## 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-GSM1606327.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606327.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606327.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 20:48:25 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	31505673	2393698	0	0	3645102	0	0.115697	125438384

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	25421255	25421255
2.0	1.777894	1882584	1882584
3.0	2.383014	332805	332805
4.0	2.853733	106951	106951
5.0	3.219903	46480	46480
6.0	3.504744	24174	24174
7.0	3.726321	13814	13814
8.0	3.898684	8850	8850
9.0	4.032764	5730	5730
10.0	4.137065	4044	4044
11.0	4.218199	2899	2899
12.0	4.281314	2176	2176
13.0	4.33041	1616	1616
14.0	4.368601	1227	1227
15.0	4.39831	928	928
16.0	4.421421	709	709
17.0	4.439398	639	639
18.0	4.453383	472	472
19.0	4.464262	419	419
20.0	4.472724	351	351
21.0	4.479307	299	299
22.0	4.484428	248	248
23.0	4.488411	215	215
24.0	4.49151	174	174
25.0	4.49392	161	161
26.0	4.495795	121	121
27.0	4.497254	115	115
28.0	4.498388	103	103
29.0	4.499271	89	89
30.0	4.499958	73	73
31.0	4.500492	72	72
32.0	4.500907	67	67
33.0	4.50123	56	56
34.0	4.501482	62	62
35.0	4.501677	58	58
36.0	4.501829	43	43
37.0	4.501948	34	34
38.0	4.50204	25	25
39.0	4.502111	37	37
40.0	4.502167	23	23
41.0	4.502211	24	24
42.0	4.502244	20	20
43.0	4.50227	28	28
44.0	4.502291	23	23
45.0	4.502307	24	24
46.0	4.502319	8	8
47.0	4.502329	7	7
48.0	4.502336	14	14
49.0	4.502342	5	5
50.0	4.502346	9	9
51.0	4.50235	11	11
52.0	4.502353	9	9
53.0	4.502355	10	10
54.0	4.502356	5	5
55.0	4.502358	3	3
56.0	4.502359	8	8
57.0	4.50236	9	9
58.0	4.50236	6	6
59.0	4.502361	9	9
60.0	4.502361	7	7
61.0	4.502361	7	7
62.0	4.502362	7	7
63.0	4.502362	6	6
64.0	4.502362	3	3
65.0	4.502362	3	3
66.0	4.502362	2	2
67.0	4.502362	6	6
68.0	4.502362	2	2
69.0	4.502362	6	6
70.0	4.502362	4	4
71.0	4.502362	2	2
72.0	4.502362	0	0
73.0	4.502362	5	5
74.0	4.502362	0	0
75.0	4.502362	5	5
76.0	4.502362	1	1
77.0	4.502362	4	4
78.0	4.502362	6	6
79.0	4.502362	1	1
80.0	4.502362	3	3
81.0	4.502362	2	2
82.0	4.502362	0	0
83.0	4.502362	0	0
84.0	4.502362	2	2
85.0	4.502362	0	0
86.0	4.502362	3	3
87.0	4.502362	0	0
88.0	4.502362	0	0
89.0	4.502362	1	1
90.0	4.502362	1	1
91.0	4.502362	1	1
92.0	4.502362	2	2
93.0	4.502362	3	3
94.0	4.502362	1	1
95.0	4.502362	0	0
96.0	4.502362	4	4
97.0	4.502362	2	2
98.0	4.502362	0	0
99.0	4.502362	3	3
100.0	4.502362	0	0
105.0	0	1	1
110.0	0	1	1
111.0	0	1	1
112.0	0	1	1
114.0	0	1	1
115.0	0	1	1
116.0	0	1	1
118.0	0	1	1
119.0	0	1	1
123.0	0	1	1
127.0	0	1	1
135.0	0	1	1
136.0	0	1	1
137.0	0	1	1
141.0	0	1	1
145.0	0	2	2
148.0	0	1	1
167.0	0	1	1
199.0	0	1	1
213.0	0	1	1
232.0	0	1	1
242.0	0	1	1
279.0	0	1	1
280.0	0	1	1
285.0	0	1	1
325.0	0	1	1
326.0	0	1	1
328.0	0	1	1
396.0	0	1	1
412.0	0	1	1
490.0	0	1	1
581.0	0	1	1
689.0	0	1	1
792.0	0	1	1
17756.0	0	1	1