## 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-GSM1606357.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606357.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606357.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 14:41:13 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	23819124	3357348	0	0	3490176	0	0.146528	73127811

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	18534474	18534474
2.0	1.722008	1238243	1238243
3.0	2.243303	272068	272068
4.0	2.619683	108798	108798
5.0	2.891432	55630	55630
6.0	3.087637	32611	32611
7.0	3.229299	21103	21103
8.0	3.331579	14111	14111
9.0	3.405427	10345	10345
10.0	3.458745	7426	7426
11.0	3.497242	5737	5737
12.0	3.525036	4359	4359
13.0	3.545104	3555	3555
14.0	3.559594	2902	2902
15.0	3.570055	2224	2224
16.0	3.577608	1825	1825
17.0	3.583062	1600	1600
18.0	3.586999	1343	1343
19.0	3.589842	1104	1104
20.0	3.591895	985	985
21.0	3.593377	853	853
22.0	3.594447	713	713
23.0	3.595219	672	672
24.0	3.595777	514	514
25.0	3.59618	484	484
26.0	3.59647	460	460
27.0	3.59668	389	389
28.0	3.596832	364	364
29.0	3.596941	335	335
30.0	3.59702	287	287
31.0	3.597077	255	255
32.0	3.597119	205	205
33.0	3.597148	222	222
34.0	3.59717	184	184
35.0	3.597185	170	170
36.0	3.597196	182	182
37.0	3.597205	164	164
38.0	3.59721	130	130
39.0	3.597215	88	88
40.0	3.597218	113	113
41.0	3.59722	103	103
42.0	3.597221	94	94
43.0	3.597223	87	87
44.0	3.597223	85	85
45.0	3.597224	66	66
46.0	3.597224	69	69
47.0	3.597225	53	53
48.0	3.597225	67	67
49.0	3.597225	53	53
50.0	3.597225	49	49
51.0	3.597225	54	54
52.0	3.597225	42	42
53.0	3.597225	38	38
54.0	3.597225	47	47
55.0	3.597225	51	51
56.0	3.597225	24	24
57.0	3.597226	23	23
58.0	3.597226	25	25
59.0	3.597226	47	47
60.0	3.597226	28	28
61.0	3.597226	25	25
62.0	3.597226	21	21
63.0	3.597226	13	13
64.0	3.597226	16	16
65.0	3.597226	23	23
66.0	3.597226	26	26
67.0	3.597226	19	19
68.0	3.597226	16	16
69.0	3.597226	28	28
70.0	3.597226	16	16
71.0	3.597226	14	14
72.0	3.597226	20	20
73.0	3.597226	12	12
74.0	3.597226	12	12
75.0	3.597226	17	17
76.0	3.597226	14	14
77.0	3.597226	12	12
78.0	3.597226	20	20
79.0	3.597226	4	4
80.0	3.597226	12	12
81.0	3.597226	9	9
82.0	3.597226	9	9
83.0	3.597226	6	6
84.0	3.597226	7	7
85.0	3.597226	9	9
86.0	3.597226	5	5
87.0	3.597226	6	6
88.0	3.597226	7	7
89.0	3.597226	10	10
90.0	3.597226	6	6
91.0	3.597226	8	8
92.0	3.597226	7	7
93.0	3.597226	7	7
94.0	3.597226	0	0
95.0	3.597226	6	6
96.0	3.597226	7	7
97.0	3.597226	5	5
98.0	3.597226	6	6
99.0	3.597226	1	1
100.0	3.597226	5	5
101.0	0	4	4
102.0	0	6	6
103.0	0	1	1
104.0	0	6	6
105.0	0	1	1
106.0	0	4	4
107.0	0	5	5
108.0	0	4	4
109.0	0	2	2
110.0	0	2	2
111.0	0	3	3
113.0	0	2	2
114.0	0	1	1
115.0	0	9	9
116.0	0	2	2
117.0	0	1	1
118.0	0	4	4
119.0	0	3	3
120.0	0	5	5
121.0	0	2	2
122.0	0	7	7
123.0	0	3	3
124.0	0	3	3
125.0	0	3	3
128.0	0	1	1
129.0	0	3	3
130.0	0	2	2
131.0	0	2	2
132.0	0	1	1
133.0	0	1	1
134.0	0	1	1
136.0	0	1	1
137.0	0	2	2
138.0	0	1	1
139.0	0	2	2
141.0	0	2	2
144.0	0	1	1
145.0	0	1	1
146.0	0	3	3
149.0	0	1	1
150.0	0	1	1
151.0	0	2	2
153.0	0	2	2
154.0	0	1	1
156.0	0	1	1
157.0	0	1	1
158.0	0	1	1
159.0	0	3	3
160.0	0	1	1
164.0	0	1	1
166.0	0	1	1
167.0	0	2	2
168.0	0	2	2
172.0	0	1	1
180.0	0	1	1
181.0	0	1	1
182.0	0	2	2
184.0	0	1	1
189.0	0	1	1
193.0	0	1	1
198.0	0	1	1
204.0	0	2	2
216.0	0	1	1
221.0	0	1	1
225.0	0	1	1
231.0	0	1	1
234.0	0	1	1
264.0	0	1	1
267.0	0	1	1
269.0	0	1	1
297.0	0	1	1
319.0	0	1	1
323.0	0	1	1
5133.0	0	1	1