## 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-GSM1606354.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606354.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606354.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 14:34:41 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	23693518	3387410	0	0	3405060	0	0.143713	74330548

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	18493448	18493448
2.0	1.727051	1257522	1257522
3.0	2.255654	268104	268104
4.0	2.639975	104762	104762
5.0	2.919396	52737	52737
6.0	3.12255	30735	30735
7.0	3.270252	19748	19748
8.0	3.37764	13392	13392
9.0	3.455716	9451	9451
10.0	3.512481	6839	6839
11.0	3.553753	5217	5217
12.0	3.583759	4091	4091
13.0	3.605575	3277	3277
14.0	3.621437	2594	2594
15.0	3.632969	2139	2139
16.0	3.641353	1751	1751
17.0	3.647449	1486	1486
18.0	3.651881	1248	1248
19.0	3.655103	1049	1049
20.0	3.657446	921	921
21.0	3.659149	819	819
22.0	3.660388	701	701
23.0	3.661288	603	603
24.0	3.661943	499	499
25.0	3.662419	452	452
26.0	3.662765	406	406
27.0	3.663016	338	338
28.0	3.663199	310	310
29.0	3.663332	285	285
30.0	3.663429	235	235
31.0	3.663499	215	215
32.0	3.66355	231	231
33.0	3.663587	211	211
34.0	3.663614	178	178
35.0	3.663634	165	165
36.0	3.663648	129	129
37.0	3.663659	132	132
38.0	3.663666	121	121
39.0	3.663672	104	104
40.0	3.663676	111	111
41.0	3.663679	92	92
42.0	3.663681	88	88
43.0	3.663682	91	91
44.0	3.663683	81	81
45.0	3.663684	69	69
46.0	3.663685	72	72
47.0	3.663685	45	45
48.0	3.663686	67	67
49.0	3.663686	44	44
50.0	3.663686	47	47
51.0	3.663686	47	47
52.0	3.663686	47	47
53.0	3.663686	45	45
54.0	3.663686	39	39
55.0	3.663686	25	25
56.0	3.663686	46	46
57.0	3.663686	32	32
58.0	3.663686	31	31
59.0	3.663686	33	33
60.0	3.663686	24	24
61.0	3.663686	24	24
62.0	3.663686	27	27
63.0	3.663686	21	21
64.0	3.663686	22	22
65.0	3.663686	27	27
66.0	3.663686	23	23
67.0	3.663686	18	18
68.0	3.663686	16	16
69.0	3.663686	21	21
70.0	3.663686	19	19
71.0	3.663686	22	22
72.0	3.663686	16	16
73.0	3.663686	16	16
74.0	3.663686	11	11
75.0	3.663686	19	19
76.0	3.663686	13	13
77.0	3.663686	15	15
78.0	3.663686	9	9
79.0	3.663686	18	18
80.0	3.663686	11	11
81.0	3.663686	14	14
82.0	3.663686	9	9
83.0	3.663686	6	6
84.0	3.663686	9	9
85.0	3.663686	6	6
86.0	3.663686	6	6
87.0	3.663686	6	6
88.0	3.663686	2	2
89.0	3.663686	6	6
90.0	3.663686	4	4
91.0	3.663686	5	5
92.0	3.663686	8	8
93.0	3.663686	4	4
94.0	3.663686	4	4
95.0	3.663686	7	7
96.0	3.663686	7	7
97.0	3.663686	6	6
98.0	3.663686	3	3
99.0	3.663686	7	7
100.0	3.663686	5	5
101.0	0	5	5
102.0	0	2	2
103.0	0	3	3
104.0	0	3	3
106.0	0	4	4
107.0	0	4	4
108.0	0	5	5
109.0	0	1	1
110.0	0	2	2
111.0	0	5	5
112.0	0	2	2
113.0	0	3	3
114.0	0	3	3
115.0	0	3	3
116.0	0	3	3
117.0	0	2	2
118.0	0	2	2
119.0	0	3	3
120.0	0	2	2
121.0	0	2	2
122.0	0	2	2
123.0	0	3	3
124.0	0	1	1
125.0	0	1	1
126.0	0	3	3
127.0	0	2	2
128.0	0	3	3
131.0	0	1	1
133.0	0	2	2
134.0	0	1	1
135.0	0	1	1
136.0	0	2	2
137.0	0	2	2
139.0	0	2	2
140.0	0	2	2
144.0	0	1	1
147.0	0	1	1
148.0	0	1	1
149.0	0	1	1
150.0	0	1	1
151.0	0	1	1
152.0	0	1	1
154.0	0	3	3
155.0	0	1	1
156.0	0	1	1
157.0	0	1	1
159.0	0	1	1
160.0	0	3	3
162.0	0	1	1
163.0	0	3	3
167.0	0	1	1
168.0	0	1	1
169.0	0	1	1
171.0	0	1	1
175.0	0	1	1
177.0	0	3	3
179.0	0	2	2
180.0	0	2	2
185.0	0	1	1
187.0	0	1	1
194.0	0	1	1
196.0	0	1	1
199.0	0	1	1
201.0	0	1	1
202.0	0	1	1
208.0	0	2	2
209.0	0	1	1
210.0	0	1	1
211.0	0	1	1
216.0	0	1	1
225.0	0	2	2
235.0	0	1	1
236.0	0	1	1
259.0	0	1	1
261.0	0	1	1
298.0	0	1	1
322.0	0	1	1
335.0	0	1	1
354.0	0	1	1
403.0	0	1	1
4901.0	0	1	1