## 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-GSM1606348.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606348.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606348.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 14:33:10 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	24449335	3794564	0	0	3676157	0	0.150358	72931417

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	18874487	18874487
2.0	1.715168	1313682	1313682
3.0	2.226634	288841	288841
4.0	2.592418	114036	114036
5.0	2.854015	58223	58223
6.0	3.041101	33796	33796
7.0	3.174899	21563	21563
8.0	3.270587	14626	14626
9.0	3.339021	10503	10503
10.0	3.387962	7669	7669
11.0	3.422963	5751	5751
12.0	3.447995	4647	4647
13.0	3.465897	3660	3660
14.0	3.478699	2927	2927
15.0	3.487856	2433	2433
16.0	3.494404	1972	1972
17.0	3.499087	1701	1701
18.0	3.502436	1390	1390
19.0	3.504831	1161	1161
20.0	3.506544	1056	1056
21.0	3.507769	853	853
22.0	3.508646	767	767
23.0	3.509272	685	685
24.0	3.50972	605	605
25.0	3.510041	561	561
26.0	3.51027	475	475
27.0	3.510434	398	398
28.0	3.510551	356	356
29.0	3.510635	335	335
30.0	3.510695	305	305
31.0	3.510738	275	275
32.0	3.510768	258	258
33.0	3.51079	236	236
34.0	3.510806	179	179
35.0	3.510817	173	173
36.0	3.510825	170	170
37.0	3.510831	147	147
38.0	3.510835	126	126
39.0	3.510838	117	117
40.0	3.51084	126	126
41.0	3.510842	125	125
42.0	3.510843	94	94
43.0	3.510844	97	97
44.0	3.510844	87	87
45.0	3.510844	74	74
46.0	3.510845	70	70
47.0	3.510845	74	74
48.0	3.510845	63	63
49.0	3.510845	56	56
50.0	3.510845	57	57
51.0	3.510845	49	49
52.0	3.510845	59	59
53.0	3.510845	44	44
54.0	3.510845	36	36
55.0	3.510845	37	37
56.0	3.510845	46	46
57.0	3.510845	46	46
58.0	3.510845	36	36
59.0	3.510845	37	37
60.0	3.510845	37	37
61.0	3.510845	34	34
62.0	3.510845	41	41
63.0	3.510845	17	17
64.0	3.510845	23	23
65.0	3.510845	26	26
66.0	3.510845	23	23
67.0	3.510845	18	18
68.0	3.510845	22	22
69.0	3.510845	26	26
70.0	3.510845	17	17
71.0	3.510845	15	15
72.0	3.510845	17	17
73.0	3.510845	10	10
74.0	3.510845	12	12
75.0	3.510845	16	16
76.0	3.510845	10	10
77.0	3.510845	10	10
78.0	3.510845	10	10
79.0	3.510845	7	7
80.0	3.510845	11	11
81.0	3.510845	12	12
82.0	3.510845	11	11
83.0	3.510845	9	9
84.0	3.510845	16	16
85.0	3.510845	14	14
86.0	3.510845	3	3
87.0	3.510845	8	8
88.0	3.510845	7	7
89.0	3.510845	8	8
90.0	3.510845	6	6
91.0	3.510845	6	6
92.0	3.510845	5	5
93.0	3.510845	5	5
94.0	3.510845	7	7
95.0	3.510845	6	6
96.0	3.510845	5	5
97.0	3.510845	4	4
98.0	3.510845	4	4
99.0	3.510845	7	7
100.0	3.510845	2	2
101.0	0	5	5
102.0	0	4	4
103.0	0	3	3
104.0	0	4	4
105.0	0	5	5
106.0	0	6	6
107.0	0	5	5
108.0	0	1	1
109.0	0	2	2
110.0	0	6	6
111.0	0	10	10
112.0	0	5	5
113.0	0	4	4
114.0	0	2	2
115.0	0	2	2
116.0	0	4	4
117.0	0	2	2
118.0	0	3	3
119.0	0	4	4
120.0	0	3	3
121.0	0	3	3
122.0	0	3	3
123.0	0	2	2
124.0	0	1	1
125.0	0	2	2
126.0	0	5	5
127.0	0	3	3
128.0	0	1	1
129.0	0	4	4
130.0	0	3	3
134.0	0	1	1
135.0	0	1	1
136.0	0	1	1
138.0	0	3	3
139.0	0	2	2
140.0	0	1	1
141.0	0	2	2
142.0	0	3	3
143.0	0	3	3
144.0	0	2	2
145.0	0	2	2
146.0	0	1	1
147.0	0	1	1
148.0	0	2	2
149.0	0	1	1
153.0	0	3	3
154.0	0	1	1
156.0	0	1	1
157.0	0	1	1
158.0	0	2	2
160.0	0	1	1
161.0	0	2	2
165.0	0	1	1
167.0	0	2	2
169.0	0	1	1
171.0	0	1	1
174.0	0	1	1
177.0	0	2	2
178.0	0	1	1
179.0	0	1	1
184.0	0	2	2
191.0	0	1	1
199.0	0	1	1
200.0	0	1	1
207.0	0	1	1
209.0	0	1	1
213.0	0	1	1
216.0	0	1	1
217.0	0	1	1
243.0	0	2	2
245.0	0	1	1
253.0	0	1	1
285.0	0	1	1
293.0	0	1	1
298.0	0	1	1
333.0	0	1	1
4788.0	0	1	1