## 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-GSM1606352.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606352.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606352.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 20:20:22 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	18910951	2713418	0	0	2453432	0	0.129736	66432122

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	15158133	15158133
2.0	1.752266	908308	908308
3.0	2.318169	194932	194932
4.0	2.743879	77077	77077
5.0	3.064126	38795	38795
6.0	3.305037	22065	22065
7.0	3.486266	14252	14252
8.0	3.622598	9692	9692
9.0	3.725156	6872	6872
10.0	3.802307	4945	4945
11.0	3.860345	3797	3797
12.0	3.904005	2991	2991
13.0	3.936849	2343	2343
14.0	3.961556	1912	1912
15.0	3.980142	1505	1505
16.0	3.994124	1240	1240
17.0	4.004643	1068	1068
18.0	4.012555	855	855
19.0	4.018507	754	754
20.0	4.022985	565	565
21.0	4.026353	550	550
22.0	4.028887	472	472
23.0	4.030794	423	423
24.0	4.032227	340	340
25.0	4.033306	319	319
26.0	4.034118	283	283
27.0	4.034728	247	247
28.0	4.035187	223	223
29.0	4.035533	216	216
30.0	4.035793	200	200
31.0	4.035988	155	155
32.0	4.036135	129	129
33.0	4.036246	131	131
34.0	4.036329	118	118
35.0	4.036392	108	108
36.0	4.036439	97	97
37.0	4.036474	85	85
38.0	4.036501	74	74
39.0	4.036521	70	70
40.0	4.036536	73	73
41.0	4.036547	58	58
42.0	4.036556	67	67
43.0	4.036562	70	70
44.0	4.036567	47	47
45.0	4.036571	55	55
46.0	4.036574	48	48
47.0	4.036576	41	41
48.0	4.036577	31	31
49.0	4.036578	38	38
50.0	4.036579	32	32
51.0	4.03658	30	30
52.0	4.03658	30	30
53.0	4.036581	32	32
54.0	4.036581	24	24
55.0	4.036581	22	22
56.0	4.036581	30	30
57.0	4.036581	16	16
58.0	4.036582	19	19
59.0	4.036582	15	15
60.0	4.036582	12	12
61.0	4.036582	18	18
62.0	4.036582	13	13
63.0	4.036582	19	19
64.0	4.036582	14	14
65.0	4.036582	7	7
66.0	4.036582	11	11
67.0	4.036582	12	12
68.0	4.036582	12	12
69.0	4.036582	11	11
70.0	4.036582	16	16
71.0	4.036582	6	6
72.0	4.036582	6	6
73.0	4.036582	12	12
74.0	4.036582	8	8
75.0	4.036582	8	8
76.0	4.036582	4	4
77.0	4.036582	5	5
78.0	4.036582	3	3
79.0	4.036582	7	7
80.0	4.036582	5	5
81.0	4.036582	7	7
82.0	4.036582	5	5
83.0	4.036582	14	14
84.0	4.036582	2	2
85.0	4.036582	7	7
86.0	4.036582	3	3
87.0	4.036582	10	10
88.0	4.036582	10	10
89.0	4.036582	3	3
90.0	4.036582	5	5
91.0	4.036582	6	6
92.0	4.036582	3	3
93.0	4.036582	6	6
94.0	4.036582	4	4
95.0	4.036582	2	2
96.0	4.036582	2	2
97.0	4.036582	6	6
98.0	4.036582	4	4
99.0	4.036582	2	2
100.0	4.036582	2	2
101.0	0	1	1
102.0	0	1	1
104.0	0	1	1
105.0	0	1	1
106.0	0	2	2
107.0	0	1	1
108.0	0	3	3
109.0	0	2	2
111.0	0	2	2
113.0	0	2	2
114.0	0	3	3
115.0	0	3	3
116.0	0	4	4
117.0	0	3	3
118.0	0	1	1
119.0	0	1	1
120.0	0	1	1
122.0	0	1	1
123.0	0	3	3
124.0	0	3	3
125.0	0	1	1
127.0	0	2	2
128.0	0	1	1
130.0	0	3	3
131.0	0	3	3
132.0	0	2	2
135.0	0	1	1
136.0	0	1	1
142.0	0	2	2
143.0	0	1	1
145.0	0	1	1
146.0	0	2	2
148.0	0	1	1
149.0	0	1	1
150.0	0	1	1
152.0	0	1	1
153.0	0	2	2
155.0	0	1	1
157.0	0	1	1
158.0	0	1	1
169.0	0	1	1
170.0	0	1	1
176.0	0	1	1
180.0	0	1	1
181.0	0	1	1
185.0	0	1	1
190.0	0	1	1
191.0	0	1	1
197.0	0	1	1
198.0	0	1	1
202.0	0	1	1
214.0	0	1	1
217.0	0	1	1
224.0	0	1	1
236.0	0	1	1
252.0	0	1	1
284.0	0	1	1
309.0	0	1	1
333.0	0	1	1
5530.0	0	1	1