## 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-GSM1606217.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606217.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606217.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 00:52:04 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	34449738	5678346	0	0	4519954	0	0.131204	119529172

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	27555774	27555774
2.0	1.749603	1650195	1650195
3.0	2.311507	360453	360453
4.0	2.732712	142612	142612
5.0	3.048448	71730	71730
6.0	3.285125	41786	41786
7.0	3.462538	26361	26361
8.0	3.595528	17757	17757
9.0	3.695217	12548	12548
10.0	3.769945	9215	9215
11.0	3.825961	7057	7057
12.0	3.867951	5312	5312
13.0	3.899426	4307	4307
14.0	3.92302	3368	3368
15.0	3.940707	2746	2746
16.0	3.953964	2278	2278
17.0	3.963902	1888	1888
18.0	3.971352	1688	1688
19.0	3.976936	1377	1377
20.0	3.981122	1177	1177
21.0	3.98426	952	952
22.0	3.986612	854	854
23.0	3.988375	771	771
24.0	3.989696	654	654
25.0	3.990687	629	629
26.0	3.99143	515	515
27.0	3.991986	424	424
28.0	3.992404	441	441
29.0	3.992717	378	378
30.0	3.992951	317	317
31.0	3.993127	293	293
32.0	3.993259	269	269
33.0	3.993357	257	257
34.0	3.993431	253	253
35.0	3.993487	204	204
36.0	3.993528	197	197
37.0	3.99356	174	174
38.0	3.993583	157	157
39.0	3.993601	116	116
40.0	3.993614	143	143
41.0	3.993624	126	126
42.0	3.993631	123	123
43.0	3.993636	110	110
44.0	3.993641	96	96
45.0	3.993644	75	75
46.0	3.993646	87	87
47.0	3.993648	73	73
48.0	3.993649	81	81
49.0	3.99365	65	65
50.0	3.993651	66	66
51.0	3.993651	64	64
52.0	3.993652	56	56
53.0	3.993652	50	50
54.0	3.993652	42	42
55.0	3.993652	63	63
56.0	3.993653	53	53
57.0	3.993653	42	42
58.0	3.993653	36	36
59.0	3.993653	49	49
60.0	3.993653	26	26
61.0	3.993653	29	29
62.0	3.993653	32	32
63.0	3.993653	38	38
64.0	3.993653	24	24
65.0	3.993653	29	29
66.0	3.993653	22	22
67.0	3.993653	20	20
68.0	3.993653	20	20
69.0	3.993653	25	25
70.0	3.993653	15	15
71.0	3.993653	19	19
72.0	3.993653	18	18
73.0	3.993653	17	17
74.0	3.993653	20	20
75.0	3.993653	15	15
76.0	3.993653	15	15
77.0	3.993653	16	16
78.0	3.993653	11	11
79.0	3.993653	16	16
80.0	3.993653	14	14
81.0	3.993653	13	13
82.0	3.993653	21	21
83.0	3.993653	8	8
84.0	3.993653	10	10
85.0	3.993653	14	14
86.0	3.993653	10	10
87.0	3.993653	8	8
88.0	3.993653	9	9
89.0	3.993653	10	10
90.0	3.993653	3	3
91.0	3.993653	3	3
92.0	3.993653	10	10
93.0	3.993653	3	3
94.0	3.993653	5	5
95.0	3.993653	9	9
96.0	3.993653	8	8
97.0	3.993653	10	10
98.0	3.993653	7	7
99.0	3.993653	3	3
100.0	3.993653	6	6
101.0	0	5	5
102.0	0	3	3
103.0	0	8	8
104.0	0	4	4
105.0	0	7	7
106.0	0	3	3
107.0	0	1	1
108.0	0	4	4
109.0	0	2	2
110.0	0	6	6
111.0	0	1	1
112.0	0	4	4
113.0	0	2	2
114.0	0	2	2
115.0	0	3	3
116.0	0	1	1
117.0	0	4	4
118.0	0	4	4
119.0	0	3	3
120.0	0	3	3
121.0	0	3	3
122.0	0	3	3
123.0	0	7	7
124.0	0	1	1
125.0	0	2	2
126.0	0	1	1
127.0	0	2	2
129.0	0	3	3
131.0	0	1	1
132.0	0	1	1
133.0	0	2	2
134.0	0	2	2
135.0	0	2	2
136.0	0	2	2
137.0	0	1	1
138.0	0	1	1
139.0	0	1	1
140.0	0	1	1
141.0	0	4	4
143.0	0	2	2
144.0	0	3	3
146.0	0	2	2
147.0	0	2	2
148.0	0	1	1
149.0	0	1	1
150.0	0	1	1
152.0	0	1	1
153.0	0	1	1
154.0	0	1	1
155.0	0	3	3
160.0	0	1	1
161.0	0	1	1
164.0	0	1	1
165.0	0	1	1
166.0	0	1	1
167.0	0	1	1
168.0	0	1	1
169.0	0	2	2
171.0	0	2	2
172.0	0	1	1
173.0	0	1	1
174.0	0	1	1
176.0	0	2	2
177.0	0	1	1
181.0	0	1	1
182.0	0	1	1
184.0	0	2	2
185.0	0	1	1
189.0	0	2	2
190.0	0	1	1
191.0	0	1	1
192.0	0	2	2
199.0	0	1	1
200.0	0	1	1
201.0	0	1	1
202.0	0	1	1
210.0	0	2	2
212.0	0	1	1
214.0	0	1	1
216.0	0	1	1
219.0	0	1	1
222.0	0	1	1
223.0	0	1	1
231.0	0	1	1
236.0	0	1	1
246.0	0	1	1
252.0	0	1	1
254.0	0	1	1
256.0	0	1	1
261.0	0	1	1
266.0	0	1	1
275.0	0	1	1
279.0	0	1	1
288.0	0	1	1
300.0	0	1	1
301.0	0	1	1
321.0	0	1	1
392.0	0	1	1
427.0	0	1	1
428.0	0	1	1
436.0	0	1	1
964.0	0	1	1
996.0	0	1	1
8143.0	0	1	1