## 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-GSM1606223.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606223.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606223.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 14:50:58 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	27190770	3696206	0	0	3861092	0	0.142	86446022

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	21230425	21230425
2.0	1.730124	1488164	1488164
3.0	2.263206	306035	306035
4.0	2.652422	119383	119383
5.0	2.936598	60196	60196
6.0	3.144081	35284	35284
7.0	3.29557	22675	22675
8.0	3.406176	15084	15084
9.0	3.486932	10734	10734
10.0	3.545894	7792	7792
11.0	3.588943	5920	5920
12.0	3.620375	4662	4662
13.0	3.643324	3568	3568
14.0	3.660079	2838	2838
15.0	3.672313	2421	2421
16.0	3.681245	1891	1891
17.0	3.687767	1625	1625
18.0	3.692528	1293	1293
19.0	3.696005	1099	1099
20.0	3.698543	976	976
21.0	3.700396	781	781
22.0	3.701749	650	650
23.0	3.702737	573	573
24.0	3.703459	532	532
25.0	3.703985	488	488
26.0	3.70437	430	430
27.0	3.70465	319	319
28.0	3.704855	321	321
29.0	3.705005	280	280
30.0	3.705114	240	240
31.0	3.705194	230	230
32.0	3.705252	194	194
33.0	3.705295	216	216
34.0	3.705326	182	182
35.0	3.705349	157	157
36.0	3.705365	127	127
37.0	3.705377	121	121
38.0	3.705386	122	122
39.0	3.705393	108	108
40.0	3.705397	114	114
41.0	3.705401	77	77
42.0	3.705403	93	93
43.0	3.705405	71	71
44.0	3.705406	72	72
45.0	3.705407	58	58
46.0	3.705408	56	56
47.0	3.705409	64	64
48.0	3.705409	53	53
49.0	3.705409	52	52
50.0	3.705409	38	38
51.0	3.70541	43	43
52.0	3.70541	41	41
53.0	3.70541	28	28
54.0	3.70541	36	36
55.0	3.70541	37	37
56.0	3.70541	34	34
57.0	3.70541	31	31
58.0	3.70541	20	20
59.0	3.70541	19	19
60.0	3.70541	18	18
61.0	3.70541	27	27
62.0	3.70541	23	23
63.0	3.70541	13	13
64.0	3.70541	17	17
65.0	3.70541	22	22
66.0	3.70541	16	16
67.0	3.70541	19	19
68.0	3.70541	9	9
69.0	3.70541	14	14
70.0	3.70541	17	17
71.0	3.70541	13	13
72.0	3.70541	15	15
73.0	3.70541	12	12
74.0	3.70541	13	13
75.0	3.70541	8	8
76.0	3.70541	9	9
77.0	3.70541	10	10
78.0	3.70541	10	10
79.0	3.70541	6	6
80.0	3.70541	9	9
81.0	3.70541	6	6
82.0	3.70541	7	7
83.0	3.70541	5	5
84.0	3.70541	11	11
85.0	3.70541	4	4
86.0	3.70541	6	6
87.0	3.70541	7	7
88.0	3.70541	4	4
89.0	3.70541	6	6
90.0	3.70541	10	10
91.0	3.70541	4	4
92.0	3.70541	7	7
93.0	3.70541	1	1
94.0	3.70541	2	2
95.0	3.70541	4	4
96.0	3.70541	6	6
97.0	3.70541	3	3
98.0	3.70541	2	2
99.0	3.70541	6	6
100.0	3.70541	5	5
101.0	0	2	2
102.0	0	2	2
103.0	0	1	1
104.0	0	2	2
105.0	0	4	4
107.0	0	3	3
108.0	0	1	1
109.0	0	6	6
110.0	0	3	3
111.0	0	1	1
112.0	0	5	5
113.0	0	1	1
115.0	0	6	6
116.0	0	4	4
117.0	0	1	1
118.0	0	2	2
119.0	0	1	1
120.0	0	3	3
121.0	0	2	2
122.0	0	2	2
123.0	0	2	2
125.0	0	1	1
126.0	0	2	2
127.0	0	2	2
129.0	0	2	2
130.0	0	1	1
131.0	0	1	1
132.0	0	2	2
133.0	0	3	3
135.0	0	1	1
136.0	0	1	1
137.0	0	1	1
138.0	0	1	1
141.0	0	1	1
144.0	0	2	2
148.0	0	2	2
150.0	0	1	1
156.0	0	1	1
158.0	0	1	1
161.0	0	1	1
169.0	0	1	1
174.0	0	2	2
177.0	0	2	2
182.0	0	1	1
185.0	0	1	1
187.0	0	1	1
200.0	0	1	1
205.0	0	1	1
209.0	0	2	2
216.0	0	1	1
221.0	0	1	1
240.0	0	1	1
244.0	0	1	1
288.0	0	1	1
1807.0	0	1	1