## 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-GSM1606337.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606337.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606337.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 13:54:00 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	27191881	3770480	0	0	4423999	0	0.162696	74233048

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	20418772	20418772
2.0	1.693292	1633651	1633651
3.0	2.173945	360049	360049
4.0	2.507179	140591	140591
5.0	2.738206	70283	70283
6.0	2.898376	40677	40677
7.0	3.009421	25599	25599
8.0	3.086407	17308	17308
9.0	3.139781	12308	12308
10.0	3.176784	8909	8909
11.0	3.202439	6761	6761
12.0	3.220224	5133	5133
13.0	3.232555	4174	4174
14.0	3.241104	3289	3289
15.0	3.247031	2702	2702
16.0	3.25114	2259	2259
17.0	3.253989	1841	1841
18.0	3.255964	1500	1500
19.0	3.257333	1277	1277
20.0	3.258283	1136	1136
21.0	3.258941	959	959
22.0	3.259397	874	874
23.0	3.259713	729	729
24.0	3.259933	610	610
25.0	3.260085	598	598
26.0	3.26019	506	506
27.0	3.260263	490	490
28.0	3.260314	385	385
29.0	3.260349	391	391
30.0	3.260373	324	324
31.0	3.26039	270	270
32.0	3.260402	237	237
33.0	3.26041	235	235
34.0	3.260416	234	234
35.0	3.26042	186	186
36.0	3.260422	192	192
37.0	3.260424	158	158
38.0	3.260425	142	142
39.0	3.260426	137	137
40.0	3.260427	122	122
41.0	3.260427	103	103
42.0	3.260428	115	115
43.0	3.260428	106	106
44.0	3.260428	95	95
45.0	3.260428	101	101
46.0	3.260428	69	69
47.0	3.260428	79	79
48.0	3.260428	78	78
49.0	3.260428	65	65
50.0	3.260428	68	68
51.0	3.260428	59	59
52.0	3.260428	47	47
53.0	3.260428	53	53
54.0	3.260428	48	48
55.0	3.260428	33	33
56.0	3.260428	37	37
57.0	3.260428	43	43
58.0	3.260428	30	30
59.0	3.260428	30	30
60.0	3.260428	30	30
61.0	3.260428	27	27
62.0	3.260428	27	27
63.0	3.260428	24	24
64.0	3.260428	28	28
65.0	3.260428	19	19
66.0	3.260428	20	20
67.0	3.260428	16	16
68.0	3.260428	17	17
69.0	3.260428	15	15
70.0	3.260428	18	18
71.0	3.260428	16	16
72.0	3.260428	10	10
73.0	3.260428	14	14
74.0	3.260428	14	14
75.0	3.260428	12	12
76.0	3.260428	13	13
77.0	3.260428	12	12
78.0	3.260428	11	11
79.0	3.260428	8	8
80.0	3.260428	13	13
81.0	3.260428	12	12
82.0	3.260428	13	13
83.0	3.260428	8	8
84.0	3.260428	5	5
85.0	3.260428	7	7
86.0	3.260428	7	7
87.0	3.260428	8	8
88.0	3.260428	7	7
89.0	3.260428	8	8
90.0	3.260428	6	6
91.0	3.260428	3	3
92.0	3.260428	6	6
93.0	3.260428	6	6
94.0	3.260428	4	4
95.0	3.260428	8	8
96.0	3.260428	7	7
97.0	3.260428	3	3
98.0	3.260428	3	3
99.0	3.260428	5	5
100.0	3.260428	2	2
101.0	0	5	5
102.0	0	6	6
103.0	0	5	5
104.0	0	4	4
105.0	0	1	1
106.0	0	3	3
107.0	0	2	2
108.0	0	1	1
109.0	0	4	4
110.0	0	1	1
111.0	0	2	2
112.0	0	6	6
113.0	0	2	2
114.0	0	4	4
115.0	0	1	1
117.0	0	3	3
118.0	0	2	2
119.0	0	1	1
120.0	0	3	3
121.0	0	1	1
123.0	0	2	2
124.0	0	2	2
125.0	0	1	1
126.0	0	1	1
127.0	0	4	4
128.0	0	1	1
129.0	0	2	2
130.0	0	1	1
131.0	0	2	2
132.0	0	1	1
133.0	0	1	1
134.0	0	3	3
135.0	0	1	1
139.0	0	1	1
141.0	0	1	1
143.0	0	2	2
146.0	0	3	3
148.0	0	1	1
149.0	0	1	1
150.0	0	2	2
151.0	0	1	1
152.0	0	1	1
153.0	0	2	2
154.0	0	2	2
155.0	0	1	1
156.0	0	1	1
159.0	0	2	2
161.0	0	1	1
164.0	0	1	1
167.0	0	1	1
171.0	0	1	1
173.0	0	2	2
174.0	0	1	1
178.0	0	2	2
179.0	0	1	1
182.0	0	1	1
183.0	0	1	1
184.0	0	1	1
186.0	0	1	1
187.0	0	1	1
188.0	0	1	1
189.0	0	1	1
191.0	0	1	1
192.0	0	1	1
196.0	0	1	1
201.0	0	1	1
202.0	0	1	1
210.0	0	1	1
214.0	0	1	1
220.0	0	1	1
247.0	0	1	1
256.0	0	1	1
270.0	0	1	1
276.0	0	1	1
298.0	0	1	1
320.0	0	1	1
392.0	0	1	1
6304.0	0	1	1