## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-139-TP4.bam --OUTPUT ACR-139-TP4.md.bam --METRICS_FILE ACR-139-TP4.md.MarkDuplicates.metrics.txt --ASSUME_SORTED true --VALIDATION_STRINGENCY LENIENT --REFERENCE_SEQUENCE Apulcra-genome.fa --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_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_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 --REMOVE_DUPLICATES 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 --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
## htsjdk.samtools.metrics.StringHeader
# Started on: Tue Jul 22 18:14:27 GMT 2025

## 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	265	15560517	3790757	0	180	8784516	3804505	0.56454	9592052

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.136072	2950209	0	3768998
2.0	1.360399	1731905	1024140	1845909
3.0	1.404694	946300	404408	736299
4.0	1.41344	502186	200254	261960
5.0	1.415167	267841	109028	91428
6.0	1.415508	148764	61248	34259
7.0	1.415575	85922	35193	14589
8.0	1.415589	51299	20424	7292
9.0	1.415591	31658	11639	4124
10.0	1.415592	19869	6966	2679
11.0	1.415592	12637	4144	1694
12.0	1.415592	8141	2469	1218
13.0	1.415592	5466	1347	994
14.0	1.415592	3683	907	720
15.0	1.415592	2492	509	598
16.0	1.415592	1674	315	449
17.0	1.415592	1236	179	350
18.0	1.415592	908	115	319
19.0	1.415592	604	76	226
20.0	1.415592	462	44	222
21.0	1.415592	380	34	183
22.0	1.415592	288	15	152
23.0	1.415592	280	16	119
24.0	1.415592	193	9	116
25.0	1.415592	176	5	86
26.0	1.415592	140	7	92
27.0	1.415592	110	0	82
28.0	1.415592	110	4	52
29.0	1.415592	88	0	60
30.0	1.415592	63	3	50
31.0	1.415592	68	1	49
32.0	1.415592	73	3	41
33.0	1.415592	51	2	35
34.0	1.415592	46	0	32
35.0	1.415592	34	0	40
36.0	1.415592	35	0	26
37.0	1.415592	38	0	27
38.0	1.415592	43	3	25
39.0	1.415592	27	0	26
40.0	1.415592	34	1	21
41.0	1.415592	28	0	29
42.0	1.415592	22	1	22
43.0	1.415592	34	1	14
44.0	1.415592	16	0	12
45.0	1.415592	15	0	16
46.0	1.415592	20	0	15
47.0	1.415592	19	1	12
48.0	1.415592	12	1	11
49.0	1.415592	12	0	11
50.0	1.415592	19	0	17
51.0	1.415592	18	0	6
52.0	1.415592	11	0	11
53.0	1.415592	11	0	6
54.0	1.415592	7	0	10
55.0	1.415592	6	0	2
56.0	1.415592	8	0	6
57.0	1.415592	4	0	8
58.0	1.415592	6	0	3
59.0	1.415592	10	2	6
60.0	1.415592	9	0	7
61.0	1.415592	5	0	6
62.0	1.415592	2	0	10
63.0	1.415592	7	0	8
64.0	1.415592	15	0	8
65.0	1.415592	8	0	5
66.0	1.415592	5	1	2
67.0	1.415592	10	0	5
68.0	1.415592	7	0	5
69.0	1.415592	3	2	4
70.0	1.415592	2	0	1
71.0	1.415592	4	0	1
72.0	1.415592	2	0	1
73.0	1.415592	4	0	8
74.0	1.415592	5	0	3
75.0	1.415592	5	0	5
76.0	1.415592	5	0	3
77.0	1.415592	6	0	2
78.0	1.415592	3	0	2
79.0	1.415592	4	0	0
80.0	1.415592	1	0	1
81.0	1.415592	6	0	1
82.0	1.415592	3	0	2
83.0	1.415592	1	0	0
84.0	1.415592	1	0	0
85.0	1.415592	1	0	2
86.0	1.415592	1	0	0
87.0	1.415592	1	0	4
88.0	1.415592	1	0	1
89.0	1.415592	0	0	2
90.0	1.415592	6	0	0
91.0	1.415592	0	1	1
92.0	1.415592	1	0	2
93.0	1.415592	3	0	2
94.0	1.415592	2	0	0
95.0	1.415592	2	0	2
96.0	1.415592	0	0	0
97.0	1.415592	0	0	0
98.0	1.415592	2	0	0
99.0	1.415592	2	0	0
100.0	1.415592	1	0	0
101.0	0	1	0	0
102.0	0	1	0	3
103.0	0	0	0	1
104.0	0	1	0	2
105.0	0	0	0	3
106.0	0	1	0	0
107.0	0	2	0	1
108.0	0	2	0	1
109.0	0	2	0	0
110.0	0	2	0	1
111.0	0	1	0	0
112.0	0	0	1	1
114.0	0	1	0	0
116.0	0	0	0	1
117.0	0	1	0	3
118.0	0	1	0	0
119.0	0	0	0	2
120.0	0	3	0	0
121.0	0	1	0	0
124.0	0	0	0	1
125.0	0	1	0	0
126.0	0	2	0	0
128.0	0	0	0	1
129.0	0	1	0	0
130.0	0	1	0	1
132.0	0	1	0	0
136.0	0	0	0	1
138.0	0	0	0	1
140.0	0	1	0	0
141.0	0	1	0	0
146.0	0	0	0	1
147.0	0	1	0	0
148.0	0	0	0	1
152.0	0	1	0	0
153.0	0	1	0	1
155.0	0	0	0	1
159.0	0	1	0	0
165.0	0	1	0	0
173.0	0	1	0	0
180.0	0	0	0	1
182.0	0	0	0	1
183.0	0	1	0	0
190.0	0	1	0	0
194.0	0	0	0	1
198.0	0	1	0	0
204.0	0	0	0	1
206.0	0	0	0	1
207.0	0	1	0	0
208.0	0	1	0	0
215.0	0	0	0	1
218.0	0	1	0	0
228.0	0	1	0	0
238.0	0	0	0	1
255.0	0	1	0	0
290.0	0	0	0	1
296.0	0	1	0	0
332.0	0	0	0	1
422.0	0	1	0	0