## 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-GSM1606200.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606200.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606200.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 14:12:57 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	30021252	5317996	0	0	4330363	0	0.144243	93796507

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	23456000	23456000
2.0	1.7261	1539926	1539926
3.0	2.253321	344741	344741
4.0	2.636135	135826	135826
5.0	2.914097	68907	68907
6.0	3.115925	40077	40077
7.0	3.262472	25560	25560
8.0	3.36888	17343	17343
9.0	3.446143	12252	12252
10.0	3.502244	9070	9070
11.0	3.542978	6866	6866
12.0	3.572555	5310	5310
13.0	3.594032	4140	4140
14.0	3.609625	3263	3263
15.0	3.620948	2709	2709
16.0	3.629169	2225	2225
17.0	3.635139	1860	1860
18.0	3.639473	1652	1652
19.0	3.642621	1434	1434
20.0	3.644906	1185	1185
21.0	3.646565	1061	1061
22.0	3.64777	901	901
23.0	3.648645	765	765
24.0	3.64928	714	714
25.0	3.649741	572	572
26.0	3.650076	534	534
27.0	3.650319	482	482
28.0	3.650496	408	408
29.0	3.650624	370	370
30.0	3.650717	326	326
31.0	3.650785	352	352
32.0	3.650834	287	287
33.0	3.650869	238	238
34.0	3.650895	214	214
35.0	3.650914	232	232
36.0	3.650928	197	197
37.0	3.650938	154	154
38.0	3.650945	156	156
39.0	3.65095	152	152
40.0	3.650954	142	142
41.0	3.650957	129	129
42.0	3.650959	121	121
43.0	3.65096	102	102
44.0	3.650961	117	117
45.0	3.650962	98	98
46.0	3.650962	90	90
47.0	3.650963	83	83
48.0	3.650963	79	79
49.0	3.650963	61	61
50.0	3.650963	71	71
51.0	3.650964	62	62
52.0	3.650964	64	64
53.0	3.650964	64	64
54.0	3.650964	43	43
55.0	3.650964	56	56
56.0	3.650964	53	53
57.0	3.650964	42	42
58.0	3.650964	52	52
59.0	3.650964	40	40
60.0	3.650964	36	36
61.0	3.650964	38	38
62.0	3.650964	32	32
63.0	3.650964	32	32
64.0	3.650964	29	29
65.0	3.650964	32	32
66.0	3.650964	27	27
67.0	3.650964	26	26
68.0	3.650964	24	24
69.0	3.650964	20	20
70.0	3.650964	25	25
71.0	3.650964	22	22
72.0	3.650964	20	20
73.0	3.650964	26	26
74.0	3.650964	13	13
75.0	3.650964	15	15
76.0	3.650964	10	10
77.0	3.650964	10	10
78.0	3.650964	10	10
79.0	3.650964	8	8
80.0	3.650964	12	12
81.0	3.650964	17	17
82.0	3.650964	13	13
83.0	3.650964	12	12
84.0	3.650964	5	5
85.0	3.650964	10	10
86.0	3.650964	9	9
87.0	3.650964	7	7
88.0	3.650964	10	10
89.0	3.650964	10	10
90.0	3.650964	10	10
91.0	3.650964	14	14
92.0	3.650964	7	7
93.0	3.650964	9	9
94.0	3.650964	5	5
95.0	3.650964	9	9
96.0	3.650964	8	8
97.0	3.650964	5	5
98.0	3.650964	4	4
99.0	3.650964	5	5
100.0	3.650964	6	6
101.0	0	9	9
102.0	0	5	5
103.0	0	6	6
104.0	0	3	3
105.0	0	7	7
106.0	0	8	8
107.0	0	5	5
108.0	0	2	2
109.0	0	6	6
110.0	0	4	4
111.0	0	3	3
112.0	0	1	1
113.0	0	2	2
114.0	0	6	6
115.0	0	3	3
116.0	0	2	2
118.0	0	5	5
119.0	0	4	4
120.0	0	3	3
121.0	0	1	1
122.0	0	5	5
123.0	0	3	3
124.0	0	1	1
125.0	0	1	1
126.0	0	2	2
127.0	0	1	1
128.0	0	3	3
129.0	0	5	5
130.0	0	1	1
131.0	0	3	3
132.0	0	3	3
133.0	0	3	3
134.0	0	1	1
135.0	0	1	1
136.0	0	4	4
137.0	0	3	3
138.0	0	2	2
139.0	0	1	1
141.0	0	3	3
142.0	0	3	3
143.0	0	1	1
144.0	0	4	4
145.0	0	1	1
146.0	0	3	3
147.0	0	4	4
148.0	0	1	1
149.0	0	2	2
150.0	0	3	3
152.0	0	1	1
154.0	0	3	3
156.0	0	1	1
157.0	0	1	1
159.0	0	2	2
161.0	0	1	1
164.0	0	2	2
166.0	0	1	1
167.0	0	3	3
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
179.0	0	2	2
181.0	0	2	2
184.0	0	1	1
185.0	0	2	2
186.0	0	1	1
188.0	0	2	2
189.0	0	2	2
190.0	0	1	1
193.0	0	1	1
194.0	0	1	1
198.0	0	3	3
199.0	0	2	2
202.0	0	1	1
203.0	0	1	1
211.0	0	1	1
212.0	0	1	1
216.0	0	1	1
220.0	0	1	1
221.0	0	1	1
242.0	0	1	1
243.0	0	1	1
267.0	0	1	1
268.0	0	1	1
302.0	0	1	1
310.0	0	1	1
339.0	0	1	1
347.0	0	1	1
372.0	0	1	1
423.0	0	1	1
443.0	0	1	1
453.0	0	1	1
558.0	0	1	1
5354.0	0	1	1