## 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-GSM1606362.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606362.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606362.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 22:35:34 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	30869615	4460976	0	0	4651975	0	0.150698	91850989

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	23822772	23822772
2.0	1.714563	1661689	1661689
3.0	2.225164	361152	361152
4.0	2.590021	142851	142851
5.0	2.850734	71966	71966
6.0	3.03703	42498	42498
7.0	3.17015	27551	27551
8.0	3.265273	18475	18475
9.0	3.333244	13450	13450
10.0	3.381814	9936	9936
11.0	3.41652	7449	7449
12.0	3.44132	5777	5777
13.0	3.459041	4532	4532
14.0	3.471704	3711	3711
15.0	3.480752	3000	3000
16.0	3.487218	2569	2569
17.0	3.491838	2112	2112
18.0	3.49514	1766	1766
19.0	3.497499	1458	1458
20.0	3.499184	1342	1342
21.0	3.500389	1109	1109
22.0	3.501249	1019	1019
23.0	3.501864	831	831
24.0	3.502304	743	743
25.0	3.502618	618	618
26.0	3.502842	545	545
27.0	3.503003	551	551
28.0	3.503117	444	444
29.0	3.503199	421	421
30.0	3.503258	402	402
31.0	3.5033	329	329
32.0	3.503329	311	311
33.0	3.503351	260	260
34.0	3.503366	257	257
35.0	3.503377	233	233
36.0	3.503385	218	218
37.0	3.50339	215	215
38.0	3.503394	186	186
39.0	3.503397	161	161
40.0	3.503399	147	147
41.0	3.503401	131	131
42.0	3.503402	131	131
43.0	3.503402	121	121
44.0	3.503403	116	116
45.0	3.503403	124	124
46.0	3.503403	110	110
47.0	3.503404	99	99
48.0	3.503404	95	95
49.0	3.503404	83	83
50.0	3.503404	72	72
51.0	3.503404	61	61
52.0	3.503404	61	61
53.0	3.503404	58	58
54.0	3.503404	59	59
55.0	3.503404	55	55
56.0	3.503404	53	53
57.0	3.503404	64	64
58.0	3.503404	43	43
59.0	3.503404	31	31
60.0	3.503404	54	54
61.0	3.503404	36	36
62.0	3.503404	33	33
63.0	3.503404	22	22
64.0	3.503404	32	32
65.0	3.503404	43	43
66.0	3.503404	30	30
67.0	3.503404	31	31
68.0	3.503404	21	21
69.0	3.503404	22	22
70.0	3.503404	22	22
71.0	3.503404	23	23
72.0	3.503404	27	27
73.0	3.503404	17	17
74.0	3.503404	21	21
75.0	3.503404	14	14
76.0	3.503404	11	11
77.0	3.503404	10	10
78.0	3.503404	22	22
79.0	3.503404	9	9
80.0	3.503404	18	18
81.0	3.503404	17	17
82.0	3.503404	17	17
83.0	3.503404	15	15
84.0	3.503404	17	17
85.0	3.503404	18	18
86.0	3.503404	12	12
87.0	3.503404	13	13
88.0	3.503404	17	17
89.0	3.503404	10	10
90.0	3.503404	11	11
91.0	3.503404	10	10
92.0	3.503404	10	10
93.0	3.503404	6	6
94.0	3.503404	10	10
95.0	3.503404	11	11
96.0	3.503404	14	14
97.0	3.503404	11	11
98.0	3.503404	10	10
99.0	3.503404	12	12
100.0	3.503404	3	3
101.0	0	6	6
102.0	0	11	11
103.0	0	7	7
104.0	0	6	6
105.0	0	5	5
106.0	0	8	8
107.0	0	7	7
108.0	0	7	7
109.0	0	5	5
110.0	0	5	5
111.0	0	8	8
112.0	0	4	4
113.0	0	4	4
114.0	0	4	4
115.0	0	5	5
116.0	0	5	5
117.0	0	2	2
118.0	0	3	3
119.0	0	3	3
120.0	0	2	2
121.0	0	2	2
122.0	0	3	3
123.0	0	1	1
124.0	0	2	2
125.0	0	3	3
126.0	0	1	1
127.0	0	6	6
128.0	0	2	2
129.0	0	3	3
130.0	0	2	2
131.0	0	2	2
132.0	0	3	3
133.0	0	2	2
134.0	0	2	2
135.0	0	2	2
137.0	0	2	2
138.0	0	3	3
139.0	0	2	2
140.0	0	2	2
141.0	0	3	3
142.0	0	2	2
143.0	0	1	1
144.0	0	5	5
146.0	0	2	2
147.0	0	2	2
149.0	0	1	1
150.0	0	2	2
151.0	0	2	2
152.0	0	2	2
153.0	0	3	3
154.0	0	2	2
155.0	0	1	1
156.0	0	2	2
157.0	0	2	2
158.0	0	3	3
161.0	0	1	1
162.0	0	1	1
164.0	0	2	2
165.0	0	2	2
166.0	0	1	1
167.0	0	2	2
171.0	0	2	2
172.0	0	4	4
174.0	0	2	2
175.0	0	1	1
176.0	0	1	1
177.0	0	2	2
178.0	0	1	1
180.0	0	3	3
186.0	0	1	1
189.0	0	1	1
190.0	0	1	1
191.0	0	2	2
192.0	0	1	1
198.0	0	1	1
199.0	0	1	1
205.0	0	1	1
206.0	0	1	1
212.0	0	1	1
213.0	0	1	1
216.0	0	1	1
218.0	0	2	2
221.0	0	1	1
230.0	0	1	1
234.0	0	1	1
237.0	0	2	2
252.0	0	1	1
258.0	0	1	1
261.0	0	1	1
263.0	0	1	1
264.0	0	1	1
274.0	0	1	1
278.0	0	1	1
280.0	0	1	1
282.0	0	1	1
288.0	0	1	1
296.0	0	1	1
300.0	0	1	1
302.0	0	1	1
315.0	0	1	1
325.0	0	1	1
333.0	0	1	1
349.0	0	1	1
377.0	0	1	1
381.0	0	1	1
399.0	0	1	1
420.0	0	1	1
454.0	0	1	1
7492.0	0	1	1