## 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-GSM1606199.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606199.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606199.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 15:09:04 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	23917462	4139822	0	0	3493817	0	0.146078	73681971

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	18613076	18613076
2.0	1.722814	1252276	1252276
3.0	2.245273	277562	277562
4.0	2.622914	108524	108524
5.0	2.895878	55489	55489
6.0	3.093179	31886	31886
7.0	3.235792	20451	20451
8.0	3.338874	13831	13831
9.0	3.413383	9914	9914
10.0	3.46724	7387	7387
11.0	3.506168	5640	5640
12.0	3.534306	4245	4245
13.0	3.554644	3306	3306
14.0	3.569345	2753	2753
15.0	3.579971	2145	2145
16.0	3.587651	1814	1814
17.0	3.593203	1553	1553
18.0	3.597216	1283	1283
19.0	3.600116	1074	1074
20.0	3.602213	957	957
21.0	3.603728	816	816
22.0	3.604823	735	735
23.0	3.605615	646	646
24.0	3.606187	547	547
25.0	3.606601	445	445
26.0	3.6069	411	411
27.0	3.607116	391	391
28.0	3.607272	335	335
29.0	3.607385	329	329
30.0	3.607467	278	278
31.0	3.607526	266	266
32.0	3.607569	219	219
33.0	3.607599	190	190
34.0	3.607622	180	180
35.0	3.607638	188	188
36.0	3.607649	143	143
37.0	3.607658	131	131
38.0	3.607664	136	136
39.0	3.607668	116	116
40.0	3.607671	127	127
41.0	3.607674	120	120
42.0	3.607675	91	91
43.0	3.607677	90	90
44.0	3.607678	81	81
45.0	3.607678	71	71
46.0	3.607679	71	71
47.0	3.607679	82	82
48.0	3.607679	67	67
49.0	3.607679	66	66
50.0	3.607679	48	48
51.0	3.60768	56	56
52.0	3.60768	54	54
53.0	3.60768	46	46
54.0	3.60768	45	45
55.0	3.60768	42	42
56.0	3.60768	33	33
57.0	3.60768	42	42
58.0	3.60768	39	39
59.0	3.60768	36	36
60.0	3.60768	23	23
61.0	3.60768	24	24
62.0	3.60768	25	25
63.0	3.60768	22	22
64.0	3.60768	23	23
65.0	3.60768	23	23
66.0	3.60768	24	24
67.0	3.60768	16	16
68.0	3.60768	14	14
69.0	3.60768	14	14
70.0	3.60768	14	14
71.0	3.60768	15	15
72.0	3.60768	10	10
73.0	3.60768	18	18
74.0	3.60768	13	13
75.0	3.60768	13	13
76.0	3.60768	14	14
77.0	3.60768	12	12
78.0	3.60768	13	13
79.0	3.60768	8	8
80.0	3.60768	7	7
81.0	3.60768	14	14
82.0	3.60768	14	14
83.0	3.60768	9	9
84.0	3.60768	4	4
85.0	3.60768	12	12
86.0	3.60768	14	14
87.0	3.60768	10	10
88.0	3.60768	7	7
89.0	3.60768	6	6
90.0	3.60768	7	7
91.0	3.60768	6	6
92.0	3.60768	3	3
93.0	3.60768	5	5
94.0	3.60768	4	4
95.0	3.60768	5	5
96.0	3.60768	6	6
97.0	3.60768	4	4
98.0	3.60768	2	2
99.0	3.60768	5	5
100.0	3.60768	5	5
101.0	0	5	5
102.0	0	5	5
103.0	0	2	2
104.0	0	2	2
105.0	0	6	6
106.0	0	3	3
107.0	0	5	5
108.0	0	5	5
109.0	0	7	7
110.0	0	3	3
111.0	0	4	4
112.0	0	5	5
113.0	0	2	2
114.0	0	4	4
115.0	0	1	1
117.0	0	1	1
118.0	0	1	1
120.0	0	6	6
121.0	0	2	2
123.0	0	1	1
125.0	0	3	3
126.0	0	2	2
127.0	0	3	3
128.0	0	2	2
129.0	0	3	3
130.0	0	5	5
131.0	0	1	1
133.0	0	4	4
134.0	0	3	3
135.0	0	4	4
136.0	0	1	1
137.0	0	1	1
140.0	0	1	1
142.0	0	2	2
143.0	0	2	2
144.0	0	2	2
145.0	0	3	3
146.0	0	2	2
150.0	0	3	3
151.0	0	1	1
152.0	0	1	1
153.0	0	2	2
155.0	0	3	3
156.0	0	2	2
157.0	0	2	2
158.0	0	1	1
163.0	0	1	1
164.0	0	2	2
165.0	0	2	2
166.0	0	3	3
167.0	0	1	1
168.0	0	1	1
170.0	0	1	1
171.0	0	1	1
172.0	0	2	2
175.0	0	1	1
178.0	0	1	1
179.0	0	2	2
182.0	0	1	1
187.0	0	1	1
196.0	0	1	1
197.0	0	2	2
203.0	0	1	1
204.0	0	1	1
205.0	0	1	1
214.0	0	1	1
223.0	0	2	2
224.0	0	2	2
227.0	0	3	3
232.0	0	1	1
234.0	0	1	1
237.0	0	1	1
244.0	0	1	1
250.0	0	1	1
259.0	0	1	1
264.0	0	1	1
266.0	0	1	1
279.0	0	1	1
291.0	0	1	1
314.0	0	1	1
321.0	0	1	1
335.0	0	1	1
338.0	0	1	1
376.0	0	1	1
415.0	0	1	1
480.0	0	1	1
540.0	0	1	1
632.0	0	1	1
1269.0	0	1	1