## 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-GSM1606359.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606359.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606359.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: Mon Nov 01 22:23:23 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	35682965	4854238	0	0	5994448	0	0.167992	93943437

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	26690969	26690969
2.0	1.683975	2046528	2046528
3.0	2.151796	460200	460200
4.0	2.471774	185216	185216
5.0	2.69063	95431	95431
6.0	2.840323	56305	56305
7.0	2.942708	36291	36291
8.0	3.012738	24920	24920
9.0	3.060636	17645	17645
10.0	3.093397	13109	13109
11.0	3.115805	9964	9964
12.0	3.131131	7745	7745
13.0	3.141614	6264	6264
14.0	3.148784	5019	5019
15.0	3.153688	4077	4077
16.0	3.157042	3403	3403
17.0	3.159337	2833	2833
18.0	3.160906	2434	2434
19.0	3.161979	2066	2066
20.0	3.162713	1832	1832
21.0	3.163215	1556	1556
22.0	3.163559	1380	1380
23.0	3.163794	1178	1178
24.0	3.163954	1005	1005
25.0	3.164064	954	954
26.0	3.164139	826	826
27.0	3.164191	750	750
28.0	3.164226	634	634
29.0	3.16425	605	605
30.0	3.164267	537	537
31.0	3.164278	476	476
32.0	3.164285	462	462
33.0	3.164291	418	418
34.0	3.164294	341	341
35.0	3.164297	343	343
36.0	3.164298	302	302
37.0	3.1643	236	236
38.0	3.1643	240	240
39.0	3.164301	241	241
40.0	3.164301	216	216
41.0	3.164302	173	173
42.0	3.164302	174	174
43.0	3.164302	193	193
44.0	3.164302	182	182
45.0	3.164302	140	140
46.0	3.164302	152	152
47.0	3.164302	132	132
48.0	3.164302	129	129
49.0	3.164302	124	124
50.0	3.164302	113	113
51.0	3.164302	100	100
52.0	3.164302	93	93
53.0	3.164302	75	75
54.0	3.164302	65	65
55.0	3.164302	67	67
56.0	3.164302	80	80
57.0	3.164302	67	67
58.0	3.164302	72	72
59.0	3.164302	74	74
60.0	3.164302	54	54
61.0	3.164302	58	58
62.0	3.164302	55	55
63.0	3.164302	46	46
64.0	3.164302	53	53
65.0	3.164302	38	38
66.0	3.164302	40	40
67.0	3.164302	43	43
68.0	3.164302	26	26
69.0	3.164302	39	39
70.0	3.164302	41	41
71.0	3.164302	28	28
72.0	3.164302	30	30
73.0	3.164302	21	21
74.0	3.164302	30	30
75.0	3.164302	20	20
76.0	3.164302	32	32
77.0	3.164302	21	21
78.0	3.164302	22	22
79.0	3.164302	23	23
80.0	3.164302	23	23
81.0	3.164302	15	15
82.0	3.164302	16	16
83.0	3.164302	22	22
84.0	3.164302	20	20
85.0	3.164302	14	14
86.0	3.164302	20	20
87.0	3.164302	26	26
88.0	3.164302	16	16
89.0	3.164302	17	17
90.0	3.164302	7	7
91.0	3.164302	9	9
92.0	3.164302	15	15
93.0	3.164302	15	15
94.0	3.164302	5	5
95.0	3.164302	9	9
96.0	3.164302	9	9
97.0	3.164302	12	12
98.0	3.164302	17	17
99.0	3.164302	14	14
100.0	3.164302	6	6
101.0	0	11	11
102.0	0	10	10
103.0	0	8	8
104.0	0	11	11
105.0	0	11	11
106.0	0	2	2
107.0	0	8	8
108.0	0	9	9
109.0	0	12	12
110.0	0	4	4
111.0	0	5	5
112.0	0	6	6
113.0	0	4	4
114.0	0	8	8
115.0	0	7	7
116.0	0	4	4
117.0	0	6	6
118.0	0	2	2
119.0	0	5	5
120.0	0	6	6
121.0	0	7	7
122.0	0	3	3
123.0	0	3	3
124.0	0	2	2
125.0	0	3	3
126.0	0	5	5
127.0	0	4	4
128.0	0	6	6
129.0	0	3	3
130.0	0	4	4
131.0	0	4	4
132.0	0	4	4
133.0	0	1	1
134.0	0	5	5
135.0	0	8	8
136.0	0	2	2
137.0	0	3	3
138.0	0	3	3
139.0	0	1	1
140.0	0	1	1
142.0	0	3	3
143.0	0	3	3
144.0	0	4	4
146.0	0	1	1
147.0	0	4	4
148.0	0	3	3
149.0	0	3	3
150.0	0	2	2
151.0	0	5	5
152.0	0	2	2
153.0	0	3	3
155.0	0	1	1
156.0	0	5	5
157.0	0	2	2
158.0	0	2	2
160.0	0	2	2
161.0	0	1	1
162.0	0	1	1
163.0	0	3	3
164.0	0	1	1
165.0	0	3	3
166.0	0	1	1
167.0	0	2	2
168.0	0	2	2
170.0	0	1	1
171.0	0	2	2
172.0	0	2	2
173.0	0	2	2
176.0	0	3	3
177.0	0	1	1
179.0	0	1	1
180.0	0	1	1
182.0	0	1	1
183.0	0	1	1
184.0	0	1	1
185.0	0	1	1
186.0	0	1	1
188.0	0	4	4
189.0	0	1	1
191.0	0	2	2
192.0	0	1	1
193.0	0	1	1
194.0	0	1	1
196.0	0	1	1
200.0	0	1	1
205.0	0	2	2
208.0	0	1	1
213.0	0	2	2
214.0	0	1	1
216.0	0	2	2
219.0	0	1	1
220.0	0	1	1
222.0	0	2	2
231.0	0	1	1
232.0	0	1	1
236.0	0	1	1
241.0	0	1	1
242.0	0	1	1
250.0	0	1	1
255.0	0	1	1
262.0	0	1	1
268.0	0	1	1
271.0	0	2	2
276.0	0	1	1
277.0	0	1	1
282.0	0	1	1
283.0	0	1	1
289.0	0	1	1
322.0	0	1	1
411.0	0	1	1
424.0	0	1	1
694.0	0	1	1
718.0	0	1	1
6171.0	0	1	1