## 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-GSM1606203.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606203.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606203.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 00:53:46 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	35669467	6334350	0	0	5236669	0	0.146811	109274903

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	27775600	27775600
2.0	1.721502	1818347	1818347
3.0	2.242068	412611	412611
4.0	2.617658	163363	163363
5.0	2.888646	83559	83559
6.0	3.084165	48175	48175
7.0	3.225233	31353	31353
8.0	3.327013	21578	21578
9.0	3.400448	15248	15248
10.0	3.453431	11222	11222
11.0	3.491659	8438	8438
12.0	3.51924	6477	6477
13.0	3.53914	5217	5217
14.0	3.553498	4191	4191
15.0	3.563858	3424	3424
16.0	3.571332	2844	2844
17.0	3.576724	2456	2456
18.0	3.580615	2045	2045
19.0	3.583423	1758	1758
20.0	3.585448	1564	1564
21.0	3.586909	1297	1297
22.0	3.587964	1106	1106
23.0	3.588724	993	993
24.0	3.589273	864	864
25.0	3.589669	722	722
26.0	3.589955	694	694
27.0	3.590161	614	614
28.0	3.59031	527	527
29.0	3.590417	473	473
30.0	3.590495	411	411
31.0	3.590551	394	394
32.0	3.590591	346	346
33.0	3.59062	312	312
34.0	3.590641	281	281
35.0	3.590656	305	305
36.0	3.590667	262	262
37.0	3.590675	225	225
38.0	3.590681	195	195
39.0	3.590685	204	204
40.0	3.590688	196	196
41.0	3.59069	161	161
42.0	3.590691	133	133
43.0	3.590692	136	136
44.0	3.590693	119	119
45.0	3.590694	119	119
46.0	3.590694	110	110
47.0	3.590694	102	102
48.0	3.590695	99	99
49.0	3.590695	99	99
50.0	3.590695	88	88
51.0	3.590695	82	82
52.0	3.590695	75	75
53.0	3.590695	78	78
54.0	3.590695	60	60
55.0	3.590695	56	56
56.0	3.590695	62	62
57.0	3.590695	48	48
58.0	3.590695	51	51
59.0	3.590695	32	32
60.0	3.590695	57	57
61.0	3.590695	46	46
62.0	3.590695	40	40
63.0	3.590695	46	46
64.0	3.590695	38	38
65.0	3.590695	34	34
66.0	3.590695	36	36
67.0	3.590695	42	42
68.0	3.590695	25	25
69.0	3.590695	37	37
70.0	3.590695	28	28
71.0	3.590695	20	20
72.0	3.590695	29	29
73.0	3.590695	24	24
74.0	3.590695	20	20
75.0	3.590695	32	32
76.0	3.590695	22	22
77.0	3.590695	27	27
78.0	3.590695	13	13
79.0	3.590695	16	16
80.0	3.590695	15	15
81.0	3.590695	14	14
82.0	3.590695	16	16
83.0	3.590695	26	26
84.0	3.590695	13	13
85.0	3.590695	22	22
86.0	3.590695	11	11
87.0	3.590695	13	13
88.0	3.590695	12	12
89.0	3.590695	17	17
90.0	3.590695	12	12
91.0	3.590695	13	13
92.0	3.590695	8	8
93.0	3.590695	14	14
94.0	3.590695	8	8
95.0	3.590695	6	6
96.0	3.590695	13	13
97.0	3.590695	12	12
98.0	3.590695	9	9
99.0	3.590695	8	8
100.0	3.590695	11	11
101.0	0	8	8
102.0	0	10	10
103.0	0	8	8
104.0	0	8	8
105.0	0	9	9
106.0	0	7	7
107.0	0	10	10
108.0	0	6	6
109.0	0	7	7
110.0	0	6	6
111.0	0	8	8
112.0	0	5	5
113.0	0	3	3
114.0	0	3	3
115.0	0	2	2
116.0	0	6	6
117.0	0	5	5
118.0	0	6	6
119.0	0	5	5
120.0	0	4	4
121.0	0	9	9
123.0	0	2	2
124.0	0	1	1
125.0	0	3	3
126.0	0	3	3
127.0	0	7	7
128.0	0	4	4
130.0	0	1	1
131.0	0	4	4
132.0	0	2	2
133.0	0	3	3
134.0	0	3	3
135.0	0	2	2
136.0	0	1	1
137.0	0	4	4
138.0	0	1	1
139.0	0	2	2
140.0	0	4	4
141.0	0	4	4
142.0	0	4	4
143.0	0	2	2
144.0	0	1	1
145.0	0	2	2
146.0	0	4	4
147.0	0	3	3
148.0	0	2	2
149.0	0	2	2
150.0	0	4	4
152.0	0	1	1
153.0	0	1	1
154.0	0	4	4
158.0	0	3	3
159.0	0	1	1
160.0	0	2	2
163.0	0	3	3
164.0	0	3	3
167.0	0	1	1
168.0	0	1	1
169.0	0	2	2
170.0	0	1	1
171.0	0	2	2
174.0	0	1	1
175.0	0	1	1
176.0	0	1	1
177.0	0	1	1
178.0	0	1	1
180.0	0	1	1
182.0	0	1	1
184.0	0	1	1
185.0	0	1	1
191.0	0	2	2
192.0	0	1	1
193.0	0	3	3
194.0	0	2	2
197.0	0	1	1
199.0	0	1	1
206.0	0	1	1
207.0	0	1	1
214.0	0	1	1
215.0	0	1	1
216.0	0	2	2
218.0	0	2	2
222.0	0	3	3
224.0	0	1	1
225.0	0	1	1
231.0	0	1	1
233.0	0	1	1
235.0	0	1	1
237.0	0	1	1
242.0	0	1	1
243.0	0	1	1
245.0	0	1	1
246.0	0	1	1
249.0	0	1	1
253.0	0	1	1
258.0	0	1	1
281.0	0	1	1
282.0	0	2	2
295.0	0	1	1
298.0	0	1	1
303.0	0	1	1
312.0	0	1	1
327.0	0	1	1
348.0	0	1	1
351.0	0	1	1
364.0	0	1	1
366.0	0	1	1
532.0	0	1	1
5352.0	0	1	1