## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-237-TP1.bam --OUTPUT ACR-237-TP1.md.bam --METRICS_FILE ACR-237-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 18:14:52 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	359	16377127	3377062	0	266	11193949	3185123	0.683512	5769468

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.047988	1403655	0	1719240
2.0	1.109304	1202664	853304	1426957
3.0	1.112891	911099	322470	952447
4.0	1.113101	616816	156098	534205
5.0	1.113113	390922	86156	268488
6.0	1.113114	240053	50183	129163
7.0	1.113114	145815	30469	62169
8.0	1.113114	90856	18729	31903
9.0	1.113114	56878	11447	17452
10.0	1.113114	36755	7259	10514
11.0	1.113114	24251	4666	6816
12.0	1.113114	16425	2910	4599
13.0	1.113114	11317	1864	3343
14.0	1.113114	8239	1127	2517
15.0	1.113114	5705	722	1902
16.0	1.113114	4114	468	1575
17.0	1.113114	3115	335	1231
18.0	1.113114	2380	192	1061
19.0	1.113114	1735	131	874
20.0	1.113114	1412	87	738
21.0	1.113114	1118	81	631
22.0	1.113114	955	42	523
23.0	1.113114	744	38	413
24.0	1.113114	635	25	406
25.0	1.113114	549	14	351
26.0	1.113114	484	11	294
27.0	1.113114	392	13	250
28.0	1.113114	341	9	241
29.0	1.113114	252	4	203
30.0	1.113114	279	5	190
31.0	1.113114	238	7	170
32.0	1.113114	201	4	153
33.0	1.113114	196	4	146
34.0	1.113114	176	1	125
35.0	1.113114	133	1	110
36.0	1.113114	133	2	111
37.0	1.113114	119	4	107
38.0	1.113114	127	2	92
39.0	1.113114	121	1	74
40.0	1.113114	99	2	77
41.0	1.113114	93	2	58
42.0	1.113114	99	0	77
43.0	1.113114	65	0	42
44.0	1.113114	74	1	58
45.0	1.113114	73	1	55
46.0	1.113114	58	0	49
47.0	1.113114	52	0	61
48.0	1.113114	53	0	40
49.0	1.113114	51	0	37
50.0	1.113114	60	1	29
51.0	1.113114	43	0	36
52.0	1.113114	44	0	37
53.0	1.113114	36	0	29
54.0	1.113114	34	0	38
55.0	1.113114	43	0	28
56.0	1.113114	27	0	27
57.0	1.113114	36	1	23
58.0	1.113114	27	0	23
59.0	1.113114	30	0	20
60.0	1.113114	28	0	24
61.0	1.113114	21	1	18
62.0	1.113114	29	0	20
63.0	1.113114	21	0	14
64.0	1.113114	23	0	19
65.0	1.113114	21	0	13
66.0	1.113114	17	0	12
67.0	1.113114	17	0	12
68.0	1.113114	13	0	17
69.0	1.113114	26	0	23
70.0	1.113114	11	0	11
71.0	1.113114	8	1	16
72.0	1.113114	15	0	10
73.0	1.113114	18	0	6
74.0	1.113114	13	1	12
75.0	1.113114	12	0	15
76.0	1.113114	14	0	13
77.0	1.113114	11	0	6
78.0	1.113114	8	0	6
79.0	1.113114	17	0	7
80.0	1.113114	9	0	10
81.0	1.113114	11	0	7
82.0	1.113114	9	0	9
83.0	1.113114	7	0	5
84.0	1.113114	14	0	8
85.0	1.113114	10	0	10
86.0	1.113114	10	0	8
87.0	1.113114	7	0	4
88.0	1.113114	10	0	5
89.0	1.113114	3	0	3
90.0	1.113114	10	0	3
91.0	1.113114	3	0	8
92.0	1.113114	2	0	6
93.0	1.113114	6	0	5
94.0	1.113114	4	0	3
95.0	1.113114	5	0	3
96.0	1.113114	5	0	2
97.0	1.113114	5	0	4
98.0	1.113114	3	0	0
99.0	1.113114	5	0	3
100.0	1.113114	0	0	8
101.0	0	6	0	1
102.0	0	2	0	3
103.0	0	2	0	3
104.0	0	5	0	3
105.0	0	8	0	5
106.0	0	4	0	4
107.0	0	5	0	4
108.0	0	7	0	3
109.0	0	5	0	2
110.0	0	3	0	2
111.0	0	5	0	6
112.0	0	3	0	2
113.0	0	5	0	3
114.0	0	1	0	3
115.0	0	2	0	1
116.0	0	3	0	2
117.0	0	2	0	1
118.0	0	2	0	2
119.0	0	3	0	0
120.0	0	1	0	4
121.0	0	1	0	1
122.0	0	4	0	1
123.0	0	2	0	2
124.0	0	2	0	1
125.0	0	2	0	1
126.0	0	3	0	3
127.0	0	2	0	2
128.0	0	3	0	1
129.0	0	1	0	1
130.0	0	2	0	1
131.0	0	0	0	1
132.0	0	2	0	2
133.0	0	0	0	6
134.0	0	2	0	1
135.0	0	3	0	1
136.0	0	2	0	0
137.0	0	0	0	3
138.0	0	2	0	3
139.0	0	3	0	0
140.0	0	1	0	0
141.0	0	1	0	2
142.0	0	0	0	1
143.0	0	1	0	2
144.0	0	1	0	3
145.0	0	5	0	0
146.0	0	2	0	1
148.0	0	0	0	1
151.0	0	3	0	1
152.0	0	3	0	0
153.0	0	1	0	1
154.0	0	1	0	1
155.0	0	1	0	1
156.0	0	0	0	2
157.0	0	0	0	1
158.0	0	3	0	1
160.0	0	1	0	0
161.0	0	1	0	2
163.0	0	1	0	1
164.0	0	1	0	0
167.0	0	1	0	0
168.0	0	1	0	1
169.0	0	0	0	1
170.0	0	1	0	0
171.0	0	1	0	0
172.0	0	1	0	0
173.0	0	0	0	4
174.0	0	1	0	0
175.0	0	1	0	0
176.0	0	0	0	2
177.0	0	2	0	0
178.0	0	0	0	2
179.0	0	1	0	1
180.0	0	1	0	0
181.0	0	1	0	0
182.0	0	0	0	2
183.0	0	1	0	2
184.0	0	2	0	0
185.0	0	1	0	2
186.0	0	2	0	0
188.0	0	1	0	1
190.0	0	1	0	0
191.0	0	1	0	0
192.0	0	1	0	0
195.0	0	2	0	0
198.0	0	0	0	1
199.0	0	1	0	0
200.0	0	1	0	1
208.0	0	0	0	2
209.0	0	0	0	1
212.0	0	0	0	2
213.0	0	0	0	1
214.0	0	2	0	0
215.0	0	0	0	1
217.0	0	1	0	0
218.0	0	1	0	0
219.0	0	1	0	0
220.0	0	1	0	3
222.0	0	1	0	0
225.0	0	1	0	0
226.0	0	1	0	0
229.0	0	1	0	0
238.0	0	0	0	1
243.0	0	0	0	1
244.0	0	0	0	1
246.0	0	0	0	1
248.0	0	1	0	0
249.0	0	1	0	0
250.0	0	1	0	0
254.0	0	1	0	0
256.0	0	0	0	1
260.0	0	0	0	1
261.0	0	0	0	1
262.0	0	1	0	0
263.0	0	1	0	0
266.0	0	0	0	1
272.0	0	1	0	1
280.0	0	1	0	0
284.0	0	0	0	1
291.0	0	1	0	0
293.0	0	1	0	0
294.0	0	2	0	0
298.0	0	0	0	1
299.0	0	0	0	1
300.0	0	0	0	1
303.0	0	1	0	0
308.0	0	1	0	0
317.0	0	1	0	0
326.0	0	0	0	1
350.0	0	1	0	0
365.0	0	0	0	1
384.0	0	1	0	0
399.0	0	0	0	1
409.0	0	0	0	1
417.0	0	1	0	0
424.0	0	0	0	1
426.0	0	1	0	0
441.0	0	1	0	1
442.0	0	0	0	1
460.0	0	1	0	0
472.0	0	1	0	0
510.0	0	0	0	1
525.0	0	1	0	0
539.0	0	0	0	1
551.0	0	0	0	1
553.0	0	1	0	0
588.0	0	1	0	0
656.0	0	0	0	1
688.0	0	0	0	1
692.0	0	1	0	0
720.0	0	1	0	0
963.0	0	0	0	1
1019.0	0	1	0	0