## 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-GSM1606222.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606222.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606222.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 00:02:15 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	36503760	5619770	0	0	5051879	0	0.138393	119412621

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	28854344	28854344
2.0	1.736612	1784693	1784693
3.0	2.279209	400383	400383
4.0	2.678892	159044	159044
5.0	2.973303	80924	80924
6.0	3.19017	47107	47107
7.0	3.349917	30486	30486
8.0	3.467588	20676	20676
9.0	3.554266	14657	14657
10.0	3.618114	10802	10802
11.0	3.665145	8280	8280
12.0	3.699789	6195	6195
13.0	3.725308	4951	4951
14.0	3.744106	4043	4043
15.0	3.757952	3240	3240
16.0	3.768152	2655	2655
17.0	3.775665	2276	2276
18.0	3.781199	1875	1875
19.0	3.785276	1638	1638
20.0	3.788279	1392	1392
21.0	3.790491	1285	1285
22.0	3.79212	1066	1066
23.0	3.79332	902	902
24.0	3.794204	815	815
25.0	3.794855	687	687
26.0	3.795335	600	600
27.0	3.795688	562	562
28.0	3.795949	482	482
29.0	3.79614	434	434
30.0	3.796282	417	417
31.0	3.796386	330	330
32.0	3.796462	289	289
33.0	3.796519	296	296
34.0	3.79656	296	296
35.0	3.796591	260	260
36.0	3.796614	213	213
37.0	3.79663	199	199
38.0	3.796642	205	205
39.0	3.796651	163	163
40.0	3.796658	144	144
41.0	3.796663	158	158
42.0	3.796667	124	124
43.0	3.796669	126	126
44.0	3.796671	126	126
45.0	3.796673	105	105
46.0	3.796674	100	100
47.0	3.796674	82	82
48.0	3.796675	109	109
49.0	3.796675	93	93
50.0	3.796676	63	63
51.0	3.796676	84	84
52.0	3.796676	64	64
53.0	3.796676	65	65
54.0	3.796676	52	52
55.0	3.796676	54	54
56.0	3.796676	69	69
57.0	3.796677	46	46
58.0	3.796677	52	52
59.0	3.796677	47	47
60.0	3.796677	36	36
61.0	3.796677	38	38
62.0	3.796677	39	39
63.0	3.796677	35	35
64.0	3.796677	38	38
65.0	3.796677	35	35
66.0	3.796677	31	31
67.0	3.796677	19	19
68.0	3.796677	26	26
69.0	3.796677	20	20
70.0	3.796677	32	32
71.0	3.796677	20	20
72.0	3.796677	18	18
73.0	3.796677	17	17
74.0	3.796677	19	19
75.0	3.796677	22	22
76.0	3.796677	16	16
77.0	3.796677	13	13
78.0	3.796677	22	22
79.0	3.796677	14	14
80.0	3.796677	16	16
81.0	3.796677	13	13
82.0	3.796677	15	15
83.0	3.796677	12	12
84.0	3.796677	18	18
85.0	3.796677	9	9
86.0	3.796677	16	16
87.0	3.796677	8	8
88.0	3.796677	11	11
89.0	3.796677	15	15
90.0	3.796677	11	11
91.0	3.796677	8	8
92.0	3.796677	8	8
93.0	3.796677	11	11
94.0	3.796677	9	9
95.0	3.796677	4	4
96.0	3.796677	4	4
97.0	3.796677	9	9
98.0	3.796677	7	7
99.0	3.796677	3	3
100.0	3.796677	5	5
101.0	0	7	7
102.0	0	7	7
103.0	0	8	8
104.0	0	7	7
105.0	0	5	5
106.0	0	6	6
107.0	0	3	3
108.0	0	5	5
109.0	0	8	8
110.0	0	2	2
111.0	0	6	6
112.0	0	2	2
113.0	0	5	5
114.0	0	3	3
115.0	0	3	3
116.0	0	1	1
117.0	0	3	3
118.0	0	7	7
119.0	0	5	5
120.0	0	2	2
121.0	0	3	3
122.0	0	7	7
123.0	0	4	4
124.0	0	2	2
125.0	0	2	2
126.0	0	4	4
127.0	0	2	2
128.0	0	1	1
129.0	0	3	3
131.0	0	1	1
132.0	0	1	1
133.0	0	5	5
134.0	0	3	3
135.0	0	1	1
136.0	0	1	1
137.0	0	1	1
139.0	0	2	2
141.0	0	1	1
142.0	0	1	1
143.0	0	2	2
144.0	0	5	5
145.0	0	4	4
146.0	0	4	4
147.0	0	1	1
148.0	0	1	1
150.0	0	5	5
151.0	0	1	1
152.0	0	2	2
153.0	0	2	2
154.0	0	2	2
155.0	0	2	2
156.0	0	2	2
157.0	0	2	2
158.0	0	1	1
159.0	0	2	2
160.0	0	1	1
161.0	0	1	1
162.0	0	1	1
163.0	0	1	1
164.0	0	1	1
165.0	0	1	1
166.0	0	2	2
167.0	0	2	2
168.0	0	1	1
169.0	0	1	1
170.0	0	1	1
171.0	0	1	1
173.0	0	1	1
175.0	0	3	3
177.0	0	1	1
178.0	0	1	1
180.0	0	3	3
181.0	0	2	2
184.0	0	2	2
190.0	0	1	1
191.0	0	2	2
192.0	0	1	1
198.0	0	2	2
201.0	0	1	1
202.0	0	1	1
206.0	0	1	1
207.0	0	1	1
214.0	0	1	1
215.0	0	1	1
222.0	0	1	1
223.0	0	1	1
227.0	0	1	1
235.0	0	2	2
238.0	0	1	1
244.0	0	1	1
255.0	0	1	1
285.0	0	1	1
306.0	0	2	2
327.0	0	1	1
330.0	0	1	1
343.0	0	1	1
368.0	0	1	1
476.0	0	1	1
2603.0	0	1	1