## 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-GSM1606194.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606194.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606194.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 15:08:55 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	21467637	3562942	0	0	2670407	0	0.124392	78975135

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	17283304	17283304
2.0	1.761985	1083399	1083399
3.0	2.342607	225024	225024
4.0	2.785033	84578	84578
5.0	3.122154	41856	41856
6.0	3.379036	23330	23330
7.0	3.574777	14499	14499
8.0	3.723928	9520	9520
9.0	3.837579	6730	6730
10.0	3.924179	4887	4887
11.0	3.990168	3592	3592
12.0	4.04045	2781	2781
13.0	4.078764	2155	2155
14.0	4.107959	1707	1707
15.0	4.130205	1337	1337
16.0	4.147156	1069	1069
17.0	4.160073	931	931
18.0	4.169915	850	850
19.0	4.177415	684	684
20.0	4.183129	574	574
21.0	4.187484	479	479
22.0	4.190802	395	395
23.0	4.19333	330	330
24.0	4.195256	306	306
25.0	4.196724	281	281
26.0	4.197843	245	245
27.0	4.198695	201	201
28.0	4.199345	185	185
29.0	4.19984	193	193
30.0	4.200217	160	160
31.0	4.200504	127	127
32.0	4.200723	112	112
33.0	4.20089	93	93
34.0	4.201017	92	92
35.0	4.201114	98	98
36.0	4.201188	86	86
37.0	4.201244	75	75
38.0	4.201287	61	61
39.0	4.20132	74	74
40.0	4.201344	55	55
41.0	4.201363	53	53
42.0	4.201378	49	49
43.0	4.201389	35	35
44.0	4.201397	43	43
45.0	4.201404	37	37
46.0	4.201408	30	30
47.0	4.201412	33	33
48.0	4.201415	19	19
49.0	4.201417	28	28
50.0	4.201419	24	24
51.0	4.20142	28	28
52.0	4.201421	21	21
53.0	4.201422	13	13
54.0	4.201422	22	22
55.0	4.201423	13	13
56.0	4.201423	18	18
57.0	4.201423	16	16
58.0	4.201423	10	10
59.0	4.201424	9	9
60.0	4.201424	12	12
61.0	4.201424	20	20
62.0	4.201424	15	15
63.0	4.201424	12	12
64.0	4.201424	11	11
65.0	4.201424	8	8
66.0	4.201424	5	5
67.0	4.201424	7	7
68.0	4.201424	6	6
69.0	4.201424	4	4
70.0	4.201424	6	6
71.0	4.201424	4	4
72.0	4.201424	6	6
73.0	4.201424	6	6
74.0	4.201424	4	4
75.0	4.201424	5	5
76.0	4.201424	8	8
77.0	4.201424	6	6
78.0	4.201424	7	7
79.0	4.201424	9	9
80.0	4.201424	1	1
81.0	4.201424	3	3
82.0	4.201424	7	7
83.0	4.201424	2	2
84.0	4.201424	5	5
85.0	4.201424	4	4
86.0	4.201424	0	0
87.0	4.201424	5	5
88.0	4.201424	2	2
89.0	4.201424	2	2
90.0	4.201424	3	3
91.0	4.201424	2	2
92.0	4.201424	0	0
93.0	4.201424	2	2
94.0	4.201424	1	1
95.0	4.201424	4	4
96.0	4.201424	2	2
97.0	4.201424	1	1
98.0	4.201424	2	2
99.0	4.201424	0	0
100.0	4.201424	2	2
101.0	0	1	1
102.0	0	3	3
103.0	0	2	2
105.0	0	1	1
107.0	0	1	1
108.0	0	4	4
109.0	0	2	2
111.0	0	2	2
112.0	0	3	3
113.0	0	1	1
114.0	0	1	1
117.0	0	1	1
121.0	0	1	1
123.0	0	2	2
124.0	0	1	1
125.0	0	2	2
135.0	0	1	1
136.0	0	1	1
138.0	0	1	1
139.0	0	1	1
140.0	0	1	1
142.0	0	2	2
149.0	0	2	2
152.0	0	1	1
157.0	0	1	1
159.0	0	1	1
163.0	0	1	1
170.0	0	1	1
171.0	0	1	1
182.0	0	1	1
183.0	0	1	1
194.0	0	1	1
196.0	0	1	1
201.0	0	1	1
202.0	0	1	1
209.0	0	1	1
211.0	0	1	1
223.0	0	1	1
225.0	0	1	1
230.0	0	1	1
243.0	0	1	1
250.0	0	1	1
278.0	0	1	1
287.0	0	1	1
323.0	0	1	1
340.0	0	1	1
360.0	0	1	1
505.0	0	1	1
2367.0	0	1	1