## 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-GSM1606202.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606202.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606202.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 13:19:15 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	35361428	6312606	0	0	5675701	0	0.160505	98023757

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	26874768	26874768
2.0	1.697158	1913988	1913988
3.0	2.183187	436186	436186
4.0	2.522026	174548	174548
5.0	2.75825	89448	89448
6.0	2.922936	52470	52470
7.0	3.037747	33800	33800
8.0	3.117789	23186	23186
9.0	3.173591	16377	16377
10.0	3.212494	12217	12217
11.0	3.239615	9454	9454
12.0	3.258523	7263	7263
13.0	3.271705	5791	5791
14.0	3.280895	4617	4617
15.0	3.287301	3911	3911
16.0	3.291768	3347	3347
17.0	3.294882	2769	2769
18.0	3.297053	2266	2266
19.0	3.298566	1951	1951
20.0	3.299621	1719	1719
21.0	3.300357	1476	1476
22.0	3.30087	1237	1237
23.0	3.301227	1140	1140
24.0	3.301476	956	956
25.0	3.30165	879	879
26.0	3.301771	733	733
27.0	3.301856	693	693
28.0	3.301915	629	629
29.0	3.301956	517	517
30.0	3.301984	520	520
31.0	3.302004	463	463
32.0	3.302018	415	415
33.0	3.302028	366	366
34.0	3.302035	356	356
35.0	3.302039	285	285
36.0	3.302043	284	284
37.0	3.302045	237	237
38.0	3.302046	269	269
39.0	3.302048	246	246
40.0	3.302048	201	201
41.0	3.302049	210	210
42.0	3.302049	168	168
43.0	3.302049	163	163
44.0	3.30205	171	171
45.0	3.30205	135	135
46.0	3.30205	134	134
47.0	3.30205	132	132
48.0	3.30205	107	107
49.0	3.30205	122	122
50.0	3.30205	113	113
51.0	3.30205	118	118
52.0	3.30205	105	105
53.0	3.30205	89	89
54.0	3.30205	91	91
55.0	3.30205	79	79
56.0	3.30205	75	75
57.0	3.30205	69	69
58.0	3.30205	57	57
59.0	3.30205	62	62
60.0	3.30205	55	55
61.0	3.30205	56	56
62.0	3.30205	51	51
63.0	3.30205	56	56
64.0	3.30205	44	44
65.0	3.30205	49	49
66.0	3.30205	44	44
67.0	3.30205	51	51
68.0	3.30205	36	36
69.0	3.30205	50	50
70.0	3.30205	37	37
71.0	3.30205	34	34
72.0	3.30205	32	32
73.0	3.30205	33	33
74.0	3.30205	25	25
75.0	3.30205	24	24
76.0	3.30205	21	21
77.0	3.30205	32	32
78.0	3.30205	22	22
79.0	3.30205	21	21
80.0	3.30205	29	29
81.0	3.30205	20	20
82.0	3.30205	17	17
83.0	3.30205	14	14
84.0	3.30205	24	24
85.0	3.30205	19	19
86.0	3.30205	23	23
87.0	3.30205	24	24
88.0	3.30205	13	13
89.0	3.30205	21	21
90.0	3.30205	10	10
91.0	3.30205	11	11
92.0	3.30205	11	11
93.0	3.30205	21	21
94.0	3.30205	18	18
95.0	3.30205	14	14
96.0	3.30205	9	9
97.0	3.30205	17	17
98.0	3.30205	15	15
99.0	3.30205	6	6
100.0	3.30205	11	11
101.0	0	5	5
102.0	0	10	10
103.0	0	10	10
104.0	0	11	11
105.0	0	11	11
106.0	0	8	8
107.0	0	9	9
108.0	0	7	7
109.0	0	13	13
110.0	0	11	11
111.0	0	7	7
112.0	0	11	11
113.0	0	5	5
114.0	0	6	6
115.0	0	9	9
116.0	0	8	8
117.0	0	8	8
118.0	0	3	3
119.0	0	5	5
120.0	0	7	7
121.0	0	3	3
122.0	0	6	6
123.0	0	7	7
124.0	0	4	4
125.0	0	5	5
126.0	0	4	4
127.0	0	6	6
128.0	0	4	4
129.0	0	7	7
130.0	0	1	1
131.0	0	8	8
132.0	0	5	5
133.0	0	3	3
134.0	0	4	4
135.0	0	3	3
136.0	0	6	6
137.0	0	3	3
138.0	0	4	4
139.0	0	5	5
140.0	0	1	1
141.0	0	4	4
142.0	0	1	1
143.0	0	3	3
144.0	0	5	5
145.0	0	6	6
146.0	0	1	1
147.0	0	2	2
148.0	0	2	2
149.0	0	2	2
150.0	0	1	1
151.0	0	3	3
152.0	0	4	4
153.0	0	2	2
154.0	0	1	1
155.0	0	1	1
156.0	0	2	2
157.0	0	5	5
158.0	0	1	1
159.0	0	1	1
160.0	0	2	2
161.0	0	1	1
163.0	0	1	1
165.0	0	3	3
166.0	0	5	5
167.0	0	5	5
168.0	0	1	1
169.0	0	1	1
170.0	0	1	1
171.0	0	2	2
172.0	0	1	1
173.0	0	1	1
175.0	0	1	1
177.0	0	2	2
178.0	0	2	2
179.0	0	1	1
180.0	0	3	3
184.0	0	1	1
185.0	0	1	1
187.0	0	4	4
188.0	0	3	3
190.0	0	2	2
192.0	0	2	2
193.0	0	1	1
194.0	0	1	1
195.0	0	2	2
196.0	0	1	1
198.0	0	2	2
199.0	0	1	1
201.0	0	2	2
202.0	0	2	2
203.0	0	2	2
204.0	0	1	1
205.0	0	1	1
206.0	0	2	2
207.0	0	1	1
208.0	0	1	1
209.0	0	1	1
210.0	0	1	1
216.0	0	1	1
218.0	0	1	1
221.0	0	1	1
222.0	0	2	2
223.0	0	1	1
227.0	0	1	1
228.0	0	1	1
229.0	0	1	1
233.0	0	2	2
234.0	0	2	2
237.0	0	1	1
242.0	0	1	1
243.0	0	2	2
247.0	0	1	1
248.0	0	1	1
249.0	0	1	1
250.0	0	1	1
254.0	0	2	2
276.0	0	2	2
287.0	0	1	1
289.0	0	1	1
295.0	0	1	1
301.0	0	1	1
306.0	0	1	1
307.0	0	1	1
310.0	0	1	1
318.0	0	1	1
321.0	0	1	1
329.0	0	1	1
341.0	0	1	1
343.0	0	1	1
345.0	0	1	1
346.0	0	1	1
354.0	0	1	1
358.0	0	1	1
368.0	0	1	1
371.0	0	1	1
391.0	0	1	1
419.0	0	1	1
430.0	0	1	1
452.0	0	1	1
464.0	0	1	1
468.0	0	1	1
485.0	0	1	1
486.0	0	1	1
527.0	0	1	1
559.0	0	1	1
560.0	0	1	1
633.0	0	1	1
672.0	0	1	1
732.0	0	1	1
961.0	0	1	1
1225.0	0	1	1
1265.0	0	1	1
10905.0	0	1	1