## 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-GSM1606267.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606267.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606267.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 14:50:43 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	26398176	3561926	0	0	4888288	0	0.185175	62177287

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	19195895	19195895
2.0	1.654056	1528649	1528649
3.0	2.081844	364840	364840
4.0	2.361642	153862	153862
5.0	2.544645	80823	80823
6.0	2.664339	48818	48818
7.0	2.742626	31554	31554
8.0	2.79383	21998	21998
9.0	2.82732	15770	15770
10.0	2.849224	11959	11959
11.0	2.863551	9026	9026
12.0	2.872921	7097	7097
13.0	2.87905	5661	5661
14.0	2.883059	4473	4473
15.0	2.88568	3676	3676
16.0	2.887395	3115	3115
17.0	2.888517	2625	2625
18.0	2.88925	2292	2292
19.0	2.88973	1948	1948
20.0	2.890044	1583	1583
21.0	2.890249	1416	1416
22.0	2.890384	1243	1243
23.0	2.890471	1046	1046
24.0	2.890529	881	881
25.0	2.890566	837	837
26.0	2.890591	765	765
27.0	2.890607	642	642
28.0	2.890618	576	576
29.0	2.890624	540	540
30.0	2.890629	457	457
31.0	2.890632	423	423
32.0	2.890634	417	417
33.0	2.890635	345	345
34.0	2.890636	297	297
35.0	2.890636	291	291
36.0	2.890637	244	244
37.0	2.890637	285	285
38.0	2.890637	211	211
39.0	2.890637	199	199
40.0	2.890637	202	202
41.0	2.890637	184	184
42.0	2.890637	152	152
43.0	2.890637	132	132
44.0	2.890637	116	116
45.0	2.890637	112	112
46.0	2.890637	114	114
47.0	2.890637	115	115
48.0	2.890637	110	110
49.0	2.890637	88	88
50.0	2.890637	93	93
51.0	2.890637	82	82
52.0	2.890637	68	68
53.0	2.890637	70	70
54.0	2.890637	46	46
55.0	2.890637	53	53
56.0	2.890637	63	63
57.0	2.890637	55	55
58.0	2.890637	63	63
59.0	2.890637	48	48
60.0	2.890637	47	47
61.0	2.890637	43	43
62.0	2.890637	55	55
63.0	2.890637	34	34
64.0	2.890637	45	45
65.0	2.890637	28	28
66.0	2.890637	34	34
67.0	2.890637	23	23
68.0	2.890637	29	29
69.0	2.890637	36	36
70.0	2.890637	30	30
71.0	2.890637	30	30
72.0	2.890637	21	21
73.0	2.890637	28	28
74.0	2.890637	31	31
75.0	2.890637	13	13
76.0	2.890637	14	14
77.0	2.890637	26	26
78.0	2.890637	20	20
79.0	2.890637	13	13
80.0	2.890637	15	15
81.0	2.890637	19	19
82.0	2.890637	28	28
83.0	2.890637	11	11
84.0	2.890637	12	12
85.0	2.890637	20	20
86.0	2.890637	12	12
87.0	2.890637	12	12
88.0	2.890637	10	10
89.0	2.890637	17	17
90.0	2.890637	11	11
91.0	2.890637	9	9
92.0	2.890637	16	16
93.0	2.890637	12	12
94.0	2.890637	12	12
95.0	2.890637	12	12
96.0	2.890637	5	5
97.0	2.890637	10	10
98.0	2.890637	2	2
99.0	2.890637	13	13
100.0	2.890637	7	7
101.0	0	9	9
102.0	0	7	7
103.0	0	4	4
104.0	0	13	13
105.0	0	8	8
106.0	0	6	6
107.0	0	3	3
108.0	0	5	5
109.0	0	9	9
110.0	0	4	4
111.0	0	9	9
112.0	0	5	5
113.0	0	6	6
114.0	0	4	4
115.0	0	5	5
116.0	0	7	7
117.0	0	4	4
118.0	0	5	5
119.0	0	4	4
120.0	0	4	4
121.0	0	5	5
122.0	0	2	2
123.0	0	4	4
124.0	0	5	5
126.0	0	5	5
127.0	0	2	2
128.0	0	2	2
129.0	0	2	2
130.0	0	3	3
131.0	0	4	4
132.0	0	2	2
133.0	0	5	5
134.0	0	2	2
135.0	0	2	2
136.0	0	2	2
137.0	0	3	3
138.0	0	1	1
139.0	0	4	4
140.0	0	5	5
141.0	0	2	2
142.0	0	1	1
143.0	0	1	1
144.0	0	3	3
145.0	0	1	1
146.0	0	4	4
147.0	0	4	4
148.0	0	2	2
149.0	0	5	5
150.0	0	2	2
151.0	0	2	2
152.0	0	1	1
153.0	0	1	1
154.0	0	1	1
156.0	0	3	3
157.0	0	1	1
160.0	0	1	1
161.0	0	1	1
163.0	0	1	1
164.0	0	1	1
166.0	0	2	2
168.0	0	4	4
169.0	0	1	1
171.0	0	1	1
172.0	0	1	1
174.0	0	1	1
177.0	0	3	3
185.0	0	1	1
186.0	0	2	2
187.0	0	1	1
188.0	0	1	1
189.0	0	1	1
191.0	0	1	1
193.0	0	2	2
195.0	0	1	1
197.0	0	2	2
200.0	0	1	1
201.0	0	1	1
206.0	0	1	1
207.0	0	1	1
212.0	0	1	1
213.0	0	1	1
216.0	0	1	1
218.0	0	1	1
219.0	0	1	1
221.0	0	1	1
223.0	0	1	1
225.0	0	1	1
227.0	0	1	1
230.0	0	1	1
232.0	0	1	1
242.0	0	1	1
245.0	0	1	1
248.0	0	1	1
250.0	0	1	1
251.0	0	1	1
252.0	0	2	2
253.0	0	1	1
259.0	0	2	2
271.0	0	1	1
283.0	0	1	1
313.0	0	1	1
322.0	0	1	1
337.0	0	1	1
345.0	0	1	1
421.0	0	1	1
434.0	0	1	1
3744.0	0	1	1