## 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-GSM1606335.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606335.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606335.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 14:42:35 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	23489842	3034350	0	0	3027051	0	0.128866	83129527

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	18690849	18690849
2.0	1.753844	1286640	1286640
3.0	2.322126	259503	259503
4.0	2.750522	95430	95430
5.0	3.073466	45796	45796
6.0	3.316915	25602	25602
7.0	3.500438	15592	15592
8.0	3.638786	10539	10539
9.0	3.743079	7200	7200
10.0	3.821699	5232	5232
11.0	3.880967	3811	3811
12.0	3.925646	2806	2806
13.0	3.959326	2212	2212
14.0	3.984716	1736	1736
15.0	4.003856	1451	1451
16.0	4.018285	1116	1116
17.0	4.029162	977	977
18.0	4.037362	812	812
19.0	4.043543	657	657
20.0	4.048203	541	541
21.0	4.051715	445	445
22.0	4.054363	428	428
23.0	4.056359	357	357
24.0	4.057864	299	299
25.0	4.058999	304	304
26.0	4.059854	244	244
27.0	4.060498	190	190
28.0	4.060984	187	187
29.0	4.061351	155	155
30.0	4.061627	146	146
31.0	4.061835	122	122
32.0	4.061992	123	123
33.0	4.06211	113	113
34.0	4.062199	85	85
35.0	4.062267	94	94
36.0	4.062317	73	73
37.0	4.062356	70	70
38.0	4.062384	64	64
39.0	4.062406	62	62
40.0	4.062422	67	67
41.0	4.062435	44	44
42.0	4.062444	42	42
43.0	4.062451	30	30
44.0	4.062456	40	40
45.0	4.06246	30	30
46.0	4.062463	32	32
47.0	4.062466	24	24
48.0	4.062467	20	20
49.0	4.062469	23	23
50.0	4.06247	16	16
51.0	4.06247	21	21
52.0	4.062471	17	17
53.0	4.062471	17	17
54.0	4.062472	18	18
55.0	4.062472	13	13
56.0	4.062472	20	20
57.0	4.062472	13	13
58.0	4.062472	7	7
59.0	4.062472	6	6
60.0	4.062472	11	11
61.0	4.062472	9	9
62.0	4.062472	13	13
63.0	4.062472	9	9
64.0	4.062473	8	8
65.0	4.062473	10	10
66.0	4.062473	6	6
67.0	4.062473	5	5
68.0	4.062473	6	6
69.0	4.062473	8	8
70.0	4.062473	9	9
71.0	4.062473	6	6
72.0	4.062473	3	3
73.0	4.062473	3	3
74.0	4.062473	3	3
75.0	4.062473	8	8
76.0	4.062473	7	7
77.0	4.062473	3	3
78.0	4.062473	1	1
79.0	4.062473	2	2
80.0	4.062473	3	3
81.0	4.062473	3	3
82.0	4.062473	2	2
83.0	4.062473	3	3
84.0	4.062473	2	2
85.0	4.062473	1	1
86.0	4.062473	0	0
87.0	4.062473	4	4
88.0	4.062473	2	2
89.0	4.062473	1	1
90.0	4.062473	4	4
91.0	4.062473	5	5
92.0	4.062473	4	4
93.0	4.062473	1	1
94.0	4.062473	1	1
95.0	4.062473	2	2
96.0	4.062473	2	2
97.0	4.062473	2	2
98.0	4.062473	1	1
99.0	4.062473	1	1
100.0	4.062473	2	2
103.0	0	2	2
104.0	0	4	4
106.0	0	2	2
108.0	0	1	1
109.0	0	1	1
110.0	0	2	2
113.0	0	2	2
115.0	0	1	1
117.0	0	2	2
118.0	0	1	1
120.0	0	2	2
121.0	0	2	2
122.0	0	1	1
124.0	0	2	2
125.0	0	1	1
127.0	0	1	1
128.0	0	1	1
132.0	0	1	1
139.0	0	1	1
142.0	0	2	2
145.0	0	1	1
152.0	0	2	2
155.0	0	1	1
156.0	0	1	1
170.0	0	1	1
173.0	0	1	1
191.0	0	1	1
202.0	0	1	1
215.0	0	1	1
237.0	0	2	2
285.0	0	2	2
287.0	0	2	2
296.0	0	1	1
356.0	0	1	1
420.0	0	1	1
10183.0	0	1	1