## 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-GSM1606342.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606342.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606342.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 14:26:14 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	24567238	3777354	0	0	3849611	0	0.156697	69967998

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	18745993	18745993
2.0	1.703899	1348986	1348986
3.0	2.199372	306931	306931
4.0	2.548134	122463	122463
5.0	2.793628	61991	61991
6.0	2.966431	35869	35869
7.0	3.088066	23259	23259
8.0	3.173685	15623	15623
9.0	3.233952	11157	11157
10.0	3.276374	8063	8063
11.0	3.306235	6173	6173
12.0	3.327254	4861	4861
13.0	3.342049	3775	3775
14.0	3.352464	2948	2948
15.0	3.359794	2510	2510
16.0	3.364954	2035	2035
17.0	3.368586	1715	1715
18.0	3.371143	1565	1565
19.0	3.372943	1287	1287
20.0	3.374209	1073	1073
21.0	3.375101	856	856
22.0	3.375729	788	788
23.0	3.37617	739	739
24.0	3.376481	566	566
25.0	3.3767	482	482
26.0	3.376854	497	497
27.0	3.376963	404	404
28.0	3.377039	393	393
29.0	3.377093	354	354
30.0	3.377131	322	322
31.0	3.377157	316	316
32.0	3.377176	267	267
33.0	3.377189	212	212
34.0	3.377199	232	232
35.0	3.377205	185	185
36.0	3.37721	176	176
37.0	3.377213	160	160
38.0	3.377215	160	160
39.0	3.377217	128	128
40.0	3.377218	144	144
41.0	3.377219	100	100
42.0	3.377219	116	116
43.0	3.37722	115	115
44.0	3.37722	89	89
45.0	3.37722	89	89
46.0	3.37722	87	87
47.0	3.37722	69	69
48.0	3.377221	72	72
49.0	3.377221	54	54
50.0	3.377221	53	53
51.0	3.377221	50	50
52.0	3.377221	47	47
53.0	3.377221	57	57
54.0	3.377221	49	49
55.0	3.377221	41	41
56.0	3.377221	47	47
57.0	3.377221	22	22
58.0	3.377221	37	37
59.0	3.377221	30	30
60.0	3.377221	38	38
61.0	3.377221	39	39
62.0	3.377221	32	32
63.0	3.377221	20	20
64.0	3.377221	30	30
65.0	3.377221	22	22
66.0	3.377221	21	21
67.0	3.377221	24	24
68.0	3.377221	22	22
69.0	3.377221	23	23
70.0	3.377221	11	11
71.0	3.377221	14	14
72.0	3.377221	17	17
73.0	3.377221	19	19
74.0	3.377221	14	14
75.0	3.377221	24	24
76.0	3.377221	22	22
77.0	3.377221	15	15
78.0	3.377221	13	13
79.0	3.377221	12	12
80.0	3.377221	12	12
81.0	3.377221	12	12
82.0	3.377221	8	8
83.0	3.377221	6	6
84.0	3.377221	10	10
85.0	3.377221	11	11
86.0	3.377221	12	12
87.0	3.377221	7	7
88.0	3.377221	6	6
89.0	3.377221	9	9
90.0	3.377221	8	8
91.0	3.377221	4	4
92.0	3.377221	6	6
93.0	3.377221	4	4
94.0	3.377221	6	6
95.0	3.377221	5	5
96.0	3.377221	4	4
97.0	3.377221	5	5
98.0	3.377221	6	6
99.0	3.377221	4	4
100.0	3.377221	8	8
101.0	0	4	4
102.0	0	6	6
103.0	0	8	8
104.0	0	3	3
105.0	0	7	7
106.0	0	2	2
107.0	0	5	5
108.0	0	4	4
109.0	0	3	3
110.0	0	4	4
112.0	0	2	2
113.0	0	5	5
114.0	0	4	4
115.0	0	2	2
116.0	0	2	2
120.0	0	1	1
121.0	0	6	6
122.0	0	2	2
123.0	0	4	4
124.0	0	4	4
125.0	0	4	4
126.0	0	1	1
127.0	0	3	3
128.0	0	1	1
129.0	0	1	1
130.0	0	1	1
131.0	0	1	1
132.0	0	4	4
134.0	0	1	1
135.0	0	1	1
136.0	0	2	2
138.0	0	2	2
139.0	0	1	1
141.0	0	2	2
142.0	0	1	1
144.0	0	1	1
145.0	0	2	2
147.0	0	1	1
148.0	0	3	3
149.0	0	3	3
150.0	0	2	2
151.0	0	2	2
154.0	0	1	1
155.0	0	1	1
156.0	0	1	1
157.0	0	1	1
158.0	0	1	1
159.0	0	1	1
161.0	0	2	2
168.0	0	1	1
169.0	0	1	1
170.0	0	1	1
172.0	0	2	2
174.0	0	3	3
177.0	0	1	1
181.0	0	2	2
182.0	0	1	1
184.0	0	1	1
185.0	0	1	1
187.0	0	1	1
188.0	0	1	1
195.0	0	1	1
196.0	0	1	1
198.0	0	1	1
208.0	0	1	1
215.0	0	1	1
225.0	0	2	2
226.0	0	1	1
235.0	0	1	1
237.0	0	2	2
244.0	0	1	1
247.0	0	1	1
248.0	0	1	1
259.0	0	1	1
322.0	0	1	1
330.0	0	1	1
3414.0	0	1	1