## 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-GSM1606268.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606268.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606268.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 14:59:02 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	25761197	3599604	0	0	5077304	0	0.197091	56450154

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	18286773	18286773
2.0	1.63359	1593495	1593495
3.0	2.035027	373211	373211
4.0	2.289373	155382	155382
5.0	2.450524	82608	82608
6.0	2.552628	50121	50121
7.0	2.61732	32352	32352
8.0	2.658308	22648	22648
9.0	2.684278	16321	16321
10.0	2.700732	12168	12168
11.0	2.711157	9472	9472
12.0	2.717762	7417	7417
13.0	2.721947	5895	5895
14.0	2.724599	4926	4926
15.0	2.726279	3964	3964
16.0	2.727344	3281	3281
17.0	2.728018	2704	2704
18.0	2.728445	2266	2266
19.0	2.728716	1970	1970
20.0	2.728888	1748	1748
21.0	2.728996	1428	1428
22.0	2.729065	1206	1206
23.0	2.729109	1151	1151
24.0	2.729136	930	930
25.0	2.729154	849	849
26.0	2.729165	788	788
27.0	2.729172	753	753
28.0	2.729176	634	634
29.0	2.729179	561	561
30.0	2.729181	500	500
31.0	2.729182	434	434
32.0	2.729183	391	391
33.0	2.729183	367	367
34.0	2.729184	344	344
35.0	2.729184	330	330
36.0	2.729184	289	289
37.0	2.729184	280	280
38.0	2.729184	257	257
39.0	2.729184	214	214
40.0	2.729184	187	187
41.0	2.729184	177	177
42.0	2.729184	168	168
43.0	2.729184	153	153
44.0	2.729184	152	152
45.0	2.729184	127	127
46.0	2.729184	133	133
47.0	2.729184	115	115
48.0	2.729184	104	104
49.0	2.729184	100	100
50.0	2.729184	99	99
51.0	2.729184	94	94
52.0	2.729184	95	95
53.0	2.729184	87	87
54.0	2.729184	67	67
55.0	2.729184	66	66
56.0	2.729184	76	76
57.0	2.729184	58	58
58.0	2.729184	66	66
59.0	2.729184	53	53
60.0	2.729184	44	44
61.0	2.729184	50	50
62.0	2.729184	44	44
63.0	2.729184	40	40
64.0	2.729184	50	50
65.0	2.729184	40	40
66.0	2.729184	42	42
67.0	2.729184	40	40
68.0	2.729184	27	27
69.0	2.729184	30	30
70.0	2.729184	36	36
71.0	2.729184	26	26
72.0	2.729184	33	33
73.0	2.729184	19	19
74.0	2.729184	30	30
75.0	2.729184	24	24
76.0	2.729184	28	28
77.0	2.729184	27	27
78.0	2.729184	15	15
79.0	2.729184	22	22
80.0	2.729184	19	19
81.0	2.729184	20	20
82.0	2.729184	25	25
83.0	2.729184	18	18
84.0	2.729184	19	19
85.0	2.729184	15	15
86.0	2.729184	16	16
87.0	2.729184	13	13
88.0	2.729184	11	11
89.0	2.729184	11	11
90.0	2.729184	10	10
91.0	2.729184	14	14
92.0	2.729184	11	11
93.0	2.729184	12	12
94.0	2.729184	14	14
95.0	2.729184	14	14
96.0	2.729184	7	7
97.0	2.729184	8	8
98.0	2.729184	9	9
99.0	2.729184	8	8
100.0	2.729184	6	6
101.0	0	11	11
102.0	0	7	7
103.0	0	11	11
104.0	0	5	5
105.0	0	9	9
106.0	0	7	7
107.0	0	10	10
108.0	0	12	12
109.0	0	7	7
110.0	0	12	12
111.0	0	6	6
112.0	0	8	8
113.0	0	4	4
114.0	0	12	12
115.0	0	2	2
116.0	0	9	9
117.0	0	5	5
118.0	0	2	2
119.0	0	9	9
120.0	0	4	4
121.0	0	6	6
122.0	0	5	5
123.0	0	2	2
124.0	0	3	3
125.0	0	6	6
126.0	0	5	5
127.0	0	2	2
128.0	0	3	3
129.0	0	4	4
130.0	0	3	3
131.0	0	4	4
132.0	0	5	5
133.0	0	5	5
134.0	0	2	2
135.0	0	2	2
136.0	0	6	6
137.0	0	3	3
138.0	0	1	1
139.0	0	1	1
140.0	0	2	2
141.0	0	4	4
142.0	0	1	1
143.0	0	3	3
144.0	0	1	1
145.0	0	4	4
146.0	0	1	1
147.0	0	3	3
148.0	0	1	1
149.0	0	1	1
150.0	0	2	2
151.0	0	5	5
154.0	0	2	2
155.0	0	3	3
156.0	0	2	2
157.0	0	4	4
158.0	0	2	2
159.0	0	1	1
160.0	0	3	3
161.0	0	1	1
163.0	0	1	1
164.0	0	1	1
168.0	0	2	2
169.0	0	1	1
170.0	0	2	2
171.0	0	3	3
172.0	0	2	2
173.0	0	3	3
182.0	0	3	3
183.0	0	3	3
185.0	0	2	2
187.0	0	1	1
188.0	0	2	2
191.0	0	1	1
193.0	0	1	1
196.0	0	2	2
197.0	0	2	2
200.0	0	1	1
201.0	0	2	2
202.0	0	1	1
204.0	0	1	1
209.0	0	1	1
211.0	0	1	1
212.0	0	1	1
213.0	0	1	1
215.0	0	2	2
219.0	0	1	1
222.0	0	1	1
224.0	0	1	1
225.0	0	1	1
230.0	0	1	1
231.0	0	2	2
234.0	0	1	1
235.0	0	1	1
243.0	0	1	1
245.0	0	1	1
247.0	0	1	1
249.0	0	1	1
255.0	0	2	2
258.0	0	1	1
263.0	0	1	1
271.0	0	1	1
278.0	0	1	1
279.0	0	1	1
289.0	0	1	1
291.0	0	1	1
301.0	0	1	1
303.0	0	1	1
320.0	0	1	1
335.0	0	1	1
356.0	0	1	1
367.0	0	1	1
388.0	0	1	1
445.0	0	1	1
536.0	0	1	1
7355.0	0	1	1