## 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-GSM1606196.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606196.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606196.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 21:29:24 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	33256290	5759292	0	0	5490326	0	0.165091	89300196

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	24974596	24974596
2.0	1.689072	1905914	1905914
3.0	2.163891	435989	435989
4.0	2.491076	173177	173177
5.0	2.71653	88253	88253
6.0	2.871884	51708	51708
7.0	2.978934	32778	32778
8.0	3.052699	22221	22221
9.0	3.103528	15841	15841
10.0	3.138553	11623	11623
11.0	3.162688	8989	8989
12.0	3.179319	6779	6779
13.0	3.190778	5448	5448
14.0	3.198675	4426	4426
15.0	3.204116	3567	3567
16.0	3.207865	3021	3021
17.0	3.210449	2432	2432
18.0	3.212229	2118	2118
19.0	3.213456	1810	1810
20.0	3.214301	1530	1530
21.0	3.214884	1357	1357
22.0	3.215285	1155	1155
23.0	3.215562	969	969
24.0	3.215753	912	912
25.0	3.215884	817	817
26.0	3.215974	618	618
27.0	3.216037	610	610
28.0	3.21608	583	583
29.0	3.216109	515	515
30.0	3.21613	482	482
31.0	3.216144	371	371
32.0	3.216153	349	349
33.0	3.21616	314	314
34.0	3.216165	320	320
35.0	3.216168	298	298
36.0	3.21617	228	228
37.0	3.216172	246	246
38.0	3.216173	198	198
39.0	3.216173	194	194
40.0	3.216174	191	191
41.0	3.216174	154	154
42.0	3.216174	135	135
43.0	3.216175	145	145
44.0	3.216175	123	123
45.0	3.216175	143	143
46.0	3.216175	124	124
47.0	3.216175	121	121
48.0	3.216175	108	108
49.0	3.216175	106	106
50.0	3.216175	116	116
51.0	3.216175	85	85
52.0	3.216175	87	87
53.0	3.216175	75	75
54.0	3.216175	64	64
55.0	3.216175	70	70
56.0	3.216175	52	52
57.0	3.216175	49	49
58.0	3.216175	57	57
59.0	3.216175	45	45
60.0	3.216175	65	65
61.0	3.216175	46	46
62.0	3.216175	47	47
63.0	3.216175	49	49
64.0	3.216175	39	39
65.0	3.216175	31	31
66.0	3.216175	47	47
67.0	3.216175	23	23
68.0	3.216175	31	31
69.0	3.216175	35	35
70.0	3.216175	20	20
71.0	3.216175	23	23
72.0	3.216175	23	23
73.0	3.216175	31	31
74.0	3.216175	22	22
75.0	3.216175	22	22
76.0	3.216175	22	22
77.0	3.216175	22	22
78.0	3.216175	16	16
79.0	3.216175	11	11
80.0	3.216175	20	20
81.0	3.216175	18	18
82.0	3.216175	16	16
83.0	3.216175	11	11
84.0	3.216175	14	14
85.0	3.216175	19	19
86.0	3.216175	19	19
87.0	3.216175	11	11
88.0	3.216175	12	12
89.0	3.216175	9	9
90.0	3.216175	16	16
91.0	3.216175	12	12
92.0	3.216175	9	9
93.0	3.216175	6	6
94.0	3.216175	12	12
95.0	3.216175	14	14
96.0	3.216175	5	5
97.0	3.216175	12	12
98.0	3.216175	3	3
99.0	3.216175	7	7
100.0	3.216175	9	9
101.0	0	8	8
102.0	0	6	6
103.0	0	6	6
104.0	0	13	13
105.0	0	8	8
106.0	0	9	9
107.0	0	3	3
108.0	0	5	5
109.0	0	6	6
110.0	0	3	3
111.0	0	7	7
112.0	0	2	2
113.0	0	3	3
114.0	0	7	7
115.0	0	4	4
116.0	0	6	6
117.0	0	4	4
118.0	0	8	8
119.0	0	1	1
120.0	0	1	1
121.0	0	4	4
122.0	0	1	1
123.0	0	3	3
124.0	0	5	5
125.0	0	1	1
126.0	0	3	3
127.0	0	6	6
128.0	0	3	3
129.0	0	3	3
130.0	0	4	4
131.0	0	3	3
132.0	0	3	3
133.0	0	3	3
134.0	0	3	3
135.0	0	3	3
136.0	0	3	3
137.0	0	4	4
138.0	0	2	2
139.0	0	3	3
140.0	0	3	3
141.0	0	3	3
142.0	0	6	6
143.0	0	2	2
144.0	0	2	2
145.0	0	1	1
146.0	0	2	2
148.0	0	1	1
149.0	0	1	1
150.0	0	1	1
151.0	0	1	1
152.0	0	3	3
153.0	0	4	4
154.0	0	1	1
155.0	0	2	2
157.0	0	1	1
158.0	0	1	1
159.0	0	2	2
163.0	0	3	3
165.0	0	1	1
168.0	0	1	1
169.0	0	1	1
170.0	0	1	1
171.0	0	1	1
172.0	0	1	1
173.0	0	1	1
174.0	0	1	1
176.0	0	1	1
177.0	0	1	1
178.0	0	1	1
180.0	0	2	2
181.0	0	1	1
183.0	0	2	2
185.0	0	1	1
188.0	0	1	1
191.0	0	1	1
192.0	0	2	2
194.0	0	2	2
197.0	0	1	1
200.0	0	1	1
201.0	0	1	1
202.0	0	1	1
205.0	0	1	1
208.0	0	2	2
209.0	0	1	1
214.0	0	1	1
215.0	0	1	1
218.0	0	1	1
227.0	0	1	1
228.0	0	2	2
231.0	0	1	1
233.0	0	1	1
239.0	0	1	1
241.0	0	1	1
247.0	0	1	1
248.0	0	1	1
252.0	0	1	1
255.0	0	1	1
266.0	0	1	1
275.0	0	1	1
283.0	0	2	2
291.0	0	1	1
295.0	0	1	1
318.0	0	1	1
324.0	0	1	1
325.0	0	1	1
328.0	0	1	1
329.0	0	1	1
351.0	0	1	1
358.0	0	1	1
365.0	0	1	1
369.0	0	1	1
379.0	0	1	1
395.0	0	1	1
405.0	0	1	1
442.0	0	1	1
473.0	0	1	1
477.0	0	1	1
575.0	0	1	1
751.0	0	1	1
3813.0	0	1	1