## 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-GSM1606343.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606343.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606343.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 22:35:41 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	31389499	4677816	0	0	5811118	0	0.185129	73954756

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	22712100	22712100
2.0	1.654135	1957002	1957002
3.0	2.082027	439804	439804
4.0	2.361926	176157	176157
5.0	2.545018	90527	90527
6.0	2.664785	53564	53564
7.0	2.743128	34310	34310
8.0	2.794375	23706	23706
9.0	2.827898	16992	16992
10.0	2.849826	12537	12537
11.0	2.86417	9710	9710
12.0	2.873553	7457	7457
13.0	2.879691	6091	6091
14.0	2.883706	4994	4994
15.0	2.886332	4080	4080
16.0	2.88805	3360	3360
17.0	2.889174	2916	2916
18.0	2.889909	2389	2389
19.0	2.89039	2017	2017
20.0	2.890704	1797	1797
21.0	2.89091	1527	1527
22.0	2.891045	1377	1377
23.0	2.891133	1232	1232
24.0	2.89119	1017	1017
25.0	2.891228	916	916
26.0	2.891253	805	805
27.0	2.891269	768	768
28.0	2.891279	635	635
29.0	2.891286	602	602
30.0	2.891291	541	541
31.0	2.891294	478	478
32.0	2.891296	491	491
33.0	2.891297	419	419
34.0	2.891298	368	368
35.0	2.891298	333	333
36.0	2.891299	352	352
37.0	2.891299	303	303
38.0	2.891299	274	274
39.0	2.891299	264	264
40.0	2.891299	214	214
41.0	2.891299	230	230
42.0	2.891299	193	193
43.0	2.891299	165	165
44.0	2.891299	163	163
45.0	2.891299	153	153
46.0	2.891299	154	154
47.0	2.891299	143	143
48.0	2.891299	136	136
49.0	2.891299	119	119
50.0	2.891299	108	108
51.0	2.891299	109	109
52.0	2.891299	95	95
53.0	2.891299	81	81
54.0	2.891299	102	102
55.0	2.891299	92	92
56.0	2.891299	89	89
57.0	2.891299	86	86
58.0	2.891299	59	59
59.0	2.891299	69	69
60.0	2.891299	70	70
61.0	2.891299	56	56
62.0	2.891299	47	47
63.0	2.891299	59	59
64.0	2.891299	47	47
65.0	2.891299	48	48
66.0	2.891299	42	42
67.0	2.891299	46	46
68.0	2.891299	47	47
69.0	2.891299	46	46
70.0	2.891299	35	35
71.0	2.891299	34	34
72.0	2.891299	30	30
73.0	2.891299	30	30
74.0	2.891299	39	39
75.0	2.891299	39	39
76.0	2.891299	19	19
77.0	2.891299	25	25
78.0	2.891299	34	34
79.0	2.891299	24	24
80.0	2.891299	21	21
81.0	2.891299	20	20
82.0	2.891299	29	29
83.0	2.891299	26	26
84.0	2.891299	13	13
85.0	2.891299	23	23
86.0	2.891299	17	17
87.0	2.891299	25	25
88.0	2.891299	19	19
89.0	2.891299	19	19
90.0	2.891299	16	16
91.0	2.891299	13	13
92.0	2.891299	16	16
93.0	2.891299	12	12
94.0	2.891299	7	7
95.0	2.891299	15	15
96.0	2.891299	9	9
97.0	2.891299	16	16
98.0	2.891299	10	10
99.0	2.891299	9	9
100.0	2.891299	11	11
101.0	0	10	10
102.0	0	12	12
103.0	0	10	10
104.0	0	8	8
105.0	0	15	15
106.0	0	15	15
107.0	0	7	7
108.0	0	6	6
109.0	0	12	12
110.0	0	6	6
111.0	0	5	5
112.0	0	8	8
113.0	0	6	6
114.0	0	5	5
115.0	0	9	9
116.0	0	5	5
117.0	0	11	11
118.0	0	4	4
119.0	0	6	6
120.0	0	4	4
121.0	0	7	7
122.0	0	8	8
123.0	0	8	8
124.0	0	5	5
125.0	0	8	8
126.0	0	5	5
127.0	0	1	1
128.0	0	5	5
129.0	0	6	6
130.0	0	4	4
131.0	0	5	5
132.0	0	5	5
133.0	0	5	5
134.0	0	3	3
135.0	0	1	1
136.0	0	2	2
137.0	0	5	5
138.0	0	3	3
139.0	0	4	4
140.0	0	3	3
141.0	0	8	8
142.0	0	4	4
143.0	0	7	7
144.0	0	3	3
145.0	0	6	6
146.0	0	2	2
147.0	0	6	6
148.0	0	1	1
149.0	0	4	4
150.0	0	2	2
151.0	0	4	4
152.0	0	2	2
153.0	0	3	3
154.0	0	3	3
155.0	0	4	4
156.0	0	6	6
157.0	0	6	6
160.0	0	3	3
161.0	0	2	2
163.0	0	3	3
164.0	0	3	3
165.0	0	2	2
166.0	0	2	2
167.0	0	1	1
168.0	0	2	2
169.0	0	3	3
171.0	0	1	1
173.0	0	1	1
174.0	0	1	1
175.0	0	2	2
177.0	0	1	1
178.0	0	5	5
179.0	0	1	1
181.0	0	4	4
182.0	0	3	3
183.0	0	2	2
184.0	0	2	2
185.0	0	2	2
189.0	0	3	3
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
195.0	0	1	1
197.0	0	2	2
198.0	0	1	1
200.0	0	1	1
201.0	0	1	1
202.0	0	1	1
203.0	0	1	1
204.0	0	3	3
205.0	0	2	2
208.0	0	1	1
209.0	0	3	3
210.0	0	2	2
212.0	0	2	2
213.0	0	1	1
218.0	0	1	1
221.0	0	1	1
223.0	0	1	1
225.0	0	2	2
227.0	0	1	1
237.0	0	2	2
242.0	0	1	1
243.0	0	1	1
246.0	0	1	1
249.0	0	1	1
250.0	0	1	1
255.0	0	1	1
257.0	0	1	1
259.0	0	1	1
264.0	0	2	2
265.0	0	1	1
273.0	0	1	1
274.0	0	1	1
275.0	0	1	1
280.0	0	1	1
286.0	0	1	1
296.0	0	1	1
299.0	0	1	1
305.0	0	1	1
318.0	0	1	1
320.0	0	1	1
333.0	0	1	1
335.0	0	1	1
341.0	0	1	1
360.0	0	1	1
368.0	0	1	1
424.0	0	1	1
506.0	0	1	1
527.0	0	1	1
546.0	0	1	1
591.0	0	1	1
594.0	0	1	1
648.0	0	1	1
10618.0	0	1	1