## 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-GSM1606220.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606220.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606220.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: Mon Nov 01 23:28:57 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	38567402	6146250	0	0	5142533	0	0.133339	131457956

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	30778785	30778785
2.0	1.745737	1813278	1813278
3.0	2.301861	410260	410260
4.0	2.716583	162852	162852
5.0	3.025857	83459	83459
6.0	3.256494	48619	48619
7.0	3.428489	30944	30944
8.0	3.556752	21218	21218
9.0	3.652402	15009	15009
10.0	3.723732	11150	11150
11.0	3.776925	8353	8353
12.0	3.816594	6540	6540
13.0	3.846176	4995	4995
14.0	3.868236	4083	4083
15.0	3.884688	3343	3343
16.0	3.896956	2743	2743
17.0	3.906105	2288	2288
18.0	3.912928	1978	1978
19.0	3.918016	1685	1685
20.0	3.92181	1422	1422
21.0	3.92464	1175	1175
22.0	3.92675	1016	1016
23.0	3.928323	895	895
24.0	3.929497	809	809
25.0	3.930372	730	730
26.0	3.931025	667	667
27.0	3.931511	512	512
28.0	3.931874	473	473
29.0	3.932145	395	395
30.0	3.932347	402	402
31.0	3.932497	353	353
32.0	3.932609	299	299
33.0	3.932693	282	282
34.0	3.932755	266	266
35.0	3.932802	247	247
36.0	3.932837	212	212
37.0	3.932863	168	168
38.0	3.932882	172	172
39.0	3.932896	189	189
40.0	3.932907	162	162
41.0	3.932915	133	133
42.0	3.932921	140	140
43.0	3.932925	124	124
44.0	3.932929	134	134
45.0	3.932931	107	107
46.0	3.932933	113	113
47.0	3.932935	99	99
48.0	3.932936	97	97
49.0	3.932936	82	82
50.0	3.932937	59	59
51.0	3.932937	61	61
52.0	3.932938	68	68
53.0	3.932938	48	48
54.0	3.932938	58	58
55.0	3.932938	50	50
56.0	3.932938	47	47
57.0	3.932938	45	45
58.0	3.932938	37	37
59.0	3.932938	38	38
60.0	3.932938	42	42
61.0	3.932938	36	36
62.0	3.932939	41	41
63.0	3.932939	41	41
64.0	3.932939	20	20
65.0	3.932939	33	33
66.0	3.932939	29	29
67.0	3.932939	25	25
68.0	3.932939	27	27
69.0	3.932939	22	22
70.0	3.932939	26	26
71.0	3.932939	20	20
72.0	3.932939	18	18
73.0	3.932939	15	15
74.0	3.932939	26	26
75.0	3.932939	13	13
76.0	3.932939	18	18
77.0	3.932939	22	22
78.0	3.932939	12	12
79.0	3.932939	10	10
80.0	3.932939	15	15
81.0	3.932939	11	11
82.0	3.932939	12	12
83.0	3.932939	8	8
84.0	3.932939	11	11
85.0	3.932939	9	9
86.0	3.932939	11	11
87.0	3.932939	14	14
88.0	3.932939	11	11
89.0	3.932939	6	6
90.0	3.932939	16	16
91.0	3.932939	3	3
92.0	3.932939	7	7
93.0	3.932939	10	10
94.0	3.932939	7	7
95.0	3.932939	7	7
96.0	3.932939	5	5
97.0	3.932939	6	6
98.0	3.932939	5	5
99.0	3.932939	6	6
100.0	3.932939	12	12
101.0	0	13	13
102.0	0	3	3
103.0	0	7	7
104.0	0	3	3
105.0	0	4	4
106.0	0	6	6
107.0	0	4	4
108.0	0	5	5
109.0	0	7	7
110.0	0	6	6
111.0	0	6	6
112.0	0	1	1
113.0	0	3	3
114.0	0	4	4
115.0	0	3	3
116.0	0	4	4
117.0	0	4	4
118.0	0	4	4
120.0	0	3	3
121.0	0	4	4
122.0	0	3	3
123.0	0	2	2
124.0	0	3	3
125.0	0	5	5
126.0	0	1	1
127.0	0	2	2
128.0	0	1	1
129.0	0	2	2
131.0	0	3	3
132.0	0	3	3
133.0	0	1	1
134.0	0	4	4
135.0	0	2	2
136.0	0	1	1
137.0	0	2	2
138.0	0	3	3
139.0	0	1	1
140.0	0	3	3
141.0	0	3	3
142.0	0	2	2
143.0	0	2	2
144.0	0	4	4
145.0	0	4	4
148.0	0	2	2
149.0	0	1	1
150.0	0	3	3
152.0	0	3	3
153.0	0	2	2
156.0	0	1	1
158.0	0	3	3
160.0	0	2	2
161.0	0	2	2
165.0	0	1	1
167.0	0	2	2
168.0	0	1	1
171.0	0	1	1
172.0	0	1	1
174.0	0	2	2
175.0	0	2	2
179.0	0	1	1
181.0	0	1	1
184.0	0	2	2
186.0	0	2	2
187.0	0	1	1
188.0	0	1	1
190.0	0	1	1
191.0	0	1	1
192.0	0	1	1
197.0	0	1	1
198.0	0	1	1
199.0	0	2	2
202.0	0	1	1
204.0	0	1	1
205.0	0	2	2
213.0	0	1	1
218.0	0	1	1
227.0	0	1	1
241.0	0	1	1
245.0	0	1	1
249.0	0	1	1
255.0	0	1	1
266.0	0	1	1
275.0	0	1	1
289.0	0	1	1
340.0	0	1	1
365.0	0	1	1
572.0	0	1	1
7504.0	0	1	1