## 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-GSM1606185.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606185.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606185.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 15:15:52 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	18798393	1870480	0	0	1127981	0	0.060004	150311636

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	16819797	16819797
2.0	1.882441	703144	703144
3.0	2.661144	96126	96126
4.0	3.348304	27054	27054
5.0	3.954683	10740	10740
6.0	4.489776	5115	5115
7.0	4.961965	2873	2873
8.0	5.378643	1672	1672
9.0	5.746338	1087	1087
10.0	6.070807	712	712
11.0	6.357132	501	501
12.0	6.609797	339	339
13.0	6.832759	259	259
14.0	7.02951	183	183
15.0	7.203132	145	145
16.0	7.356342	109	109
17.0	7.491541	90	90
18.0	7.610847	69	69
19.0	7.716127	59	59
20.0	7.809031	40	40
21.0	7.891013	35	35
22.0	7.963357	42	42
23.0	8.027197	20	20
24.0	8.083531	27	27
25.0	8.133243	19	19
26.0	8.177111	13	13
27.0	8.215822	11	11
28.0	8.249983	14	14
29.0	8.280127	11	11
30.0	8.306728	9	9
31.0	8.330201	7	7
32.0	8.350915	6	6
33.0	8.369194	6	6
34.0	8.385324	6	6
35.0	8.399558	5	5
36.0	8.412118	5	5
37.0	8.423202	5	5
38.0	8.432983	1	1
39.0	8.441614	1	1
40.0	8.449231	1	1
41.0	8.455952	0	0
42.0	8.461883	2	2
43.0	8.467116	1	1
44.0	8.471735	3	3
45.0	8.47581	2	2
46.0	8.479407	3	3
47.0	8.48258	2	2
48.0	8.485381	0	0
49.0	8.487852	1	1
50.0	8.490033	2	2
51.0	8.491957	1	1
52.0	8.493655	1	1
53.0	8.495154	0	0
54.0	8.496476	0	0
55.0	8.497643	1	1
56.0	8.498673	4	4
57.0	8.499582	1	1
58.0	8.500383	1	1
59.0	8.501091	2	2
60.0	8.501715	0	0
61.0	8.502266	2	2
62.0	8.502753	1	1
63.0	8.503182	0	0
64.0	8.50356	0	0
65.0	8.503894	0	0
66.0	8.504189	1	1
67.0	8.504449	0	0
68.0	8.504679	1	1
69.0	8.504882	0	0
70.0	8.50506	1	1
71.0	8.505218	1	1
72.0	8.505357	0	0
73.0	8.50548	0	0
74.0	8.505589	0	0
75.0	8.505684	1	1
76.0	8.505769	0	0
77.0	8.505843	1	1
78.0	8.505909	0	0
79.0	8.505967	1	1
80.0	8.506018	1	1
81.0	8.506063	1	1
82.0	8.506103	0	0
83.0	8.506138	0	0
84.0	8.506169	0	0
85.0	8.506197	0	0
86.0	8.506221	0	0
87.0	8.506242	0	0
88.0	8.506261	0	0
89.0	8.506278	0	0
90.0	8.506292	0	0
91.0	8.506305	0	0
92.0	8.506317	0	0
93.0	8.506327	0	0
94.0	8.506336	0	0
95.0	8.506344	0	0
96.0	8.506351	0	0
97.0	8.506357	0	0
98.0	8.506362	0	0
99.0	8.506367	0	0
100.0	8.506371	0	0
106.0	0	1	1
123.0	0	1	1
133.0	0	1	1
137.0	0	2	2
140.0	0	1	1
156.0	0	1	1
183.0	0	1	1
215.0	0	1	1
265.0	0	1	1
300.0	0	1	1
308.0	0	1	1
339.0	0	1	1
403.0	0	1	1
5347.0	0	1	1