## 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-GSM1606186.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606186.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606186.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 22:28:58 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	44238105	5064440	0	0	4986150	0	0.112712	181203530

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	35929091	35929091
2.0	1.783382	2553889	2553889
3.0	2.397069	458017	458017
4.0	2.877821	148591	148591
5.0	3.254433	64630	64630
6.0	3.549464	33310	33310
7.0	3.780586	19269	19269
8.0	3.961643	11987	11987
9.0	4.10348	8003	8003
10.0	4.214592	5644	5644
11.0	4.301635	4127	4127
12.0	4.369823	2906	2906
13.0	4.423241	2254	2254
14.0	4.465087	1712	1712
15.0	4.497869	1329	1329
16.0	4.523549	1022	1022
17.0	4.543667	823	823
18.0	4.559426	739	739
19.0	4.571772	580	580
20.0	4.581444	493	493
21.0	4.589021	413	413
22.0	4.594956	355	355
23.0	4.599605	291	291
24.0	4.603248	241	241
25.0	4.606101	234	234
26.0	4.608337	200	200
27.0	4.610088	168	168
28.0	4.61146	161	161
29.0	4.612534	157	157
30.0	4.613376	113	113
31.0	4.614036	100	100
32.0	4.614552	84	84
33.0	4.614957	93	93
34.0	4.615274	82	82
35.0	4.615522	64	64
36.0	4.615717	58	58
37.0	4.615869	49	49
38.0	4.615989	48	48
39.0	4.616082	52	52
40.0	4.616156	39	39
41.0	4.616213	44	44
42.0	4.616258	30	30
43.0	4.616293	30	30
44.0	4.616321	19	19
45.0	4.616342	28	28
46.0	4.616359	22	22
47.0	4.616373	23	23
48.0	4.616383	21	21
49.0	4.616391	25	25
50.0	4.616397	12	12
51.0	4.616402	11	11
52.0	4.616406	15	15
53.0	4.616409	6	6
54.0	4.616412	16	16
55.0	4.616414	5	5
56.0	4.616415	13	13
57.0	4.616416	14	14
58.0	4.616417	10	10
59.0	4.616418	8	8
60.0	4.616418	9	9
61.0	4.616419	9	9
62.0	4.616419	5	5
63.0	4.61642	9	9
64.0	4.61642	12	12
65.0	4.61642	7	7
66.0	4.61642	7	7
67.0	4.61642	5	5
68.0	4.61642	1	1
69.0	4.61642	6	6
70.0	4.61642	6	6
71.0	4.61642	4	4
72.0	4.61642	3	3
73.0	4.61642	1	1
74.0	4.61642	4	4
75.0	4.61642	2	2
76.0	4.61642	2	2
77.0	4.61642	1	1
78.0	4.61642	3	3
79.0	4.61642	4	4
80.0	4.61642	2	2
81.0	4.61642	3	3
82.0	4.61642	1	1
83.0	4.61642	2	2
84.0	4.616421	3	3
85.0	4.616421	1	1
86.0	4.616421	2	2
87.0	4.616421	1	1
88.0	4.616421	4	4
89.0	4.616421	2	2
90.0	4.616421	1	1
91.0	4.616421	1	1
92.0	4.616421	3	3
93.0	4.616421	1	1
94.0	4.616421	2	2
95.0	4.616421	1	1
96.0	4.616421	0	0
97.0	4.616421	4	4
98.0	4.616421	1	1
99.0	4.616421	1	1
100.0	4.616421	0	0
101.0	0	1	1
102.0	0	1	1
108.0	0	1	1
109.0	0	1	1
114.0	0	1	1
115.0	0	1	1
117.0	0	1	1
119.0	0	2	2
121.0	0	1	1
122.0	0	2	2
123.0	0	1	1
125.0	0	1	1
127.0	0	1	1
129.0	0	1	1
130.0	0	1	1
131.0	0	1	1
136.0	0	1	1
148.0	0	1	1
158.0	0	1	1
159.0	0	1	1
167.0	0	2	2
168.0	0	2	2
169.0	0	1	1
173.0	0	2	2
178.0	0	1	1
210.0	0	1	1
217.0	0	2	2
239.0	0	1	1
252.0	0	1	1
330.0	0	1	1
343.0	0	1	1
350.0	0	1	1
371.0	0	1	1
399.0	0	1	1
409.0	0	1	1
575.0	0	1	1
607.0	0	1	1
671.0	0	1	1
737.0	0	1	1
790.0	0	1	1
894.0	0	1	1
928.0	0	1	1
13101.0	0	1	1