## 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-GSM1606366.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606366.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606366.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 14:02:46 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	28177536	3816636	0	0	4170201	0	0.147997	85551571

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	21878013	21878013
2.0	1.719382	1465856	1465856
3.0	2.236892	323626	323626
4.0	2.609179	129492	129492
5.0	2.876996	66874	66874
6.0	3.069658	39238	39238
7.0	3.208256	25154	25154
8.0	3.307961	17144	17144
9.0	3.379686	12175	12175
10.0	3.431285	8857	8857
11.0	3.468403	6786	6786
12.0	3.495106	5296	5296
13.0	3.514315	4135	4135
14.0	3.528134	3301	3301
15.0	3.538075	2776	2776
16.0	3.545227	2279	2279
17.0	3.550371	1849	1849
18.0	3.554072	1602	1602
19.0	3.556735	1365	1365
20.0	3.55865	1239	1239
21.0	3.560028	1029	1029
22.0	3.561019	897	897
23.0	3.561732	761	761
24.0	3.562245	637	637
25.0	3.562614	614	614
26.0	3.562879	519	519
27.0	3.56307	426	426
28.0	3.563208	429	429
29.0	3.563306	389	389
30.0	3.563377	326	326
31.0	3.563429	304	304
32.0	3.563465	286	286
33.0	3.563492	259	259
34.0	3.563511	207	207
35.0	3.563525	192	192
36.0	3.563534	192	192
37.0	3.563542	176	176
38.0	3.563547	156	156
39.0	3.56355	142	142
40.0	3.563553	132	132
41.0	3.563555	126	126
42.0	3.563556	116	116
43.0	3.563557	101	101
44.0	3.563558	86	86
45.0	3.563558	79	79
46.0	3.563559	71	71
47.0	3.563559	78	78
48.0	3.563559	77	77
49.0	3.563559	70	70
50.0	3.563559	57	57
51.0	3.563559	70	70
52.0	3.56356	64	64
53.0	3.56356	47	47
54.0	3.56356	52	52
55.0	3.56356	61	61
56.0	3.56356	42	42
57.0	3.56356	50	50
58.0	3.56356	34	34
59.0	3.56356	44	44
60.0	3.56356	29	29
61.0	3.56356	28	28
62.0	3.56356	39	39
63.0	3.56356	39	39
64.0	3.56356	29	29
65.0	3.56356	30	30
66.0	3.56356	22	22
67.0	3.56356	29	29
68.0	3.56356	24	24
69.0	3.56356	25	25
70.0	3.56356	18	18
71.0	3.56356	19	19
72.0	3.56356	19	19
73.0	3.56356	23	23
74.0	3.56356	19	19
75.0	3.56356	17	17
76.0	3.56356	15	15
77.0	3.56356	22	22
78.0	3.56356	12	12
79.0	3.56356	19	19
80.0	3.56356	20	20
81.0	3.56356	6	6
82.0	3.56356	12	12
83.0	3.56356	12	12
84.0	3.56356	7	7
85.0	3.56356	12	12
86.0	3.56356	9	9
87.0	3.56356	12	12
88.0	3.56356	6	6
89.0	3.56356	11	11
90.0	3.56356	6	6
91.0	3.56356	13	13
92.0	3.56356	9	9
93.0	3.56356	4	4
94.0	3.56356	11	11
95.0	3.56356	9	9
96.0	3.56356	7	7
97.0	3.56356	9	9
98.0	3.56356	6	6
99.0	3.56356	2	2
100.0	3.56356	5	5
101.0	0	8	8
102.0	0	3	3
103.0	0	5	5
104.0	0	2	2
105.0	0	11	11
106.0	0	3	3
107.0	0	6	6
108.0	0	7	7
109.0	0	4	4
110.0	0	3	3
111.0	0	4	4
112.0	0	6	6
113.0	0	5	5
114.0	0	4	4
115.0	0	4	4
116.0	0	2	2
117.0	0	4	4
118.0	0	4	4
120.0	0	8	8
121.0	0	1	1
122.0	0	2	2
123.0	0	3	3
124.0	0	3	3
125.0	0	3	3
126.0	0	2	2
127.0	0	1	1
128.0	0	3	3
129.0	0	2	2
130.0	0	2	2
131.0	0	3	3
132.0	0	2	2
133.0	0	3	3
135.0	0	3	3
136.0	0	2	2
137.0	0	1	1
138.0	0	1	1
140.0	0	2	2
141.0	0	2	2
142.0	0	3	3
144.0	0	3	3
146.0	0	1	1
147.0	0	2	2
148.0	0	1	1
152.0	0	1	1
153.0	0	3	3
154.0	0	1	1
155.0	0	1	1
156.0	0	1	1
158.0	0	1	1
159.0	0	1	1
162.0	0	2	2
163.0	0	3	3
164.0	0	1	1
165.0	0	2	2
166.0	0	3	3
169.0	0	2	2
171.0	0	1	1
172.0	0	1	1
173.0	0	2	2
175.0	0	1	1
180.0	0	1	1
183.0	0	2	2
184.0	0	1	1
185.0	0	2	2
186.0	0	1	1
189.0	0	1	1
194.0	0	3	3
198.0	0	1	1
200.0	0	1	1
202.0	0	1	1
203.0	0	1	1
206.0	0	1	1
210.0	0	1	1
214.0	0	1	1
216.0	0	1	1
217.0	0	1	1
218.0	0	1	1
225.0	0	2	2
232.0	0	1	1
233.0	0	1	1
235.0	0	1	1
247.0	0	1	1
251.0	0	1	1
254.0	0	1	1
256.0	0	1	1
267.0	0	2	2
274.0	0	1	1
279.0	0	1	1
282.0	0	1	1
303.0	0	1	1
336.0	0	1	1
343.0	0	1	1
344.0	0	1	1
403.0	0	1	1
411.0	0	1	1
420.0	0	1	1
427.0	0	1	1
6816.0	0	1	1