## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-229-TP2.bam --OUTPUT ACR-229-TP2.md.bam --METRICS_FILE ACR-229-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 18:14:49 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	160	15091177	3413337	0	97	8189458	3905314	0.542666	10570403

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.164194	3348324	0	4362271
2.0	1.443443	1709892	1061950	1682912
3.0	1.510425	850358	419797	547961
4.0	1.526491	427370	207803	171613
5.0	1.530345	225908	111118	59970
6.0	1.531269	126091	60749	25619
7.0	1.531491	73479	34660	13638
8.0	1.531544	44763	19716	8251
9.0	1.531557	28300	11191	5763
10.0	1.53156	18122	6608	4105
11.0	1.531561	12052	3895	2989
12.0	1.531561	8207	2366	2498
13.0	1.531561	5653	1409	1901
14.0	1.531561	4148	882	1479
15.0	1.531561	3077	566	1260
16.0	1.531561	2202	382	1082
17.0	1.531561	1767	275	854
18.0	1.531561	1424	195	737
19.0	1.531561	1130	151	704
20.0	1.531561	963	112	567
21.0	1.531561	901	81	501
22.0	1.531561	728	69	402
23.0	1.531561	549	60	367
24.0	1.531561	492	45	334
25.0	1.531561	454	38	249
26.0	1.531561	388	35	246
27.0	1.531561	347	27	242
28.0	1.531561	324	23	216
29.0	1.531561	309	19	216
30.0	1.531561	252	22	167
31.0	1.531561	214	20	173
32.0	1.531561	216	13	138
33.0	1.531561	193	10	136
34.0	1.531561	174	17	112
35.0	1.531561	165	10	132
36.0	1.531561	163	8	100
37.0	1.531561	149	7	95
38.0	1.531561	139	4	93
39.0	1.531561	122	4	73
40.0	1.531561	96	4	79
41.0	1.531561	115	3	72
42.0	1.531561	110	6	67
43.0	1.531561	92	2	57
44.0	1.531561	69	0	54
45.0	1.531561	86	3	59
46.0	1.531561	71	6	50
47.0	1.531561	68	7	41
48.0	1.531561	63	4	49
49.0	1.531561	59	2	48
50.0	1.531561	68	5	40
51.0	1.531561	59	5	45
52.0	1.531561	53	3	35
53.0	1.531561	46	2	29
54.0	1.531561	47	1	43
55.0	1.531561	44	3	34
56.0	1.531561	43	2	23
57.0	1.531561	34	1	22
58.0	1.531561	39	2	31
59.0	1.531561	25	1	25
60.0	1.531561	25	3	30
61.0	1.531561	36	1	28
62.0	1.531561	31	1	20
63.0	1.531561	32	2	19
64.0	1.531561	26	1	11
65.0	1.531561	29	0	14
66.0	1.531561	25	0	18
67.0	1.531561	13	0	23
68.0	1.531561	27	0	13
69.0	1.531561	26	0	14
70.0	1.531561	28	1	7
71.0	1.531561	17	0	15
72.0	1.531561	17	1	11
73.0	1.531561	17	0	13
74.0	1.531561	23	0	7
75.0	1.531561	18	0	8
76.0	1.531561	10	0	7
77.0	1.531561	14	0	9
78.0	1.531561	11	1	7
79.0	1.531561	7	0	13
80.0	1.531561	14	1	11
81.0	1.531561	11	0	8
82.0	1.531561	15	0	7
83.0	1.531561	11	0	9
84.0	1.531561	8	0	12
85.0	1.531561	11	0	6
86.0	1.531561	8	0	10
87.0	1.531561	16	1	9
88.0	1.531561	14	0	7
89.0	1.531561	7	0	2
90.0	1.531561	13	0	6
91.0	1.531561	11	0	3
92.0	1.531561	8	2	1
93.0	1.531561	2	1	7
94.0	1.531561	6	1	6
95.0	1.531561	5	0	12
96.0	1.531561	6	0	4
97.0	1.531561	10	0	4
98.0	1.531561	5	0	4
99.0	1.531561	4	0	8
100.0	1.531561	8	1	6
101.0	0	9	0	7
102.0	0	5	0	0
103.0	0	9	0	3
104.0	0	3	0	6
105.0	0	7	0	5
106.0	0	6	0	3
107.0	0	4	1	6
108.0	0	4	0	2
109.0	0	5	0	1
110.0	0	2	0	4
111.0	0	6	0	6
112.0	0	3	0	2
113.0	0	2	0	3
114.0	0	2	0	1
115.0	0	5	0	3
116.0	0	4	0	7
117.0	0	9	1	2
118.0	0	4	1	2
119.0	0	3	1	1
120.0	0	2	0	7
121.0	0	3	0	2
122.0	0	2	0	0
123.0	0	6	0	1
124.0	0	1	0	3
125.0	0	2	0	3
126.0	0	4	0	1
127.0	0	4	0	7
128.0	0	2	0	0
129.0	0	3	0	2
130.0	0	6	0	2
131.0	0	1	0	2
132.0	0	3	0	2
133.0	0	0	0	4
134.0	0	2	0	2
135.0	0	4	0	2
136.0	0	2	0	2
137.0	0	2	0	3
138.0	0	1	0	4
139.0	0	5	1	1
140.0	0	3	0	5
141.0	0	2	0	2
142.0	0	5	0	1
143.0	0	1	0	0
144.0	0	3	0	1
145.0	0	2	0	2
146.0	0	2	0	2
147.0	0	4	0	0
148.0	0	1	0	0
149.0	0	3	0	0
150.0	0	2	0	1
151.0	0	5	0	3
152.0	0	2	0	1
153.0	0	2	0	3
154.0	0	3	0	1
155.0	0	0	0	1
156.0	0	2	0	3
157.0	0	2	0	3
158.0	0	1	0	0
159.0	0	3	0	0
160.0	0	1	0	0
162.0	0	2	0	0
163.0	0	2	0	1
164.0	0	1	0	1
165.0	0	1	0	0
166.0	0	2	0	1
167.0	0	0	0	2
168.0	0	2	0	0
169.0	0	1	0	1
170.0	0	4	0	0
172.0	0	1	0	4
174.0	0	1	0	1
175.0	0	1	0	0
176.0	0	2	0	3
177.0	0	2	0	0
178.0	0	2	0	0
179.0	0	1	0	0
180.0	0	0	0	1
182.0	0	0	0	1
183.0	0	0	0	1
185.0	0	1	0	0
186.0	0	0	0	1
188.0	0	1	0	1
191.0	0	0	0	1
192.0	0	1	0	1
193.0	0	2	0	1
194.0	0	1	0	1
195.0	0	1	0	0
196.0	0	0	0	2
197.0	0	2	0	0
200.0	0	2	0	2
201.0	0	1	0	2
202.0	0	2	0	0
205.0	0	1	0	1
206.0	0	1	0	0
207.0	0	0	0	1
208.0	0	0	0	2
209.0	0	1	0	1
210.0	0	2	0	0
211.0	0	0	0	1
212.0	0	1	0	0
213.0	0	2	0	0
214.0	0	3	0	0
215.0	0	0	0	1
216.0	0	0	0	2
217.0	0	1	0	1
218.0	0	0	0	2
219.0	0	0	0	1
220.0	0	2	0	2
222.0	0	1	0	0
223.0	0	1	0	0
225.0	0	2	0	0
227.0	0	1	0	0
228.0	0	3	0	1
230.0	0	1	0	0
231.0	0	1	0	0
234.0	0	0	0	1
235.0	0	0	0	2
236.0	0	1	0	0
237.0	0	0	0	1
239.0	0	2	0	0
240.0	0	1	0	0
242.0	0	1	0	0
243.0	0	1	0	0
244.0	0	1	0	0
246.0	0	2	0	0
251.0	0	0	0	1
254.0	0	1	0	1
257.0	0	1	0	0
259.0	0	0	0	1
263.0	0	0	0	1
264.0	0	1	0	0
276.0	0	0	0	1
283.0	0	0	0	1
285.0	0	0	0	1
286.0	0	0	0	1
289.0	0	1	0	0
292.0	0	0	0	1
293.0	0	1	0	0
295.0	0	1	0	0
301.0	0	0	0	1
302.0	0	1	0	0
303.0	0	1	0	0
309.0	0	0	0	2
315.0	0	1	0	0
319.0	0	0	0	1
321.0	0	1	0	0
322.0	0	1	0	0
324.0	0	1	0	0
331.0	0	0	0	1
342.0	0	1	0	0
348.0	0	1	0	0
350.0	0	1	0	0
351.0	0	0	0	1
360.0	0	1	0	0
363.0	0	0	0	1
374.0	0	1	0	0
386.0	0	0	0	1
389.0	0	0	0	1
404.0	0	1	0	0
405.0	0	0	0	1
408.0	0	0	0	1
409.0	0	1	0	0
417.0	0	1	0	0
426.0	0	1	0	0
460.0	0	0	0	1
479.0	0	0	0	1
495.0	0	0	0	1
502.0	0	1	0	0
517.0	0	1	0	0
521.0	0	1	0	0
524.0	0	0	0	1
533.0	0	1	0	0
552.0	0	0	0	1
619.0	0	0	0	1
626.0	0	0	0	1
629.0	0	1	0	0
637.0	0	1	0	0
649.0	0	1	0	0
737.0	0	0	0	1
758.0	0	1	0	0
831.0	0	0	0	1
893.0	0	1	0	0