## 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-GSM1606334.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606334.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606334.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 13:31:22 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	29066173	3704146	0	0	4125202	0	0.141924	92463042

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	22497656	22497656
2.0	1.73026	1790989	1790989
3.0	2.26354	354130	354130
4.0	2.652973	127326	127326
5.0	2.93736	60176	60176
6.0	3.145037	33615	33615
7.0	3.296695	20757	20757
8.0	3.407445	13338	13338
9.0	3.488321	9217	9217
10.0	3.547382	6825	6825
11.0	3.590511	4911	4911
12.0	3.622007	3879	3879
13.0	3.645007	2878	2878
14.0	3.661803	2310	2310
15.0	3.674069	1892	1892
16.0	3.683026	1478	1478
17.0	3.689567	1265	1265
18.0	3.694344	991	991
19.0	3.697832	844	844
20.0	3.700379	751	751
21.0	3.702239	649	649
22.0	3.703598	537	537
23.0	3.70459	469	469
24.0	3.705314	399	399
25.0	3.705843	360	360
26.0	3.706229	284	284
27.0	3.706511	272	272
28.0	3.706717	239	239
29.0	3.706868	208	208
30.0	3.706978	166	166
31.0	3.707058	168	168
32.0	3.707117	164	164
33.0	3.707159	138	138
34.0	3.707191	135	135
35.0	3.707213	128	128
36.0	3.70723	97	97
37.0	3.707242	97	97
38.0	3.707251	78	78
39.0	3.707258	69	69
40.0	3.707262	71	71
41.0	3.707266	50	50
42.0	3.707268	49	49
43.0	3.70727	58	58
44.0	3.707272	43	43
45.0	3.707272	47	47
46.0	3.707273	42	42
47.0	3.707274	32	32
48.0	3.707274	42	42
49.0	3.707274	38	38
50.0	3.707275	28	28
51.0	3.707275	38	38
52.0	3.707275	31	31
53.0	3.707275	23	23
54.0	3.707275	19	19
55.0	3.707275	23	23
56.0	3.707275	16	16
57.0	3.707275	32	32
58.0	3.707275	21	21
59.0	3.707275	10	10
60.0	3.707275	23	23
61.0	3.707275	17	17
62.0	3.707275	15	15
63.0	3.707275	15	15
64.0	3.707275	17	17
65.0	3.707275	10	10
66.0	3.707275	8	8
67.0	3.707275	11	11
68.0	3.707275	11	11
69.0	3.707275	14	14
70.0	3.707275	9	9
71.0	3.707275	8	8
72.0	3.707275	7	7
73.0	3.707275	5	5
74.0	3.707275	7	7
75.0	3.707275	8	8
76.0	3.707275	5	5
77.0	3.707275	3	3
78.0	3.707275	5	5
79.0	3.707275	9	9
80.0	3.707275	4	4
81.0	3.707275	5	5
82.0	3.707275	11	11
83.0	3.707275	4	4
84.0	3.707275	3	3
85.0	3.707275	3	3
86.0	3.707275	5	5
87.0	3.707275	5	5
88.0	3.707275	5	5
89.0	3.707275	3	3
90.0	3.707275	2	2
91.0	3.707275	4	4
92.0	3.707275	5	5
93.0	3.707275	2	2
94.0	3.707275	4	4
95.0	3.707275	1	1
96.0	3.707275	3	3
97.0	3.707275	3	3
98.0	3.707275	1	1
99.0	3.707275	4	4
100.0	3.707275	5	5
101.0	0	2	2
102.0	0	2	2
104.0	0	2	2
105.0	0	1	1
106.0	0	2	2
107.0	0	3	3
108.0	0	1	1
109.0	0	2	2
111.0	0	1	1
112.0	0	2	2
113.0	0	2	2
114.0	0	1	1
115.0	0	3	3
118.0	0	1	1
119.0	0	1	1
121.0	0	1	1
122.0	0	1	1
123.0	0	1	1
127.0	0	1	1
128.0	0	1	1
132.0	0	3	3
133.0	0	2	2
134.0	0	2	2
136.0	0	1	1
138.0	0	1	1
142.0	0	1	1
143.0	0	1	1
146.0	0	1	1
147.0	0	1	1
149.0	0	2	2
151.0	0	3	3
156.0	0	1	1
159.0	0	1	1
160.0	0	1	1
168.0	0	1	1
172.0	0	1	1
173.0	0	1	1
179.0	0	1	1
190.0	0	1	1
192.0	0	1	1
198.0	0	1	1
202.0	0	1	1
208.0	0	1	1
213.0	0	1	1
215.0	0	1	1
217.0	0	1	1
233.0	0	1	1
257.0	0	1	1
262.0	0	1	1
286.0	0	1	1
288.0	0	2	2
316.0	0	1	1
347.0	0	1	1
348.0	0	1	1
432.0	0	1	1
437.0	0	1	1
457.0	0	1	1
507.0	0	1	1
598.0	0	1	1
599.0	0	2	2
611.0	0	1	1
708.0	0	1	1
840.0	0	1	1
20132.0	0	1	1