## 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-GSM1606226.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606226.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606226.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 13:19:15 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	32943348	4810528	0	0	5080609	0	0.154223	95515252

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	25392992	25392992
2.0	1.70829	1666676	1666676
3.0	2.209965	381073	381073
4.0	2.565297	156356	156356
5.0	2.816974	81553	81553
6.0	2.995235	48416	48416
7.0	3.121496	31400	31400
8.0	3.210925	21758	21758
9.0	3.274266	15457	15457
10.0	3.319131	11774	11774
11.0	3.350908	8765	8765
12.0	3.373415	6915	6915
13.0	3.389357	5543	5543
14.0	3.400648	4516	4516
15.0	3.408645	3708	3708
16.0	3.41431	2907	2907
17.0	3.418322	2630	2630
18.0	3.421164	2163	2163
19.0	3.423177	1904	1904
20.0	3.424602	1653	1653
21.0	3.425612	1392	1392
22.0	3.426327	1191	1191
23.0	3.426834	1059	1059
24.0	3.427193	966	966
25.0	3.427447	833	833
26.0	3.427627	738	738
27.0	3.427754	655	655
28.0	3.427845	592	592
29.0	3.427909	509	509
30.0	3.427954	466	466
31.0	3.427986	421	421
32.0	3.428009	383	383
33.0	3.428025	348	348
34.0	3.428036	305	305
35.0	3.428044	275	275
36.0	3.42805	269	269
37.0	3.428054	215	215
38.0	3.428057	187	187
39.0	3.428059	235	235
40.0	3.42806	202	202
41.0	3.428062	197	197
42.0	3.428062	170	170
43.0	3.428063	143	143
44.0	3.428063	135	135
45.0	3.428063	135	135
46.0	3.428064	123	123
47.0	3.428064	127	127
48.0	3.428064	110	110
49.0	3.428064	89	89
50.0	3.428064	85	85
51.0	3.428064	81	81
52.0	3.428064	91	91
53.0	3.428064	91	91
54.0	3.428064	78	78
55.0	3.428064	87	87
56.0	3.428064	72	72
57.0	3.428064	56	56
58.0	3.428064	71	71
59.0	3.428064	46	46
60.0	3.428064	67	67
61.0	3.428064	65	65
62.0	3.428064	43	43
63.0	3.428064	50	50
64.0	3.428064	38	38
65.0	3.428064	42	42
66.0	3.428064	44	44
67.0	3.428064	38	38
68.0	3.428064	33	33
69.0	3.428064	39	39
70.0	3.428064	40	40
71.0	3.428064	30	30
72.0	3.428064	31	31
73.0	3.428064	27	27
74.0	3.428064	25	25
75.0	3.428064	27	27
76.0	3.428064	22	22
77.0	3.428064	18	18
78.0	3.428064	17	17
79.0	3.428064	16	16
80.0	3.428064	15	15
81.0	3.428064	25	25
82.0	3.428064	17	17
83.0	3.428064	15	15
84.0	3.428064	28	28
85.0	3.428064	17	17
86.0	3.428064	17	17
87.0	3.428064	19	19
88.0	3.428064	10	10
89.0	3.428064	18	18
90.0	3.428064	18	18
91.0	3.428064	6	6
92.0	3.428064	13	13
93.0	3.428064	11	11
94.0	3.428064	10	10
95.0	3.428064	8	8
96.0	3.428064	9	9
97.0	3.428064	18	18
98.0	3.428064	17	17
99.0	3.428064	9	9
100.0	3.428064	15	15
101.0	0	9	9
102.0	0	15	15
103.0	0	6	6
104.0	0	4	4
105.0	0	6	6
106.0	0	3	3
107.0	0	7	7
108.0	0	4	4
109.0	0	5	5
110.0	0	7	7
111.0	0	4	4
112.0	0	4	4
113.0	0	3	3
114.0	0	6	6
115.0	0	4	4
116.0	0	7	7
117.0	0	5	5
118.0	0	3	3
119.0	0	2	2
120.0	0	5	5
121.0	0	7	7
122.0	0	4	4
123.0	0	4	4
124.0	0	10	10
125.0	0	4	4
126.0	0	7	7
127.0	0	2	2
128.0	0	2	2
129.0	0	4	4
130.0	0	5	5
131.0	0	2	2
132.0	0	7	7
133.0	0	2	2
134.0	0	2	2
135.0	0	3	3
136.0	0	1	1
137.0	0	3	3
138.0	0	2	2
139.0	0	2	2
141.0	0	1	1
142.0	0	1	1
143.0	0	1	1
144.0	0	4	4
145.0	0	2	2
147.0	0	8	8
148.0	0	1	1
149.0	0	4	4
150.0	0	3	3
151.0	0	3	3
152.0	0	1	1
153.0	0	2	2
154.0	0	3	3
156.0	0	4	4
158.0	0	3	3
159.0	0	2	2
160.0	0	1	1
161.0	0	6	6
162.0	0	1	1
163.0	0	2	2
164.0	0	1	1
165.0	0	2	2
166.0	0	2	2
167.0	0	1	1
168.0	0	1	1
169.0	0	2	2
170.0	0	2	2
171.0	0	2	2
172.0	0	1	1
173.0	0	1	1
174.0	0	5	5
178.0	0	2	2
179.0	0	4	4
180.0	0	1	1
182.0	0	1	1
184.0	0	2	2
185.0	0	2	2
186.0	0	1	1
187.0	0	1	1
191.0	0	1	1
194.0	0	1	1
195.0	0	1	1
196.0	0	1	1
198.0	0	1	1
199.0	0	1	1
203.0	0	3	3
204.0	0	1	1
207.0	0	4	4
209.0	0	1	1
211.0	0	1	1
213.0	0	1	1
215.0	0	1	1
218.0	0	1	1
224.0	0	1	1
227.0	0	1	1
229.0	0	1	1
232.0	0	1	1
233.0	0	1	1
234.0	0	1	1
236.0	0	1	1
241.0	0	2	2
242.0	0	1	1
246.0	0	1	1
247.0	0	1	1
251.0	0	1	1
262.0	0	1	1
263.0	0	1	1
266.0	0	1	1
269.0	0	1	1
274.0	0	1	1
284.0	0	1	1
288.0	0	1	1
292.0	0	1	1
293.0	0	1	1
298.0	0	1	1
299.0	0	1	1
303.0	0	1	1
314.0	0	1	1
327.0	0	1	1
334.0	0	1	1
367.0	0	1	1
428.0	0	1	1
433.0	0	1	1
451.0	0	1	1
512.0	0	1	1
584.0	0	1	1
602.0	0	1	1
615.0	0	1	1
2716.0	0	1	1