## 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-GSM1606215.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606215.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606215.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 13:56:15 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	31951694	5167204	0	0	4204431	0	0.131587	110506777

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	25561011	25561011
2.0	1.748909	1513866	1513866
3.0	2.309774	332264	332264
4.0	2.72981	132465	132465
5.0	3.044379	66820	66820
6.0	3.279963	39091	39091
7.0	3.456393	24924	24924
8.0	3.588524	16848	16848
9.0	3.687478	11819	11819
10.0	3.761585	8811	8811
11.0	3.817085	6600	6600
12.0	3.858649	5194	5194
13.0	3.889777	4123	4123
14.0	3.913089	3105	3105
15.0	3.930547	2615	2615
16.0	3.943622	2169	2169
17.0	3.953414	1875	1875
18.0	3.960747	1516	1516
19.0	3.966239	1298	1298
20.0	3.970352	1139	1139
21.0	3.973432	897	897
22.0	3.975739	820	820
23.0	3.977466	766	766
24.0	3.97876	632	632
25.0	3.979729	538	538
26.0	3.980455	471	471
27.0	3.980998	434	434
28.0	3.981405	410	410
29.0	3.98171	351	351
30.0	3.981938	316	316
31.0	3.982109	305	305
32.0	3.982237	276	276
33.0	3.982333	228	228
34.0	3.982405	196	196
35.0	3.982459	188	188
36.0	3.982499	169	169
37.0	3.982529	173	173
38.0	3.982552	142	142
39.0	3.982569	140	140
40.0	3.982581	131	131
41.0	3.982591	103	103
42.0	3.982598	116	116
43.0	3.982603	94	94
44.0	3.982607	115	115
45.0	3.98261	105	105
46.0	3.982612	75	75
47.0	3.982614	95	95
48.0	3.982615	90	90
49.0	3.982616	68	68
50.0	3.982617	62	62
51.0	3.982617	69	69
52.0	3.982618	56	56
53.0	3.982618	61	61
54.0	3.982618	42	42
55.0	3.982619	40	40
56.0	3.982619	37	37
57.0	3.982619	41	41
58.0	3.982619	31	31
59.0	3.982619	30	30
60.0	3.982619	36	36
61.0	3.982619	28	28
62.0	3.982619	27	27
63.0	3.982619	30	30
64.0	3.982619	26	26
65.0	3.982619	17	17
66.0	3.982619	25	25
67.0	3.982619	28	28
68.0	3.982619	28	28
69.0	3.982619	19	19
70.0	3.982619	20	20
71.0	3.982619	14	14
72.0	3.982619	23	23
73.0	3.982619	22	22
74.0	3.982619	25	25
75.0	3.982619	13	13
76.0	3.982619	14	14
77.0	3.982619	12	12
78.0	3.982619	12	12
79.0	3.982619	8	8
80.0	3.982619	14	14
81.0	3.982619	9	9
82.0	3.982619	9	9
83.0	3.982619	13	13
84.0	3.982619	7	7
85.0	3.982619	10	10
86.0	3.982619	8	8
87.0	3.982619	10	10
88.0	3.982619	10	10
89.0	3.982619	9	9
90.0	3.982619	4	4
91.0	3.982619	9	9
92.0	3.982619	5	5
93.0	3.982619	15	15
94.0	3.982619	8	8
95.0	3.982619	7	7
96.0	3.982619	7	7
97.0	3.982619	9	9
98.0	3.982619	5	5
99.0	3.982619	9	9
100.0	3.982619	7	7
101.0	0	1	1
102.0	0	2	2
103.0	0	7	7
104.0	0	2	2
105.0	0	3	3
106.0	0	3	3
107.0	0	4	4
108.0	0	4	4
109.0	0	2	2
110.0	0	2	2
111.0	0	8	8
112.0	0	1	1
113.0	0	3	3
114.0	0	1	1
115.0	0	4	4
116.0	0	3	3
117.0	0	2	2
118.0	0	2	2
119.0	0	3	3
120.0	0	7	7
121.0	0	4	4
122.0	0	3	3
123.0	0	4	4
124.0	0	6	6
125.0	0	3	3
126.0	0	4	4
127.0	0	3	3
128.0	0	1	1
130.0	0	1	1
132.0	0	1	1
133.0	0	4	4
134.0	0	1	1
135.0	0	2	2
137.0	0	2	2
138.0	0	1	1
139.0	0	2	2
140.0	0	1	1
142.0	0	2	2
143.0	0	1	1
145.0	0	2	2
146.0	0	1	1
147.0	0	1	1
148.0	0	1	1
149.0	0	1	1
150.0	0	1	1
151.0	0	2	2
152.0	0	2	2
153.0	0	1	1
154.0	0	2	2
157.0	0	1	1
159.0	0	2	2
161.0	0	1	1
165.0	0	3	3
166.0	0	1	1
168.0	0	1	1
170.0	0	1	1
172.0	0	1	1
173.0	0	3	3
174.0	0	1	1
176.0	0	1	1
177.0	0	1	1
181.0	0	2	2
184.0	0	1	1
187.0	0	2	2
188.0	0	1	1
189.0	0	2	2
194.0	0	3	3
195.0	0	1	1
201.0	0	1	1
202.0	0	1	1
204.0	0	1	1
206.0	0	2	2
210.0	0	1	1
214.0	0	1	1
223.0	0	1	1
239.0	0	1	1
240.0	0	1	1
243.0	0	1	1
245.0	0	1	1
251.0	0	1	1
255.0	0	1	1
263.0	0	1	1
267.0	0	1	1
273.0	0	1	1
282.0	0	1	1
293.0	0	1	1
294.0	0	1	1
321.0	0	1	1
326.0	0	1	1
340.0	0	1	1
351.0	0	2	2
354.0	0	1	1
360.0	0	1	1
390.0	0	1	1
425.0	0	1	1
646.0	0	1	1
699.0	0	1	1
745.0	0	1	1
6086.0	0	1	1