## 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-GSM1606367.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606367.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606367.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 20:52:10 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	32887237	4316656	0	0	5988458	0	0.182091	78972628

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	23986114	23986114
2.0	1.659391	1977934	1977934
3.0	2.094188	446304	446304
4.0	2.380889	180443	180443
5.0	2.569937	93923	93923
6.0	2.694594	55881	55881
7.0	2.776791	35832	35832
8.0	2.830991	25196	25196
9.0	2.866731	18067	18067
10.0	2.890297	13577	13577
11.0	2.905836	10458	10458
12.0	2.916082	8146	8146
13.0	2.922839	6417	6417
14.0	2.927294	5284	5284
15.0	2.930232	4341	4341
16.0	2.932169	3716	3716
17.0	2.933446	2981	2981
18.0	2.934288	2565	2565
19.0	2.934844	2185	2185
20.0	2.93521	1869	1869
21.0	2.935451	1607	1607
22.0	2.93561	1391	1391
23.0	2.935715	1301	1301
24.0	2.935785	1136	1136
25.0	2.93583	1014	1014
26.0	2.93586	830	830
27.0	2.93588	767	767
28.0	2.935893	735	735
29.0	2.935902	610	610
30.0	2.935908	593	593
31.0	2.935911	553	553
32.0	2.935914	496	496
33.0	2.935916	406	406
34.0	2.935917	374	374
35.0	2.935917	327	327
36.0	2.935918	332	332
37.0	2.935918	265	265
38.0	2.935918	275	275
39.0	2.935918	249	249
40.0	2.935919	198	198
41.0	2.935919	226	226
42.0	2.935919	205	205
43.0	2.935919	201	201
44.0	2.935919	155	155
45.0	2.935919	169	169
46.0	2.935919	140	140
47.0	2.935919	125	125
48.0	2.935919	136	136
49.0	2.935919	145	145
50.0	2.935919	137	137
51.0	2.935919	116	116
52.0	2.935919	104	104
53.0	2.935919	95	95
54.0	2.935919	94	94
55.0	2.935919	75	75
56.0	2.935919	82	82
57.0	2.935919	72	72
58.0	2.935919	80	80
59.0	2.935919	60	60
60.0	2.935919	66	66
61.0	2.935919	64	64
62.0	2.935919	65	65
63.0	2.935919	56	56
64.0	2.935919	51	51
65.0	2.935919	50	50
66.0	2.935919	46	46
67.0	2.935919	36	36
68.0	2.935919	44	44
69.0	2.935919	41	41
70.0	2.935919	37	37
71.0	2.935919	39	39
72.0	2.935919	34	34
73.0	2.935919	43	43
74.0	2.935919	40	40
75.0	2.935919	31	31
76.0	2.935919	29	29
77.0	2.935919	28	28
78.0	2.935919	23	23
79.0	2.935919	22	22
80.0	2.935919	15	15
81.0	2.935919	28	28
82.0	2.935919	23	23
83.0	2.935919	24	24
84.0	2.935919	15	15
85.0	2.935919	24	24
86.0	2.935919	18	18
87.0	2.935919	14	14
88.0	2.935919	23	23
89.0	2.935919	22	22
90.0	2.935919	21	21
91.0	2.935919	16	16
92.0	2.935919	13	13
93.0	2.935919	24	24
94.0	2.935919	13	13
95.0	2.935919	17	17
96.0	2.935919	12	12
97.0	2.935919	9	9
98.0	2.935919	15	15
99.0	2.935919	17	17
100.0	2.935919	19	19
101.0	0	17	17
102.0	0	11	11
103.0	0	6	6
104.0	0	8	8
105.0	0	12	12
106.0	0	8	8
107.0	0	10	10
108.0	0	11	11
109.0	0	9	9
110.0	0	9	9
111.0	0	8	8
112.0	0	7	7
113.0	0	9	9
114.0	0	6	6
115.0	0	6	6
116.0	0	11	11
117.0	0	8	8
118.0	0	4	4
119.0	0	6	6
120.0	0	10	10
121.0	0	10	10
122.0	0	5	5
123.0	0	3	3
124.0	0	4	4
125.0	0	6	6
126.0	0	7	7
127.0	0	4	4
128.0	0	2	2
129.0	0	4	4
130.0	0	3	3
131.0	0	6	6
132.0	0	6	6
133.0	0	7	7
134.0	0	7	7
135.0	0	7	7
136.0	0	3	3
137.0	0	3	3
138.0	0	3	3
139.0	0	4	4
140.0	0	2	2
141.0	0	3	3
142.0	0	2	2
143.0	0	3	3
144.0	0	6	6
145.0	0	1	1
146.0	0	2	2
147.0	0	4	4
148.0	0	4	4
149.0	0	4	4
150.0	0	2	2
151.0	0	5	5
152.0	0	5	5
153.0	0	3	3
154.0	0	3	3
156.0	0	2	2
157.0	0	1	1
159.0	0	1	1
160.0	0	2	2
162.0	0	1	1
163.0	0	1	1
165.0	0	1	1
167.0	0	1	1
168.0	0	2	2
169.0	0	4	4
170.0	0	2	2
171.0	0	2	2
172.0	0	1	1
173.0	0	1	1
175.0	0	1	1
176.0	0	1	1
177.0	0	5	5
179.0	0	1	1
180.0	0	1	1
181.0	0	3	3
182.0	0	5	5
183.0	0	3	3
184.0	0	2	2
186.0	0	1	1
187.0	0	3	3
189.0	0	1	1
191.0	0	1	1
193.0	0	1	1
195.0	0	1	1
196.0	0	1	1
198.0	0	1	1
200.0	0	3	3
201.0	0	1	1
203.0	0	1	1
204.0	0	2	2
205.0	0	2	2
207.0	0	1	1
208.0	0	1	1
209.0	0	2	2
210.0	0	2	2
212.0	0	1	1
214.0	0	1	1
215.0	0	2	2
216.0	0	1	1
217.0	0	4	4
224.0	0	1	1
225.0	0	1	1
227.0	0	2	2
229.0	0	2	2
232.0	0	1	1
235.0	0	1	1
238.0	0	1	1
240.0	0	1	1
242.0	0	1	1
246.0	0	1	1
247.0	0	1	1
254.0	0	1	1
263.0	0	1	1
270.0	0	1	1
272.0	0	1	1
276.0	0	1	1
287.0	0	1	1
288.0	0	1	1
289.0	0	1	1
290.0	0	2	2
307.0	0	1	1
308.0	0	1	1
316.0	0	1	1
318.0	0	1	1
332.0	0	1	1
337.0	0	1	1
341.0	0	1	1
346.0	0	1	1
356.0	0	1	1
361.0	0	1	1
366.0	0	1	1
371.0	0	1	1
385.0	0	1	1
404.0	0	1	1
406.0	0	1	1
432.0	0	1	1
437.0	0	1	1
446.0	0	1	1
462.0	0	1	1
526.0	0	1	1
528.0	0	1	1
919.0	0	1	1
17128.0	0	1	1