## 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-GSM1606332.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606332.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606332.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 00:34:30 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	31592168	4270506	0	0	4158526	0	0.131632	109222716

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	24760263	24760263
2.0	1.748828	2046384	2046384
3.0	2.309572	364834	364834
4.0	2.729473	119591	119591
5.0	3.043907	53844	53844
6.0	3.279364	28410	28410
7.0	3.455681	17076	17076
8.0	3.587712	10996	10996
9.0	3.686581	7518	7518
10.0	3.760617	5295	5295
11.0	3.816057	3760	3760
12.0	3.857572	2851	2851
13.0	3.888659	2101	2101
14.0	3.911939	1715	1715
15.0	3.929371	1405	1405
16.0	3.942425	1100	1100
17.0	3.9522	854	854
18.0	3.959519	769	769
19.0	3.965001	572	572
20.0	3.969105	533	533
21.0	3.972179	395	395
22.0	3.97448	358	358
23.0	3.976204	297	297
24.0	3.977494	263	263
25.0	3.978461	244	244
26.0	3.979185	221	221
27.0	3.979727	194	194
28.0	3.980132	156	156
29.0	3.980436	153	153
30.0	3.980664	107	107
31.0	3.980834	107	107
32.0	3.980962	98	98
33.0	3.981057	96	96
34.0	3.981129	69	69
35.0	3.981182	78	78
36.0	3.981223	66	66
37.0	3.981253	53	53
38.0	3.981275	50	50
39.0	3.981292	46	46
40.0	3.981305	41	41
41.0	3.981314	45	45
42.0	3.981321	28	28
43.0	3.981326	27	27
44.0	3.98133	26	26
45.0	3.981333	39	39
46.0	3.981336	29	29
47.0	3.981337	24	24
48.0	3.981338	25	25
49.0	3.981339	16	16
50.0	3.98134	22	22
51.0	3.981341	25	25
52.0	3.981341	18	18
53.0	3.981341	19	19
54.0	3.981342	10	10
55.0	3.981342	8	8
56.0	3.981342	9	9
57.0	3.981342	14	14
58.0	3.981342	14	14
59.0	3.981342	7	7
60.0	3.981342	14	14
61.0	3.981342	9	9
62.0	3.981342	7	7
63.0	3.981342	8	8
64.0	3.981342	7	7
65.0	3.981342	6	6
66.0	3.981342	5	5
67.0	3.981342	4	4
68.0	3.981342	9	9
69.0	3.981342	9	9
70.0	3.981342	6	6
71.0	3.981342	4	4
72.0	3.981342	7	7
73.0	3.981342	4	4
74.0	3.981342	5	5
75.0	3.981342	4	4
76.0	3.981342	4	4
77.0	3.981342	3	3
78.0	3.981342	4	4
79.0	3.981342	1	1
80.0	3.981342	3	3
81.0	3.981342	1	1
82.0	3.981342	3	3
83.0	3.981342	5	5
84.0	3.981342	3	3
85.0	3.981342	5	5
86.0	3.981342	3	3
87.0	3.981342	0	0
88.0	3.981342	0	0
89.0	3.981342	4	4
90.0	3.981342	3	3
91.0	3.981342	3	3
92.0	3.981342	1	1
93.0	3.981342	5	5
94.0	3.981342	1	1
95.0	3.981342	4	4
96.0	3.981342	2	2
97.0	3.981342	3	3
98.0	3.981342	3	3
99.0	3.981342	2	2
100.0	3.981342	3	3
101.0	0	1	1
103.0	0	4	4
105.0	0	1	1
106.0	0	1	1
107.0	0	3	3
108.0	0	2	2
109.0	0	1	1
110.0	0	1	1
111.0	0	1	1
115.0	0	5	5
118.0	0	1	1
121.0	0	1	1
122.0	0	1	1
123.0	0	1	1
124.0	0	2	2
125.0	0	1	1
127.0	0	1	1
131.0	0	2	2
133.0	0	1	1
134.0	0	1	1
136.0	0	3	3
138.0	0	1	1
141.0	0	1	1
142.0	0	2	2
144.0	0	1	1
145.0	0	1	1
150.0	0	1	1
152.0	0	1	1
161.0	0	1	1
164.0	0	1	1
167.0	0	1	1
168.0	0	1	1
170.0	0	1	1
175.0	0	2	2
178.0	0	1	1
179.0	0	1	1
181.0	0	1	1
192.0	0	1	1
198.0	0	1	1
207.0	0	1	1
208.0	0	1	1
218.0	0	1	1
219.0	0	2	2
222.0	0	1	1
224.0	0	1	1
225.0	0	1	1
229.0	0	1	1
237.0	0	1	1
242.0	0	1	1
244.0	0	1	1
245.0	0	1	1
246.0	0	1	1
259.0	0	1	1
269.0	0	1	1
272.0	0	1	1
279.0	0	1	1
313.0	0	1	1
328.0	0	1	1
333.0	0	1	1
350.0	0	1	1
410.0	0	1	1
440.0	0	1	1
457.0	0	1	1
458.0	0	1	1
474.0	0	1	1
558.0	0	1	1
563.0	0	1	1
572.0	0	1	1
575.0	0	1	1
603.0	0	1	1
650.0	0	1	1
779.0	0	1	1
785.0	0	1	1
871.0	0	1	1
895.0	0	1	1
904.0	0	1	1
939.0	0	1	1
1122.0	0	1	1
2561.0	0	1	1
40121.0	0	1	1