## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-186-TP1.bam --OUTPUT ACR-186-TP1.md.bam --METRICS_FILE ACR-186-TP1.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 18:15:23 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	326	8478682	1624754	0	247	7532535	1497531	0.888406	946741

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000499	84597	0	90236
2.0	1.000628	37212	175016	43517
3.0	1.000628	37986	83002	49649
4.0	1.000628	46626	47588	64012
5.0	1.000628	57905	31587	79781
6.0	1.000628	67550	22920	90375
7.0	1.000628	74548	17163	95106
8.0	1.000628	76768	13322	91433
9.0	1.000628	75124	10648	82364
10.0	1.000628	69060	8469	68636
11.0	1.000628	61018	6529	53840
12.0	1.000628	51634	5361	40103
13.0	1.000628	42139	4303	28132
14.0	1.000628	33835	3187	19828
15.0	1.000628	26638	2567	13475
16.0	1.000628	20937	2048	9152
17.0	1.000628	16312	1605	6187
18.0	1.000628	12965	1236	4435
19.0	1.000628	9990	898	3268
20.0	1.000628	7985	772	2468
21.0	1.000628	6576	551	1977
22.0	1.000628	5193	462	1582
23.0	1.000628	4396	296	1237
24.0	1.000628	3525	267	1038
25.0	1.000628	2741	200	702
26.0	1.000628	2364	127	613
27.0	1.000628	1871	98	480
28.0	1.000628	1457	97	356
29.0	1.000628	1265	64	297
30.0	1.000628	1035	38	230
31.0	1.000628	805	24	200
32.0	1.000628	662	25	144
33.0	1.000628	534	18	136
34.0	1.000628	435	16	112
35.0	1.000628	337	6	112
36.0	1.000628	275	8	89
37.0	1.000628	261	5	72
38.0	1.000628	195	3	77
39.0	1.000628	177	8	57
40.0	1.000628	138	3	49
41.0	1.000628	130	0	49
42.0	1.000628	96	3	36
43.0	1.000628	77	1	46
44.0	1.000628	73	1	31
45.0	1.000628	73	0	36
46.0	1.000628	49	1	23
47.0	1.000628	42	1	26
48.0	1.000628	54	1	26
49.0	1.000628	31	0	19
50.0	1.000628	45	0	18
51.0	1.000628	26	2	18
52.0	1.000628	25	0	22
53.0	1.000628	22	0	14
54.0	1.000628	21	0	9
55.0	1.000628	22	0	13
56.0	1.000628	16	0	17
57.0	1.000628	17	0	14
58.0	1.000628	21	0	6
59.0	1.000628	12	0	11
60.0	1.000628	18	0	14
61.0	1.000628	13	0	12
62.0	1.000628	14	0	7
63.0	1.000628	10	0	7
64.0	1.000628	14	0	8
65.0	1.000628	9	0	7
66.0	1.000628	12	0	5
67.0	1.000628	7	0	3
68.0	1.000628	5	0	3
69.0	1.000628	4	0	5
70.0	1.000628	9	0	4
71.0	1.000628	7	0	6
72.0	1.000628	4	0	4
73.0	1.000628	5	0	4
74.0	1.000628	3	0	3
75.0	1.000628	7	0	4
76.0	1.000628	1	0	5
77.0	1.000628	3	0	0
78.0	1.000628	5	0	1
79.0	1.000628	5	0	3
80.0	1.000628	1	0	0
81.0	1.000628	0	0	2
82.0	1.000628	5	0	1
83.0	1.000628	4	0	4
84.0	1.000628	1	0	3
85.0	1.000628	3	0	1
86.0	1.000628	2	0	2
87.0	1.000628	3	0	2
88.0	1.000628	3	0	0
89.0	1.000628	2	0	0
90.0	1.000628	0	0	1
91.0	1.000628	1	0	1
92.0	1.000628	2	0	1
93.0	1.000628	1	0	2
94.0	1.000628	1	0	1
95.0	1.000628	1	0	1
96.0	1.000628	2	0	1
97.0	1.000628	1	0	3
98.0	1.000628	4	0	1
99.0	1.000628	0	0	1
100.0	1.000628	0	0	0
102.0	0	1	0	0
104.0	0	2	0	0
105.0	0	0	0	3
106.0	0	0	0	1
107.0	0	3	0	0
109.0	0	1	0	1
110.0	0	1	0	0
111.0	0	1	0	2
113.0	0	3	0	0
114.0	0	1	0	1
115.0	0	1	0	1
118.0	0	1	0	1
120.0	0	2	0	0
123.0	0	1	0	0
126.0	0	1	0	0
130.0	0	0	0	2
132.0	0	1	0	0
134.0	0	0	0	1
136.0	0	1	0	0
138.0	0	1	0	1
140.0	0	1	0	0
153.0	0	0	0	1
155.0	0	1	0	1
159.0	0	0	0	1
161.0	0	1	0	0
162.0	0	0	0	1
164.0	0	1	0	0
166.0	0	1	0	0
177.0	0	0	0	1
179.0	0	0	0	1
184.0	0	1	0	0
194.0	0	1	0	0
246.0	0	0	0	1
249.0	0	1	0	0
251.0	0	0	0	1
255.0	0	1	0	0
278.0	0	0	0	1
288.0	0	1	0	0