## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606266.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606266.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606266.samtools-coordinate.metrics.txt TMP_DIR=[/scratch/siebrenf/tmp]    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Tue Nov 02 15:29:06 CET 2021

## METRICS CLASS	picard.sam.DuplicationMetrics
LIBRARY	UNPAIRED_READS_EXAMINED	READ_PAIRS_EXAMINED	SECONDARY_OR_SUPPLEMENTARY_RDS	UNMAPPED_READS	UNPAIRED_READ_DUPLICATES	READ_PAIR_DUPLICATES	READ_PAIR_OPTICAL_DUPLICATES	PERCENT_DUPLICATION	ESTIMATED_LIBRARY_SIZE
Unknown Library	0	13884650	2347778	0	0	1346165	0	0.096953	66897568

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	11687215	11687215
2.0	1.812572	650790	650790
3.0	2.472845	109920	109920
4.0	3.009364	38710	38710
5.0	3.445325	18742	18742
6.0	3.799574	10238	10238
7.0	4.087427	6387	6387
8.0	4.321328	4095	4095
9.0	4.51139	2725	2725
10.0	4.665829	1995	1995
11.0	4.791321	1400	1400
12.0	4.893293	1124	1124
13.0	4.976152	874	874
14.0	5.043481	705	705
15.0	5.098191	535	535
16.0	5.142647	455	455
17.0	5.17877	370	370
18.0	5.208123	279	279
19.0	5.231974	241	241
20.0	5.251355	195	195
21.0	5.267104	159	159
22.0	5.2799	164	164
23.0	5.290299	123	123
24.0	5.298748	121	121
25.0	5.305614	97	97
26.0	5.311192	81	81
27.0	5.315726	66	66
28.0	5.319409	60	60
29.0	5.322402	49	49
30.0	5.324835	55	55
31.0	5.326811	39	39
32.0	5.328417	47	47
33.0	5.329722	41	41
34.0	5.330782	27	27
35.0	5.331644	29	29
36.0	5.332344	23	23
37.0	5.332913	23	23
38.0	5.333375	24	24
39.0	5.33375	15	15
40.0	5.334056	19	19
41.0	5.334304	23	23
42.0	5.334505	15	15
43.0	5.334669	19	19
44.0	5.334802	8	8
45.0	5.33491	16	16
46.0	5.334998	15	15
47.0	5.335069	8	8
48.0	5.335127	6	6
49.0	5.335175	6	6
50.0	5.335213	7	7
51.0	5.335244	7	7
52.0	5.335269	7	7
53.0	5.33529	4	4
54.0	5.335306	5	5
55.0	5.33532	3	3
56.0	5.335331	2	2
57.0	5.33534	5	5
58.0	5.335347	6	6
59.0	5.335353	8	8
60.0	5.335358	3	3
61.0	5.335362	2	2
62.0	5.335365	5	5
63.0	5.335368	2	2
64.0	5.33537	4	4
65.0	5.335371	0	0
66.0	5.335373	1	1
67.0	5.335374	2	2
68.0	5.335375	2	2
69.0	5.335376	3	3
70.0	5.335376	1	1
71.0	5.335377	1	1
72.0	5.335377	0	0
73.0	5.335377	1	1
74.0	5.335378	1	1
75.0	5.335378	1	1
76.0	5.335378	3	3
77.0	5.335378	1	1
78.0	5.335378	2	2
79.0	5.335378	1	1
80.0	5.335379	1	1
81.0	5.335379	1	1
82.0	5.335379	1	1
83.0	5.335379	0	0
84.0	5.335379	0	0
85.0	5.335379	2	2
86.0	5.335379	1	1
87.0	5.335379	2	2
88.0	5.335379	0	0
89.0	5.335379	0	0
90.0	5.335379	1	1
91.0	5.335379	0	0
92.0	5.335379	0	0
93.0	5.335379	0	0
94.0	5.335379	0	0
95.0	5.335379	1	1
96.0	5.335379	0	0
97.0	5.335379	0	0
98.0	5.335379	1	1
99.0	5.335379	2	2
100.0	5.335379	0	0
108.0	0	1	1
114.0	0	2	2
119.0	0	1	1
120.0	0	1	1
125.0	0	1	1
142.0	0	1	1
156.0	0	1	1
2641.0	0	1	1