## 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-GSM1606189.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606189.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606189.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 13:44:10 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	33073758	4558158	0	0	3863263	0	0.116808	130320054

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	26797147	26797147
2.0	1.775856	1808258	1808258
3.0	2.377808	339729	339729
4.0	2.844836	117986	117986
5.0	3.207182	54439	54439
6.0	3.488311	29557	29557
7.0	3.706426	17699	17699
8.0	3.875652	11132	11132
9.0	4.006946	8007	8007
10.0	4.108812	5488	5488
11.0	4.187846	4086	4086
12.0	4.249164	2935	2935
13.0	4.296738	2357	2357
14.0	4.333649	1851	1851
15.0	4.362286	1481	1481
16.0	4.384505	1123	1123
17.0	4.401743	950	950
18.0	4.415118	840	840
19.0	4.425494	665	665
20.0	4.433545	569	569
21.0	4.439791	496	496
22.0	4.444637	398	398
23.0	4.448397	310	310
24.0	4.451314	303	303
25.0	4.453578	239	239
26.0	4.455334	259	259
27.0	4.456696	206	206
28.0	4.457753	179	179
29.0	4.458573	170	170
30.0	4.45921	141	141
31.0	4.459703	112	112
32.0	4.460086	112	112
33.0	4.460383	108	108
34.0	4.460614	104	104
35.0	4.460793	71	71
36.0	4.460932	80	80
37.0	4.461039	51	51
38.0	4.461123	78	78
39.0	4.461188	53	53
40.0	4.461238	45	45
41.0	4.461277	48	48
42.0	4.461307	31	31
43.0	4.461331	42	42
44.0	4.461349	41	41
45.0	4.461363	34	34
46.0	4.461374	27	27
47.0	4.461383	25	25
48.0	4.461389	17	17
49.0	4.461394	26	26
50.0	4.461398	18	18
51.0	4.461401	18	18
52.0	4.461404	17	17
53.0	4.461406	17	17
54.0	4.461407	19	19
55.0	4.461408	14	14
56.0	4.461409	15	15
57.0	4.46141	9	9
58.0	4.46141	12	12
59.0	4.461411	11	11
60.0	4.461411	9	9
61.0	4.461411	8	8
62.0	4.461411	7	7
63.0	4.461412	9	9
64.0	4.461412	12	12
65.0	4.461412	7	7
66.0	4.461412	2	2
67.0	4.461412	9	9
68.0	4.461412	10	10
69.0	4.461412	9	9
70.0	4.461412	10	10
71.0	4.461412	11	11
72.0	4.461412	4	4
73.0	4.461412	5	5
74.0	4.461412	3	3
75.0	4.461412	6	6
76.0	4.461412	6	6
77.0	4.461412	5	5
78.0	4.461412	1	1
79.0	4.461412	4	4
80.0	4.461412	2	2
81.0	4.461412	2	2
82.0	4.461412	2	2
83.0	4.461412	4	4
84.0	4.461412	0	0
85.0	4.461412	3	3
86.0	4.461412	3	3
87.0	4.461412	4	4
88.0	4.461412	2	2
89.0	4.461412	0	0
90.0	4.461412	2	2
91.0	4.461412	3	3
92.0	4.461412	2	2
93.0	4.461412	2	2
94.0	4.461412	4	4
95.0	4.461412	1	1
96.0	4.461412	1	1
97.0	4.461412	2	2
98.0	4.461412	2	2
99.0	4.461412	0	0
100.0	4.461412	0	0
101.0	0	2	2
102.0	0	3	3
105.0	0	1	1
107.0	0	3	3
108.0	0	1	1
109.0	0	2	2
111.0	0	1	1
112.0	0	2	2
113.0	0	2	2
115.0	0	2	2
117.0	0	1	1
118.0	0	1	1
120.0	0	2	2
123.0	0	1	1
126.0	0	1	1
127.0	0	1	1
128.0	0	1	1
131.0	0	1	1
136.0	0	2	2
150.0	0	1	1
158.0	0	1	1
159.0	0	1	1
162.0	0	1	1
164.0	0	1	1
168.0	0	1	1
169.0	0	1	1
176.0	0	2	2
181.0	0	1	1
188.0	0	2	2
189.0	0	1	1
196.0	0	1	1
198.0	0	1	1
200.0	0	1	1
216.0	0	1	1
231.0	0	1	1
248.0	0	1	1
255.0	0	1	1
261.0	0	1	1
269.0	0	1	1
270.0	0	1	1
306.0	0	1	1
310.0	0	1	1
419.0	0	1	1
453.0	0	1	1
463.0	0	1	1
603.0	0	1	1
657.0	0	1	1
745.0	0	1	1
7151.0	0	1	1