## 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-GSM1606355.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606355.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606355.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 21:30:36 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	27487163	3932414	0	0	4310593	0	0.156822	78213808

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	20930261	20930261
2.0	1.703677	1572881	1572881
3.0	2.198838	333705	333705
4.0	2.547271	130109	130109
5.0	2.792455	66402	66402
6.0	2.964986	38829	38829
7.0	3.086392	25011	25011
8.0	3.171822	16705	16705
9.0	3.231937	12156	12156
10.0	3.274239	9002	9002
11.0	3.304006	6652	6652
12.0	3.324952	5379	5379
13.0	3.339692	4354	4354
14.0	3.350063	3325	3325
15.0	3.357362	2814	2814
16.0	3.362497	2227	2227
17.0	3.366111	1965	1965
18.0	3.368654	1549	1549
19.0	3.370444	1382	1382
20.0	3.371703	1200	1200
21.0	3.372589	1035	1035
22.0	3.373212	919	919
23.0	3.373651	821	821
24.0	3.37396	656	656
25.0	3.374177	603	603
26.0	3.37433	506	506
27.0	3.374438	479	479
28.0	3.374513	427	427
29.0	3.374566	404	404
30.0	3.374604	315	315
31.0	3.37463	321	321
32.0	3.374649	304	304
33.0	3.374662	280	280
34.0	3.374671	237	237
35.0	3.374678	206	206
36.0	3.374682	196	196
37.0	3.374685	176	176
38.0	3.374688	154	154
39.0	3.374689	149	149
40.0	3.37469	146	146
41.0	3.374691	132	132
42.0	3.374692	123	123
43.0	3.374692	95	95
44.0	3.374692	98	98
45.0	3.374693	89	89
46.0	3.374693	83	83
47.0	3.374693	76	76
48.0	3.374693	87	87
49.0	3.374693	72	72
50.0	3.374693	70	70
51.0	3.374693	52	52
52.0	3.374693	67	67
53.0	3.374693	60	60
54.0	3.374693	54	54
55.0	3.374693	53	53
56.0	3.374693	51	51
57.0	3.374693	42	42
58.0	3.374693	43	43
59.0	3.374693	39	39
60.0	3.374693	35	35
61.0	3.374693	47	47
62.0	3.374693	38	38
63.0	3.374693	34	34
64.0	3.374693	30	30
65.0	3.374693	28	28
66.0	3.374693	27	27
67.0	3.374693	25	25
68.0	3.374693	20	20
69.0	3.374693	22	22
70.0	3.374693	16	16
71.0	3.374693	20	20
72.0	3.374693	20	20
73.0	3.374693	20	20
74.0	3.374693	21	21
75.0	3.374693	17	17
76.0	3.374693	21	21
77.0	3.374693	16	16
78.0	3.374693	15	15
79.0	3.374693	12	12
80.0	3.374693	17	17
81.0	3.374693	15	15
82.0	3.374693	15	15
83.0	3.374693	12	12
84.0	3.374693	15	15
85.0	3.374693	10	10
86.0	3.374693	14	14
87.0	3.374693	12	12
88.0	3.374693	7	7
89.0	3.374693	9	9
90.0	3.374693	10	10
91.0	3.374693	12	12
92.0	3.374693	13	13
93.0	3.374693	14	14
94.0	3.374693	13	13
95.0	3.374693	8	8
96.0	3.374693	6	6
97.0	3.374693	5	5
98.0	3.374693	5	5
99.0	3.374693	5	5
100.0	3.374693	8	8
101.0	0	4	4
102.0	0	1	1
103.0	0	6	6
104.0	0	5	5
105.0	0	6	6
106.0	0	4	4
107.0	0	1	1
108.0	0	7	7
109.0	0	12	12
110.0	0	9	9
111.0	0	5	5
112.0	0	3	3
113.0	0	3	3
114.0	0	3	3
115.0	0	2	2
116.0	0	6	6
117.0	0	4	4
118.0	0	6	6
119.0	0	7	7
120.0	0	4	4
121.0	0	5	5
122.0	0	6	6
123.0	0	1	1
124.0	0	1	1
125.0	0	3	3
126.0	0	2	2
127.0	0	1	1
128.0	0	4	4
129.0	0	2	2
130.0	0	2	2
131.0	0	3	3
132.0	0	4	4
133.0	0	4	4
134.0	0	1	1
135.0	0	3	3
136.0	0	2	2
137.0	0	2	2
138.0	0	3	3
139.0	0	3	3
140.0	0	1	1
142.0	0	1	1
143.0	0	1	1
144.0	0	1	1
145.0	0	2	2
146.0	0	3	3
147.0	0	2	2
150.0	0	2	2
152.0	0	2	2
153.0	0	1	1
155.0	0	1	1
156.0	0	1	1
159.0	0	3	3
163.0	0	1	1
164.0	0	1	1
165.0	0	2	2
166.0	0	2	2
167.0	0	1	1
169.0	0	2	2
170.0	0	1	1
171.0	0	1	1
172.0	0	1	1
173.0	0	1	1
174.0	0	1	1
175.0	0	2	2
177.0	0	1	1
178.0	0	1	1
179.0	0	2	2
181.0	0	1	1
183.0	0	2	2
184.0	0	1	1
190.0	0	1	1
194.0	0	1	1
199.0	0	2	2
201.0	0	1	1
203.0	0	2	2
207.0	0	1	1
209.0	0	1	1
215.0	0	1	1
217.0	0	2	2
224.0	0	1	1
225.0	0	2	2
226.0	0	1	1
229.0	0	1	1
234.0	0	1	1
235.0	0	1	1
238.0	0	1	1
240.0	0	1	1
244.0	0	1	1
248.0	0	1	1
263.0	0	1	1
266.0	0	1	1
278.0	0	1	1
283.0	0	1	1
287.0	0	1	1
288.0	0	1	1
311.0	0	1	1
312.0	0	1	1
326.0	0	1	1
392.0	0	1	1
394.0	0	1	1
451.0	0	1	1
455.0	0	1	1
505.0	0	1	1
5966.0	0	1	1