## 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-GSM1606208.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606208.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606208.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 15:00:19 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	26098605	4746088	0	0	3205707	0	0.122831	97347867

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	21166629	21166629
2.0	1.764834	1215800	1215800
3.0	2.349805	257791	257791
4.0	2.797211	100353	100353
5.0	3.139403	49932	49932
6.0	3.401122	28711	28711
7.0	3.601294	18430	18430
8.0	3.754393	12086	12086
9.0	3.871488	8755	8755
10.0	3.961046	6224	6224
11.0	4.029543	4746	4746
12.0	4.081932	3794	3794
13.0	4.122001	3052	3052
14.0	4.152647	2378	2378
15.0	4.176086	1859	1859
16.0	4.194013	1602	1602
17.0	4.207724	1287	1287
18.0	4.218211	1104	1104
19.0	4.226232	877	877
20.0	4.232366	720	720
21.0	4.237058	648	648
22.0	4.240646	586	586
23.0	4.243391	512	512
24.0	4.24549	497	497
25.0	4.247096	372	372
26.0	4.248324	345	345
27.0	4.249263	299	299
28.0	4.249981	292	292
29.0	4.250531	249	249
30.0	4.250951	207	207
31.0	4.251272	208	208
32.0	4.251518	196	196
33.0	4.251706	166	166
34.0	4.25185	169	169
35.0	4.25196	113	113
36.0	4.252044	131	131
37.0	4.252108	118	118
38.0	4.252157	100	100
39.0	4.252195	104	104
40.0	4.252224	103	103
41.0	4.252246	102	102
42.0	4.252263	65	65
43.0	4.252275	60	60
44.0	4.252285	61	61
45.0	4.252293	65	65
46.0	4.252299	42	42
47.0	4.252303	56	56
48.0	4.252306	49	49
49.0	4.252309	56	56
50.0	4.252311	40	40
51.0	4.252312	45	45
52.0	4.252314	30	30
53.0	4.252314	31	31
54.0	4.252315	26	26
55.0	4.252316	26	26
56.0	4.252316	27	27
57.0	4.252316	26	26
58.0	4.252317	21	21
59.0	4.252317	18	18
60.0	4.252317	22	22
61.0	4.252317	18	18
62.0	4.252317	15	15
63.0	4.252317	18	18
64.0	4.252317	21	21
65.0	4.252317	22	22
66.0	4.252317	13	13
67.0	4.252317	15	15
68.0	4.252317	13	13
69.0	4.252317	15	15
70.0	4.252317	8	8
71.0	4.252317	11	11
72.0	4.252317	11	11
73.0	4.252317	8	8
74.0	4.252317	8	8
75.0	4.252317	6	6
76.0	4.252317	12	12
77.0	4.252317	12	12
78.0	4.252317	13	13
79.0	4.252317	8	8
80.0	4.252317	7	7
81.0	4.252317	6	6
82.0	4.252317	8	8
83.0	4.252317	9	9
84.0	4.252317	8	8
85.0	4.252317	6	6
86.0	4.252317	6	6
87.0	4.252317	13	13
88.0	4.252317	6	6
89.0	4.252317	0	0
90.0	4.252317	4	4
91.0	4.252317	5	5
92.0	4.252317	5	5
93.0	4.252317	7	7
94.0	4.252317	4	4
95.0	4.252317	6	6
96.0	4.252317	1	1
97.0	4.252317	7	7
98.0	4.252317	2	2
99.0	4.252317	5	5
100.0	4.252317	4	4
101.0	0	3	3
103.0	0	1	1
104.0	0	5	5
105.0	0	4	4
106.0	0	5	5
107.0	0	3	3
108.0	0	3	3
109.0	0	1	1
110.0	0	1	1
111.0	0	2	2
112.0	0	2	2
113.0	0	2	2
114.0	0	2	2
116.0	0	1	1
117.0	0	2	2
120.0	0	4	4
121.0	0	1	1
122.0	0	1	1
123.0	0	4	4
127.0	0	2	2
128.0	0	1	1
129.0	0	2	2
130.0	0	2	2
131.0	0	2	2
132.0	0	2	2
133.0	0	1	1
134.0	0	1	1
136.0	0	2	2
137.0	0	1	1
138.0	0	2	2
139.0	0	1	1
142.0	0	1	1
143.0	0	2	2
144.0	0	1	1
145.0	0	2	2
147.0	0	1	1
148.0	0	2	2
149.0	0	2	2
150.0	0	1	1
151.0	0	1	1
154.0	0	1	1
155.0	0	1	1
164.0	0	1	1
166.0	0	1	1
168.0	0	1	1
170.0	0	3	3
176.0	0	1	1
179.0	0	1	1
185.0	0	1	1
186.0	0	1	1
187.0	0	1	1
188.0	0	1	1
194.0	0	1	1
195.0	0	1	1
201.0	0	1	1
203.0	0	1	1
205.0	0	2	2
207.0	0	1	1
215.0	0	2	2
219.0	0	1	1
221.0	0	1	1
231.0	0	1	1
245.0	0	1	1
246.0	0	1	1
247.0	0	1	1
251.0	0	1	1
253.0	0	1	1
277.0	0	1	1
288.0	0	1	1
292.0	0	1	1
390.0	0	1	1
402.0	0	1	1
410.0	0	1	1
656.0	0	1	1
733.0	0	1	1
4353.0	0	1	1