## 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-GSM1606360.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606360.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606360.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 14:51:53 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	22877946	3217730	0	0	3045318	0	0.133112	78126904

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	18204855	18204855
2.0	1.746149	1144865	1144865
3.0	2.302886	242328	242328
4.0	2.718295	94141	94141
5.0	3.028252	47656	47656
6.0	3.259526	27559	27559
7.0	3.43209	17468	17468
8.0	3.560849	12012	12012
9.0	3.656923	8299	8299
10.0	3.728607	6021	6021
11.0	3.782095	4617	4617
12.0	3.822005	3652	3652
13.0	3.851783	2936	2936
14.0	3.874002	2280	2280
15.0	3.890581	1907	1907
16.0	3.902952	1461	1461
17.0	3.912182	1250	1250
18.0	3.919069	1021	1021
19.0	3.924207	910	910
20.0	3.928042	742	742
21.0	3.930903	637	637
22.0	3.933037	545	545
23.0	3.93463	535	535
24.0	3.935818	420	420
25.0	3.936705	409	409
26.0	3.937367	375	375
27.0	3.937861	336	336
28.0	3.938229	286	286
29.0	3.938504	252	252
30.0	3.938709	201	201
31.0	3.938862	213	213
32.0	3.938976	168	168
33.0	3.939061	127	127
34.0	3.939125	143	143
35.0	3.939172	140	140
36.0	3.939208	112	112
37.0	3.939234	115	115
38.0	3.939254	106	106
39.0	3.939269	85	85
40.0	3.939279	87	87
41.0	3.939288	87	87
42.0	3.939294	72	72
43.0	3.939298	80	80
44.0	3.939302	61	61
45.0	3.939304	52	52
46.0	3.939306	56	56
47.0	3.939308	53	53
48.0	3.939309	53	53
49.0	3.939309	27	27
50.0	3.93931	43	43
51.0	3.93931	32	32
52.0	3.939311	31	31
53.0	3.939311	24	24
54.0	3.939311	40	40
55.0	3.939311	32	32
56.0	3.939311	30	30
57.0	3.939312	18	18
58.0	3.939312	21	21
59.0	3.939312	28	28
60.0	3.939312	18	18
61.0	3.939312	18	18
62.0	3.939312	26	26
63.0	3.939312	13	13
64.0	3.939312	20	20
65.0	3.939312	20	20
66.0	3.939312	17	17
67.0	3.939312	12	12
68.0	3.939312	18	18
69.0	3.939312	16	16
70.0	3.939312	17	17
71.0	3.939312	13	13
72.0	3.939312	8	8
73.0	3.939312	11	11
74.0	3.939312	9	9
75.0	3.939312	12	12
76.0	3.939312	7	7
77.0	3.939312	12	12
78.0	3.939312	7	7
79.0	3.939312	11	11
80.0	3.939312	7	7
81.0	3.939312	12	12
82.0	3.939312	7	7
83.0	3.939312	6	6
84.0	3.939312	9	9
85.0	3.939312	0	0
86.0	3.939312	6	6
87.0	3.939312	8	8
88.0	3.939312	7	7
89.0	3.939312	9	9
90.0	3.939312	5	5
91.0	3.939312	4	4
92.0	3.939312	4	4
93.0	3.939312	2	2
94.0	3.939312	2	2
95.0	3.939312	10	10
96.0	3.939312	6	6
97.0	3.939312	6	6
98.0	3.939312	2	2
99.0	3.939312	1	1
100.0	3.939312	3	3
101.0	0	1	1
102.0	0	2	2
103.0	0	4	4
104.0	0	1	1
105.0	0	2	2
106.0	0	4	4
107.0	0	2	2
108.0	0	4	4
109.0	0	3	3
110.0	0	1	1
111.0	0	1	1
112.0	0	2	2
113.0	0	1	1
115.0	0	1	1
116.0	0	2	2
117.0	0	1	1
118.0	0	2	2
119.0	0	1	1
120.0	0	5	5
121.0	0	2	2
122.0	0	1	1
123.0	0	4	4
124.0	0	1	1
125.0	0	3	3
126.0	0	2	2
127.0	0	1	1
128.0	0	1	1
129.0	0	2	2
130.0	0	2	2
131.0	0	1	1
132.0	0	2	2
133.0	0	1	1
136.0	0	2	2
137.0	0	2	2
139.0	0	2	2
141.0	0	1	1
143.0	0	2	2
144.0	0	1	1
145.0	0	2	2
146.0	0	2	2
147.0	0	1	1
148.0	0	1	1
149.0	0	1	1
150.0	0	2	2
151.0	0	1	1
154.0	0	1	1
161.0	0	1	1
162.0	0	2	2
167.0	0	1	1
168.0	0	1	1
174.0	0	1	1
176.0	0	2	2
177.0	0	2	2
178.0	0	1	1
184.0	0	1	1
186.0	0	3	3
200.0	0	1	1
208.0	0	1	1
211.0	0	1	1
218.0	0	1	1
220.0	0	1	1
233.0	0	1	1
235.0	0	1	1
238.0	0	2	2
249.0	0	1	1
250.0	0	1	1
265.0	0	1	1
283.0	0	1	1
302.0	0	1	1
314.0	0	1	1
4887.0	0	1	1