## 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-GSM1606228.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606228.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606228.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 21:09:58 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	37496990	5122766	0	0	6128410	0	0.163437	101840803

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	28424375	28424375
2.0	1.691984	1973443	1973443
3.0	2.170826	457374	457374
4.0	2.502177	188505	188505
5.0	2.731467	99458	99458
6.0	2.890132	58603	58603
7.0	2.999926	38700	38700
8.0	3.075901	26409	26409
9.0	3.128475	18983	18983
10.0	3.164855	14210	14210
11.0	3.19003	11001	11001
12.0	3.20745	8555	8555
13.0	3.219505	6871	6871
14.0	3.227846	5608	5608
15.0	3.233618	4481	4481
16.0	3.237613	3850	3850
17.0	3.240377	3190	3190
18.0	3.242289	2680	2680
19.0	3.243613	2294	2294
20.0	3.244529	1838	1838
21.0	3.245163	1638	1638
22.0	3.245601	1542	1542
23.0	3.245905	1351	1351
24.0	3.246115	1211	1211
25.0	3.24626	1057	1057
26.0	3.24636	934	934
27.0	3.24643	755	755
28.0	3.246478	703	703
29.0	3.246511	683	683
30.0	3.246535	606	606
31.0	3.24655	540	540
32.0	3.246562	442	442
33.0	3.246569	433	433
34.0	3.246574	383	383
35.0	3.246578	355	355
36.0	3.246581	342	342
37.0	3.246582	316	316
38.0	3.246584	289	289
39.0	3.246584	261	261
40.0	3.246585	276	276
41.0	3.246585	219	219
42.0	3.246586	206	206
43.0	3.246586	198	198
44.0	3.246586	199	199
45.0	3.246586	165	165
46.0	3.246586	142	142
47.0	3.246586	132	132
48.0	3.246586	154	154
49.0	3.246586	128	128
50.0	3.246586	139	139
51.0	3.246586	116	116
52.0	3.246586	100	100
53.0	3.246586	87	87
54.0	3.246586	88	88
55.0	3.246586	70	70
56.0	3.246586	77	77
57.0	3.246586	69	69
58.0	3.246586	80	80
59.0	3.246586	65	65
60.0	3.246586	60	60
61.0	3.246586	65	65
62.0	3.246586	53	53
63.0	3.246586	60	60
64.0	3.246586	50	50
65.0	3.246586	58	58
66.0	3.246586	48	48
67.0	3.246586	32	32
68.0	3.246586	41	41
69.0	3.246586	41	41
70.0	3.246586	53	53
71.0	3.246586	33	33
72.0	3.246586	35	35
73.0	3.246586	33	33
74.0	3.246586	34	34
75.0	3.246586	33	33
76.0	3.246586	35	35
77.0	3.246586	30	30
78.0	3.246586	27	27
79.0	3.246586	29	29
80.0	3.246586	28	28
81.0	3.246586	27	27
82.0	3.246586	28	28
83.0	3.246586	18	18
84.0	3.246586	15	15
85.0	3.246586	27	27
86.0	3.246586	28	28
87.0	3.246586	14	14
88.0	3.246586	14	14
89.0	3.246586	11	11
90.0	3.246586	11	11
91.0	3.246586	16	16
92.0	3.246586	17	17
93.0	3.246586	17	17
94.0	3.246586	18	18
95.0	3.246586	12	12
96.0	3.246586	9	9
97.0	3.246586	13	13
98.0	3.246586	12	12
99.0	3.246586	12	12
100.0	3.246586	10	10
101.0	0	15	15
102.0	0	7	7
103.0	0	11	11
104.0	0	4	4
105.0	0	8	8
106.0	0	8	8
107.0	0	5	5
108.0	0	5	5
109.0	0	7	7
110.0	0	4	4
111.0	0	8	8
112.0	0	8	8
113.0	0	8	8
114.0	0	10	10
115.0	0	6	6
116.0	0	14	14
117.0	0	10	10
118.0	0	7	7
119.0	0	6	6
120.0	0	6	6
121.0	0	6	6
122.0	0	8	8
123.0	0	4	4
124.0	0	4	4
125.0	0	2	2
126.0	0	2	2
127.0	0	5	5
128.0	0	3	3
129.0	0	5	5
130.0	0	3	3
131.0	0	7	7
132.0	0	2	2
133.0	0	7	7
134.0	0	2	2
135.0	0	1	1
136.0	0	6	6
137.0	0	3	3
138.0	0	6	6
139.0	0	2	2
140.0	0	3	3
141.0	0	6	6
142.0	0	3	3
143.0	0	1	1
144.0	0	3	3
145.0	0	3	3
146.0	0	5	5
147.0	0	3	3
148.0	0	2	2
149.0	0	1	1
150.0	0	1	1
151.0	0	2	2
152.0	0	4	4
153.0	0	2	2
154.0	0	3	3
156.0	0	3	3
157.0	0	1	1
158.0	0	4	4
160.0	0	2	2
161.0	0	2	2
162.0	0	2	2
163.0	0	1	1
164.0	0	1	1
165.0	0	1	1
166.0	0	4	4
167.0	0	2	2
169.0	0	3	3
170.0	0	3	3
171.0	0	3	3
173.0	0	1	1
175.0	0	4	4
176.0	0	3	3
177.0	0	2	2
178.0	0	3	3
179.0	0	1	1
180.0	0	1	1
181.0	0	2	2
182.0	0	1	1
184.0	0	1	1
186.0	0	1	1
188.0	0	1	1
190.0	0	2	2
191.0	0	2	2
194.0	0	2	2
199.0	0	2	2
200.0	0	1	1
207.0	0	1	1
208.0	0	1	1
210.0	0	2	2
211.0	0	1	1
213.0	0	3	3
217.0	0	1	1
219.0	0	1	1
220.0	0	1	1
223.0	0	1	1
224.0	0	1	1
226.0	0	1	1
227.0	0	1	1
233.0	0	1	1
234.0	0	1	1
236.0	0	2	2
237.0	0	2	2
238.0	0	1	1
239.0	0	1	1
241.0	0	1	1
247.0	0	1	1
252.0	0	1	1
254.0	0	1	1
255.0	0	3	3
256.0	0	1	1
260.0	0	1	1
261.0	0	1	1
264.0	0	1	1
270.0	0	1	1
276.0	0	1	1
277.0	0	1	1
301.0	0	1	1
316.0	0	1	1
319.0	0	1	1
325.0	0	1	1
328.0	0	1	1
338.0	0	1	1
370.0	0	1	1
376.0	0	1	1
377.0	0	1	1
384.0	0	1	1
390.0	0	1	1
408.0	0	1	1
414.0	0	1	1
416.0	0	1	1
417.0	0	1	1
418.0	0	1	1
656.0	0	1	1
2654.0	0	1	1