## 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-GSM919923.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919923.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919923.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 15:56:19 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	7974760	1306342	0	0	765610	0	0.096004	38830300

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	6697848	6697848
2.0	1.814342	404032	404032
3.0	2.477495	62143	62143
4.0	3.017529	20229	20229
5.0	3.457301	9203	9203
6.0	3.815426	4932	4932
7.0	4.107062	2962	2962
8.0	4.344554	1863	1863
9.0	4.537953	1274	1274
10.0	4.695447	928	928
11.0	4.8237	671	671
12.0	4.928142	506	506
13.0	5.013194	403	403
14.0	5.082455	320	320
15.0	5.138857	266	266
16.0	5.184788	177	177
17.0	5.222192	197	197
18.0	5.252651	126	126
19.0	5.277455	128	128
20.0	5.297654	131	131
21.0	5.314103	78	78
22.0	5.327498	73	73
23.0	5.338406	57	57
24.0	5.347289	55	55
25.0	5.354523	51	51
26.0	5.360414	44	44
27.0	5.365211	44	44
28.0	5.369117	32	32
29.0	5.372299	24	24
30.0	5.374889	25	25
31.0	5.376999	27	27
32.0	5.378717	23	23
33.0	5.380116	19	19
34.0	5.381255	21	21
35.0	5.382183	8	8
36.0	5.382938	10	10
37.0	5.383554	13	13
38.0	5.384055	8	8
39.0	5.384463	9	9
40.0	5.384795	6	6
41.0	5.385065	13	13
42.0	5.385286	12	12
43.0	5.385465	9	9
44.0	5.385611	2	2
45.0	5.38573	8	8
46.0	5.385827	7	7
47.0	5.385906	7	7
48.0	5.38597	5	5
49.0	5.386023	4	4
50.0	5.386065	6	6
51.0	5.3861	7	7
52.0	5.386128	7	7
53.0	5.386151	3	3
54.0	5.38617	3	3
55.0	5.386185	5	5
56.0	5.386198	3	3
57.0	5.386208	6	6
58.0	5.386216	3	3
59.0	5.386223	3	3
60.0	5.386228	5	5
61.0	5.386233	6	6
62.0	5.386236	1	1
63.0	5.386239	0	0
64.0	5.386242	4	4
65.0	5.386244	0	0
66.0	5.386245	2	2
67.0	5.386247	1	1
68.0	5.386248	2	2
69.0	5.386248	5	5
70.0	5.386249	0	0
71.0	5.38625	0	0
72.0	5.38625	0	0
73.0	5.386251	2	2
74.0	5.386251	4	4
75.0	5.386251	2	2
76.0	5.386251	1	1
77.0	5.386251	0	0
78.0	5.386252	0	0
79.0	5.386252	1	1
80.0	5.386252	0	0
81.0	5.386252	0	0
82.0	5.386252	0	0
83.0	5.386252	1	1
84.0	5.386252	1	1
85.0	5.386252	2	2
86.0	5.386252	0	0
87.0	5.386252	0	0
88.0	5.386252	0	0
89.0	5.386252	2	2
90.0	5.386252	3	3
91.0	5.386252	0	0
92.0	5.386252	1	1
93.0	5.386252	0	0
94.0	5.386252	0	0
95.0	5.386252	1	1
96.0	5.386252	0	0
97.0	5.386252	0	0
98.0	5.386252	1	1
99.0	5.386252	0	0
100.0	5.386252	0	0
101.0	0	1	1
104.0	0	2	2
105.0	0	2	2
106.0	0	2	2
108.0	0	2	2
111.0	0	1	1
113.0	0	1	1
115.0	0	2	2
122.0	0	1	1
125.0	0	1	1
132.0	0	3	3
137.0	0	1	1
196.0	0	1	1
230.0	0	1	1
254.0	0	1	1
316.0	0	1	1