## 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-GSM1606363.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606363.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606363.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 14:04:40 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	28058808	4268274	0	0	3654243	0	0.130235	98152232

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	22480730	22480730
2.0	1.75136	1338749	1338749
3.0	2.315902	291162	291162
4.0	2.740076	114575	114575
5.0	3.058784	58182	58182
6.0	3.298248	33878	33878
7.0	3.478172	21642	21642
8.0	3.613359	14294	14294
9.0	3.714934	10115	10115
10.0	3.791253	7574	7574
11.0	3.848596	5701	5701
12.0	3.891681	4325	4325
13.0	3.924054	3527	3527
14.0	3.948377	2837	2837
15.0	3.966653	2259	2259
16.0	3.980385	1896	1896
17.0	3.990702	1534	1534
18.0	3.998454	1292	1292
19.0	4.004279	1124	1124
20.0	4.008655	979	979
21.0	4.011943	816	816
22.0	4.014414	740	740
23.0	4.01627	685	685
24.0	4.017665	605	605
25.0	4.018713	504	504
26.0	4.019501	371	371
27.0	4.020092	379	379
28.0	4.020537	319	319
29.0	4.020871	280	280
30.0	4.021122	265	265
31.0	4.02131	226	226
32.0	4.021452	181	181
33.0	4.021558	194	194
34.0	4.021638	173	173
35.0	4.021698	185	185
36.0	4.021744	138	138
37.0	4.021777	135	135
38.0	4.021803	136	136
39.0	4.021822	106	106
40.0	4.021837	114	114
41.0	4.021847	114	114
42.0	4.021855	90	90
43.0	4.021862	74	74
44.0	4.021866	78	78
45.0	4.02187	69	69
46.0	4.021872	61	61
47.0	4.021874	50	50
48.0	4.021876	56	56
49.0	4.021877	39	39
50.0	4.021878	46	46
51.0	4.021878	40	40
52.0	4.021879	42	42
53.0	4.021879	50	50
54.0	4.021879	33	33
55.0	4.021879	35	35
56.0	4.02188	36	36
57.0	4.02188	38	38
58.0	4.02188	37	37
59.0	4.02188	29	29
60.0	4.02188	26	26
61.0	4.02188	36	36
62.0	4.02188	16	16
63.0	4.02188	30	30
64.0	4.02188	21	21
65.0	4.02188	18	18
66.0	4.02188	15	15
67.0	4.02188	13	13
68.0	4.02188	16	16
69.0	4.02188	20	20
70.0	4.02188	22	22
71.0	4.02188	13	13
72.0	4.02188	18	18
73.0	4.02188	12	12
74.0	4.02188	5	5
75.0	4.02188	14	14
76.0	4.02188	13	13
77.0	4.02188	8	8
78.0	4.02188	8	8
79.0	4.02188	11	11
80.0	4.02188	9	9
81.0	4.02188	6	6
82.0	4.02188	11	11
83.0	4.02188	13	13
84.0	4.02188	11	11
85.0	4.02188	10	10
86.0	4.02188	8	8
87.0	4.02188	7	7
88.0	4.02188	5	5
89.0	4.02188	4	4
90.0	4.02188	10	10
91.0	4.02188	4	4
92.0	4.02188	5	5
93.0	4.02188	3	3
94.0	4.02188	3	3
95.0	4.02188	5	5
96.0	4.02188	4	4
97.0	4.02188	5	5
98.0	4.02188	9	9
99.0	4.02188	2	2
100.0	4.02188	2	2
101.0	0	5	5
102.0	0	7	7
103.0	0	5	5
104.0	0	3	3
105.0	0	1	1
106.0	0	4	4
107.0	0	2	2
108.0	0	5	5
109.0	0	2	2
110.0	0	3	3
111.0	0	1	1
112.0	0	2	2
113.0	0	4	4
114.0	0	7	7
115.0	0	1	1
116.0	0	2	2
117.0	0	3	3
118.0	0	5	5
119.0	0	2	2
120.0	0	4	4
121.0	0	5	5
123.0	0	1	1
124.0	0	2	2
125.0	0	3	3
126.0	0	1	1
127.0	0	1	1
128.0	0	1	1
129.0	0	2	2
130.0	0	5	5
131.0	0	1	1
132.0	0	2	2
134.0	0	1	1
135.0	0	2	2
136.0	0	3	3
138.0	0	1	1
139.0	0	2	2
140.0	0	3	3
144.0	0	1	1
147.0	0	2	2
149.0	0	2	2
150.0	0	1	1
151.0	0	1	1
152.0	0	2	2
155.0	0	1	1
157.0	0	2	2
158.0	0	1	1
159.0	0	1	1
161.0	0	1	1
164.0	0	2	2
165.0	0	1	1
166.0	0	2	2
167.0	0	1	1
168.0	0	1	1
170.0	0	1	1
172.0	0	1	1
173.0	0	1	1
177.0	0	1	1
180.0	0	1	1
184.0	0	3	3
197.0	0	1	1
198.0	0	1	1
200.0	0	1	1
202.0	0	1	1
203.0	0	1	1
214.0	0	1	1
230.0	0	1	1
243.0	0	1	1
248.0	0	1	1
261.0	0	1	1
266.0	0	1	1
281.0	0	1	1
290.0	0	1	1
316.0	0	1	1
364.0	0	1	1
6590.0	0	1	1