## 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-GSM1606345.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606345.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606345.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 14:23:23 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	25087442	3825980	0	0	4013845	0	0.159994	69794298

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	19033707	19033707
2.0	1.698061	1399609	1399609
3.0	2.185351	314773	314773
4.0	2.525509	125070	125070
5.0	2.76296	63527	63527
6.0	2.928716	37108	37108
7.0	3.044423	23753	23753
8.0	3.125194	16055	16055
9.0	3.181577	11541	11541
10.0	3.220936	8512	8512
11.0	3.248411	6353	6353
12.0	3.26759	5176	5176
13.0	3.280978	3934	3934
14.0	3.290324	3231	3231
15.0	3.296848	2720	2720
16.0	3.301402	2165	2165
17.0	3.304581	1811	1811
18.0	3.3068	1561	1561
19.0	3.308349	1365	1365
20.0	3.309431	1196	1196
21.0	3.310186	1032	1032
22.0	3.310713	921	921
23.0	3.311081	776	776
24.0	3.311337	632	632
25.0	3.311517	583	583
26.0	3.311642	530	530
27.0	3.311729	466	466
28.0	3.31179	433	433
29.0	3.311833	396	396
30.0	3.311862	327	327
31.0	3.311883	314	314
32.0	3.311897	251	251
33.0	3.311908	246	246
34.0	3.311915	235	235
35.0	3.31192	211	211
36.0	3.311923	178	178
37.0	3.311925	170	170
38.0	3.311927	164	164
39.0	3.311928	130	130
40.0	3.311929	115	115
41.0	3.31193	129	129
42.0	3.31193	140	140
43.0	3.31193	127	127
44.0	3.31193	118	118
45.0	3.311931	106	106
46.0	3.311931	83	83
47.0	3.311931	73	73
48.0	3.311931	86	86
49.0	3.311931	69	69
50.0	3.311931	73	73
51.0	3.311931	66	66
52.0	3.311931	54	54
53.0	3.311931	54	54
54.0	3.311931	61	61
55.0	3.311931	66	66
56.0	3.311931	49	49
57.0	3.311931	40	40
58.0	3.311931	47	47
59.0	3.311931	31	31
60.0	3.311931	27	27
61.0	3.311931	31	31
62.0	3.311931	19	19
63.0	3.311931	31	31
64.0	3.311931	37	37
65.0	3.311931	27	27
66.0	3.311931	31	31
67.0	3.311931	25	25
68.0	3.311931	23	23
69.0	3.311931	18	18
70.0	3.311931	21	21
71.0	3.311931	26	26
72.0	3.311931	19	19
73.0	3.311931	22	22
74.0	3.311931	20	20
75.0	3.311931	15	15
76.0	3.311931	14	14
77.0	3.311931	11	11
78.0	3.311931	18	18
79.0	3.311931	13	13
80.0	3.311931	12	12
81.0	3.311931	11	11
82.0	3.311931	13	13
83.0	3.311931	10	10
84.0	3.311931	17	17
85.0	3.311931	14	14
86.0	3.311931	5	5
87.0	3.311931	14	14
88.0	3.311931	13	13
89.0	3.311931	11	11
90.0	3.311931	9	9
91.0	3.311931	8	8
92.0	3.311931	6	6
93.0	3.311931	9	9
94.0	3.311931	5	5
95.0	3.311931	1	1
96.0	3.311931	11	11
97.0	3.311931	6	6
98.0	3.311931	5	5
99.0	3.311931	7	7
100.0	3.311931	2	2
101.0	0	3	3
102.0	0	3	3
103.0	0	7	7
104.0	0	5	5
105.0	0	7	7
106.0	0	5	5
107.0	0	7	7
108.0	0	3	3
109.0	0	2	2
110.0	0	4	4
111.0	0	4	4
112.0	0	5	5
113.0	0	7	7
114.0	0	5	5
115.0	0	6	6
116.0	0	2	2
117.0	0	6	6
118.0	0	3	3
119.0	0	3	3
120.0	0	2	2
121.0	0	7	7
122.0	0	2	2
123.0	0	5	5
124.0	0	3	3
125.0	0	2	2
126.0	0	5	5
127.0	0	2	2
128.0	0	2	2
129.0	0	2	2
130.0	0	4	4
131.0	0	2	2
132.0	0	3	3
133.0	0	3	3
134.0	0	4	4
135.0	0	3	3
136.0	0	1	1
137.0	0	3	3
138.0	0	1	1
139.0	0	4	4
140.0	0	2	2
141.0	0	3	3
142.0	0	1	1
143.0	0	1	1
146.0	0	2	2
147.0	0	2	2
149.0	0	2	2
150.0	0	1	1
151.0	0	1	1
152.0	0	2	2
154.0	0	1	1
155.0	0	2	2
156.0	0	1	1
157.0	0	2	2
158.0	0	1	1
162.0	0	3	3
163.0	0	1	1
164.0	0	1	1
165.0	0	1	1
170.0	0	1	1
171.0	0	1	1
172.0	0	1	1
174.0	0	2	2
177.0	0	1	1
178.0	0	1	1
182.0	0	2	2
184.0	0	1	1
187.0	0	1	1
189.0	0	2	2
191.0	0	1	1
193.0	0	1	1
197.0	0	1	1
198.0	0	1	1
213.0	0	1	1
214.0	0	1	1
215.0	0	1	1
221.0	0	1	1
222.0	0	1	1
250.0	0	1	1
257.0	0	1	1
260.0	0	1	1
272.0	0	1	1
274.0	0	1	1
282.0	0	1	1
287.0	0	1	1
313.0	0	1	1
316.0	0	1	1
334.0	0	1	1
354.0	0	1	1
7293.0	0	1	1