## 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-GSM1606232.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606232.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606232.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 14:14:39 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	28147787	4045804	0	0	4891456	0	0.173778	71305061

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	20978897	20978897
2.0	1.673847	1475022	1475022
3.0	2.127918	370950	370950
4.0	2.433892	157988	157988
5.0	2.640072	83139	83139
6.0	2.779005	50301	50301
7.0	2.872626	33148	33148
8.0	2.935711	22490	22490
9.0	2.978221	16249	16249
10.0	3.006867	12107	12107
11.0	3.026169	9177	9177
12.0	3.039176	7286	7286
13.0	3.047941	5700	5700
14.0	3.053847	4522	4522
15.0	3.057827	3776	3776
16.0	3.060509	3152	3152
17.0	3.062316	2667	2667
18.0	3.063534	2142	2142
19.0	3.064354	1834	1834
20.0	3.064907	1609	1609
21.0	3.06528	1417	1417
22.0	3.065531	1231	1231
23.0	3.0657	1058	1058
24.0	3.065814	898	898
25.0	3.065891	908	908
26.0	3.065943	700	700
27.0	3.065977	637	637
28.0	3.066001	566	566
29.0	3.066017	571	571
30.0	3.066027	441	441
31.0	3.066035	396	396
32.0	3.066039	340	340
33.0	3.066043	348	348
34.0	3.066045	312	312
35.0	3.066046	321	321
36.0	3.066047	257	257
37.0	3.066048	250	250
38.0	3.066049	219	219
39.0	3.066049	202	202
40.0	3.066049	194	194
41.0	3.066049	155	155
42.0	3.066049	153	153
43.0	3.066049	142	142
44.0	3.066049	127	127
45.0	3.066049	137	137
46.0	3.066049	118	118
47.0	3.066049	104	104
48.0	3.066049	108	108
49.0	3.066049	93	93
50.0	3.066049	86	86
51.0	3.066049	73	73
52.0	3.066049	67	67
53.0	3.066049	69	69
54.0	3.066049	63	63
55.0	3.066049	66	66
56.0	3.066049	73	73
57.0	3.066049	60	60
58.0	3.066049	70	70
59.0	3.066049	46	46
60.0	3.066049	47	47
61.0	3.066049	41	41
62.0	3.066049	47	47
63.0	3.066049	36	36
64.0	3.066049	29	29
65.0	3.066049	40	40
66.0	3.066049	31	31
67.0	3.066049	36	36
68.0	3.066049	42	42
69.0	3.066049	21	21
70.0	3.066049	26	26
71.0	3.066049	29	29
72.0	3.066049	18	18
73.0	3.066049	25	25
74.0	3.066049	26	26
75.0	3.066049	20	20
76.0	3.066049	25	25
77.0	3.066049	28	28
78.0	3.066049	16	16
79.0	3.066049	14	14
80.0	3.066049	15	15
81.0	3.066049	17	17
82.0	3.066049	17	17
83.0	3.066049	15	15
84.0	3.066049	15	15
85.0	3.066049	15	15
86.0	3.066049	12	12
87.0	3.066049	15	15
88.0	3.066049	9	9
89.0	3.066049	6	6
90.0	3.066049	14	14
91.0	3.066049	16	16
92.0	3.066049	8	8
93.0	3.066049	9	9
94.0	3.066049	15	15
95.0	3.066049	12	12
96.0	3.066049	9	9
97.0	3.066049	8	8
98.0	3.066049	9	9
99.0	3.066049	8	8
100.0	3.066049	9	9
101.0	0	8	8
102.0	0	3	3
103.0	0	4	4
104.0	0	6	6
105.0	0	7	7
106.0	0	4	4
107.0	0	6	6
108.0	0	7	7
109.0	0	6	6
110.0	0	6	6
111.0	0	2	2
112.0	0	3	3
113.0	0	5	5
114.0	0	5	5
115.0	0	5	5
116.0	0	4	4
117.0	0	3	3
118.0	0	3	3
119.0	0	4	4
120.0	0	6	6
121.0	0	4	4
122.0	0	5	5
123.0	0	2	2
124.0	0	5	5
125.0	0	1	1
126.0	0	1	1
127.0	0	3	3
128.0	0	5	5
129.0	0	4	4
130.0	0	2	2
131.0	0	5	5
132.0	0	4	4
133.0	0	2	2
134.0	0	4	4
135.0	0	1	1
136.0	0	5	5
137.0	0	1	1
138.0	0	3	3
140.0	0	3	3
141.0	0	2	2
143.0	0	1	1
144.0	0	4	4
145.0	0	1	1
146.0	0	2	2
149.0	0	3	3
150.0	0	1	1
151.0	0	2	2
152.0	0	1	1
153.0	0	2	2
154.0	0	1	1
155.0	0	1	1
157.0	0	2	2
158.0	0	2	2
159.0	0	1	1
160.0	0	2	2
163.0	0	1	1
164.0	0	2	2
165.0	0	1	1
167.0	0	2	2
172.0	0	2	2
174.0	0	1	1
175.0	0	2	2
176.0	0	2	2
177.0	0	1	1
178.0	0	1	1
179.0	0	1	1
186.0	0	2	2
189.0	0	1	1
192.0	0	3	3
193.0	0	1	1
194.0	0	1	1
195.0	0	1	1
197.0	0	1	1
198.0	0	1	1
201.0	0	1	1
203.0	0	1	1
204.0	0	1	1
205.0	0	2	2
206.0	0	1	1
209.0	0	1	1
210.0	0	1	1
211.0	0	1	1
212.0	0	3	3
215.0	0	1	1
218.0	0	1	1
219.0	0	1	1
220.0	0	1	1
221.0	0	1	1
222.0	0	1	1
226.0	0	1	1
233.0	0	1	1
234.0	0	1	1
235.0	0	1	1
236.0	0	1	1
237.0	0	1	1
238.0	0	1	1
248.0	0	1	1
266.0	0	1	1
269.0	0	1	1
277.0	0	1	1
286.0	0	1	1
329.0	0	1	1
339.0	0	1	1
402.0	0	1	1
419.0	0	1	1
439.0	0	1	1
524.0	0	1	1
1146.0	0	1	1