## 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-GSM1606361.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606361.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606361.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 14:41:03 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	24978731	3545588	0	0	4121642	0	0.165006	67112442

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	18837594	18837594
2.0	1.689222	1366512	1366512
3.0	2.164248	312198	312198
4.0	2.491647	127292	127292
5.0	2.717297	66169	66169
6.0	2.87282	39035	39035
7.0	2.98001	25082	25082
8.0	3.053888	17400	17400
9.0	3.104806	12288	12288
10.0	3.1399	9400	9400
11.0	3.164087	7125	7125
12.0	3.180758	5524	5524
13.0	3.192247	4399	4399
14.0	3.200166	3490	3490
15.0	3.205624	2874	2874
16.0	3.209386	2466	2466
17.0	3.211978	2172	2172
18.0	3.213765	1711	1711
19.0	3.214997	1524	1524
20.0	3.215846	1292	1292
21.0	3.216431	1042	1042
22.0	3.216834	1019	1019
23.0	3.217112	847	847
24.0	3.217303	754	754
25.0	3.217435	682	682
26.0	3.217526	547	547
27.0	3.217589	511	511
28.0	3.217632	498	498
29.0	3.217662	445	445
30.0	3.217683	369	369
31.0	3.217697	343	343
32.0	3.217707	284	284
33.0	3.217713	270	270
34.0	3.217718	246	246
35.0	3.217721	230	230
36.0	3.217723	201	201
37.0	3.217725	190	190
38.0	3.217726	156	156
39.0	3.217727	156	156
40.0	3.217727	175	175
41.0	3.217727	126	126
42.0	3.217728	130	130
43.0	3.217728	117	117
44.0	3.217728	135	135
45.0	3.217728	93	93
46.0	3.217728	101	101
47.0	3.217728	82	82
48.0	3.217728	98	98
49.0	3.217728	72	72
50.0	3.217728	76	76
51.0	3.217728	62	62
52.0	3.217728	65	65
53.0	3.217728	55	55
54.0	3.217728	52	52
55.0	3.217728	54	54
56.0	3.217728	55	55
57.0	3.217728	49	49
58.0	3.217728	49	49
59.0	3.217728	56	56
60.0	3.217728	49	49
61.0	3.217728	40	40
62.0	3.217728	34	34
63.0	3.217728	36	36
64.0	3.217728	37	37
65.0	3.217728	29	29
66.0	3.217728	34	34
67.0	3.217728	27	27
68.0	3.217728	28	28
69.0	3.217728	29	29
70.0	3.217728	27	27
71.0	3.217728	22	22
72.0	3.217728	30	30
73.0	3.217728	23	23
74.0	3.217728	23	23
75.0	3.217728	21	21
76.0	3.217728	20	20
77.0	3.217728	14	14
78.0	3.217728	13	13
79.0	3.217728	13	13
80.0	3.217728	13	13
81.0	3.217728	14	14
82.0	3.217728	15	15
83.0	3.217728	18	18
84.0	3.217728	13	13
85.0	3.217728	14	14
86.0	3.217728	13	13
87.0	3.217728	10	10
88.0	3.217728	16	16
89.0	3.217728	12	12
90.0	3.217728	8	8
91.0	3.217728	7	7
92.0	3.217728	15	15
93.0	3.217728	8	8
94.0	3.217728	14	14
95.0	3.217728	11	11
96.0	3.217728	7	7
97.0	3.217728	4	4
98.0	3.217728	6	6
99.0	3.217728	9	9
100.0	3.217728	6	6
101.0	0	6	6
102.0	0	12	12
103.0	0	6	6
104.0	0	8	8
105.0	0	10	10
106.0	0	7	7
107.0	0	8	8
108.0	0	3	3
109.0	0	6	6
110.0	0	5	5
111.0	0	3	3
112.0	0	2	2
113.0	0	8	8
114.0	0	8	8
115.0	0	5	5
116.0	0	4	4
117.0	0	3	3
118.0	0	5	5
119.0	0	1	1
120.0	0	5	5
121.0	0	3	3
122.0	0	3	3
123.0	0	3	3
124.0	0	1	1
125.0	0	5	5
126.0	0	3	3
127.0	0	3	3
128.0	0	4	4
129.0	0	4	4
130.0	0	2	2
131.0	0	3	3
132.0	0	3	3
133.0	0	3	3
134.0	0	7	7
135.0	0	3	3
136.0	0	3	3
137.0	0	2	2
138.0	0	3	3
140.0	0	1	1
142.0	0	3	3
143.0	0	1	1
144.0	0	4	4
145.0	0	1	1
146.0	0	1	1
147.0	0	1	1
148.0	0	2	2
150.0	0	1	1
151.0	0	1	1
154.0	0	1	1
155.0	0	1	1
157.0	0	2	2
158.0	0	2	2
159.0	0	1	1
162.0	0	1	1
163.0	0	1	1
164.0	0	2	2
165.0	0	2	2
166.0	0	1	1
167.0	0	3	3
168.0	0	1	1
169.0	0	1	1
170.0	0	1	1
171.0	0	1	1
173.0	0	2	2
174.0	0	1	1
176.0	0	1	1
178.0	0	1	1
180.0	0	1	1
182.0	0	1	1
183.0	0	1	1
185.0	0	2	2
188.0	0	1	1
190.0	0	2	2
192.0	0	2	2
194.0	0	1	1
195.0	0	2	2
203.0	0	1	1
204.0	0	1	1
206.0	0	1	1
217.0	0	1	1
220.0	0	3	3
222.0	0	2	2
227.0	0	1	1
228.0	0	1	1
229.0	0	1	1
230.0	0	1	1
232.0	0	1	1
233.0	0	2	2
239.0	0	1	1
240.0	0	1	1
245.0	0	1	1
249.0	0	1	1
253.0	0	1	1
259.0	0	2	2
260.0	0	1	1
262.0	0	1	1
268.0	0	1	1
278.0	0	1	1
288.0	0	1	1
290.0	0	1	1
305.0	0	1	1
307.0	0	1	1
327.0	0	1	1
346.0	0	1	1
367.0	0	1	1
377.0	0	1	1
452.0	0	1	1
456.0	0	1	1
462.0	0	1	1
556.0	0	1	1
7570.0	0	1	1