## 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-GSM1606205.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606205.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606205.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: Mon Nov 01 23:56:40 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	39406836	6984560	0	0	5876201	0	0.149116	118643648

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	30574037	30574037
2.0	1.717384	2019571	2019571
3.0	2.232023	459037	459037
4.0	2.601217	182863	182863
5.0	2.86607	93283	93283
6.0	3.056072	54264	54264
7.0	3.192376	34795	34795
8.0	3.290158	24098	24098
9.0	3.360306	17147	17147
10.0	3.410628	12529	12529
11.0	3.446729	9652	9652
12.0	3.472627	7291	7291
13.0	3.491206	5908	5908
14.0	3.504534	4754	4754
15.0	3.514095	3933	3933
16.0	3.520955	3148	3148
17.0	3.525875	2719	2719
18.0	3.529405	2293	2293
19.0	3.531938	2000	2000
20.0	3.533754	1667	1667
21.0	3.535058	1484	1484
22.0	3.535992	1297	1297
23.0	3.536663	1178	1178
24.0	3.537144	965	965
25.0	3.53749	852	852
26.0	3.537737	789	789
27.0	3.537915	726	726
28.0	3.538042	623	623
29.0	3.538134	602	602
30.0	3.538199	474	474
31.0	3.538246	463	463
32.0	3.53828	394	394
33.0	3.538304	342	342
34.0	3.538322	359	359
35.0	3.538334	330	330
36.0	3.538343	287	287
37.0	3.538349	270	270
38.0	3.538354	252	252
39.0	3.538357	219	219
40.0	3.53836	199	199
41.0	3.538361	189	189
42.0	3.538363	190	190
43.0	3.538363	170	170
44.0	3.538364	150	150
45.0	3.538365	156	156
46.0	3.538365	119	119
47.0	3.538365	129	129
48.0	3.538365	111	111
49.0	3.538365	89	89
50.0	3.538365	102	102
51.0	3.538366	102	102
52.0	3.538366	93	93
53.0	3.538366	89	89
54.0	3.538366	80	80
55.0	3.538366	82	82
56.0	3.538366	60	60
57.0	3.538366	72	72
58.0	3.538366	70	70
59.0	3.538366	67	67
60.0	3.538366	67	67
61.0	3.538366	64	64
62.0	3.538366	47	47
63.0	3.538366	53	53
64.0	3.538366	38	38
65.0	3.538366	38	38
66.0	3.538366	40	40
67.0	3.538366	51	51
68.0	3.538366	35	35
69.0	3.538366	38	38
70.0	3.538366	30	30
71.0	3.538366	33	33
72.0	3.538366	26	26
73.0	3.538366	28	28
74.0	3.538366	21	21
75.0	3.538366	25	25
76.0	3.538366	26	26
77.0	3.538366	14	14
78.0	3.538366	23	23
79.0	3.538366	28	28
80.0	3.538366	15	15
81.0	3.538366	29	29
82.0	3.538366	26	26
83.0	3.538366	20	20
84.0	3.538366	17	17
85.0	3.538366	19	19
86.0	3.538366	16	16
87.0	3.538366	15	15
88.0	3.538366	12	12
89.0	3.538366	11	11
90.0	3.538366	12	12
91.0	3.538366	16	16
92.0	3.538366	12	12
93.0	3.538366	13	13
94.0	3.538366	10	10
95.0	3.538366	9	9
96.0	3.538366	18	18
97.0	3.538366	11	11
98.0	3.538366	12	12
99.0	3.538366	12	12
100.0	3.538366	12	12
101.0	0	10	10
102.0	0	11	11
103.0	0	10	10
104.0	0	7	7
105.0	0	6	6
106.0	0	11	11
107.0	0	11	11
108.0	0	9	9
109.0	0	5	5
110.0	0	7	7
111.0	0	11	11
112.0	0	7	7
113.0	0	4	4
114.0	0	8	8
115.0	0	9	9
116.0	0	8	8
117.0	0	8	8
118.0	0	2	2
119.0	0	8	8
120.0	0	5	5
121.0	0	2	2
122.0	0	6	6
123.0	0	6	6
124.0	0	2	2
125.0	0	6	6
126.0	0	4	4
127.0	0	6	6
128.0	0	3	3
129.0	0	6	6
130.0	0	3	3
131.0	0	3	3
132.0	0	4	4
133.0	0	5	5
134.0	0	1	1
135.0	0	2	2
136.0	0	7	7
137.0	0	3	3
138.0	0	4	4
139.0	0	4	4
140.0	0	1	1
141.0	0	3	3
142.0	0	3	3
143.0	0	2	2
144.0	0	4	4
145.0	0	2	2
146.0	0	3	3
147.0	0	2	2
148.0	0	3	3
149.0	0	1	1
150.0	0	2	2
152.0	0	3	3
153.0	0	2	2
154.0	0	1	1
156.0	0	6	6
157.0	0	2	2
158.0	0	3	3
159.0	0	1	1
160.0	0	4	4
161.0	0	2	2
162.0	0	4	4
163.0	0	4	4
164.0	0	2	2
165.0	0	1	1
167.0	0	2	2
171.0	0	1	1
173.0	0	1	1
174.0	0	2	2
176.0	0	1	1
177.0	0	1	1
178.0	0	2	2
179.0	0	2	2
180.0	0	3	3
181.0	0	1	1
182.0	0	2	2
184.0	0	1	1
185.0	0	3	3
186.0	0	2	2
187.0	0	2	2
188.0	0	2	2
189.0	0	2	2
190.0	0	1	1
191.0	0	1	1
192.0	0	1	1
193.0	0	2	2
195.0	0	2	2
197.0	0	1	1
198.0	0	1	1
203.0	0	1	1
204.0	0	1	1
206.0	0	1	1
211.0	0	2	2
212.0	0	1	1
216.0	0	1	1
220.0	0	2	2
222.0	0	1	1
223.0	0	1	1
226.0	0	1	1
227.0	0	1	1
228.0	0	1	1
234.0	0	1	1
235.0	0	1	1
236.0	0	1	1
237.0	0	1	1
247.0	0	1	1
249.0	0	1	1
251.0	0	1	1
255.0	0	1	1
258.0	0	1	1
259.0	0	1	1
265.0	0	2	2
272.0	0	1	1
277.0	0	1	1
292.0	0	1	1
293.0	0	1	1
302.0	0	1	1
304.0	0	1	1
322.0	0	1	1
336.0	0	1	1
343.0	0	1	1
349.0	0	1	1
382.0	0	1	1
396.0	0	1	1
406.0	0	1	1
473.0	0	1	1
498.0	0	1	1
509.0	0	1	1
563.0	0	1	1
676.0	0	1	1
7196.0	0	1	1