## 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-GSM919956.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919956.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919956.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 15:34:26 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	10539146	2135208	0	0	2420427	0	0.229661	19278011

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	7150760	7150760
2.0	1.578861	601642	601642
3.0	1.913941	158051	158051
4.0	2.107906	69697	69697
5.0	2.220185	38445	38445
6.0	2.285179	23631	23631
7.0	2.322801	16105	16105
8.0	2.34458	11325	11325
9.0	2.357186	8257	8257
10.0	2.364483	6343	6343
11.0	2.368708	4915	4915
12.0	2.371153	3951	3951
13.0	2.372568	3327	3327
14.0	2.373388	2509	2509
15.0	2.373862	2278	2278
16.0	2.374137	1808	1808
17.0	2.374295	1635	1635
18.0	2.374387	1297	1297
19.0	2.374441	1159	1159
20.0	2.374472	1012	1012
21.0	2.374489	901	901
22.0	2.3745	785	785
23.0	2.374506	697	697
24.0	2.374509	621	621
25.0	2.374511	534	534
26.0	2.374512	489	489
27.0	2.374513	446	446
28.0	2.374513	424	424
29.0	2.374514	371	371
30.0	2.374514	310	310
31.0	2.374514	301	301
32.0	2.374514	267	267
33.0	2.374514	265	265
34.0	2.374514	234	234
35.0	2.374514	217	217
36.0	2.374514	169	169
37.0	2.374514	183	183
38.0	2.374514	168	168
39.0	2.374514	151	151
40.0	2.374514	142	142
41.0	2.374514	145	145
42.0	2.374514	147	147
43.0	2.374514	126	126
44.0	2.374514	93	93
45.0	2.374514	82	82
46.0	2.374514	82	82
47.0	2.374514	87	87
48.0	2.374514	85	85
49.0	2.374514	80	80
50.0	2.374514	89	89
51.0	2.374514	71	71
52.0	2.374514	85	85
53.0	2.374514	64	64
54.0	2.374514	64	64
55.0	2.374514	53	53
56.0	2.374514	65	65
57.0	2.374514	55	55
58.0	2.374514	56	56
59.0	2.374514	55	55
60.0	2.374514	52	52
61.0	2.374514	53	53
62.0	2.374514	31	31
63.0	2.374514	40	40
64.0	2.374514	42	42
65.0	2.374514	31	31
66.0	2.374514	31	31
67.0	2.374514	39	39
68.0	2.374514	23	23
69.0	2.374514	21	21
70.0	2.374514	27	27
71.0	2.374514	29	29
72.0	2.374514	30	30
73.0	2.374514	38	38
74.0	2.374514	21	21
75.0	2.374514	25	25
76.0	2.374514	25	25
77.0	2.374514	17	17
78.0	2.374514	17	17
79.0	2.374514	25	25
80.0	2.374514	20	20
81.0	2.374514	16	16
82.0	2.374514	15	15
83.0	2.374514	10	10
84.0	2.374514	13	13
85.0	2.374514	16	16
86.0	2.374514	21	21
87.0	2.374514	13	13
88.0	2.374514	16	16
89.0	2.374514	15	15
90.0	2.374514	16	16
91.0	2.374514	10	10
92.0	2.374514	20	20
93.0	2.374514	12	12
94.0	2.374514	10	10
95.0	2.374514	14	14
96.0	2.374514	10	10
97.0	2.374514	8	8
98.0	2.374514	10	10
99.0	2.374514	12	12
100.0	2.374514	10	10
101.0	0	8	8
102.0	0	5	5
103.0	0	2	2
104.0	0	7	7
105.0	0	7	7
106.0	0	18	18
107.0	0	11	11
108.0	0	8	8
109.0	0	5	5
110.0	0	7	7
111.0	0	5	5
112.0	0	8	8
113.0	0	5	5
114.0	0	6	6
115.0	0	10	10
116.0	0	8	8
117.0	0	6	6
118.0	0	4	4
119.0	0	7	7
120.0	0	3	3
121.0	0	6	6
122.0	0	3	3
123.0	0	9	9
124.0	0	2	2
125.0	0	5	5
126.0	0	3	3
127.0	0	8	8
128.0	0	4	4
129.0	0	5	5
130.0	0	5	5
131.0	0	6	6
132.0	0	1	1
133.0	0	4	4
134.0	0	10	10
135.0	0	3	3
136.0	0	6	6
137.0	0	4	4
138.0	0	4	4
139.0	0	3	3
140.0	0	3	3
141.0	0	4	4
142.0	0	2	2
143.0	0	2	2
144.0	0	2	2
145.0	0	1	1
146.0	0	2	2
147.0	0	3	3
148.0	0	1	1
149.0	0	3	3
150.0	0	3	3
151.0	0	4	4
152.0	0	1	1
153.0	0	1	1
154.0	0	2	2
155.0	0	3	3
156.0	0	3	3
157.0	0	1	1
158.0	0	2	2
159.0	0	1	1
160.0	0	2	2
161.0	0	3	3
162.0	0	2	2
164.0	0	3	3
165.0	0	3	3
166.0	0	5	5
167.0	0	3	3
168.0	0	1	1
170.0	0	1	1
171.0	0	1	1
173.0	0	2	2
174.0	0	3	3
175.0	0	2	2
176.0	0	1	1
178.0	0	2	2
179.0	0	1	1
180.0	0	2	2
182.0	0	1	1
183.0	0	3	3
185.0	0	3	3
187.0	0	1	1
190.0	0	1	1
191.0	0	1	1
193.0	0	1	1
194.0	0	4	4
195.0	0	3	3
196.0	0	1	1
197.0	0	2	2
198.0	0	1	1
199.0	0	3	3
200.0	0	1	1
201.0	0	1	1
203.0	0	3	3
204.0	0	2	2
205.0	0	1	1
206.0	0	1	1
207.0	0	1	1
209.0	0	2	2
213.0	0	1	1
215.0	0	1	1
220.0	0	1	1
223.0	0	2	2
224.0	0	1	1
229.0	0	2	2
231.0	0	1	1
232.0	0	1	1
234.0	0	2	2
236.0	0	1	1
237.0	0	1	1
239.0	0	1	1
242.0	0	1	1
251.0	0	1	1
252.0	0	1	1
257.0	0	1	1
258.0	0	1	1
259.0	0	2	2
260.0	0	1	1
266.0	0	1	1
268.0	0	1	1
269.0	0	1	1
270.0	0	1	1
271.0	0	1	1
278.0	0	1	1
279.0	0	1	1
280.0	0	2	2
282.0	0	1	1
284.0	0	1	1
286.0	0	1	1
287.0	0	1	1
291.0	0	1	1
295.0	0	2	2
297.0	0	1	1
298.0	0	1	1
335.0	0	1	1
344.0	0	1	1
346.0	0	2	2
354.0	0	1	1
358.0	0	1	1
362.0	0	1	1
373.0	0	1	1
376.0	0	1	1
390.0	0	1	1
393.0	0	1	1
477.0	0	1	1
520.0	0	1	1
530.0	0	1	1
547.0	0	1	1
563.0	0	1	1
564.0	0	1	1
682.0	0	1	1
687.0	0	1	1