## 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-GSM1606201.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606201.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606201.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 20:48:48 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	40649096	7070482	0	0	6847215	0	0.168447	106689810

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	30578479	30578479
2.0	1.683176	2128674	2128674
3.0	2.149906	520480	520480
4.0	2.468764	213822	213822
5.0	2.686601	110636	110636
6.0	2.835421	65666	65666
7.0	2.937092	42395	42395
8.0	3.006551	29027	29027
9.0	3.054004	20737	20737
10.0	3.086423	15444	15444
11.0	3.10857	11980	11980
12.0	3.123701	9404	9404
13.0	3.134038	7532	7532
14.0	3.1411	5984	5984
15.0	3.145924	5027	5027
16.0	3.14922	4122	4122
17.0	3.151472	3532	3532
18.0	3.15301	2907	2907
19.0	3.154061	2510	2510
20.0	3.154779	2200	2200
21.0	3.15527	1895	1895
22.0	3.155605	1635	1635
23.0	3.155834	1459	1459
24.0	3.15599	1344	1344
25.0	3.156097	1172	1172
26.0	3.15617	1017	1017
27.0	3.15622	889	889
28.0	3.156254	806	806
29.0	3.156277	813	813
30.0	3.156293	694	694
31.0	3.156304	613	613
32.0	3.156312	597	597
33.0	3.156317	531	531
34.0	3.15632	468	468
35.0	3.156322	408	408
36.0	3.156324	425	425
37.0	3.156325	384	384
38.0	3.156326	344	344
39.0	3.156326	319	319
40.0	3.156327	315	315
41.0	3.156327	255	255
42.0	3.156327	271	271
43.0	3.156327	242	242
44.0	3.156327	200	200
45.0	3.156327	213	213
46.0	3.156328	171	171
47.0	3.156328	185	185
48.0	3.156328	169	169
49.0	3.156328	157	157
50.0	3.156328	149	149
51.0	3.156328	145	145
52.0	3.156328	133	133
53.0	3.156328	104	104
54.0	3.156328	102	102
55.0	3.156328	96	96
56.0	3.156328	99	99
57.0	3.156328	94	94
58.0	3.156328	105	105
59.0	3.156328	90	90
60.0	3.156328	79	79
61.0	3.156328	86	86
62.0	3.156328	69	69
63.0	3.156328	85	85
64.0	3.156328	73	73
65.0	3.156328	63	63
66.0	3.156328	66	66
67.0	3.156328	58	58
68.0	3.156328	52	52
69.0	3.156328	52	52
70.0	3.156328	54	54
71.0	3.156328	49	49
72.0	3.156328	49	49
73.0	3.156328	50	50
74.0	3.156328	34	34
75.0	3.156328	47	47
76.0	3.156328	36	36
77.0	3.156328	47	47
78.0	3.156328	40	40
79.0	3.156328	33	33
80.0	3.156328	29	29
81.0	3.156328	36	36
82.0	3.156328	26	26
83.0	3.156328	28	28
84.0	3.156328	34	34
85.0	3.156328	30	30
86.0	3.156328	24	24
87.0	3.156328	31	31
88.0	3.156328	23	23
89.0	3.156328	25	25
90.0	3.156328	30	30
91.0	3.156328	29	29
92.0	3.156328	12	12
93.0	3.156328	27	27
94.0	3.156328	15	15
95.0	3.156328	19	19
96.0	3.156328	17	17
97.0	3.156328	13	13
98.0	3.156328	17	17
99.0	3.156328	16	16
100.0	3.156328	17	17
101.0	0	15	15
102.0	0	14	14
103.0	0	15	15
104.0	0	15	15
105.0	0	12	12
106.0	0	11	11
107.0	0	4	4
108.0	0	12	12
109.0	0	16	16
110.0	0	7	7
111.0	0	15	15
112.0	0	14	14
113.0	0	7	7
114.0	0	10	10
115.0	0	7	7
116.0	0	3	3
117.0	0	11	11
118.0	0	9	9
119.0	0	4	4
120.0	0	8	8
121.0	0	12	12
122.0	0	9	9
123.0	0	10	10
124.0	0	8	8
125.0	0	9	9
126.0	0	7	7
127.0	0	7	7
128.0	0	10	10
129.0	0	7	7
130.0	0	3	3
131.0	0	6	6
132.0	0	5	5
133.0	0	4	4
134.0	0	6	6
135.0	0	1	1
136.0	0	2	2
137.0	0	4	4
138.0	0	5	5
139.0	0	2	2
140.0	0	3	3
141.0	0	6	6
142.0	0	2	2
143.0	0	4	4
144.0	0	3	3
145.0	0	5	5
146.0	0	2	2
147.0	0	1	1
148.0	0	3	3
149.0	0	5	5
150.0	0	6	6
151.0	0	4	4
152.0	0	4	4
153.0	0	4	4
154.0	0	1	1
155.0	0	4	4
156.0	0	6	6
157.0	0	2	2
158.0	0	5	5
159.0	0	2	2
160.0	0	5	5
161.0	0	3	3
162.0	0	5	5
163.0	0	5	5
164.0	0	3	3
165.0	0	5	5
166.0	0	1	1
167.0	0	3	3
168.0	0	6	6
169.0	0	3	3
171.0	0	7	7
172.0	0	2	2
174.0	0	3	3
175.0	0	1	1
176.0	0	3	3
177.0	0	4	4
178.0	0	2	2
179.0	0	4	4
180.0	0	1	1
181.0	0	3	3
182.0	0	2	2
183.0	0	3	3
184.0	0	2	2
186.0	0	1	1
189.0	0	1	1
190.0	0	2	2
191.0	0	1	1
192.0	0	2	2
193.0	0	1	1
196.0	0	2	2
197.0	0	2	2
198.0	0	1	1
199.0	0	1	1
201.0	0	1	1
202.0	0	3	3
203.0	0	1	1
204.0	0	2	2
205.0	0	2	2
206.0	0	2	2
208.0	0	4	4
210.0	0	1	1
211.0	0	3	3
212.0	0	3	3
213.0	0	1	1
214.0	0	3	3
215.0	0	1	1
216.0	0	1	1
218.0	0	1	1
219.0	0	1	1
220.0	0	2	2
221.0	0	1	1
226.0	0	2	2
228.0	0	2	2
230.0	0	1	1
232.0	0	1	1
237.0	0	2	2
238.0	0	2	2
240.0	0	2	2
241.0	0	1	1
245.0	0	2	2
247.0	0	1	1
249.0	0	1	1
252.0	0	1	1
253.0	0	1	1
254.0	0	1	1
257.0	0	2	2
259.0	0	2	2
260.0	0	1	1
263.0	0	1	1
264.0	0	1	1
265.0	0	2	2
266.0	0	1	1
267.0	0	1	1
268.0	0	1	1
270.0	0	1	1
271.0	0	1	1
273.0	0	1	1
275.0	0	2	2
278.0	0	1	1
280.0	0	1	1
282.0	0	2	2
284.0	0	1	1
285.0	0	1	1
286.0	0	2	2
288.0	0	1	1
289.0	0	2	2
290.0	0	1	1
301.0	0	1	1
321.0	0	1	1
322.0	0	1	1
324.0	0	1	1
326.0	0	2	2
329.0	0	1	1
334.0	0	1	1
361.0	0	3	3
373.0	0	1	1
375.0	0	1	1
389.0	0	1	1
393.0	0	1	1
458.0	0	1	1
476.0	0	1	1
481.0	0	1	1
548.0	0	1	1
602.0	0	1	1
643.0	0	1	1
652.0	0	1	1
667.0	0	1	1
872.0	0	1	1
7619.0	0	1	1