## 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-GSM1606358.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606358.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606358.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 13:41:59 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	28312452	3788364	0	0	4407471	0	0.155673	81230869

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	21653424	21653424
2.0	1.705716	1548383	1548383
3.0	2.20375	344131	344131
4.0	2.555221	137220	137220
5.0	2.803259	69864	69864
6.0	2.978303	41564	41564
7.0	3.101835	26372	26372
8.0	3.189013	18041	18041
9.0	3.250536	12791	12791
10.0	3.293954	9626	9626
11.0	3.324595	7238	7238
12.0	3.346218	5583	5583
13.0	3.361478	4311	4311
14.0	3.372247	3631	3631
15.0	3.379847	2980	2980
16.0	3.385211	2475	2475
17.0	3.388996	1947	1947
18.0	3.391667	1708	1708
19.0	3.393552	1506	1506
20.0	3.394883	1225	1225
21.0	3.395822	1097	1097
22.0	3.396484	925	925
23.0	3.396952	807	807
24.0	3.397282	706	706
25.0	3.397514	647	647
26.0	3.397679	558	558
27.0	3.397795	536	536
28.0	3.397877	449	449
29.0	3.397934	370	370
30.0	3.397975	357	357
31.0	3.398004	314	314
32.0	3.398024	267	267
33.0	3.398039	250	250
34.0	3.398049	250	250
35.0	3.398056	233	233
36.0	3.398061	238	238
37.0	3.398064	186	186
38.0	3.398067	172	172
39.0	3.398069	178	178
40.0	3.39807	126	126
41.0	3.398071	133	133
42.0	3.398071	139	139
43.0	3.398072	128	128
44.0	3.398072	117	117
45.0	3.398072	105	105
46.0	3.398073	89	89
47.0	3.398073	82	82
48.0	3.398073	63	63
49.0	3.398073	63	63
50.0	3.398073	68	68
51.0	3.398073	71	71
52.0	3.398073	50	50
53.0	3.398073	66	66
54.0	3.398073	46	46
55.0	3.398073	57	57
56.0	3.398073	41	41
57.0	3.398073	44	44
58.0	3.398073	39	39
59.0	3.398073	39	39
60.0	3.398073	34	34
61.0	3.398073	36	36
62.0	3.398073	33	33
63.0	3.398073	34	34
64.0	3.398073	31	31
65.0	3.398073	29	29
66.0	3.398073	21	21
67.0	3.398073	29	29
68.0	3.398073	30	30
69.0	3.398073	24	24
70.0	3.398073	25	25
71.0	3.398073	18	18
72.0	3.398073	12	12
73.0	3.398073	22	22
74.0	3.398073	14	14
75.0	3.398073	17	17
76.0	3.398073	11	11
77.0	3.398073	18	18
78.0	3.398073	16	16
79.0	3.398073	10	10
80.0	3.398073	9	9
81.0	3.398073	12	12
82.0	3.398073	12	12
83.0	3.398073	13	13
84.0	3.398073	11	11
85.0	3.398073	13	13
86.0	3.398073	8	8
87.0	3.398073	7	7
88.0	3.398073	4	4
89.0	3.398073	8	8
90.0	3.398073	20	20
91.0	3.398073	18	18
92.0	3.398073	9	9
93.0	3.398073	11	11
94.0	3.398073	5	5
95.0	3.398073	5	5
96.0	3.398073	8	8
97.0	3.398073	3	3
98.0	3.398073	4	4
99.0	3.398073	5	5
100.0	3.398073	8	8
101.0	0	3	3
102.0	0	4	4
103.0	0	6	6
104.0	0	5	5
105.0	0	2	2
106.0	0	7	7
107.0	0	10	10
108.0	0	7	7
109.0	0	3	3
110.0	0	3	3
111.0	0	7	7
112.0	0	5	5
113.0	0	5	5
114.0	0	5	5
115.0	0	2	2
116.0	0	1	1
117.0	0	5	5
118.0	0	3	3
119.0	0	2	2
120.0	0	1	1
121.0	0	1	1
122.0	0	7	7
123.0	0	1	1
124.0	0	3	3
125.0	0	3	3
126.0	0	1	1
127.0	0	5	5
128.0	0	1	1
130.0	0	4	4
131.0	0	2	2
132.0	0	1	1
133.0	0	1	1
134.0	0	2	2
135.0	0	5	5
136.0	0	4	4
137.0	0	2	2
138.0	0	2	2
140.0	0	1	1
144.0	0	1	1
146.0	0	4	4
148.0	0	2	2
150.0	0	2	2
151.0	0	1	1
153.0	0	1	1
154.0	0	1	1
155.0	0	1	1
160.0	0	3	3
161.0	0	1	1
163.0	0	1	1
164.0	0	3	3
165.0	0	1	1
166.0	0	1	1
167.0	0	2	2
168.0	0	1	1
169.0	0	1	1
171.0	0	1	1
174.0	0	1	1
176.0	0	1	1
178.0	0	2	2
179.0	0	1	1
182.0	0	3	3
184.0	0	1	1
185.0	0	1	1
186.0	0	2	2
192.0	0	1	1
193.0	0	1	1
196.0	0	1	1
197.0	0	2	2
207.0	0	1	1
208.0	0	1	1
209.0	0	1	1
211.0	0	1	1
213.0	0	1	1
216.0	0	1	1
223.0	0	1	1
227.0	0	2	2
229.0	0	1	1
242.0	0	1	1
244.0	0	1	1
246.0	0	1	1
253.0	0	1	1
270.0	0	1	1
308.0	0	1	1
383.0	0	1	1
431.0	0	1	1
448.0	0	1	1
619.0	0	1	1
6148.0	0	1	1