## 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-GSM1606230.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606230.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606230.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 15:16:57 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	16844122	2319354	0	0	2035757	0	0.120859	63949503

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	13731393	13731393
2.0	1.768437	737240	737240
3.0	2.358931	167915	167915
4.0	2.812689	68276	68276
5.0	3.161373	34686	34686
6.0	3.429315	19854	19854
7.0	3.635211	12545	12545
8.0	3.793429	8582	8582
9.0	3.91501	6000	6000
10.0	4.008437	4336	4336
11.0	4.080229	3134	3134
12.0	4.135398	2425	2425
13.0	4.177791	1965	1965
14.0	4.210367	1532	1532
15.0	4.2354	1174	1174
16.0	4.254637	962	962
17.0	4.269418	799	799
18.0	4.280777	655	655
19.0	4.289506	587	587
20.0	4.296213	510	510
21.0	4.301368	429	429
22.0	4.305328	353	353
23.0	4.308372	297	297
24.0	4.31071	258	258
25.0	4.312508	230	230
26.0	4.313889	205	205
27.0	4.31495	182	182
28.0	4.315765	187	187
29.0	4.316392	132	132
30.0	4.316874	131	131
31.0	4.317244	113	113
32.0	4.317528	103	103
33.0	4.317746	98	98
34.0	4.317914	80	80
35.0	4.318043	87	87
36.0	4.318143	63	63
37.0	4.318219	60	60
38.0	4.318277	58	58
39.0	4.318322	39	39
40.0	4.318357	58	58
41.0	4.318383	44	44
42.0	4.318404	24	24
43.0	4.318419	33	33
44.0	4.318432	37	37
45.0	4.318441	33	33
46.0	4.318448	25	25
47.0	4.318453	24	24
48.0	4.318458	26	26
49.0	4.318461	19	19
50.0	4.318463	27	27
51.0	4.318465	18	18
52.0	4.318467	15	15
53.0	4.318468	21	21
54.0	4.318469	17	17
55.0	4.318469	13	13
56.0	4.31847	14	14
57.0	4.31847	8	8
58.0	4.318471	9	9
59.0	4.318471	7	7
60.0	4.318471	8	8
61.0	4.318471	8	8
62.0	4.318471	8	8
63.0	4.318471	8	8
64.0	4.318471	6	6
65.0	4.318471	11	11
66.0	4.318471	14	14
67.0	4.318471	8	8
68.0	4.318471	3	3
69.0	4.318471	8	8
70.0	4.318472	5	5
71.0	4.318472	6	6
72.0	4.318472	5	5
73.0	4.318472	1	1
74.0	4.318472	7	7
75.0	4.318472	1	1
76.0	4.318472	3	3
77.0	4.318472	5	5
78.0	4.318472	5	5
79.0	4.318472	4	4
80.0	4.318472	4	4
81.0	4.318472	1	1
82.0	4.318472	3	3
83.0	4.318472	5	5
84.0	4.318472	4	4
85.0	4.318472	0	0
86.0	4.318472	2	2
87.0	4.318472	4	4
88.0	4.318472	2	2
89.0	4.318472	3	3
90.0	4.318472	1	1
91.0	4.318472	0	0
92.0	4.318472	5	5
93.0	4.318472	2	2
94.0	4.318472	1	1
95.0	4.318472	0	0
96.0	4.318472	1	1
97.0	4.318472	1	1
98.0	4.318472	1	1
99.0	4.318472	3	3
100.0	4.318472	2	2
101.0	0	2	2
102.0	0	1	1
103.0	0	3	3
105.0	0	3	3
106.0	0	2	2
107.0	0	2	2
108.0	0	2	2
111.0	0	1	1
113.0	0	1	1
116.0	0	1	1
117.0	0	1	1
120.0	0	1	1
121.0	0	2	2
123.0	0	2	2
124.0	0	1	1
126.0	0	1	1
128.0	0	1	1
132.0	0	3	3
134.0	0	1	1
136.0	0	1	1
137.0	0	1	1
139.0	0	1	1
146.0	0	1	1
147.0	0	1	1
149.0	0	1	1
162.0	0	1	1
168.0	0	1	1
176.0	0	2	2
185.0	0	1	1
190.0	0	2	2
191.0	0	1	1
198.0	0	1	1
199.0	0	1	1
297.0	0	1	1
921.0	0	1	1