## 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-GSM1606218.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606218.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606218.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 22:37:59 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	40526645	6709996	0	0	6037126	0	0.148967	122151830

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	31443097	31443097
2.0	1.71765	2081919	2081919
3.0	2.232673	473315	473315
4.0	2.602278	188319	188319
5.0	2.867526	95482	95482
6.0	3.057881	56291	56291
7.0	3.19449	36235	36235
8.0	3.292527	24470	24470
9.0	3.362883	17326	17326
10.0	3.413375	12939	12939
11.0	3.44961	9845	9845
12.0	3.475614	7490	7490
13.0	3.494276	6046	6046
14.0	3.507668	4918	4918
15.0	3.51728	3912	3912
16.0	3.524177	3301	3301
17.0	3.529127	2757	2757
18.0	3.53268	2393	2393
19.0	3.535229	2054	2054
20.0	3.537059	1765	1765
21.0	3.538371	1433	1433
22.0	3.539314	1318	1318
23.0	3.53999	1139	1139
24.0	3.540475	943	943
25.0	3.540824	848	848
26.0	3.541073	803	803
27.0	3.541253	709	709
28.0	3.541382	597	597
29.0	3.541474	572	572
30.0	3.54154	514	514
31.0	3.541588	506	506
32.0	3.541622	393	393
33.0	3.541646	394	394
34.0	3.541664	346	346
35.0	3.541677	317	317
36.0	3.541686	298	298
37.0	3.541692	282	282
38.0	3.541697	263	263
39.0	3.5417	249	249
40.0	3.541703	202	202
41.0	3.541704	199	199
42.0	3.541706	197	197
43.0	3.541706	144	144
44.0	3.541707	149	149
45.0	3.541708	157	157
46.0	3.541708	136	136
47.0	3.541708	119	119
48.0	3.541708	121	121
49.0	3.541708	120	120
50.0	3.541708	100	100
51.0	3.541709	89	89
52.0	3.541709	78	78
53.0	3.541709	95	95
54.0	3.541709	97	97
55.0	3.541709	81	81
56.0	3.541709	70	70
57.0	3.541709	59	59
58.0	3.541709	58	58
59.0	3.541709	63	63
60.0	3.541709	42	42
61.0	3.541709	54	54
62.0	3.541709	58	58
63.0	3.541709	44	44
64.0	3.541709	47	47
65.0	3.541709	54	54
66.0	3.541709	45	45
67.0	3.541709	34	34
68.0	3.541709	40	40
69.0	3.541709	26	26
70.0	3.541709	42	42
71.0	3.541709	43	43
72.0	3.541709	29	29
73.0	3.541709	32	32
74.0	3.541709	19	19
75.0	3.541709	30	30
76.0	3.541709	23	23
77.0	3.541709	22	22
78.0	3.541709	22	22
79.0	3.541709	21	21
80.0	3.541709	18	18
81.0	3.541709	19	19
82.0	3.541709	23	23
83.0	3.541709	27	27
84.0	3.541709	12	12
85.0	3.541709	16	16
86.0	3.541709	13	13
87.0	3.541709	14	14
88.0	3.541709	10	10
89.0	3.541709	17	17
90.0	3.541709	15	15
91.0	3.541709	8	8
92.0	3.541709	19	19
93.0	3.541709	11	11
94.0	3.541709	11	11
95.0	3.541709	12	12
96.0	3.541709	13	13
97.0	3.541709	20	20
98.0	3.541709	9	9
99.0	3.541709	10	10
100.0	3.541709	11	11
101.0	0	11	11
102.0	0	9	9
103.0	0	12	12
104.0	0	7	7
105.0	0	6	6
106.0	0	6	6
107.0	0	6	6
108.0	0	8	8
109.0	0	6	6
110.0	0	8	8
111.0	0	10	10
112.0	0	7	7
113.0	0	9	9
114.0	0	7	7
115.0	0	5	5
116.0	0	2	2
117.0	0	9	9
118.0	0	5	5
119.0	0	1	1
120.0	0	7	7
121.0	0	6	6
122.0	0	3	3
123.0	0	3	3
124.0	0	4	4
125.0	0	8	8
126.0	0	2	2
127.0	0	5	5
128.0	0	4	4
129.0	0	2	2
130.0	0	2	2
131.0	0	1	1
132.0	0	5	5
133.0	0	2	2
134.0	0	3	3
135.0	0	3	3
136.0	0	5	5
137.0	0	7	7
138.0	0	1	1
139.0	0	2	2
140.0	0	4	4
141.0	0	3	3
142.0	0	2	2
143.0	0	6	6
144.0	0	2	2
145.0	0	4	4
146.0	0	3	3
147.0	0	4	4
148.0	0	3	3
150.0	0	4	4
151.0	0	2	2
152.0	0	1	1
153.0	0	4	4
154.0	0	3	3
156.0	0	3	3
158.0	0	1	1
159.0	0	1	1
160.0	0	3	3
161.0	0	1	1
163.0	0	3	3
164.0	0	2	2
166.0	0	3	3
167.0	0	2	2
169.0	0	2	2
172.0	0	1	1
174.0	0	2	2
176.0	0	1	1
177.0	0	1	1
178.0	0	1	1
179.0	0	2	2
182.0	0	1	1
183.0	0	1	1
185.0	0	1	1
187.0	0	1	1
188.0	0	2	2
189.0	0	2	2
190.0	0	1	1
191.0	0	1	1
193.0	0	1	1
201.0	0	3	3
205.0	0	4	4
207.0	0	1	1
208.0	0	2	2
211.0	0	1	1
212.0	0	1	1
214.0	0	1	1
216.0	0	1	1
217.0	0	1	1
219.0	0	1	1
222.0	0	1	1
223.0	0	1	1
226.0	0	1	1
228.0	0	3	3
229.0	0	1	1
230.0	0	1	1
232.0	0	1	1
233.0	0	1	1
235.0	0	1	1
238.0	0	1	1
241.0	0	1	1
245.0	0	1	1
246.0	0	1	1
253.0	0	1	1
258.0	0	1	1
259.0	0	1	1
267.0	0	2	2
276.0	0	1	1
280.0	0	1	1
281.0	0	1	1
284.0	0	1	1
290.0	0	1	1
296.0	0	1	1
305.0	0	1	1
310.0	0	1	1
317.0	0	1	1
331.0	0	1	1
333.0	0	1	1
348.0	0	1	1
371.0	0	1	1
406.0	0	1	1
410.0	0	1	1
438.0	0	1	1
475.0	0	1	1
513.0	0	1	1
657.0	0	1	1
1168.0	0	1	1
1194.0	0	1	1
9979.0	0	1	1