## 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-GSM1606192.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606192.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606192.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 15:09:25 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	24798120	3720000	0	0	2489375	0	0.100386	115102008

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	20729641	20729641
2.0	1.806183	1179354	1179354
3.0	2.456114	223999	223999
4.0	2.980077	79018	79018
5.0	3.402487	36683	36683
6.0	3.743026	19962	19962
7.0	4.017564	11826	11826
8.0	4.238891	7816	7816
9.0	4.417321	5027	5027
10.0	4.561168	3478	3478
11.0	4.677136	2573	2573
12.0	4.770626	1859	1859
13.0	4.845997	1367	1367
14.0	4.90676	1103	1103
15.0	4.955745	851	851
16.0	4.995237	689	689
17.0	5.027074	528	528
18.0	5.052741	460	460
19.0	5.073433	350	350
20.0	5.090115	285	285
21.0	5.103563	276	276
22.0	5.114405	198	198
23.0	5.123145	164	164
24.0	5.130192	146	146
25.0	5.135873	109	109
26.0	5.140452	110	110
27.0	5.144144	91	91
28.0	5.147121	91	91
29.0	5.149521	64	64
30.0	5.151455	66	66
31.0	5.153015	57	57
32.0	5.154272	49	49
33.0	5.155286	40	40
34.0	5.156103	41	41
35.0	5.156762	34	34
36.0	5.157293	28	28
37.0	5.157721	21	21
38.0	5.158066	30	30
39.0	5.158344	23	23
40.0	5.158569	16	16
41.0	5.158749	24	24
42.0	5.158895	16	16
43.0	5.159013	7	7
44.0	5.159108	18	18
45.0	5.159184	8	8
46.0	5.159246	15	15
47.0	5.159295	9	9
48.0	5.159335	11	11
49.0	5.159367	6	6
50.0	5.159393	7	7
51.0	5.159414	3	3
52.0	5.159431	7	7
53.0	5.159445	6	6
54.0	5.159456	14	14
55.0	5.159465	7	7
56.0	5.159472	7	7
57.0	5.159478	2	2
58.0	5.159482	6	6
59.0	5.159486	3	3
60.0	5.159489	2	2
61.0	5.159492	4	4
62.0	5.159494	0	0
63.0	5.159495	1	1
64.0	5.159496	1	1
65.0	5.159497	1	1
66.0	5.159498	0	0
67.0	5.159499	1	1
68.0	5.159499	2	2
69.0	5.1595	2	2
70.0	5.1595	3	3
71.0	5.159501	1	1
72.0	5.159501	1	1
73.0	5.159501	5	5
74.0	5.159501	0	0
75.0	5.159501	1	1
76.0	5.159501	1	1
77.0	5.159501	0	0
78.0	5.159501	1	1
79.0	5.159502	1	1
80.0	5.159502	0	0
81.0	5.159502	0	0
82.0	5.159502	1	1
83.0	5.159502	0	0
84.0	5.159502	1	1
85.0	5.159502	1	1
86.0	5.159502	1	1
87.0	5.159502	0	0
88.0	5.159502	0	0
89.0	5.159502	0	0
90.0	5.159502	0	0
91.0	5.159502	0	0
92.0	5.159502	2	2
93.0	5.159502	0	0
94.0	5.159502	0	0
95.0	5.159502	2	2
96.0	5.159502	0	0
97.0	5.159502	0	0
98.0	5.159502	1	1
99.0	5.159502	2	2
100.0	5.159502	0	0
106.0	0	1	1
109.0	0	2	2
112.0	0	1	1
131.0	0	1	1
134.0	0	1	1
376.0	0	1	1