## 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-GSM1606339.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606339.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606339.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 14:47:44 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	22963776	3393848	0	0	3847278	0	0.167537	60643655

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	17127829	17127829
2.0	1.684773	1370183	1370183
3.0	2.153688	306714	306714
4.0	2.474788	121098	121098
5.0	2.694669	61301	61301
6.0	2.845237	35639	35639
7.0	2.948343	22539	22539
8.0	3.018946	15297	15297
9.0	3.067294	10948	10948
10.0	3.100401	8054	8054
11.0	3.123072	6136	6136
12.0	3.138596	4753	4753
13.0	3.149227	3732	3732
14.0	3.156507	2940	2940
15.0	3.161492	2486	2486
16.0	3.164905	2076	2076
17.0	3.167243	1692	1692
18.0	3.168843	1467	1467
19.0	3.169939	1218	1218
20.0	3.17069	1091	1091
21.0	3.171204	893	893
22.0	3.171556	793	793
23.0	3.171797	765	765
24.0	3.171962	614	614
25.0	3.172075	527	527
26.0	3.172152	523	523
27.0	3.172205	426	426
28.0	3.172241	361	361
29.0	3.172266	355	355
30.0	3.172283	325	325
31.0	3.172295	289	289
32.0	3.172303	258	258
33.0	3.172308	209	209
34.0	3.172312	195	195
35.0	3.172315	170	170
36.0	3.172317	210	210
37.0	3.172318	152	152
38.0	3.172319	155	155
39.0	3.172319	112	112
40.0	3.172319	106	106
41.0	3.17232	115	115
42.0	3.17232	108	108
43.0	3.17232	82	82
44.0	3.17232	88	88
45.0	3.17232	80	80
46.0	3.17232	58	58
47.0	3.17232	80	80
48.0	3.17232	74	74
49.0	3.17232	58	58
50.0	3.17232	55	55
51.0	3.17232	52	52
52.0	3.17232	61	61
53.0	3.17232	43	43
54.0	3.17232	39	39
55.0	3.17232	34	34
56.0	3.17232	43	43
57.0	3.17232	38	38
58.0	3.17232	35	35
59.0	3.17232	36	36
60.0	3.17232	34	34
61.0	3.17232	28	28
62.0	3.17232	36	36
63.0	3.17232	18	18
64.0	3.17232	32	32
65.0	3.17232	28	28
66.0	3.17232	21	21
67.0	3.17232	14	14
68.0	3.17232	27	27
69.0	3.17232	18	18
70.0	3.17232	21	21
71.0	3.17232	7	7
72.0	3.17232	13	13
73.0	3.17232	11	11
74.0	3.17232	12	12
75.0	3.17232	9	9
76.0	3.17232	15	15
77.0	3.17232	12	12
78.0	3.17232	11	11
79.0	3.17232	12	12
80.0	3.17232	12	12
81.0	3.17232	9	9
82.0	3.17232	5	5
83.0	3.17232	9	9
84.0	3.17232	7	7
85.0	3.17232	12	12
86.0	3.17232	10	10
87.0	3.17232	8	8
88.0	3.17232	7	7
89.0	3.17232	10	10
90.0	3.17232	11	11
91.0	3.17232	9	9
92.0	3.17232	7	7
93.0	3.17232	4	4
94.0	3.17232	9	9
95.0	3.17232	4	4
96.0	3.17232	6	6
97.0	3.17232	5	5
98.0	3.17232	4	4
99.0	3.17232	4	4
100.0	3.17232	6	6
101.0	0	3	3
102.0	0	8	8
103.0	0	5	5
104.0	0	3	3
105.0	0	4	4
106.0	0	3	3
107.0	0	5	5
108.0	0	1	1
109.0	0	2	2
110.0	0	5	5
111.0	0	5	5
112.0	0	3	3
113.0	0	2	2
114.0	0	3	3
115.0	0	1	1
116.0	0	2	2
118.0	0	3	3
120.0	0	2	2
122.0	0	2	2
123.0	0	4	4
124.0	0	3	3
126.0	0	3	3
127.0	0	3	3
128.0	0	3	3
129.0	0	1	1
130.0	0	1	1
131.0	0	2	2
132.0	0	1	1
133.0	0	1	1
134.0	0	1	1
135.0	0	1	1
136.0	0	2	2
137.0	0	1	1
138.0	0	2	2
139.0	0	3	3
140.0	0	1	1
141.0	0	1	1
142.0	0	2	2
143.0	0	1	1
144.0	0	1	1
146.0	0	3	3
147.0	0	1	1
148.0	0	1	1
151.0	0	1	1
152.0	0	1	1
153.0	0	1	1
154.0	0	1	1
155.0	0	2	2
156.0	0	1	1
159.0	0	1	1
160.0	0	1	1
161.0	0	1	1
163.0	0	1	1
165.0	0	1	1
166.0	0	2	2
167.0	0	1	1
168.0	0	1	1
169.0	0	1	1
172.0	0	1	1
173.0	0	2	2
174.0	0	1	1
176.0	0	1	1
177.0	0	2	2
179.0	0	1	1
182.0	0	1	1
184.0	0	1	1
199.0	0	1	1
203.0	0	1	1
206.0	0	1	1
210.0	0	1	1
217.0	0	1	1
220.0	0	1	1
237.0	0	1	1
240.0	0	1	1
250.0	0	1	1
257.0	0	2	2
301.0	0	1	1
302.0	0	1	1
305.0	0	1	1
312.0	0	1	1
326.0	0	1	1
354.0	0	1	1
421.0	0	1	1
7350.0	0	1	1