## 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-GSM1606210.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606210.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606210.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 14:07:21 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	30418667	5396028	0	0	4119266	0	0.135419	101926537

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	24179245	24179245
2.0	1.741977	1464983	1464983
3.0	2.292507	323856	323856
4.0	2.700987	127968	127968
5.0	3.00407	65067	65067
6.0	3.22895	38260	38260
7.0	3.395807	23952	23952
8.0	3.51961	16447	16447
9.0	3.611469	11735	11735
10.0	3.679627	8553	8553
11.0	3.730198	6559	6559
12.0	3.767721	5080	5080
13.0	3.795562	3975	3975
14.0	3.816219	3184	3184
15.0	3.831547	2627	2627
16.0	3.842919	2189	2189
17.0	3.851357	1819	1819
18.0	3.857618	1521	1521
19.0	3.862263	1306	1306
20.0	3.86571	1064	1064
21.0	3.868268	967	967
22.0	3.870165	829	829
23.0	3.871573	718	718
24.0	3.872618	658	658
25.0	3.873393	578	578
26.0	3.873968	526	526
27.0	3.874395	433	433
28.0	3.874712	360	360
29.0	3.874946	364	364
30.0	3.875121	317	317
31.0	3.87525	304	304
32.0	3.875346	264	264
33.0	3.875417	240	240
34.0	3.87547	221	221
35.0	3.875509	203	203
36.0	3.875538	199	199
37.0	3.87556	191	191
38.0	3.875576	165	165
39.0	3.875588	149	149
40.0	3.875597	144	144
41.0	3.875603	122	122
42.0	3.875608	105	105
43.0	3.875612	87	87
44.0	3.875614	101	101
45.0	3.875616	100	100
46.0	3.875618	86	86
47.0	3.875619	77	77
48.0	3.87562	72	72
49.0	3.87562	59	59
50.0	3.875621	69	69
51.0	3.875621	57	57
52.0	3.875621	69	69
53.0	3.875621	64	64
54.0	3.875622	57	57
55.0	3.875622	42	42
56.0	3.875622	45	45
57.0	3.875622	42	42
58.0	3.875622	35	35
59.0	3.875622	41	41
60.0	3.875622	41	41
61.0	3.875622	23	23
62.0	3.875622	31	31
63.0	3.875622	24	24
64.0	3.875622	25	25
65.0	3.875622	23	23
66.0	3.875622	22	22
67.0	3.875622	23	23
68.0	3.875622	23	23
69.0	3.875622	26	26
70.0	3.875622	17	17
71.0	3.875622	21	21
72.0	3.875622	20	20
73.0	3.875622	17	17
74.0	3.875622	12	12
75.0	3.875622	18	18
76.0	3.875622	7	7
77.0	3.875622	11	11
78.0	3.875622	17	17
79.0	3.875622	14	14
80.0	3.875622	15	15
81.0	3.875622	16	16
82.0	3.875622	12	12
83.0	3.875622	12	12
84.0	3.875622	6	6
85.0	3.875622	17	17
86.0	3.875622	9	9
87.0	3.875622	11	11
88.0	3.875622	9	9
89.0	3.875622	11	11
90.0	3.875622	9	9
91.0	3.875622	12	12
92.0	3.875622	9	9
93.0	3.875622	6	6
94.0	3.875622	5	5
95.0	3.875622	7	7
96.0	3.875622	9	9
97.0	3.875622	6	6
98.0	3.875622	8	8
99.0	3.875622	5	5
100.0	3.875622	3	3
101.0	0	2	2
102.0	0	9	9
103.0	0	13	13
104.0	0	7	7
105.0	0	9	9
106.0	0	4	4
107.0	0	6	6
108.0	0	1	1
109.0	0	6	6
110.0	0	5	5
111.0	0	2	2
112.0	0	5	5
113.0	0	4	4
114.0	0	5	5
115.0	0	1	1
116.0	0	2	2
117.0	0	5	5
118.0	0	5	5
119.0	0	4	4
120.0	0	3	3
121.0	0	6	6
122.0	0	2	2
123.0	0	1	1
124.0	0	4	4
125.0	0	2	2
126.0	0	5	5
128.0	0	2	2
129.0	0	1	1
130.0	0	1	1
131.0	0	2	2
132.0	0	2	2
133.0	0	2	2
134.0	0	2	2
135.0	0	3	3
136.0	0	3	3
139.0	0	1	1
140.0	0	3	3
141.0	0	1	1
142.0	0	4	4
143.0	0	2	2
146.0	0	2	2
147.0	0	2	2
148.0	0	3	3
149.0	0	2	2
151.0	0	1	1
152.0	0	1	1
154.0	0	4	4
156.0	0	1	1
158.0	0	2	2
159.0	0	1	1
161.0	0	2	2
162.0	0	3	3
164.0	0	1	1
165.0	0	2	2
167.0	0	1	1
169.0	0	3	3
170.0	0	1	1
171.0	0	1	1
172.0	0	1	1
173.0	0	1	1
174.0	0	1	1
175.0	0	1	1
179.0	0	1	1
180.0	0	2	2
181.0	0	1	1
182.0	0	1	1
183.0	0	1	1
184.0	0	1	1
185.0	0	1	1
186.0	0	1	1
188.0	0	1	1
191.0	0	1	1
192.0	0	1	1
193.0	0	1	1
195.0	0	1	1
199.0	0	1	1
200.0	0	1	1
205.0	0	1	1
206.0	0	1	1
207.0	0	1	1
210.0	0	1	1
211.0	0	1	1
213.0	0	1	1
220.0	0	1	1
223.0	0	1	1
224.0	0	1	1
225.0	0	1	1
238.0	0	1	1
245.0	0	1	1
255.0	0	1	1
257.0	0	1	1
260.0	0	1	1
268.0	0	1	1
270.0	0	1	1
280.0	0	1	1
293.0	0	1	1
299.0	0	1	1
300.0	0	1	1
309.0	0	1	1
310.0	0	1	1
325.0	0	1	1
326.0	0	1	1
335.0	0	1	1
341.0	0	1	1
350.0	0	1	1
359.0	0	1	1
368.0	0	1	1
441.0	0	1	1
491.0	0	1	1
530.0	0	1	1
618.0	0	1	1
796.0	0	1	1
826.0	0	1	1
1394.0	0	1	1
1646.0	0	1	1
8775.0	0	1	1