## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-237-TP2.bam --OUTPUT ACR-237-TP2.md.bam --METRICS_FILE ACR-237-TP2.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 18:13:40 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	187	11927400	2587117	0	126	8007176	3121072	0.671326	4597178

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.085103	1201744	0	1571209
2.0	1.166142	928897	650668	1125240
3.0	1.172194	648167	283990	644157
4.0	1.172646	417084	153888	312124
5.0	1.17268	258349	91180	138394
6.0	1.172682	159170	56462	59569
7.0	1.172682	99936	35230	26952
8.0	1.172682	63632	22539	13528
9.0	1.172682	41996	14429	7413
10.0	1.172682	28483	9422	4541
11.0	1.172682	19352	6061	3125
12.0	1.172682	13510	3937	2234
13.0	1.172682	9454	2555	1774
14.0	1.172682	6816	1728	1362
15.0	1.172682	4942	1129	1083
16.0	1.172682	3558	748	878
17.0	1.172682	2699	530	755
18.0	1.172682	1965	320	616
19.0	1.172682	1593	269	509
20.0	1.172682	1211	166	431
21.0	1.172682	927	109	374
22.0	1.172682	768	94	377
23.0	1.172682	643	73	280
24.0	1.172682	528	60	268
25.0	1.172682	421	48	250
26.0	1.172682	385	31	200
27.0	1.172682	320	31	153
28.0	1.172682	278	25	142
29.0	1.172682	220	20	142
30.0	1.172682	211	19	126
31.0	1.172682	205	16	129
32.0	1.172682	168	16	114
33.0	1.172682	168	12	120
34.0	1.172682	152	15	89
35.0	1.172682	129	6	110
36.0	1.172682	134	3	78
37.0	1.172682	130	6	71
38.0	1.172682	112	4	79
39.0	1.172682	88	4	49
40.0	1.172682	94	3	60
41.0	1.172682	59	10	47
42.0	1.172682	77	6	61
43.0	1.172682	63	2	42
44.0	1.172682	60	1	32
45.0	1.172682	60	0	47
46.0	1.172682	56	3	40
47.0	1.172682	45	1	33
48.0	1.172682	47	1	31
49.0	1.172682	51	7	26
50.0	1.172682	41	2	33
51.0	1.172682	38	3	34
52.0	1.172682	48	1	26
53.0	1.172682	44	0	24
54.0	1.172682	44	0	25
55.0	1.172682	33	1	22
56.0	1.172682	22	1	25
57.0	1.172682	26	2	23
58.0	1.172682	34	1	18
59.0	1.172682	25	0	19
60.0	1.172682	21	0	18
61.0	1.172682	27	1	17
62.0	1.172682	20	1	19
63.0	1.172682	24	0	13
64.0	1.172682	23	0	15
65.0	1.172682	21	0	18
66.0	1.172682	19	0	13
67.0	1.172682	18	1	14
68.0	1.172682	13	1	15
69.0	1.172682	21	2	12
70.0	1.172682	15	0	16
71.0	1.172682	15	0	7
72.0	1.172682	16	1	7
73.0	1.172682	15	0	12
74.0	1.172682	11	0	14
75.0	1.172682	13	1	12
76.0	1.172682	13	1	7
77.0	1.172682	14	1	8
78.0	1.172682	11	1	2
79.0	1.172682	7	1	9
80.0	1.172682	9	0	5
81.0	1.172682	9	0	8
82.0	1.172682	9	1	10
83.0	1.172682	6	0	7
84.0	1.172682	7	0	4
85.0	1.172682	7	0	5
86.0	1.172682	7	0	10
87.0	1.172682	13	0	10
88.0	1.172682	11	1	7
89.0	1.172682	9	0	4
90.0	1.172682	6	0	5
91.0	1.172682	10	0	3
92.0	1.172682	5	0	4
93.0	1.172682	4	0	5
94.0	1.172682	8	0	4
95.0	1.172682	10	1	8
96.0	1.172682	8	1	2
97.0	1.172682	7	0	3
98.0	1.172682	6	0	5
99.0	1.172682	3	0	5
100.0	1.172682	6	0	2
101.0	0	7	0	3
102.0	0	5	0	2
103.0	0	5	0	6
104.0	0	2	0	1
105.0	0	1	0	1
106.0	0	5	0	1
107.0	0	2	0	3
108.0	0	0	0	4
109.0	0	2	0	2
110.0	0	3	0	3
111.0	0	4	0	2
112.0	0	5	1	4
113.0	0	4	0	2
114.0	0	1	0	1
115.0	0	3	0	1
116.0	0	3	0	5
117.0	0	5	0	1
118.0	0	4	0	1
119.0	0	2	0	0
120.0	0	7	0	2
121.0	0	4	0	2
122.0	0	0	1	3
123.0	0	1	0	2
124.0	0	3	1	3
125.0	0	4	0	2
126.0	0	3	0	1
127.0	0	3	1	2
128.0	0	3	0	3
129.0	0	3	0	2
130.0	0	1	0	2
131.0	0	2	0	2
132.0	0	3	0	1
133.0	0	1	1	0
134.0	0	3	0	2
135.0	0	1	0	0
136.0	0	3	0	1
137.0	0	4	0	1
138.0	0	2	0	0
139.0	0	1	0	0
140.0	0	5	0	1
141.0	0	0	0	1
142.0	0	2	0	0
143.0	0	2	0	1
144.0	0	3	0	3
145.0	0	3	0	2
146.0	0	3	0	1
147.0	0	1	0	1
148.0	0	0	0	1
149.0	0	1	0	1
151.0	0	1	0	0
152.0	0	3	0	3
153.0	0	0	0	3
155.0	0	3	0	0
156.0	0	1	0	1
157.0	0	1	0	0
158.0	0	1	0	3
159.0	0	0	0	1
160.0	0	1	0	0
162.0	0	1	0	2
164.0	0	1	0	2
165.0	0	3	0	1
166.0	0	1	0	0
167.0	0	1	0	1
168.0	0	4	0	0
169.0	0	1	0	1
170.0	0	1	0	0
171.0	0	0	0	2
172.0	0	0	0	1
173.0	0	1	0	0
175.0	0	2	0	1
176.0	0	1	0	2
179.0	0	3	0	1
180.0	0	1	0	0
181.0	0	2	0	0
182.0	0	1	0	0
184.0	0	0	1	0
185.0	0	2	0	0
186.0	0	1	0	0
190.0	0	1	0	1
191.0	0	0	0	1
194.0	0	0	0	1
195.0	0	1	0	0
197.0	0	0	0	1
201.0	0	0	0	1
203.0	0	1	0	0
205.0	0	1	0	0
206.0	0	1	0	1
208.0	0	1	0	1
209.0	0	1	0	0
213.0	0	0	0	1
214.0	0	1	0	0
215.0	0	1	0	1
222.0	0	1	0	0
223.0	0	0	0	1
224.0	0	0	0	1
225.0	0	1	0	0
228.0	0	1	0	0
232.0	0	1	0	0
238.0	0	1	0	0
240.0	0	1	0	1
241.0	0	0	0	2
247.0	0	1	0	0
250.0	0	0	0	1
252.0	0	1	0	0
260.0	0	0	0	1
262.0	0	1	0	0
270.0	0	1	0	1
277.0	0	0	0	1
278.0	0	1	0	0
279.0	0	1	0	1
280.0	0	1	0	0
281.0	0	1	0	0
283.0	0	0	0	1
287.0	0	1	0	0
291.0	0	1	0	0
292.0	0	1	0	0
295.0	0	0	0	1
299.0	0	0	0	1
307.0	0	0	0	1
311.0	0	1	0	0
320.0	0	1	0	0
322.0	0	0	0	1
325.0	0	0	0	1
335.0	0	1	0	0
343.0	0	0	0	1
345.0	0	0	0	1
346.0	0	1	0	0
351.0	0	1	0	0
355.0	0	0	0	1
358.0	0	1	0	0
369.0	0	0	0	1
370.0	0	1	0	0
371.0	0	1	0	0
375.0	0	1	0	0
383.0	0	0	0	1
387.0	0	0	0	1
393.0	0	1	0	0
398.0	0	1	0	0
403.0	0	0	0	1
408.0	0	0	0	1
436.0	0	1	0	0
439.0	0	0	0	1
461.0	0	1	0	0
529.0	0	1	0	0
599.0	0	0	0	1
615.0	0	0	0	1
620.0	0	1	0	0
639.0	0	1	0	0