## 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-GSM1606336.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606336.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606336.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 20:51:51 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	27973841	3759162	0	0	4393228	0	0.157048	79470046

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	21196189	21196189
2.0	1.703277	1673757	1673757
3.0	2.197875	363828	363828
4.0	2.545714	139039	139039
5.0	2.790342	68900	68900
6.0	2.962382	39529	39529
7.0	3.083374	24823	24823
8.0	3.168465	16507	16507
9.0	3.228308	11992	11992
10.0	3.270394	8462	8462
11.0	3.299992	6509	6509
12.0	3.320807	4926	4926
13.0	3.335447	3945	3945
14.0	3.345742	3136	3136
15.0	3.352982	2600	2600
16.0	3.358074	2098	2098
17.0	3.361656	1666	1666
18.0	3.364174	1524	1524
19.0	3.365945	1268	1268
20.0	3.367191	1069	1069
21.0	3.368067	892	892
22.0	3.368683	713	713
23.0	3.369116	722	722
24.0	3.369421	612	612
25.0	3.369635	559	559
26.0	3.369786	490	490
27.0	3.369892	405	405
28.0	3.369967	399	399
29.0	3.370019	315	315
30.0	3.370056	297	297
31.0	3.370082	241	241
32.0	3.3701	232	232
33.0	3.370113	222	222
34.0	3.370122	209	209
35.0	3.370128	188	188
36.0	3.370133	165	165
37.0	3.370136	134	134
38.0	3.370138	147	147
39.0	3.37014	120	120
40.0	3.370141	106	106
41.0	3.370142	104	104
42.0	3.370142	87	87
43.0	3.370142	104	104
44.0	3.370143	92	92
45.0	3.370143	84	84
46.0	3.370143	58	58
47.0	3.370143	55	55
48.0	3.370143	57	57
49.0	3.370143	50	50
50.0	3.370143	60	60
51.0	3.370143	45	45
52.0	3.370143	48	48
53.0	3.370143	49	49
54.0	3.370143	47	47
55.0	3.370143	40	40
56.0	3.370143	40	40
57.0	3.370143	33	33
58.0	3.370143	27	27
59.0	3.370143	24	24
60.0	3.370143	23	23
61.0	3.370143	23	23
62.0	3.370143	17	17
63.0	3.370143	28	28
64.0	3.370143	15	15
65.0	3.370143	25	25
66.0	3.370143	22	22
67.0	3.370143	22	22
68.0	3.370143	21	21
69.0	3.370143	19	19
70.0	3.370143	15	15
71.0	3.370143	14	14
72.0	3.370143	10	10
73.0	3.370143	21	21
74.0	3.370143	11	11
75.0	3.370143	13	13
76.0	3.370143	11	11
77.0	3.370143	9	9
78.0	3.370143	11	11
79.0	3.370143	7	7
80.0	3.370143	8	8
81.0	3.370143	5	5
82.0	3.370143	8	8
83.0	3.370143	8	8
84.0	3.370143	7	7
85.0	3.370143	9	9
86.0	3.370143	3	3
87.0	3.370143	3	3
88.0	3.370143	12	12
89.0	3.370143	5	5
90.0	3.370143	6	6
91.0	3.370143	7	7
92.0	3.370143	4	4
93.0	3.370143	6	6
94.0	3.370143	3	3
95.0	3.370143	3	3
96.0	3.370143	2	2
97.0	3.370143	2	2
98.0	3.370143	1	1
99.0	3.370143	6	6
100.0	3.370143	8	8
101.0	0	6	6
102.0	0	2	2
103.0	0	3	3
104.0	0	1	1
105.0	0	1	1
106.0	0	2	2
107.0	0	2	2
108.0	0	4	4
109.0	0	5	5
110.0	0	4	4
112.0	0	1	1
113.0	0	1	1
115.0	0	1	1
116.0	0	2	2
117.0	0	3	3
118.0	0	6	6
119.0	0	2	2
120.0	0	1	1
121.0	0	1	1
122.0	0	2	2
123.0	0	2	2
124.0	0	2	2
125.0	0	2	2
126.0	0	4	4
129.0	0	3	3
130.0	0	1	1
131.0	0	2	2
133.0	0	1	1
134.0	0	1	1
135.0	0	1	1
136.0	0	3	3
137.0	0	1	1
139.0	0	2	2
140.0	0	1	1
142.0	0	1	1
143.0	0	1	1
146.0	0	1	1
147.0	0	1	1
149.0	0	2	2
151.0	0	1	1
152.0	0	5	5
156.0	0	1	1
157.0	0	2	2
160.0	0	1	1
163.0	0	1	1
166.0	0	3	3
167.0	0	1	1
169.0	0	1	1
170.0	0	1	1
179.0	0	1	1
181.0	0	1	1
183.0	0	2	2
187.0	0	2	2
188.0	0	1	1
196.0	0	1	1
198.0	0	1	1
206.0	0	1	1
207.0	0	1	1
213.0	0	1	1
220.0	0	1	1
223.0	0	1	1
236.0	0	1	1
248.0	0	1	1
264.0	0	1	1
273.0	0	1	1
344.0	0	1	1
348.0	0	1	1
360.0	0	1	1
5501.0	0	1	1