## 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-GSM1606197.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606197.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606197.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 00:20:38 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	39000781	6879978	0	0	7020006	0	0.179997	94904692

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	28493865	28493865
2.0	1.663022	2370921	2370921
3.0	2.102621	543264	543264
4.0	2.394084	217135	217135
5.0	2.587331	111272	111272
6.0	2.715458	65045	65045
7.0	2.800409	42030	42030
8.0	2.856733	28648	28648
9.0	2.894077	20893	20893
10.0	2.918838	15370	15370
11.0	2.935254	11566	11566
12.0	2.946139	8858	8858
13.0	2.953355	7095	7095
14.0	2.95814	5849	5849
15.0	2.961313	4716	4716
16.0	2.963416	3993	3993
17.0	2.964811	3508	3508
18.0	2.965735	2775	2775
19.0	2.966348	2491	2491
20.0	2.966755	2105	2105
21.0	2.967024	1758	1758
22.0	2.967203	1607	1607
23.0	2.967321	1402	1402
24.0	2.9674	1131	1131
25.0	2.967452	1097	1097
26.0	2.967487	930	930
27.0	2.967509	883	883
28.0	2.967525	801	801
29.0	2.967535	665	665
30.0	2.967541	675	675
31.0	2.967546	546	546
32.0	2.967549	523	523
33.0	2.967551	457	457
34.0	2.967552	416	416
35.0	2.967553	409	409
36.0	2.967553	371	371
37.0	2.967554	342	342
38.0	2.967554	296	296
39.0	2.967554	273	273
40.0	2.967554	289	289
41.0	2.967554	234	234
42.0	2.967554	237	237
43.0	2.967554	203	203
44.0	2.967554	189	189
45.0	2.967554	191	191
46.0	2.967554	166	166
47.0	2.967554	170	170
48.0	2.967554	143	143
49.0	2.967554	120	120
50.0	2.967554	123	123
51.0	2.967554	122	122
52.0	2.967554	121	121
53.0	2.967554	114	114
54.0	2.967554	88	88
55.0	2.967554	109	109
56.0	2.967554	97	97
57.0	2.967554	97	97
58.0	2.967554	80	80
59.0	2.967554	61	61
60.0	2.967554	78	78
61.0	2.967554	68	68
62.0	2.967554	57	57
63.0	2.967554	70	70
64.0	2.967554	70	70
65.0	2.967554	73	73
66.0	2.967554	43	43
67.0	2.967554	52	52
68.0	2.967554	58	58
69.0	2.967554	48	48
70.0	2.967554	50	50
71.0	2.967554	42	42
72.0	2.967554	38	38
73.0	2.967554	34	34
74.0	2.967554	34	34
75.0	2.967554	40	40
76.0	2.967554	34	34
77.0	2.967554	25	25
78.0	2.967554	38	38
79.0	2.967554	24	24
80.0	2.967554	28	28
81.0	2.967554	31	31
82.0	2.967554	18	18
83.0	2.967554	16	16
84.0	2.967554	28	28
85.0	2.967554	24	24
86.0	2.967554	21	21
87.0	2.967554	12	12
88.0	2.967554	28	28
89.0	2.967554	19	19
90.0	2.967554	21	21
91.0	2.967554	16	16
92.0	2.967554	14	14
93.0	2.967554	6	6
94.0	2.967554	17	17
95.0	2.967554	15	15
96.0	2.967554	16	16
97.0	2.967554	16	16
98.0	2.967554	13	13
99.0	2.967554	11	11
100.0	2.967554	18	18
101.0	0	14	14
102.0	0	12	12
103.0	0	17	17
104.0	0	10	10
105.0	0	10	10
106.0	0	8	8
107.0	0	8	8
108.0	0	9	9
109.0	0	8	8
110.0	0	6	6
111.0	0	8	8
112.0	0	10	10
113.0	0	11	11
114.0	0	10	10
115.0	0	8	8
116.0	0	7	7
117.0	0	11	11
118.0	0	11	11
119.0	0	7	7
120.0	0	7	7
121.0	0	6	6
122.0	0	4	4
123.0	0	11	11
124.0	0	5	5
125.0	0	5	5
126.0	0	4	4
127.0	0	8	8
128.0	0	5	5
129.0	0	6	6
130.0	0	5	5
131.0	0	9	9
132.0	0	3	3
133.0	0	2	2
134.0	0	3	3
135.0	0	4	4
136.0	0	4	4
137.0	0	5	5
138.0	0	3	3
139.0	0	3	3
140.0	0	4	4
141.0	0	3	3
142.0	0	6	6
143.0	0	5	5
144.0	0	6	6
146.0	0	6	6
147.0	0	3	3
149.0	0	2	2
151.0	0	3	3
152.0	0	4	4
154.0	0	5	5
155.0	0	4	4
156.0	0	2	2
157.0	0	1	1
158.0	0	1	1
159.0	0	3	3
160.0	0	1	1
161.0	0	5	5
162.0	0	1	1
163.0	0	2	2
164.0	0	2	2
165.0	0	1	1
167.0	0	1	1
168.0	0	1	1
169.0	0	1	1
170.0	0	1	1
172.0	0	1	1
173.0	0	2	2
174.0	0	2	2
175.0	0	1	1
176.0	0	1	1
177.0	0	2	2
178.0	0	1	1
179.0	0	2	2
180.0	0	4	4
181.0	0	1	1
182.0	0	2	2
183.0	0	2	2
184.0	0	3	3
185.0	0	1	1
187.0	0	1	1
188.0	0	1	1
189.0	0	2	2
190.0	0	2	2
191.0	0	2	2
192.0	0	1	1
194.0	0	1	1
196.0	0	1	1
197.0	0	3	3
198.0	0	1	1
199.0	0	2	2
200.0	0	2	2
201.0	0	1	1
202.0	0	1	1
205.0	0	3	3
206.0	0	2	2
207.0	0	1	1
208.0	0	2	2
212.0	0	1	1
213.0	0	1	1
215.0	0	1	1
216.0	0	1	1
217.0	0	2	2
218.0	0	3	3
219.0	0	1	1
222.0	0	3	3
223.0	0	1	1
226.0	0	1	1
232.0	0	1	1
233.0	0	1	1
236.0	0	1	1
238.0	0	2	2
239.0	0	1	1
242.0	0	1	1
247.0	0	2	2
250.0	0	1	1
251.0	0	3	3
255.0	0	1	1
269.0	0	1	1
273.0	0	1	1
282.0	0	1	1
285.0	0	1	1
291.0	0	1	1
294.0	0	1	1
300.0	0	2	2
312.0	0	1	1
321.0	0	1	1
331.0	0	1	1
339.0	0	1	1
345.0	0	1	1
356.0	0	1	1
380.0	0	1	1
381.0	0	1	1
408.0	0	1	1
409.0	0	1	1
410.0	0	1	1
411.0	0	1	1
427.0	0	1	1
451.0	0	1	1
452.0	0	1	1
454.0	0	1	1
486.0	0	1	1
576.0	0	1	1
590.0	0	1	1
741.0	0	1	1
753.0	0	1	1
790.0	0	1	1
977.0	0	1	1
4363.0	0	1	1