## 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-GSM919924.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919924.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919924.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 15:51:58 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	8763800	1425486	0	0	993298	0	0.113341	35681141

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	7112322	7112322
2.0	1.782224	516210	516210
3.0	2.394098	82159	82159
4.0	2.87272	26799	26799
5.0	3.24711	12158	12158
6.0	3.539967	6553	6553
7.0	3.769047	3889	3889
8.0	3.948238	2463	2463
9.0	4.088406	1803	1803
10.0	4.198049	1251	1251
11.0	4.283814	894	894
12.0	4.350901	668	668
13.0	4.403379	488	488
14.0	4.444428	457	457
15.0	4.476537	335	335
16.0	4.501654	275	275
17.0	4.521301	240	240
18.0	4.53667	183	183
19.0	4.548691	165	165
20.0	4.558095	158	158
21.0	4.56545	106	106
22.0	4.571204	90	90
23.0	4.575705	85	85
24.0	4.579225	77	77
25.0	4.581979	62	62
26.0	4.584133	55	55
27.0	4.585818	34	34
28.0	4.587136	43	43
29.0	4.588167	49	49
30.0	4.588974	39	39
31.0	4.589605	24	24
32.0	4.590098	28	28
33.0	4.590484	29	29
34.0	4.590786	20	20
35.0	4.591022	17	17
36.0	4.591207	15	15
37.0	4.591352	16	16
38.0	4.591465	9	9
39.0	4.591553	14	14
40.0	4.591622	10	10
41.0	4.591676	8	8
42.0	4.591719	13	13
43.0	4.591752	14	14
44.0	4.591778	5	5
45.0	4.591798	11	11
46.0	4.591814	6	6
47.0	4.591826	7	7
48.0	4.591836	7	7
49.0	4.591844	6	6
50.0	4.591849	5	5
51.0	4.591854	4	4
52.0	4.591858	6	6
53.0	4.591861	9	9
54.0	4.591863	4	4
55.0	4.591865	4	4
56.0	4.591866	6	6
57.0	4.591867	5	5
58.0	4.591868	0	0
59.0	4.591868	3	3
60.0	4.591869	3	3
61.0	4.591869	5	5
62.0	4.59187	2	2
63.0	4.59187	2	2
64.0	4.59187	2	2
65.0	4.59187	3	3
66.0	4.59187	1	1
67.0	4.59187	3	3
68.0	4.591871	2	2
69.0	4.591871	4	4
70.0	4.591871	1	1
71.0	4.591871	5	5
72.0	4.591871	1	1
73.0	4.591871	1	1
74.0	4.591871	1	1
75.0	4.591871	1	1
76.0	4.591871	2	2
77.0	4.591871	3	3
78.0	4.591871	1	1
79.0	4.591871	1	1
80.0	4.591871	1	1
81.0	4.591871	2	2
82.0	4.591871	3	3
83.0	4.591871	2	2
84.0	4.591871	1	1
85.0	4.591871	3	3
86.0	4.591871	0	0
87.0	4.591871	2	2
88.0	4.591871	0	0
89.0	4.591871	1	1
90.0	4.591871	1	1
91.0	4.591871	1	1
92.0	4.591871	1	1
93.0	4.591871	3	3
94.0	4.591871	3	3
95.0	4.591871	0	0
96.0	4.591871	0	0
97.0	4.591871	0	0
98.0	4.591871	0	0
99.0	4.591871	0	0
100.0	4.591871	0	0
101.0	0	1	1
109.0	0	1	1
110.0	0	3	3
113.0	0	2	2
116.0	0	1	1
120.0	0	1	1
125.0	0	1	1
129.0	0	1	1
138.0	0	1	1
142.0	0	1	1
148.0	0	1	1
155.0	0	1	1
180.0	0	1	1
282.0	0	1	1
286.0	0	1	1
357.0	0	1	1