## 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-GSM1606206.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606206.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606206.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 23:19:29 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	41188081	7266998	0	0	6289143	0	0.152693	120761476

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	31777611	31777611
2.0	1.711009	2122514	2122514
3.0	2.216544	486389	486389
4.0	2.575983	193780	193780
5.0	2.831548	99154	99154
6.0	3.013257	58706	58706
7.0	3.142454	37711	37711
8.0	3.234314	25781	25781
9.0	3.299628	18553	18553
10.0	3.346066	13595	13595
11.0	3.379084	10458	10458
12.0	3.40256	8257	8257
13.0	3.419252	6412	6412
14.0	3.43112	5122	5122
15.0	3.439559	4298	4298
16.0	3.445558	3583	3583
17.0	3.449824	3047	3047
18.0	3.452857	2529	2529
19.0	3.455014	2173	2173
20.0	3.456547	1864	1864
21.0	3.457637	1659	1659
22.0	3.458412	1383	1383
23.0	3.458964	1232	1232
24.0	3.459355	1113	1113
25.0	3.459634	978	978
26.0	3.459832	829	829
27.0	3.459973	842	842
28.0	3.460073	721	721
29.0	3.460144	633	633
30.0	3.460195	508	508
31.0	3.460231	503	503
32.0	3.460257	447	447
33.0	3.460275	396	396
34.0	3.460288	394	394
35.0	3.460297	323	323
36.0	3.460303	332	332
37.0	3.460308	291	291
38.0	3.460311	285	285
39.0	3.460314	236	236
40.0	3.460315	231	231
41.0	3.460317	195	195
42.0	3.460317	214	214
43.0	3.460318	185	185
44.0	3.460318	197	197
45.0	3.460319	165	165
46.0	3.460319	147	147
47.0	3.460319	131	131
48.0	3.460319	134	134
49.0	3.460319	124	124
50.0	3.460319	123	123
51.0	3.460319	91	91
52.0	3.460319	91	91
53.0	3.460319	91	91
54.0	3.460319	100	100
55.0	3.460319	92	92
56.0	3.460319	91	91
57.0	3.460319	66	66
58.0	3.460319	65	65
59.0	3.46032	72	72
60.0	3.46032	66	66
61.0	3.46032	95	95
62.0	3.46032	76	76
63.0	3.46032	45	45
64.0	3.46032	55	55
65.0	3.46032	56	56
66.0	3.46032	59	59
67.0	3.46032	36	36
68.0	3.46032	39	39
69.0	3.46032	37	37
70.0	3.46032	43	43
71.0	3.46032	36	36
72.0	3.46032	40	40
73.0	3.46032	36	36
74.0	3.46032	21	21
75.0	3.46032	32	32
76.0	3.46032	26	26
77.0	3.46032	39	39
78.0	3.46032	22	22
79.0	3.46032	24	24
80.0	3.46032	19	19
81.0	3.46032	23	23
82.0	3.46032	24	24
83.0	3.46032	18	18
84.0	3.46032	13	13
85.0	3.46032	14	14
86.0	3.46032	23	23
87.0	3.46032	20	20
88.0	3.46032	18	18
89.0	3.46032	20	20
90.0	3.46032	15	15
91.0	3.46032	19	19
92.0	3.46032	12	12
93.0	3.46032	21	21
94.0	3.46032	13	13
95.0	3.46032	12	12
96.0	3.46032	12	12
97.0	3.46032	15	15
98.0	3.46032	7	7
99.0	3.46032	13	13
100.0	3.46032	15	15
101.0	0	14	14
102.0	0	7	7
103.0	0	7	7
104.0	0	14	14
105.0	0	8	8
106.0	0	9	9
107.0	0	13	13
108.0	0	18	18
109.0	0	8	8
110.0	0	9	9
111.0	0	7	7
112.0	0	15	15
113.0	0	5	5
114.0	0	10	10
115.0	0	8	8
116.0	0	6	6
117.0	0	5	5
118.0	0	7	7
119.0	0	7	7
120.0	0	7	7
121.0	0	7	7
122.0	0	6	6
123.0	0	7	7
124.0	0	4	4
125.0	0	2	2
126.0	0	8	8
127.0	0	10	10
128.0	0	17	17
129.0	0	4	4
130.0	0	1	1
131.0	0	8	8
132.0	0	3	3
133.0	0	4	4
134.0	0	3	3
135.0	0	3	3
136.0	0	7	7
137.0	0	3	3
138.0	0	4	4
139.0	0	4	4
141.0	0	1	1
142.0	0	5	5
143.0	0	1	1
144.0	0	5	5
145.0	0	5	5
146.0	0	1	1
147.0	0	4	4
149.0	0	4	4
150.0	0	4	4
152.0	0	2	2
153.0	0	3	3
154.0	0	5	5
155.0	0	3	3
156.0	0	2	2
157.0	0	2	2
158.0	0	1	1
159.0	0	5	5
160.0	0	1	1
161.0	0	1	1
162.0	0	4	4
163.0	0	1	1
164.0	0	1	1
165.0	0	1	1
166.0	0	1	1
169.0	0	2	2
171.0	0	6	6
172.0	0	2	2
173.0	0	3	3
174.0	0	1	1
176.0	0	1	1
177.0	0	2	2
178.0	0	2	2
180.0	0	1	1
181.0	0	2	2
182.0	0	2	2
184.0	0	3	3
186.0	0	4	4
187.0	0	1	1
188.0	0	1	1
192.0	0	2	2
193.0	0	1	1
194.0	0	1	1
195.0	0	1	1
196.0	0	1	1
200.0	0	2	2
202.0	0	2	2
203.0	0	2	2
204.0	0	2	2
207.0	0	2	2
208.0	0	2	2
209.0	0	2	2
210.0	0	2	2
211.0	0	1	1
212.0	0	1	1
213.0	0	1	1
214.0	0	1	1
216.0	0	2	2
218.0	0	1	1
220.0	0	1	1
225.0	0	1	1
226.0	0	2	2
227.0	0	1	1
232.0	0	2	2
233.0	0	1	1
234.0	0	1	1
239.0	0	1	1
241.0	0	1	1
245.0	0	1	1
246.0	0	2	2
248.0	0	1	1
249.0	0	1	1
252.0	0	1	1
261.0	0	1	1
262.0	0	1	1
266.0	0	1	1
267.0	0	1	1
269.0	0	1	1
280.0	0	1	1
283.0	0	1	1
284.0	0	1	1
294.0	0	1	1
296.0	0	1	1
298.0	0	1	1
305.0	0	1	1
310.0	0	2	2
319.0	0	2	2
321.0	0	2	2
328.0	0	1	1
329.0	0	1	1
351.0	0	1	1
364.0	0	1	1
409.0	0	1	1
425.0	0	1	1
498.0	0	1	1
511.0	0	1	1
533.0	0	1	1
549.0	0	1	1
579.0	0	1	1
664.0	0	1	1
6202.0	0	1	1