## 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-GSM1606346.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606346.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606346.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 14:21:06 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	33838340	5053972	0	0	6585551	0	0.194618	75246217

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	23902164	23902164
2.0	1.637818	2333108	2333108
3.0	2.044631	502847	502847
4.0	2.304103	194646	194646
5.0	2.4696	99959	99959
6.0	2.575156	58062	58062
7.0	2.642482	37300	37300
8.0	2.685424	25563	25563
9.0	2.712813	18498	18498
10.0	2.730282	13731	13731
11.0	2.741425	10569	10569
12.0	2.748531	8169	8169
13.0	2.753064	6502	6502
14.0	2.755955	5335	5335
15.0	2.757799	4530	4530
16.0	2.758975	3639	3639
17.0	2.759725	3081	3081
18.0	2.760204	2624	2624
19.0	2.760509	2201	2201
20.0	2.760704	1909	1909
21.0	2.760828	1650	1650
22.0	2.760907	1472	1472
23.0	2.760958	1300	1300
24.0	2.76099	1114	1114
25.0	2.76101	985	985
26.0	2.761023	862	862
27.0	2.761032	852	852
28.0	2.761037	737	737
29.0	2.76104	663	663
30.0	2.761043	597	597
31.0	2.761044	527	527
32.0	2.761045	497	497
33.0	2.761045	471	471
34.0	2.761046	419	419
35.0	2.761046	399	399
36.0	2.761046	350	350
37.0	2.761046	305	305
38.0	2.761046	308	308
39.0	2.761046	258	258
40.0	2.761046	242	242
41.0	2.761046	256	256
42.0	2.761046	199	199
43.0	2.761046	191	191
44.0	2.761046	168	168
45.0	2.761046	181	181
46.0	2.761046	166	166
47.0	2.761046	143	143
48.0	2.761046	137	137
49.0	2.761046	148	148
50.0	2.761046	136	136
51.0	2.761046	110	110
52.0	2.761046	107	107
53.0	2.761046	114	114
54.0	2.761046	90	90
55.0	2.761046	103	103
56.0	2.761046	71	71
57.0	2.761046	81	81
58.0	2.761046	86	86
59.0	2.761046	64	64
60.0	2.761046	68	68
61.0	2.761046	57	57
62.0	2.761046	67	67
63.0	2.761046	65	65
64.0	2.761046	49	49
65.0	2.761046	61	61
66.0	2.761046	51	51
67.0	2.761046	52	52
68.0	2.761046	43	43
69.0	2.761046	47	47
70.0	2.761046	35	35
71.0	2.761046	45	45
72.0	2.761046	35	35
73.0	2.761046	27	27
74.0	2.761046	27	27
75.0	2.761046	39	39
76.0	2.761046	42	42
77.0	2.761046	37	37
78.0	2.761046	33	33
79.0	2.761046	34	34
80.0	2.761046	27	27
81.0	2.761046	25	25
82.0	2.761046	22	22
83.0	2.761046	22	22
84.0	2.761046	21	21
85.0	2.761046	21	21
86.0	2.761046	20	20
87.0	2.761046	16	16
88.0	2.761046	31	31
89.0	2.761046	15	15
90.0	2.761046	17	17
91.0	2.761046	17	17
92.0	2.761046	21	21
93.0	2.761046	20	20
94.0	2.761046	20	20
95.0	2.761046	9	9
96.0	2.761046	14	14
97.0	2.761046	13	13
98.0	2.761046	14	14
99.0	2.761046	14	14
100.0	2.761046	10	10
101.0	0	8	8
102.0	0	10	10
103.0	0	16	16
104.0	0	7	7
105.0	0	10	10
106.0	0	11	11
107.0	0	6	6
108.0	0	7	7
109.0	0	12	12
110.0	0	9	9
111.0	0	16	16
112.0	0	10	10
113.0	0	6	6
114.0	0	9	9
115.0	0	10	10
116.0	0	8	8
117.0	0	9	9
118.0	0	10	10
119.0	0	4	4
120.0	0	4	4
121.0	0	8	8
122.0	0	9	9
123.0	0	7	7
124.0	0	7	7
125.0	0	6	6
126.0	0	9	9
127.0	0	6	6
128.0	0	9	9
129.0	0	4	4
130.0	0	4	4
131.0	0	5	5
132.0	0	7	7
133.0	0	2	2
134.0	0	3	3
135.0	0	6	6
136.0	0	5	5
137.0	0	3	3
138.0	0	3	3
139.0	0	4	4
140.0	0	2	2
141.0	0	4	4
142.0	0	4	4
144.0	0	3	3
145.0	0	4	4
146.0	0	4	4
147.0	0	3	3
148.0	0	3	3
149.0	0	1	1
150.0	0	2	2
151.0	0	8	8
152.0	0	2	2
153.0	0	1	1
154.0	0	5	5
155.0	0	3	3
156.0	0	2	2
157.0	0	3	3
158.0	0	2	2
159.0	0	5	5
160.0	0	3	3
161.0	0	1	1
162.0	0	1	1
163.0	0	3	3
164.0	0	2	2
165.0	0	3	3
166.0	0	5	5
167.0	0	2	2
168.0	0	4	4
169.0	0	1	1
170.0	0	3	3
171.0	0	2	2
172.0	0	2	2
173.0	0	3	3
174.0	0	1	1
175.0	0	1	1
176.0	0	2	2
177.0	0	2	2
178.0	0	2	2
179.0	0	1	1
180.0	0	2	2
181.0	0	1	1
182.0	0	1	1
183.0	0	4	4
184.0	0	2	2
185.0	0	2	2
186.0	0	3	3
187.0	0	1	1
188.0	0	1	1
189.0	0	2	2
190.0	0	1	1
191.0	0	2	2
192.0	0	1	1
197.0	0	1	1
198.0	0	4	4
199.0	0	1	1
201.0	0	1	1
202.0	0	1	1
203.0	0	1	1
206.0	0	1	1
207.0	0	2	2
208.0	0	1	1
209.0	0	1	1
212.0	0	2	2
213.0	0	1	1
214.0	0	1	1
216.0	0	1	1
219.0	0	1	1
220.0	0	1	1
221.0	0	1	1
222.0	0	2	2
223.0	0	1	1
225.0	0	1	1
226.0	0	1	1
230.0	0	1	1
231.0	0	2	2
233.0	0	2	2
234.0	0	1	1
235.0	0	1	1
238.0	0	1	1
240.0	0	1	1
241.0	0	1	1
242.0	0	1	1
244.0	0	3	3
248.0	0	1	1
252.0	0	2	2
253.0	0	1	1
256.0	0	2	2
259.0	0	2	2
265.0	0	1	1
270.0	0	1	1
279.0	0	1	1
289.0	0	1	1
292.0	0	1	1
295.0	0	1	1
303.0	0	1	1
317.0	0	1	1
335.0	0	1	1
358.0	0	1	1
363.0	0	1	1
364.0	0	1	1
366.0	0	1	1
367.0	0	1	1
375.0	0	1	1
377.0	0	1	1
381.0	0	1	1
401.0	0	1	1
434.0	0	1	1
442.0	0	1	1
464.0	0	1	1
466.0	0	1	1
620.0	0	1	1
9687.0	0	1	1