## 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-GSM1606209.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606209.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606209.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 13:31:51 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	33928405	6006630	0	0	4843851	0	0.142767	107223290

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	26624432	26624432
2.0	1.728748	1694091	1694091
3.0	2.259821	376111	376111
4.0	2.64684	149904	149904
5.0	2.928879	76240	76240
6.0	3.134414	44042	44042
7.0	3.284197	28876	28876
8.0	3.393351	19181	19181
9.0	3.472897	13791	13791
10.0	3.530866	10096	10096
11.0	3.573111	7771	7771
12.0	3.603897	6080	6080
13.0	3.626332	4792	4792
14.0	3.642681	3934	3934
15.0	3.654596	3125	3125
16.0	3.663279	2560	2560
17.0	3.669606	2168	2168
18.0	3.674217	1796	1796
19.0	3.677578	1606	1606
20.0	3.680027	1442	1442
21.0	3.681811	1166	1166
22.0	3.683112	1017	1017
23.0	3.68406	943	943
24.0	3.68475	760	760
25.0	3.685254	724	724
26.0	3.685621	654	654
27.0	3.685888	514	514
28.0	3.686083	501	501
29.0	3.686225	453	453
30.0	3.686328	393	393
31.0	3.686403	359	359
32.0	3.686458	322	322
33.0	3.686498	303	303
34.0	3.686528	266	266
35.0	3.686549	243	243
36.0	3.686564	238	238
37.0	3.686576	223	223
38.0	3.686584	210	210
39.0	3.68659	174	174
40.0	3.686594	153	153
41.0	3.686597	166	166
42.0	3.6866	135	135
43.0	3.686601	132	132
44.0	3.686603	111	111
45.0	3.686604	123	123
46.0	3.686604	114	114
47.0	3.686605	108	108
48.0	3.686605	101	101
49.0	3.686605	96	96
50.0	3.686605	81	81
51.0	3.686606	86	86
52.0	3.686606	68	68
53.0	3.686606	59	59
54.0	3.686606	72	72
55.0	3.686606	67	67
56.0	3.686606	49	49
57.0	3.686606	54	54
58.0	3.686606	45	45
59.0	3.686606	52	52
60.0	3.686606	50	50
61.0	3.686606	52	52
62.0	3.686606	34	34
63.0	3.686606	37	37
64.0	3.686606	37	37
65.0	3.686606	36	36
66.0	3.686606	36	36
67.0	3.686606	32	32
68.0	3.686606	45	45
69.0	3.686606	27	27
70.0	3.686606	30	30
71.0	3.686606	32	32
72.0	3.686606	22	22
73.0	3.686606	23	23
74.0	3.686606	32	32
75.0	3.686606	19	19
76.0	3.686606	21	21
77.0	3.686606	19	19
78.0	3.686606	15	15
79.0	3.686606	13	13
80.0	3.686606	20	20
81.0	3.686606	18	18
82.0	3.686606	14	14
83.0	3.686606	11	11
84.0	3.686606	13	13
85.0	3.686606	16	16
86.0	3.686606	17	17
87.0	3.686606	17	17
88.0	3.686606	13	13
89.0	3.686606	13	13
90.0	3.686606	11	11
91.0	3.686606	16	16
92.0	3.686606	14	14
93.0	3.686606	9	9
94.0	3.686606	11	11
95.0	3.686606	7	7
96.0	3.686606	8	8
97.0	3.686606	11	11
98.0	3.686606	9	9
99.0	3.686606	9	9
100.0	3.686606	7	7
101.0	0	6	6
102.0	0	9	9
103.0	0	9	9
104.0	0	5	5
105.0	0	5	5
106.0	0	6	6
107.0	0	5	5
108.0	0	7	7
109.0	0	5	5
110.0	0	8	8
111.0	0	9	9
112.0	0	4	4
113.0	0	5	5
114.0	0	6	6
115.0	0	5	5
116.0	0	6	6
117.0	0	4	4
118.0	0	6	6
119.0	0	2	2
120.0	0	2	2
121.0	0	4	4
122.0	0	1	1
123.0	0	2	2
124.0	0	5	5
125.0	0	1	1
126.0	0	4	4
127.0	0	1	1
128.0	0	4	4
129.0	0	6	6
130.0	0	6	6
131.0	0	5	5
132.0	0	4	4
133.0	0	3	3
134.0	0	3	3
135.0	0	1	1
136.0	0	2	2
138.0	0	1	1
139.0	0	3	3
140.0	0	4	4
141.0	0	1	1
142.0	0	4	4
143.0	0	1	1
144.0	0	1	1
145.0	0	2	2
146.0	0	1	1
147.0	0	2	2
148.0	0	7	7
149.0	0	2	2
150.0	0	1	1
151.0	0	1	1
152.0	0	2	2
153.0	0	4	4
154.0	0	1	1
155.0	0	1	1
156.0	0	1	1
157.0	0	1	1
158.0	0	2	2
159.0	0	1	1
160.0	0	1	1
161.0	0	2	2
162.0	0	1	1
163.0	0	1	1
164.0	0	1	1
166.0	0	1	1
167.0	0	3	3
168.0	0	2	2
169.0	0	2	2
172.0	0	1	1
173.0	0	2	2
174.0	0	1	1
177.0	0	1	1
178.0	0	1	1
179.0	0	2	2
180.0	0	2	2
181.0	0	1	1
182.0	0	1	1
184.0	0	1	1
185.0	0	1	1
186.0	0	1	1
187.0	0	1	1
188.0	0	4	4
189.0	0	2	2
190.0	0	1	1
191.0	0	1	1
194.0	0	1	1
198.0	0	1	1
200.0	0	1	1
202.0	0	2	2
205.0	0	1	1
208.0	0	1	1
210.0	0	1	1
219.0	0	1	1
220.0	0	1	1
222.0	0	1	1
223.0	0	1	1
226.0	0	2	2
227.0	0	1	1
230.0	0	1	1
244.0	0	1	1
247.0	0	1	1
250.0	0	1	1
254.0	0	1	1
258.0	0	1	1
260.0	0	2	2
264.0	0	2	2
274.0	0	1	1
279.0	0	2	2
282.0	0	1	1
286.0	0	1	1
287.0	0	1	1
296.0	0	1	1
308.0	0	2	2
322.0	0	2	2
339.0	0	1	1
343.0	0	1	1
360.0	0	1	1
361.0	0	1	1
362.0	0	1	1
392.0	0	1	1
395.0	0	1	1
412.0	0	1	1
433.0	0	2	2
452.0	0	1	1
457.0	0	1	1
478.0	0	1	1
498.0	0	1	1
545.0	0	1	1
683.0	0	1	1
713.0	0	1	1
774.0	0	1	1
1284.0	0	1	1
1443.0	0	1	1
8232.0	0	1	1