fasta, reads1, reads2, tmp_dir)
         samqc.run()
 
@@ -103,6 +124,7 @@ def test_run(self):
             "het_snps.het_calls.vcf",
             "het_snps.per_contig.tsv",
             "het_snps.summary.tsv",
+            "samtools_qc.depths",
             "samtools_qc.plot-acgt-cycles.png",
             "samtools_qc.plot-coverage.png",
             "samtools_qc.plot-gc-content.png",
diff --git a/python/setup.py b/python/setup.py
index e346b74..0eff21d 100644
--- a/python/setup.py
+++ b/python/setup.py
@@ -16,7 +16,7 @@
     install_requires=[
         "cluster_vcf_records >= 0.11.1",
         "python-dateutil >= 2.6.1",
-        "openpyxl >= 2.4.7",
+        "openpyxl == 2.5.0",
         "pyfastaq >= 3.14.0",
         "pymysql >= 0.7.11",
         "pysam >= 0.11.2.1",
diff --git a/vagrant/Vagrantfile b/vagrant/Vagrantfile
index b81afd8..e7c0c23 100644
--- a/vagrant/Vagrantfile
+++ b/vagrant/Vagrantfile
@@ -7,8 +7,8 @@ Vagrant.configure(2) do |config|
   config.disksize.size = '40GB'
 
   # Edit these if you want to mount whatever dirs...
-  config.vm.synced_folder "/Users/mhunt/git/", "/home/vagrant/git"
-  config.vm.synced_folder "/Users/mhunt/vm_share/", "/home/vagrant/vm_share"
+#  config.vm.synced_folder "/Users/mhunt/git/", "/home/vagrant/git"
+#  config.vm.synced_folder "/Users/mhunt/vm_share/", "/home/vagrant/vm_share"
 
   # Provider-specific configuration so you can fine-tune various
   # backing providers for Vagrant. These expose provider-specific options.