## 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-GSM1606231.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606231.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606231.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 21:28:44 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	33715728	4443186	0	0	5583076	0	0.165593	90223638

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	25524119	25524119
2.0	1.68819	1711285	1711285
3.0	2.161795	417450	417450
4.0	2.487725	174358	174358
5.0	2.712027	92019	92019
6.0	2.866389	56108	56108
7.0	2.97262	36342	36342
8.0	3.045727	25194	25194
9.0	3.096038	17886	17886
10.0	3.130662	13360	13360
11.0	3.154489	10385	10385
12.0	3.170887	8004	8004
13.0	3.182172	6568	6568
14.0	3.189938	5360	5360
15.0	3.195283	4216	4216
16.0	3.198961	3567	3567
17.0	3.201492	3065	3065
18.0	3.203234	2513	2513
19.0	3.204433	2190	2190
20.0	3.205258	1863	1863
21.0	3.205826	1642	1642
22.0	3.206217	1438	1438
23.0	3.206486	1200	1200
24.0	3.206671	1042	1042
25.0	3.206798	944	944
26.0	3.206886	837	837
27.0	3.206946	735	735
28.0	3.206987	693	693
29.0	3.207016	618	618
30.0	3.207036	550	550
31.0	3.207049	486	486
32.0	3.207058	469	469
33.0	3.207065	379	379
34.0	3.207069	379	379
35.0	3.207072	324	324
36.0	3.207074	325	325
37.0	3.207076	309	309
38.0	3.207077	237	237
39.0	3.207078	255	255
40.0	3.207078	206	206
41.0	3.207078	229	229
42.0	3.207079	190	190
43.0	3.207079	182	182
44.0	3.207079	167	167
45.0	3.207079	136	136
46.0	3.207079	149	149
47.0	3.207079	152	152
48.0	3.207079	118	118
49.0	3.207079	113	113
50.0	3.207079	118	118
51.0	3.207079	81	81
52.0	3.207079	95	95
53.0	3.207079	90	90
54.0	3.207079	84	84
55.0	3.207079	72	72
56.0	3.207079	82	82
57.0	3.207079	58	58
58.0	3.207079	60	60
59.0	3.207079	75	75
60.0	3.207079	56	56
61.0	3.207079	64	64
62.0	3.207079	49	49
63.0	3.207079	63	63
64.0	3.207079	59	59
65.0	3.207079	31	31
66.0	3.207079	40	40
67.0	3.207079	45	45
68.0	3.207079	43	43
69.0	3.207079	41	41
70.0	3.207079	41	41
71.0	3.207079	32	32
72.0	3.207079	29	29
73.0	3.207079	27	27
74.0	3.207079	26	26
75.0	3.207079	30	30
76.0	3.207079	24	24
77.0	3.207079	15	15
78.0	3.207079	24	24
79.0	3.207079	14	14
80.0	3.207079	13	13
81.0	3.207079	18	18
82.0	3.207079	16	16
83.0	3.207079	31	31
84.0	3.207079	19	19
85.0	3.207079	18	18
86.0	3.207079	23	23
87.0	3.207079	18	18
88.0	3.207079	8	8
89.0	3.207079	11	11
90.0	3.207079	13	13
91.0	3.207079	19	19
92.0	3.207079	13	13
93.0	3.207079	17	17
94.0	3.207079	18	18
95.0	3.207079	9	9
96.0	3.207079	14	14
97.0	3.207079	16	16
98.0	3.207079	12	12
99.0	3.207079	19	19
100.0	3.207079	10	10
101.0	0	16	16
102.0	0	16	16
103.0	0	8	8
104.0	0	12	12
105.0	0	7	7
106.0	0	10	10
107.0	0	12	12
108.0	0	11	11
109.0	0	9	9
110.0	0	13	13
111.0	0	12	12
112.0	0	2	2
113.0	0	4	4
114.0	0	3	3
115.0	0	7	7
116.0	0	6	6
117.0	0	8	8
118.0	0	1	1
119.0	0	5	5
120.0	0	7	7
121.0	0	6	6
122.0	0	11	11
123.0	0	2	2
124.0	0	4	4
125.0	0	7	7
126.0	0	6	6
127.0	0	1	1
128.0	0	1	1
129.0	0	1	1
130.0	0	4	4
131.0	0	5	5
132.0	0	8	8
133.0	0	2	2
134.0	0	2	2
136.0	0	3	3
137.0	0	1	1
138.0	0	4	4
139.0	0	8	8
140.0	0	2	2
141.0	0	7	7
142.0	0	3	3
144.0	0	2	2
145.0	0	2	2
146.0	0	2	2
147.0	0	1	1
150.0	0	5	5
151.0	0	1	1
152.0	0	1	1
153.0	0	3	3
154.0	0	1	1
155.0	0	2	2
156.0	0	2	2
159.0	0	3	3
160.0	0	1	1
162.0	0	2	2
164.0	0	1	1
165.0	0	3	3
166.0	0	2	2
167.0	0	2	2
168.0	0	1	1
169.0	0	2	2
171.0	0	2	2
172.0	0	1	1
173.0	0	1	1
174.0	0	1	1
175.0	0	2	2
178.0	0	2	2
179.0	0	3	3
180.0	0	1	1
181.0	0	4	4
184.0	0	3	3
186.0	0	1	1
187.0	0	1	1
188.0	0	1	1
189.0	0	2	2
190.0	0	1	1
191.0	0	2	2
193.0	0	1	1
195.0	0	1	1
197.0	0	1	1
198.0	0	2	2
199.0	0	1	1
200.0	0	1	1
201.0	0	1	1
202.0	0	1	1
203.0	0	1	1
204.0	0	1	1
205.0	0	2	2
206.0	0	1	1
208.0	0	1	1
211.0	0	1	1
214.0	0	1	1
215.0	0	1	1
217.0	0	1	1
219.0	0	1	1
221.0	0	2	2
222.0	0	1	1
224.0	0	2	2
225.0	0	1	1
228.0	0	1	1
229.0	0	2	2
230.0	0	2	2
231.0	0	1	1
232.0	0	2	2
236.0	0	1	1
239.0	0	1	1
241.0	0	1	1
242.0	0	1	1
243.0	0	2	2
246.0	0	1	1
247.0	0	1	1
249.0	0	1	1
250.0	0	1	1
251.0	0	1	1
262.0	0	1	1
263.0	0	1	1
275.0	0	1	1
284.0	0	1	1
287.0	0	1	1
300.0	0	1	1
312.0	0	2	2
324.0	0	1	1
332.0	0	1	1
334.0	0	1	1
344.0	0	1	1
346.0	0	1	1
364.0	0	1	1
381.0	0	1	1
383.0	0	1	1
389.0	0	1	1
408.0	0	1	1
415.0	0	1	1
417.0	0	1	1
438.0	0	1	1
464.0	0	1	1
754.0	0	1	1
1919.0	0	1	1