## 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-GSM1606224.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606224.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606224.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 00:19:28 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	35602073	4760254	0	0	5725329	0	0.160814	98476958

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	27091125	27091125
2.0	1.696612	1877928	1877928
3.0	2.18188	431184	431184
4.0	2.519923	176237	176237
5.0	2.755408	92591	92591
6.0	2.91945	54885	54885
7.0	3.033723	35341	35341
8.0	3.113328	24502	24502
9.0	3.168781	17693	17693
10.0	3.20741	13038	13038
11.0	3.23432	10129	10129
12.0	3.253066	7656	7656
13.0	3.266124	6284	6284
14.0	3.275221	5002	5002
15.0	3.281557	4181	4181
16.0	3.285972	3327	3327
17.0	3.289047	2941	2941
18.0	3.291189	2507	2507
19.0	3.292681	2037	2037
20.0	3.293721	1797	1797
21.0	3.294445	1540	1540
22.0	3.294949	1324	1324
23.0	3.295301	1156	1156
24.0	3.295545	1062	1062
25.0	3.295716	937	937
26.0	3.295835	838	838
27.0	3.295917	700	700
28.0	3.295975	693	693
29.0	3.296015	608	608
30.0	3.296043	516	516
31.0	3.296063	454	454
32.0	3.296076	429	429
33.0	3.296086	394	394
34.0	3.296092	359	359
35.0	3.296097	339	339
36.0	3.2961	329	329
37.0	3.296102	288	288
38.0	3.296104	270	270
39.0	3.296105	223	223
40.0	3.296106	203	203
41.0	3.296106	203	203
42.0	3.296107	184	184
43.0	3.296107	156	156
44.0	3.296107	186	186
45.0	3.296107	158	158
46.0	3.296107	143	143
47.0	3.296107	117	117
48.0	3.296107	147	147
49.0	3.296107	102	102
50.0	3.296107	110	110
51.0	3.296107	107	107
52.0	3.296107	99	99
53.0	3.296107	91	91
54.0	3.296107	75	75
55.0	3.296107	94	94
56.0	3.296107	80	80
57.0	3.296107	66	66
58.0	3.296107	57	57
59.0	3.296107	64	64
60.0	3.296107	53	53
61.0	3.296107	68	68
62.0	3.296107	55	55
63.0	3.296107	50	50
64.0	3.296107	50	50
65.0	3.296107	42	42
66.0	3.296107	44	44
67.0	3.296107	55	55
68.0	3.296107	38	38
69.0	3.296107	41	41
70.0	3.296107	42	42
71.0	3.296107	32	32
72.0	3.296107	23	23
73.0	3.296107	27	27
74.0	3.296107	29	29
75.0	3.296107	20	20
76.0	3.296107	38	38
77.0	3.296107	23	23
78.0	3.296107	20	20
79.0	3.296107	37	37
80.0	3.296107	18	18
81.0	3.296107	18	18
82.0	3.296107	21	21
83.0	3.296107	11	11
84.0	3.296107	16	16
85.0	3.296107	11	11
86.0	3.296107	19	19
87.0	3.296107	13	13
88.0	3.296107	14	14
89.0	3.296107	18	18
90.0	3.296107	13	13
91.0	3.296107	11	11
92.0	3.296107	24	24
93.0	3.296107	16	16
94.0	3.296107	9	9
95.0	3.296107	22	22
96.0	3.296107	7	7
97.0	3.296107	8	8
98.0	3.296107	14	14
99.0	3.296107	13	13
100.0	3.296107	9	9
101.0	0	8	8
102.0	0	9	9
103.0	0	10	10
104.0	0	7	7
105.0	0	7	7
106.0	0	8	8
107.0	0	11	11
108.0	0	9	9
110.0	0	8	8
111.0	0	6	6
112.0	0	8	8
113.0	0	10	10
114.0	0	7	7
115.0	0	13	13
116.0	0	2	2
117.0	0	4	4
118.0	0	7	7
119.0	0	8	8
120.0	0	4	4
121.0	0	6	6
122.0	0	7	7
123.0	0	6	6
124.0	0	6	6
125.0	0	1	1
126.0	0	6	6
127.0	0	3	3
128.0	0	2	2
129.0	0	3	3
130.0	0	4	4
131.0	0	5	5
132.0	0	4	4
133.0	0	3	3
134.0	0	1	1
135.0	0	3	3
136.0	0	5	5
137.0	0	5	5
138.0	0	3	3
139.0	0	2	2
140.0	0	4	4
141.0	0	1	1
142.0	0	1	1
143.0	0	4	4
144.0	0	3	3
145.0	0	2	2
146.0	0	4	4
147.0	0	3	3
148.0	0	4	4
149.0	0	3	3
150.0	0	2	2
151.0	0	1	1
152.0	0	3	3
153.0	0	3	3
154.0	0	2	2
155.0	0	3	3
156.0	0	3	3
158.0	0	1	1
159.0	0	2	2
161.0	0	2	2
163.0	0	1	1
164.0	0	1	1
167.0	0	1	1
168.0	0	1	1
171.0	0	1	1
172.0	0	2	2
173.0	0	1	1
174.0	0	2	2
175.0	0	2	2
176.0	0	1	1
177.0	0	1	1
178.0	0	1	1
179.0	0	2	2
181.0	0	2	2
182.0	0	1	1
183.0	0	2	2
184.0	0	3	3
185.0	0	2	2
187.0	0	3	3
188.0	0	1	1
189.0	0	1	1
190.0	0	1	1
191.0	0	1	1
192.0	0	1	1
193.0	0	1	1
194.0	0	1	1
196.0	0	1	1
198.0	0	2	2
202.0	0	2	2
205.0	0	1	1
208.0	0	1	1
209.0	0	1	1
210.0	0	1	1
211.0	0	2	2
213.0	0	2	2
214.0	0	1	1
215.0	0	1	1
216.0	0	1	1
223.0	0	1	1
224.0	0	2	2
225.0	0	2	2
228.0	0	1	1
230.0	0	1	1
233.0	0	1	1
235.0	0	1	1
236.0	0	1	1
239.0	0	1	1
242.0	0	1	1
244.0	0	1	1
247.0	0	1	1
249.0	0	1	1
253.0	0	1	1
257.0	0	1	1
259.0	0	1	1
260.0	0	1	1
268.0	0	1	1
283.0	0	1	1
300.0	0	1	1
301.0	0	1	1
304.0	0	1	1
306.0	0	1	1
307.0	0	1	1
320.0	0	1	1
323.0	0	1	1
362.0	0	1	1
366.0	0	1	1
373.0	0	1	1
383.0	0	1	1
384.0	0	1	1
413.0	0	2	2
423.0	0	2	2
466.0	0	1	1
481.0	0	1	1
652.0	0	1	1
1952.0	0	1	1