## 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-GSM1606227.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606227.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606227.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 14:59:28 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	24167524	3125462	0	0	3406729	0	0.140963	77462049

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	19034061	19034061
2.0	1.731988	1171805	1171805
3.0	2.267793	268893	268893
4.0	2.659996	109552	109552
5.0	2.947084	56295	56295
6.0	3.157229	32833	32833
7.0	3.311052	21300	21300
8.0	3.423649	14431	14431
9.0	3.506068	10431	10431
10.0	3.566398	7583	7583
11.0	3.610559	5731	5731
12.0	3.642884	4402	4402
13.0	3.666546	3522	3522
14.0	3.683866	2825	2825
15.0	3.696544	2271	2271
16.0	3.705824	1894	1894
17.0	3.712617	1555	1555
18.0	3.717589	1343	1343
19.0	3.721229	1085	1085
20.0	3.723893	958	958
21.0	3.725843	838	838
22.0	3.727271	718	718
23.0	3.728316	570	570
24.0	3.729081	524	524
25.0	3.729641	464	464
26.0	3.73005	407	407
27.0	3.73035	423	423
28.0	3.73057	299	299
29.0	3.730731	322	322
30.0	3.730848	261	261
31.0	3.730934	243	243
32.0	3.730998	232	232
33.0	3.731044	188	188
34.0	3.731077	182	182
35.0	3.731102	145	145
36.0	3.73112	153	153
37.0	3.731134	120	120
38.0	3.731143	130	130
39.0	3.73115	110	110
40.0	3.731155	102	102
41.0	3.731159	95	95
42.0	3.731162	85	85
43.0	3.731164	85	85
44.0	3.731166	75	75
45.0	3.731167	64	64
46.0	3.731168	64	64
47.0	3.731168	62	62
48.0	3.731169	52	52
49.0	3.731169	48	48
50.0	3.731169	44	44
51.0	3.731169	29	29
52.0	3.731169	45	45
53.0	3.731169	40	40
54.0	3.73117	42	42
55.0	3.73117	39	39
56.0	3.73117	34	34
57.0	3.73117	31	31
58.0	3.73117	29	29
59.0	3.73117	40	40
60.0	3.73117	31	31
61.0	3.73117	23	23
62.0	3.73117	23	23
63.0	3.73117	27	27
64.0	3.73117	23	23
65.0	3.73117	18	18
66.0	3.73117	18	18
67.0	3.73117	24	24
68.0	3.73117	16	16
69.0	3.73117	16	16
70.0	3.73117	21	21
71.0	3.73117	10	10
72.0	3.73117	16	16
73.0	3.73117	11	11
74.0	3.73117	14	14
75.0	3.73117	8	8
76.0	3.73117	18	18
77.0	3.73117	9	9
78.0	3.73117	5	5
79.0	3.73117	9	9
80.0	3.73117	8	8
81.0	3.73117	8	8
82.0	3.73117	10	10
83.0	3.73117	12	12
84.0	3.73117	7	7
85.0	3.73117	7	7
86.0	3.73117	4	4
87.0	3.73117	3	3
88.0	3.73117	6	6
89.0	3.73117	4	4
90.0	3.73117	8	8
91.0	3.73117	4	4
92.0	3.73117	4	4
93.0	3.73117	4	4
94.0	3.73117	7	7
95.0	3.73117	1	1
96.0	3.73117	3	3
97.0	3.73117	6	6
98.0	3.73117	5	5
99.0	3.73117	5	5
100.0	3.73117	5	5
101.0	0	3	3
102.0	0	3	3
103.0	0	4	4
104.0	0	5	5
105.0	0	3	3
106.0	0	6	6
107.0	0	4	4
108.0	0	3	3
109.0	0	1	1
111.0	0	2	2
112.0	0	4	4
113.0	0	2	2
115.0	0	2	2
116.0	0	3	3
117.0	0	3	3
118.0	0	3	3
120.0	0	3	3
121.0	0	1	1
122.0	0	2	2
123.0	0	1	1
125.0	0	3	3
126.0	0	4	4
127.0	0	3	3
128.0	0	1	1
129.0	0	1	1
130.0	0	1	1
134.0	0	3	3
135.0	0	1	1
138.0	0	1	1
139.0	0	1	1
140.0	0	1	1
142.0	0	1	1
143.0	0	1	1
145.0	0	2	2
149.0	0	1	1
153.0	0	1	1
154.0	0	2	2
155.0	0	2	2
156.0	0	1	1
157.0	0	1	1
158.0	0	1	1
160.0	0	1	1
162.0	0	1	1
163.0	0	1	1
164.0	0	1	1
165.0	0	4	4
167.0	0	1	1
170.0	0	1	1
175.0	0	1	1
177.0	0	1	1
178.0	0	2	2
182.0	0	1	1
185.0	0	1	1
189.0	0	1	1
193.0	0	1	1
194.0	0	1	1
197.0	0	1	1
203.0	0	1	1
204.0	0	1	1
208.0	0	1	1
209.0	0	1	1
214.0	0	1	1
220.0	0	1	1
222.0	0	1	1
224.0	0	2	2
227.0	0	2	2
253.0	0	1	1
255.0	0	1	1
273.0	0	1	1
282.0	0	1	1
294.0	0	1	1
316.0	0	1	1
424.0	0	1	1
1525.0	0	1	1