## 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-GSM1606347.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606347.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606347.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 13:19:15 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	29915937	4631708	0	0	5079328	0	0.169787	77815564

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	22311734	22311734
2.0	1.680827	1722616	1722616
3.0	2.144353	389090	389090
4.0	2.459934	155759	155759
5.0	2.67479	80569	80569
6.0	2.82107	47013	47013
7.0	2.920661	30282	30282
8.0	2.988466	20545	20545
9.0	3.034629	14878	14878
10.0	3.066058	11045	11045
11.0	3.087456	8428	8428
12.0	3.102024	6656	6656
13.0	3.111942	5233	5233
14.0	3.118695	4275	4275
15.0	3.123293	3528	3528
16.0	3.126423	2898	2898
17.0	3.128554	2427	2427
18.0	3.130005	2061	2061
19.0	3.130992	1774	1774
20.0	3.131665	1532	1532
21.0	3.132123	1319	1319
22.0	3.132434	1132	1132
23.0	3.132647	1086	1086
24.0	3.132791	892	892
25.0	3.13289	817	817
26.0	3.132957	715	715
27.0	3.133002	652	652
28.0	3.133033	605	605
29.0	3.133054	500	500
30.0	3.133069	461	461
31.0	3.133078	448	448
32.0	3.133085	398	398
33.0	3.13309	301	301
34.0	3.133093	331	331
35.0	3.133095	313	313
36.0	3.133096	258	258
37.0	3.133097	247	247
38.0	3.133098	207	207
39.0	3.133098	185	185
40.0	3.133099	198	198
41.0	3.133099	167	167
42.0	3.133099	155	155
43.0	3.133099	159	159
44.0	3.133099	134	134
45.0	3.133099	126	126
46.0	3.133099	117	117
47.0	3.133099	118	118
48.0	3.133099	96	96
49.0	3.133099	97	97
50.0	3.133099	87	87
51.0	3.133099	96	96
52.0	3.133099	93	93
53.0	3.133099	69	69
54.0	3.133099	73	73
55.0	3.133099	65	65
56.0	3.133099	61	61
57.0	3.133099	69	69
58.0	3.133099	64	64
59.0	3.133099	52	52
60.0	3.133099	46	46
61.0	3.133099	45	45
62.0	3.133099	50	50
63.0	3.133099	51	51
64.0	3.133099	49	49
65.0	3.133099	53	53
66.0	3.133099	42	42
67.0	3.133099	35	35
68.0	3.133099	30	30
69.0	3.133099	36	36
70.0	3.133099	37	37
71.0	3.133099	29	29
72.0	3.133099	21	21
73.0	3.133099	25	25
74.0	3.133099	21	21
75.0	3.133099	30	30
76.0	3.133099	25	25
77.0	3.133099	24	24
78.0	3.133099	20	20
79.0	3.133099	27	27
80.0	3.133099	20	20
81.0	3.133099	21	21
82.0	3.133099	18	18
83.0	3.133099	18	18
84.0	3.133099	19	19
85.0	3.133099	20	20
86.0	3.133099	13	13
87.0	3.133099	15	15
88.0	3.133099	7	7
89.0	3.133099	17	17
90.0	3.133099	10	10
91.0	3.133099	15	15
92.0	3.133099	9	9
93.0	3.133099	10	10
94.0	3.133099	14	14
95.0	3.133099	18	18
96.0	3.133099	5	5
97.0	3.133099	11	11
98.0	3.133099	11	11
99.0	3.133099	9	9
100.0	3.133099	8	8
101.0	0	7	7
102.0	0	4	4
103.0	0	8	8
104.0	0	13	13
105.0	0	2	2
106.0	0	9	9
107.0	0	4	4
108.0	0	8	8
109.0	0	4	4
110.0	0	7	7
111.0	0	3	3
112.0	0	5	5
113.0	0	4	4
114.0	0	4	4
115.0	0	7	7
116.0	0	7	7
117.0	0	5	5
118.0	0	4	4
119.0	0	5	5
120.0	0	5	5
121.0	0	3	3
122.0	0	5	5
123.0	0	4	4
124.0	0	6	6
125.0	0	7	7
126.0	0	2	2
128.0	0	8	8
129.0	0	2	2
130.0	0	1	1
131.0	0	3	3
132.0	0	3	3
133.0	0	3	3
134.0	0	9	9
135.0	0	5	5
136.0	0	5	5
137.0	0	4	4
139.0	0	1	1
140.0	0	4	4
141.0	0	5	5
142.0	0	2	2
143.0	0	2	2
144.0	0	2	2
145.0	0	4	4
146.0	0	1	1
147.0	0	2	2
148.0	0	1	1
149.0	0	5	5
150.0	0	3	3
151.0	0	5	5
153.0	0	4	4
154.0	0	2	2
155.0	0	2	2
156.0	0	1	1
157.0	0	3	3
158.0	0	2	2
159.0	0	1	1
160.0	0	1	1
161.0	0	1	1
162.0	0	3	3
163.0	0	2	2
164.0	0	5	5
165.0	0	2	2
166.0	0	2	2
167.0	0	4	4
168.0	0	1	1
170.0	0	3	3
172.0	0	2	2
173.0	0	2	2
175.0	0	3	3
176.0	0	1	1
178.0	0	2	2
179.0	0	2	2
180.0	0	1	1
182.0	0	1	1
183.0	0	1	1
184.0	0	4	4
189.0	0	1	1
190.0	0	2	2
196.0	0	1	1
198.0	0	1	1
199.0	0	1	1
200.0	0	1	1
202.0	0	1	1
203.0	0	1	1
204.0	0	1	1
206.0	0	2	2
209.0	0	1	1
210.0	0	1	1
213.0	0	1	1
217.0	0	2	2
221.0	0	1	1
223.0	0	1	1
225.0	0	1	1
227.0	0	1	1
234.0	0	2	2
245.0	0	1	1
249.0	0	1	1
255.0	0	1	1
283.0	0	1	1
291.0	0	1	1
297.0	0	1	1
302.0	0	1	1
329.0	0	1	1
355.0	0	1	1
372.0	0	1	1
388.0	0	1	1
401.0	0	1	1
425.0	0	1	1
444.0	0	1	1
470.0	0	1	1
8699.0	0	1	1