## 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-GSM1606233.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606233.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606233.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 21:14:58 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	36898592	5320582	0	0	7190531	0	0.194873	81926710

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	26543074	26543074
2.0	1.637382	2015296	2015296
3.0	2.043639	516656	516656
4.0	2.30258	223339	223339
5.0	2.467624	120782	120782
6.0	2.57282	73481	73481
7.0	2.639871	48093	48093
8.0	2.682607	33553	33553
9.0	2.709847	24642	24642
10.0	2.727209	18193	18193
11.0	2.738275	14246	14246
12.0	2.745329	10998	10998
13.0	2.749824	9134	9134
14.0	2.75269	7257	7257
15.0	2.754516	5981	5981
16.0	2.75568	5004	5004
17.0	2.756422	4253	4253
18.0	2.756895	3665	3665
19.0	2.757197	3173	3173
20.0	2.757389	2642	2642
21.0	2.757511	2302	2302
22.0	2.757589	2017	2017
23.0	2.757639	1767	1767
24.0	2.757671	1552	1552
25.0	2.757691	1344	1344
26.0	2.757704	1162	1162
27.0	2.757712	1076	1076
28.0	2.757717	949	949
29.0	2.757721	924	924
30.0	2.757723	796	796
31.0	2.757724	713	713
32.0	2.757725	685	685
33.0	2.757726	660	660
34.0	2.757726	543	543
35.0	2.757726	501	501
36.0	2.757726	452	452
37.0	2.757726	414	414
38.0	2.757726	407	407
39.0	2.757727	380	380
40.0	2.757727	315	315
41.0	2.757727	326	326
42.0	2.757727	303	303
43.0	2.757727	257	257
44.0	2.757727	236	236
45.0	2.757727	235	235
46.0	2.757727	201	201
47.0	2.757727	172	172
48.0	2.757727	197	197
49.0	2.757727	167	167
50.0	2.757727	167	167
51.0	2.757727	169	169
52.0	2.757727	162	162
53.0	2.757727	130	130
54.0	2.757727	123	123
55.0	2.757727	104	104
56.0	2.757727	107	107
57.0	2.757727	112	112
58.0	2.757727	101	101
59.0	2.757727	98	98
60.0	2.757727	91	91
61.0	2.757727	89	89
62.0	2.757727	84	84
63.0	2.757727	69	69
64.0	2.757727	69	69
65.0	2.757727	71	71
66.0	2.757727	64	64
67.0	2.757727	53	53
68.0	2.757727	55	55
69.0	2.757727	51	51
70.0	2.757727	59	59
71.0	2.757727	41	41
72.0	2.757727	53	53
73.0	2.757727	56	56
74.0	2.757727	54	54
75.0	2.757727	44	44
76.0	2.757727	31	31
77.0	2.757727	39	39
78.0	2.757727	33	33
79.0	2.757727	37	37
80.0	2.757727	39	39
81.0	2.757727	38	38
82.0	2.757727	40	40
83.0	2.757727	32	32
84.0	2.757727	39	39
85.0	2.757727	26	26
86.0	2.757727	18	18
87.0	2.757727	24	24
88.0	2.757727	19	19
89.0	2.757727	25	25
90.0	2.757727	22	22
91.0	2.757727	25	25
92.0	2.757727	14	14
93.0	2.757727	16	16
94.0	2.757727	23	23
95.0	2.757727	28	28
96.0	2.757727	17	17
97.0	2.757727	17	17
98.0	2.757727	16	16
99.0	2.757727	15	15
100.0	2.757727	15	15
101.0	0	9	9
102.0	0	18	18
103.0	0	15	15
104.0	0	18	18
105.0	0	10	10
106.0	0	18	18
107.0	0	14	14
108.0	0	8	8
109.0	0	10	10
110.0	0	11	11
111.0	0	14	14
112.0	0	17	17
113.0	0	12	12
114.0	0	10	10
115.0	0	11	11
116.0	0	20	20
117.0	0	5	5
118.0	0	5	5
119.0	0	10	10
120.0	0	10	10
121.0	0	5	5
122.0	0	6	6
123.0	0	14	14
124.0	0	8	8
125.0	0	10	10
126.0	0	5	5
127.0	0	13	13
128.0	0	7	7
129.0	0	8	8
130.0	0	5	5
131.0	0	11	11
132.0	0	2	2
133.0	0	6	6
134.0	0	4	4
135.0	0	6	6
136.0	0	5	5
137.0	0	10	10
138.0	0	3	3
139.0	0	3	3
140.0	0	4	4
141.0	0	9	9
142.0	0	2	2
143.0	0	7	7
144.0	0	2	2
145.0	0	7	7
146.0	0	1	1
147.0	0	2	2
148.0	0	3	3
149.0	0	1	1
150.0	0	7	7
151.0	0	7	7
152.0	0	4	4
153.0	0	3	3
154.0	0	4	4
155.0	0	7	7
156.0	0	1	1
157.0	0	3	3
158.0	0	4	4
159.0	0	2	2
160.0	0	3	3
161.0	0	3	3
162.0	0	5	5
163.0	0	2	2
165.0	0	3	3
166.0	0	2	2
167.0	0	1	1
168.0	0	2	2
169.0	0	4	4
170.0	0	4	4
171.0	0	3	3
172.0	0	3	3
174.0	0	1	1
175.0	0	1	1
176.0	0	3	3
177.0	0	2	2
179.0	0	1	1
180.0	0	2	2
181.0	0	3	3
182.0	0	2	2
183.0	0	1	1
184.0	0	4	4
185.0	0	2	2
186.0	0	3	3
189.0	0	3	3
190.0	0	1	1
191.0	0	2	2
194.0	0	1	1
195.0	0	1	1
196.0	0	2	2
198.0	0	3	3
199.0	0	3	3
200.0	0	1	1
201.0	0	2	2
203.0	0	1	1
205.0	0	2	2
207.0	0	1	1
208.0	0	2	2
209.0	0	1	1
210.0	0	1	1
214.0	0	1	1
216.0	0	1	1
217.0	0	3	3
218.0	0	1	1
219.0	0	2	2
220.0	0	1	1
222.0	0	5	5
223.0	0	1	1
227.0	0	1	1
229.0	0	1	1
232.0	0	2	2
233.0	0	2	2
235.0	0	1	1
237.0	0	1	1
238.0	0	1	1
241.0	0	1	1
245.0	0	1	1
246.0	0	1	1
247.0	0	1	1
248.0	0	1	1
249.0	0	1	1
250.0	0	1	1
252.0	0	2	2
254.0	0	1	1
262.0	0	1	1
266.0	0	1	1
269.0	0	1	1
270.0	0	1	1
271.0	0	1	1
272.0	0	1	1
273.0	0	1	1
276.0	0	1	1
277.0	0	2	2
279.0	0	1	1
287.0	0	1	1
291.0	0	2	2
294.0	0	1	1
298.0	0	1	1
299.0	0	1	1
300.0	0	1	1
302.0	0	1	1
303.0	0	1	1
304.0	0	1	1
310.0	0	1	1
318.0	0	1	1
319.0	0	1	1
327.0	0	1	1
336.0	0	1	1
340.0	0	1	1
342.0	0	1	1
350.0	0	1	1
377.0	0	1	1
388.0	0	1	1
391.0	0	1	1
411.0	0	1	1
426.0	0	1	1
432.0	0	1	1
434.0	0	1	1
452.0	0	1	1
458.0	0	1	1
459.0	0	1	1
466.0	0	1	1
472.0	0	1	1
507.0	0	1	1
523.0	0	1	1
681.0	0	1	1
1919.0	0	1	1