## 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-GSM1606365.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606365.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606365.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 13:45:05 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	29206972	3926128	0	0	4611849	0	0.157902	82468274

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	22314902	22314902
2.0	1.701763	1542360	1542360
3.0	2.194233	354604	354604
4.0	2.539831	144034	144034
5.0	2.782358	74615	74615
6.0	2.952555	44155	44155
7.0	3.071993	28664	28664
8.0	3.15581	19166	19166
9.0	3.214629	14022	14022
10.0	3.255907	10419	10419
11.0	3.284873	8018	8018
12.0	3.305201	6074	6074
13.0	3.319467	4979	4979
14.0	3.329478	3955	3955
15.0	3.336503	3225	3225
16.0	3.341433	2649	2649
17.0	3.344893	2111	2111
18.0	3.347321	1869	1869
19.0	3.349024	1602	1602
20.0	3.35022	1382	1382
21.0	3.351059	1228	1228
22.0	3.351648	1038	1038
23.0	3.352061	899	899
24.0	3.352351	794	794
25.0	3.352555	703	703
26.0	3.352698	645	645
27.0	3.352798	539	539
28.0	3.352868	489	489
29.0	3.352917	421	421
30.0	3.352952	415	415
31.0	3.352976	355	355
32.0	3.352993	332	332
33.0	3.353005	268	268
34.0	3.353014	258	258
35.0	3.35302	261	261
36.0	3.353024	235	235
37.0	3.353027	201	201
38.0	3.353029	211	211
39.0	3.35303	167	167
40.0	3.353031	168	168
41.0	3.353032	142	142
42.0	3.353032	129	129
43.0	3.353033	122	122
44.0	3.353033	122	122
45.0	3.353033	118	118
46.0	3.353033	110	110
47.0	3.353033	99	99
48.0	3.353033	87	87
49.0	3.353034	91	91
50.0	3.353034	85	85
51.0	3.353034	71	71
52.0	3.353034	63	63
53.0	3.353034	82	82
54.0	3.353034	60	60
55.0	3.353034	45	45
56.0	3.353034	48	48
57.0	3.353034	55	55
58.0	3.353034	40	40
59.0	3.353034	55	55
60.0	3.353034	33	33
61.0	3.353034	47	47
62.0	3.353034	37	37
63.0	3.353034	27	27
64.0	3.353034	33	33
65.0	3.353034	36	36
66.0	3.353034	33	33
67.0	3.353034	35	35
68.0	3.353034	34	34
69.0	3.353034	22	22
70.0	3.353034	16	16
71.0	3.353034	38	38
72.0	3.353034	28	28
73.0	3.353034	29	29
74.0	3.353034	22	22
75.0	3.353034	20	20
76.0	3.353034	21	21
77.0	3.353034	22	22
78.0	3.353034	14	14
79.0	3.353034	16	16
80.0	3.353034	11	11
81.0	3.353034	14	14
82.0	3.353034	19	19
83.0	3.353034	13	13
84.0	3.353034	12	12
85.0	3.353034	17	17
86.0	3.353034	18	18
87.0	3.353034	13	13
88.0	3.353034	11	11
89.0	3.353034	8	8
90.0	3.353034	10	10
91.0	3.353034	14	14
92.0	3.353034	12	12
93.0	3.353034	11	11
94.0	3.353034	12	12
95.0	3.353034	4	4
96.0	3.353034	12	12
97.0	3.353034	12	12
98.0	3.353034	5	5
99.0	3.353034	7	7
100.0	3.353034	2	2
101.0	0	8	8
102.0	0	7	7
103.0	0	4	4
104.0	0	12	12
105.0	0	6	6
106.0	0	7	7
107.0	0	5	5
108.0	0	1	1
109.0	0	4	4
110.0	0	10	10
111.0	0	5	5
112.0	0	7	7
113.0	0	4	4
114.0	0	3	3
115.0	0	9	9
116.0	0	4	4
117.0	0	7	7
118.0	0	3	3
119.0	0	7	7
120.0	0	2	2
121.0	0	1	1
122.0	0	1	1
123.0	0	3	3
124.0	0	4	4
125.0	0	3	3
126.0	0	3	3
127.0	0	1	1
128.0	0	4	4
130.0	0	2	2
131.0	0	3	3
132.0	0	4	4
133.0	0	2	2
134.0	0	2	2
135.0	0	4	4
136.0	0	1	1
137.0	0	3	3
138.0	0	1	1
141.0	0	4	4
142.0	0	1	1
143.0	0	2	2
147.0	0	3	3
148.0	0	1	1
149.0	0	3	3
150.0	0	4	4
152.0	0	1	1
153.0	0	1	1
154.0	0	5	5
155.0	0	1	1
156.0	0	2	2
157.0	0	2	2
158.0	0	1	1
159.0	0	3	3
160.0	0	2	2
162.0	0	1	1
163.0	0	3	3
164.0	0	1	1
165.0	0	1	1
167.0	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
176.0	0	2	2
178.0	0	1	1
180.0	0	3	3
181.0	0	2	2
182.0	0	2	2
184.0	0	1	1
185.0	0	2	2
187.0	0	1	1
188.0	0	1	1
189.0	0	1	1
190.0	0	1	1
193.0	0	1	1
194.0	0	2	2
196.0	0	1	1
198.0	0	1	1
199.0	0	1	1
203.0	0	1	1
204.0	0	1	1
205.0	0	1	1
206.0	0	1	1
208.0	0	2	2
209.0	0	2	2
210.0	0	1	1
218.0	0	1	1
221.0	0	1	1
222.0	0	1	1
224.0	0	1	1
229.0	0	1	1
230.0	0	1	1
237.0	0	1	1
251.0	0	1	1
261.0	0	1	1
263.0	0	1	1
265.0	0	1	1
267.0	0	1	1
272.0	0	1	1
286.0	0	1	1
287.0	0	1	1
289.0	0	1	1
294.0	0	1	1
309.0	0	1	1
311.0	0	1	1
334.0	0	1	1
337.0	0	1	1
347.0	0	1	1
357.0	0	1	1
382.0	0	1	1
470.0	0	1	1
472.0	0	1	1
7118.0	0	1	1