## 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-GSM1606190.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606190.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606190.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 14:13:53 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	30511522	4235494	0	0	3655563	0	0.119809	116946025

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	24606181	24606181
2.0	1.770356	1673007	1673007
3.0	2.363804	319181	319181
4.0	2.820971	113100	113100
5.0	3.173152	52720	52720
6.0	3.444456	28335	28335
7.0	3.653457	17459	17459
8.0	3.814463	11350	11350
9.0	3.938494	7910	7910
10.0	4.034042	5495	5495
11.0	4.107648	4009	4009
12.0	4.164351	3137	3137
13.0	4.208033	2290	2290
14.0	4.241683	1880	1880
15.0	4.267606	1488	1488
16.0	4.287576	1122	1122
17.0	4.302959	951	951
18.0	4.31481	833	833
19.0	4.32394	635	635
20.0	4.330973	578	578
21.0	4.336391	498	498
22.0	4.340564	412	412
23.0	4.34378	358	358
24.0	4.346256	298	298
25.0	4.348164	316	316
26.0	4.349634	240	240
27.0	4.350767	206	206
28.0	4.351639	193	193
29.0	4.352311	153	153
30.0	4.352829	138	138
31.0	4.353227	114	114
32.0	4.353535	108	108
33.0	4.353771	112	112
34.0	4.353954	96	96
35.0	4.354094	77	77
36.0	4.354202	82	82
37.0	4.354286	71	71
38.0	4.35435	58	58
39.0	4.354399	53	53
40.0	4.354437	53	53
41.0	4.354467	43	43
42.0	4.354489	35	35
43.0	4.354507	42	42
44.0	4.35452	33	33
45.0	4.354531	30	30
46.0	4.354539	35	35
47.0	4.354545	22	22
48.0	4.354549	30	30
49.0	4.354553	25	25
50.0	4.354556	15	15
51.0	4.354558	27	27
52.0	4.35456	22	22
53.0	4.354561	14	14
54.0	4.354562	11	11
55.0	4.354563	13	13
56.0	4.354563	9	9
57.0	4.354564	7	7
58.0	4.354564	11	11
59.0	4.354564	13	13
60.0	4.354565	11	11
61.0	4.354565	11	11
62.0	4.354565	16	16
63.0	4.354565	8	8
64.0	4.354565	10	10
65.0	4.354565	11	11
66.0	4.354565	5	5
67.0	4.354565	7	7
68.0	4.354565	4	4
69.0	4.354565	10	10
70.0	4.354565	6	6
71.0	4.354565	6	6
72.0	4.354565	5	5
73.0	4.354565	6	6
74.0	4.354565	4	4
75.0	4.354565	3	3
76.0	4.354565	3	3
77.0	4.354565	3	3
78.0	4.354565	2	2
79.0	4.354565	2	2
80.0	4.354565	4	4
81.0	4.354565	1	1
82.0	4.354565	4	4
83.0	4.354565	2	2
84.0	4.354565	0	0
85.0	4.354565	1	1
86.0	4.354565	2	2
87.0	4.354565	1	1
88.0	4.354565	2	2
89.0	4.354565	3	3
90.0	4.354565	2	2
91.0	4.354565	6	6
92.0	4.354565	4	4
93.0	4.354565	0	0
94.0	4.354565	2	2
95.0	4.354565	0	0
96.0	4.354565	0	0
97.0	4.354565	0	0
98.0	4.354565	1	1
99.0	4.354565	2	2
100.0	4.354565	1	1
101.0	0	2	2
106.0	0	1	1
107.0	0	2	2
108.0	0	2	2
111.0	0	1	1
112.0	0	2	2
114.0	0	1	1
115.0	0	3	3
116.0	0	1	1
119.0	0	1	1
120.0	0	1	1
121.0	0	3	3
124.0	0	1	1
126.0	0	1	1
127.0	0	1	1
128.0	0	1	1
134.0	0	1	1
138.0	0	2	2
139.0	0	1	1
144.0	0	2	2
147.0	0	1	1
149.0	0	2	2
155.0	0	1	1
157.0	0	1	1
164.0	0	1	1
172.0	0	1	1
173.0	0	1	1
177.0	0	1	1
178.0	0	1	1
179.0	0	1	1
184.0	0	1	1
185.0	0	1	1
208.0	0	1	1
218.0	0	1	1
232.0	0	1	1
265.0	0	1	1
266.0	0	1	1
279.0	0	1	1
365.0	0	1	1
410.0	0	1	1
414.0	0	1	1
482.0	0	1	1
4603.0	0	1	1