## 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-GSM1606191.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606191.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606191.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 15:13:59 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	21280556	3077128	0	0	2157355	0	0.101377	97737380

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	17775682	17775682
2.0	1.804341	1009633	1009633
3.0	2.451305	188221	188221
4.0	2.971685	66276	66276
5.0	3.390248	30620	30620
6.0	3.726916	16733	16733
7.0	3.997711	10062	10062
8.0	4.215523	6503	6503
9.0	4.390718	4552	4552
10.0	4.531634	3211	3211
11.0	4.644979	2259	2259
12.0	4.736147	1717	1717
13.0	4.809477	1270	1270
14.0	4.868459	1039	1039
15.0	4.915901	825	825
16.0	4.954061	653	653
17.0	4.984754	531	531
18.0	5.009442	452	452
19.0	5.029299	386	386
20.0	5.045272	326	326
21.0	5.058119	267	267
22.0	5.068452	232	232
23.0	5.076764	200	200
24.0	5.083449	193	193
25.0	5.088826	158	158
26.0	5.093151	104	104
27.0	5.09663	99	99
28.0	5.099429	92	92
29.0	5.101679	80	80
30.0	5.10349	68	68
31.0	5.104946	64	64
32.0	5.106117	69	69
33.0	5.107059	46	46
34.0	5.107817	50	50
35.0	5.108426	33	33
36.0	5.108917	37	37
37.0	5.109311	36	36
38.0	5.109628	36	36
39.0	5.109883	30	30
40.0	5.110088	21	21
41.0	5.110254	26	26
42.0	5.110386	19	19
43.0	5.110493	24	24
44.0	5.110579	16	16
45.0	5.110648	13	13
46.0	5.110704	12	12
47.0	5.110748	10	10
48.0	5.110784	11	11
49.0	5.110813	8	8
50.0	5.110836	11	11
51.0	5.110855	12	12
52.0	5.11087	12	12
53.0	5.110882	9	9
54.0	5.110892	11	11
55.0	5.1109	4	4
56.0	5.110906	9	9
57.0	5.110911	8	8
58.0	5.110915	8	8
59.0	5.110919	7	7
60.0	5.110921	3	3
61.0	5.110923	7	7
62.0	5.110925	2	2
63.0	5.110926	1	1
64.0	5.110927	1	1
65.0	5.110928	3	3
66.0	5.110929	4	4
67.0	5.11093	3	3
68.0	5.11093	1	1
69.0	5.11093	0	0
70.0	5.110931	2	2
71.0	5.110931	3	3
72.0	5.110931	2	2
73.0	5.110931	2	2
74.0	5.110931	3	3
75.0	5.110932	2	2
76.0	5.110932	1	1
77.0	5.110932	3	3
78.0	5.110932	4	4
79.0	5.110932	7	7
80.0	5.110932	3	3
81.0	5.110932	1	1
82.0	5.110932	1	1
83.0	5.110932	0	0
84.0	5.110932	1	1
85.0	5.110932	2	2
86.0	5.110932	1	1
87.0	5.110932	2	2
88.0	5.110932	0	0
89.0	5.110932	1	1
90.0	5.110932	0	0
91.0	5.110932	2	2
92.0	5.110932	0	0
93.0	5.110932	1	1
94.0	5.110932	1	1
95.0	5.110932	0	0
96.0	5.110932	0	0
97.0	5.110932	1	1
98.0	5.110932	1	1
99.0	5.110932	0	0
100.0	5.110932	0	0
101.0	0	1	1
107.0	0	2	2
111.0	0	1	1
114.0	0	1	1
115.0	0	1	1
116.0	0	1	1
117.0	0	2	2
121.0	0	1	1
122.0	0	1	1
125.0	0	1	1
126.0	0	1	1
131.0	0	1	1
135.0	0	2	2
139.0	0	2	2
145.0	0	1	1
147.0	0	1	1
157.0	0	1	1
172.0	0	1	1
180.0	0	1	1
191.0	0	1	1
205.0	0	1	1
208.0	0	1	1
222.0	0	1	1
243.0	0	1	1
295.0	0	1	1
363.0	0	2	2
398.0	0	1	1
3794.0	0	1	1