## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT DE-H3K9me3_R1.target.filtered.sorted.bam --OUTPUT DE-H3K9me3_R1.target.markdup.bam --METRICS_FILE DE-H3K9me3_R1.target.markdup.MarkDuplicates.metrics.txt --REMOVE_DUPLICATES false --ASSUME_SORT_ORDER coordinate --TMP_DIR tmp --VALIDATION_STRINGENCY LENIENT --REFERENCE_SEQUENCE GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --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 --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
## htsjdk.samtools.metrics.StringHeader
# Started on: Thu Jun 15 15:10:37 GMT 2023

## 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	9433736	0	0	0	243663	1827	0.025829	180770581

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000189	8953702	0	8955393
2.0	1.94952	230502	1827	228940
3.0	2.85058	5364	0	5242
4.0	3.705822	287	0	280
5.0	4.517578	73	0	73
6.0	5.288057	37	0	37
7.0	6.019359	24	0	24
8.0	6.713476	19	0	19
9.0	7.372298	11	0	11
10.0	7.997621	14	0	14
11.0	8.591147	8	0	8
12.0	9.154494	6	0	6
13.0	9.689196	7	0	7
14.0	10.196709	1	0	1
15.0	10.678416	0	0	0
16.0	11.13563	4	0	4
17.0	11.569595	3	0	3
18.0	11.981494	1	0	1
19.0	12.372449	0	0	0
20.0	12.743524	3	0	3
21.0	13.095731	0	0	0
22.0	13.430029	2	0	2
23.0	13.747329	0	0	0
24.0	14.048495	2	0	2
25.0	14.334347	0	0	0
26.0	14.605664	0	0	0
27.0	14.863185	1	0	1
28.0	15.107612	1	0	1
29.0	15.33961	0	0	0
30.0	15.559811	0	0	0
31.0	15.768816	0	0	0
32.0	15.967193	0	0	0
33.0	16.155483	0	0	0
34.0	16.3342	0	0	0
35.0	16.503828	0	0	0
36.0	16.664832	0	0	0
37.0	16.817648	0	0	0
38.0	16.962695	0	0	0
39.0	17.100366	1	0	1
40.0	17.231037	0	0	0
41.0	17.355063	0	0	0
42.0	17.472783	0	0	0
43.0	17.584517	0	0	0
44.0	17.69057	0	0	0
45.0	17.79123	0	0	0
46.0	17.886772	0	0	0
47.0	17.977455	0	0	0
48.0	18.063528	0	0	0
49.0	18.145224	0	0	0
50.0	18.222766	0	0	0
51.0	18.296365	0	0	0
52.0	18.366221	0	0	0
53.0	18.432526	0	0	0
54.0	18.495459	0	0	0
55.0	18.555192	0	0	0
56.0	18.611888	0	0	0
57.0	18.665701	0	0	0
58.0	18.716778	0	0	0
59.0	18.765257	0	0	0
60.0	18.811272	0	0	0
61.0	18.854947	0	0	0
62.0	18.896401	0	0	0
63.0	18.935747	0	0	0
64.0	18.973092	0	0	0
65.0	19.008539	0	0	0
66.0	19.042183	0	0	0
67.0	19.074116	0	0	0
68.0	19.104426	0	0	0
69.0	19.133194	0	0	0
70.0	19.1605	0	0	0
71.0	19.186417	0	0	0
72.0	19.211017	0	0	0
73.0	19.234365	0	0	0
74.0	19.256527	0	0	0
75.0	19.277561	0	0	0
76.0	19.297526	0	0	0
77.0	19.316476	0	0	0
78.0	19.334462	0	0	0
79.0	19.351533	0	0	0
80.0	19.367737	0	0	0
81.0	19.383117	0	0	0
82.0	19.397714	0	0	0
83.0	19.41157	0	0	0
84.0	19.424721	0	0	0
85.0	19.437203	0	0	0
86.0	19.44905	0	0	0
87.0	19.460295	0	0	0
88.0	19.470968	0	0	0
89.0	19.481099	0	0	0
90.0	19.490714	0	0	0
91.0	19.499841	0	0	0
92.0	19.508503	0	0	0
93.0	19.516725	0	0	0
94.0	19.524529	0	0	0
95.0	19.531936	0	0	0
96.0	19.538967	0	0	0
97.0	19.54564	0	0	0
98.0	19.551973	0	0	0
99.0	19.557985	0	0	0
100.0	19.563691	0	0	0