## 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-GSM1606187.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606187.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606187.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: Mon Nov 01 20:39:44 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	42190624	5189872	0	0	4776599	0	0.113215	171983892

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	34282540	34282540
2.0	1.782456	2389223	2389223
3.0	2.394694	435139	435139
4.0	2.873743	143804	143804
5.0	3.248578	63878	63878
6.0	3.54187	33299	33299
7.0	3.771358	19408	19408
8.0	3.950923	12194	12194
9.0	4.091424	8248	8248
10.0	4.20136	5718	5718
11.0	4.287381	4220	4220
12.0	4.354688	3104	3104
13.0	4.407352	2221	2221
14.0	4.44856	1825	1825
15.0	4.480804	1470	1470
16.0	4.506033	1150	1150
17.0	4.525773	937	937
18.0	4.54122	736	736
19.0	4.553306	645	645
20.0	4.562762	520	520
21.0	4.570162	442	442
22.0	4.575952	396	396
23.0	4.580482	314	314
24.0	4.584026	270	270
25.0	4.5868	238	238
26.0	4.58897	188	188
27.0	4.590668	183	183
28.0	4.591997	145	145
29.0	4.593037	131	131
30.0	4.59385	117	117
31.0	4.594487	114	114
32.0	4.594985	96	96
33.0	4.595374	100	100
34.0	4.595679	88	88
35.0	4.595918	76	76
36.0	4.596105	62	62
37.0	4.596251	45	45
38.0	4.596365	60	60
39.0	4.596454	48	48
40.0	4.596524	43	43
41.0	4.596579	39	39
42.0	4.596622	42	42
43.0	4.596655	45	45
44.0	4.596682	24	24
45.0	4.596702	23	23
46.0	4.596718	36	36
47.0	4.596731	17	17
48.0	4.596741	16	16
49.0	4.596748	17	17
50.0	4.596754	18	18
51.0	4.596759	17	17
52.0	4.596763	22	22
53.0	4.596766	13	13
54.0	4.596768	15	15
55.0	4.59677	11	11
56.0	4.596771	11	11
57.0	4.596772	9	9
58.0	4.596773	11	11
59.0	4.596774	13	13
60.0	4.596774	6	6
61.0	4.596775	9	9
62.0	4.596775	8	8
63.0	4.596775	11	11
64.0	4.596775	6	6
65.0	4.596775	7	7
66.0	4.596776	5	5
67.0	4.596776	7	7
68.0	4.596776	2	2
69.0	4.596776	5	5
70.0	4.596776	4	4
71.0	4.596776	7	7
72.0	4.596776	3	3
73.0	4.596776	3	3
74.0	4.596776	3	3
75.0	4.596776	6	6
76.0	4.596776	3	3
77.0	4.596776	1	1
78.0	4.596776	3	3
79.0	4.596776	5	5
80.0	4.596776	2	2
81.0	4.596776	1	1
82.0	4.596776	0	0
83.0	4.596776	2	2
84.0	4.596776	4	4
85.0	4.596776	3	3
86.0	4.596776	1	1
87.0	4.596776	3	3
88.0	4.596776	1	1
89.0	4.596776	0	0
90.0	4.596776	2	2
91.0	4.596776	2	2
92.0	4.596776	1	1
93.0	4.596776	1	1
94.0	4.596776	2	2
95.0	4.596776	0	0
96.0	4.596776	2	2
97.0	4.596776	0	0
98.0	4.596776	1	1
99.0	4.596776	3	3
100.0	4.596776	2	2
101.0	0	1	1
103.0	0	2	2
104.0	0	2	2
106.0	0	1	1
109.0	0	1	1
111.0	0	1	1
112.0	0	1	1
114.0	0	1	1
115.0	0	1	1
116.0	0	1	1
118.0	0	2	2
120.0	0	1	1
123.0	0	1	1
124.0	0	1	1
126.0	0	1	1
131.0	0	1	1
132.0	0	1	1
137.0	0	1	1
141.0	0	2	2
144.0	0	1	1
147.0	0	1	1
150.0	0	2	2
157.0	0	1	1
164.0	0	1	1
167.0	0	1	1
169.0	0	1	1
173.0	0	1	1
174.0	0	1	1
176.0	0	1	1
186.0	0	1	1
193.0	0	1	1
220.0	0	1	1
233.0	0	1	1
245.0	0	1	1
252.0	0	1	1
255.0	0	1	1
266.0	0	1	1
292.0	0	1	1
295.0	0	1	1
304.0	0	1	1
360.0	0	1	1
367.0	0	1	1
378.0	0	1	1
418.0	0	1	1
508.0	0	1	1
615.0	0	1	1
636.0	0	1	1
691.0	0	1	1
10279.0	0	1	1