## 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-GSM1606225.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606225.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606225.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 23:10:13 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	40200346	5956410	0	0	6687967	0	0.166366	107010254

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	30346488	30346488
2.0	1.68683	2113947	2113947
3.0	2.158566	492901	492901
4.0	2.482568	204108	204108
5.0	2.705103	107080	107080
6.0	2.857946	64027	64027
7.0	2.962924	41569	41569
8.0	3.035026	29123	29123
9.0	3.084547	20804	20804
10.0	3.11856	15745	15745
11.0	3.141921	12030	12030
12.0	3.157967	9331	9331
13.0	3.168987	7529	7529
14.0	3.176556	6116	6116
15.0	3.181755	5070	5070
16.0	3.185325	4302	4302
17.0	3.187778	3573	3573
18.0	3.189462	3104	3104
19.0	3.190619	2616	2616
20.0	3.191413	2217	2217
21.0	3.191959	1924	1924
22.0	3.192334	1749	1749
23.0	3.192591	1468	1468
24.0	3.192768	1295	1295
25.0	3.19289	1140	1140
26.0	3.192973	1001	1001
27.0	3.19303	957	957
28.0	3.19307	783	783
29.0	3.193097	723	723
30.0	3.193115	673	673
31.0	3.193128	602	602
32.0	3.193137	525	525
33.0	3.193143	463	463
34.0	3.193147	430	430
35.0	3.19315	419	419
36.0	3.193152	390	390
37.0	3.193153	400	400
38.0	3.193154	351	351
39.0	3.193155	274	274
40.0	3.193155	273	273
41.0	3.193155	269	269
42.0	3.193156	263	263
43.0	3.193156	211	211
44.0	3.193156	211	211
45.0	3.193156	186	186
46.0	3.193156	178	178
47.0	3.193156	184	184
48.0	3.193156	181	181
49.0	3.193156	151	151
50.0	3.193156	144	144
51.0	3.193156	125	125
52.0	3.193156	118	118
53.0	3.193156	119	119
54.0	3.193156	83	83
55.0	3.193156	90	90
56.0	3.193156	97	97
57.0	3.193156	103	103
58.0	3.193156	91	91
59.0	3.193156	86	86
60.0	3.193156	78	78
61.0	3.193156	74	74
62.0	3.193156	70	70
63.0	3.193156	80	80
64.0	3.193156	62	62
65.0	3.193156	53	53
66.0	3.193156	59	59
67.0	3.193156	46	46
68.0	3.193156	65	65
69.0	3.193156	55	55
70.0	3.193156	37	37
71.0	3.193156	39	39
72.0	3.193156	46	46
73.0	3.193156	34	34
74.0	3.193156	36	36
75.0	3.193156	42	42
76.0	3.193156	23	23
77.0	3.193156	34	34
78.0	3.193156	32	32
79.0	3.193156	29	29
80.0	3.193156	36	36
81.0	3.193156	29	29
82.0	3.193156	19	19
83.0	3.193156	22	22
84.0	3.193156	31	31
85.0	3.193156	22	22
86.0	3.193156	30	30
87.0	3.193156	23	23
88.0	3.193156	20	20
89.0	3.193156	22	22
90.0	3.193156	23	23
91.0	3.193156	16	16
92.0	3.193156	25	25
93.0	3.193156	19	19
94.0	3.193156	18	18
95.0	3.193156	19	19
96.0	3.193156	8	8
97.0	3.193156	25	25
98.0	3.193156	16	16
99.0	3.193156	19	19
100.0	3.193156	14	14
101.0	0	8	8
102.0	0	13	13
103.0	0	18	18
104.0	0	15	15
105.0	0	6	6
106.0	0	6	6
107.0	0	10	10
108.0	0	11	11
109.0	0	12	12
110.0	0	11	11
111.0	0	13	13
112.0	0	14	14
113.0	0	12	12
114.0	0	10	10
115.0	0	6	6
116.0	0	11	11
117.0	0	12	12
118.0	0	5	5
119.0	0	13	13
120.0	0	7	7
121.0	0	9	9
122.0	0	5	5
123.0	0	7	7
124.0	0	9	9
125.0	0	3	3
126.0	0	6	6
127.0	0	5	5
128.0	0	5	5
129.0	0	9	9
130.0	0	2	2
131.0	0	5	5
132.0	0	3	3
133.0	0	7	7
134.0	0	3	3
135.0	0	5	5
136.0	0	6	6
137.0	0	3	3
138.0	0	1	1
139.0	0	4	4
140.0	0	4	4
141.0	0	4	4
142.0	0	4	4
143.0	0	3	3
144.0	0	4	4
145.0	0	3	3
146.0	0	6	6
147.0	0	3	3
148.0	0	5	5
149.0	0	2	2
150.0	0	2	2
151.0	0	3	3
152.0	0	4	4
153.0	0	4	4
154.0	0	4	4
155.0	0	2	2
156.0	0	2	2
157.0	0	4	4
158.0	0	3	3
159.0	0	2	2
160.0	0	2	2
161.0	0	1	1
162.0	0	3	3
163.0	0	3	3
164.0	0	2	2
165.0	0	2	2
166.0	0	3	3
167.0	0	1	1
169.0	0	2	2
170.0	0	1	1
171.0	0	1	1
172.0	0	1	1
173.0	0	1	1
174.0	0	5	5
175.0	0	3	3
176.0	0	2	2
177.0	0	1	1
179.0	0	2	2
180.0	0	3	3
181.0	0	1	1
183.0	0	1	1
184.0	0	1	1
185.0	0	1	1
188.0	0	2	2
189.0	0	6	6
190.0	0	1	1
192.0	0	2	2
193.0	0	1	1
195.0	0	1	1
197.0	0	1	1
198.0	0	1	1
199.0	0	2	2
202.0	0	2	2
204.0	0	2	2
207.0	0	2	2
208.0	0	1	1
210.0	0	2	2
211.0	0	1	1
212.0	0	1	1
213.0	0	1	1
215.0	0	1	1
216.0	0	1	1
218.0	0	3	3
219.0	0	2	2
220.0	0	1	1
221.0	0	2	2
226.0	0	1	1
227.0	0	1	1
228.0	0	2	2
229.0	0	2	2
231.0	0	1	1
235.0	0	1	1
236.0	0	1	1
240.0	0	1	1
241.0	0	2	2
242.0	0	1	1
244.0	0	1	1
245.0	0	1	1
247.0	0	1	1
250.0	0	1	1
251.0	0	2	2
255.0	0	1	1
260.0	0	1	1
261.0	0	2	2
262.0	0	1	1
269.0	0	1	1
270.0	0	2	2
277.0	0	1	1
279.0	0	1	1
281.0	0	1	1
282.0	0	1	1
286.0	0	1	1
291.0	0	1	1
302.0	0	1	1
306.0	0	1	1
312.0	0	1	1
313.0	0	1	1
314.0	0	1	1
315.0	0	1	1
316.0	0	1	1
319.0	0	1	1
330.0	0	1	1
331.0	0	1	1
334.0	0	1	1
337.0	0	1	1
353.0	0	1	1
363.0	0	1	1
372.0	0	1	1
377.0	0	1	1
382.0	0	1	1
388.0	0	1	1
399.0	0	1	1
424.0	0	1	1
431.0	0	1	1
468.0	0	1	1
521.0	0	1	1
647.0	0	1	1
654.0	0	1	1
2368.0	0	1	1