## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-145-TP4.bam --OUTPUT ACR-145-TP4.md.bam --METRICS_FILE ACR-145-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 18:15:55 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	290	15064168	3340717	0	201	11485105	3067837	0.762412	3728395

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.023399	607905	0	728903
2.0	1.041401	619106	630362	775260
3.0	1.041718	593904	265985	715077
4.0	1.041724	498343	141056	540386
5.0	1.041724	379893	84250	352474
6.0	1.041724	271796	53753	205919
7.0	1.041724	186785	35421	112258
8.0	1.041724	126715	23460	59585
9.0	1.041724	85939	15699	32020
10.0	1.041724	58787	10765	18020
11.0	1.041724	40987	7260	10605
12.0	1.041724	28723	4775	6787
13.0	1.041724	20043	3312	4489
14.0	1.041724	14468	2219	3157
15.0	1.041724	10572	1560	2303
16.0	1.041724	7540	1065	1676
17.0	1.041724	5654	694	1316
18.0	1.041724	4352	481	1077
19.0	1.041724	3143	355	822
20.0	1.041724	2416	211	752
21.0	1.041724	1882	154	603
22.0	1.041724	1499	112	559
23.0	1.041724	1139	81	458
24.0	1.041724	919	62	377
25.0	1.041724	761	45	332
26.0	1.041724	599	35	289
27.0	1.041724	502	14	275
28.0	1.041724	417	15	242
29.0	1.041724	385	11	200
30.0	1.041724	312	14	218
31.0	1.041724	278	11	174
32.0	1.041724	251	9	174
33.0	1.041724	206	6	124
34.0	1.041724	168	8	132
35.0	1.041724	168	3	93
36.0	1.041724	144	6	100
37.0	1.041724	130	1	99
38.0	1.041724	119	2	87
39.0	1.041724	102	4	76
40.0	1.041724	93	2	73
41.0	1.041724	100	2	62
42.0	1.041724	107	2	72
43.0	1.041724	83	3	46
44.0	1.041724	74	2	61
45.0	1.041724	56	1	70
46.0	1.041724	57	1	53
47.0	1.041724	81	2	44
48.0	1.041724	59	0	47
49.0	1.041724	60	3	34
50.0	1.041724	50	3	37
51.0	1.041724	49	1	35
52.0	1.041724	51	0	39
53.0	1.041724	33	3	28
54.0	1.041724	40	0	34
55.0	1.041724	37	2	38
56.0	1.041724	27	0	24
57.0	1.041724	37	0	29
58.0	1.041724	34	0	21
59.0	1.041724	28	3	18
60.0	1.041724	25	0	23
61.0	1.041724	29	1	19
62.0	1.041724	19	1	24
63.0	1.041724	29	0	25
64.0	1.041724	22	0	8
65.0	1.041724	22	2	15
66.0	1.041724	18	2	15
67.0	1.041724	10	1	22
68.0	1.041724	14	1	13
69.0	1.041724	23	1	14
70.0	1.041724	17	0	12
71.0	1.041724	17	0	10
72.0	1.041724	20	0	16
73.0	1.041724	15	0	13
74.0	1.041724	11	0	11
75.0	1.041724	12	1	14
76.0	1.041724	16	0	9
77.0	1.041724	14	1	7
78.0	1.041724	17	0	14
79.0	1.041724	5	0	5
80.0	1.041724	17	0	11
81.0	1.041724	7	0	5
82.0	1.041724	10	0	13
83.0	1.041724	14	0	13
84.0	1.041724	12	0	8
85.0	1.041724	5	1	10
86.0	1.041724	5	0	7
87.0	1.041724	11	0	10
88.0	1.041724	9	0	6
89.0	1.041724	14	0	11
90.0	1.041724	6	0	12
91.0	1.041724	12	0	4
92.0	1.041724	9	0	7
93.0	1.041724	12	1	2
94.0	1.041724	12	0	5
95.0	1.041724	8	0	5
96.0	1.041724	6	0	5
97.0	1.041724	4	0	2
98.0	1.041724	6	0	3
99.0	1.041724	7	0	6
100.0	1.041724	7	0	8
101.0	0	3	0	3
102.0	0	4	0	4
103.0	0	3	0	3
104.0	0	5	1	4
105.0	0	5	0	3
106.0	0	6	0	5
107.0	0	2	0	4
108.0	0	5	0	4
109.0	0	5	0	3
110.0	0	4	0	5
111.0	0	3	0	2
112.0	0	4	0	3
113.0	0	4	0	2
114.0	0	4	0	2
115.0	0	2	0	2
116.0	0	4	0	6
117.0	0	1	0	3
118.0	0	3	0	5
119.0	0	2	0	2
120.0	0	3	0	4
121.0	0	8	0	3
122.0	0	4	0	5
123.0	0	5	0	8
124.0	0	1	0	2
125.0	0	4	0	1
126.0	0	5	0	4
127.0	0	3	0	1
128.0	0	5	0	2
129.0	0	5	0	2
130.0	0	1	0	1
131.0	0	1	0	2
132.0	0	1	0	4
133.0	0	0	0	1
134.0	0	5	0	2
135.0	0	1	0	0
136.0	0	2	0	1
137.0	0	1	0	0
138.0	0	1	0	4
139.0	0	3	0	1
140.0	0	6	0	1
141.0	0	1	0	2
142.0	0	4	0	3
143.0	0	2	0	1
144.0	0	1	0	4
145.0	0	6	0	3
146.0	0	1	0	0
147.0	0	2	0	1
148.0	0	1	0	1
149.0	0	4	0	1
150.0	0	4	0	1
151.0	0	0	0	3
152.0	0	1	0	1
153.0	0	3	0	1
154.0	0	1	0	1
155.0	0	2	0	2
156.0	0	4	0	3
157.0	0	2	0	0
158.0	0	2	0	1
159.0	0	2	0	2
160.0	0	1	0	0
161.0	0	0	0	3
162.0	0	0	0	4
163.0	0	2	0	1
164.0	0	1	0	1
166.0	0	4	0	5
167.0	0	3	0	1
168.0	0	0	0	3
169.0	0	2	0	2
170.0	0	1	0	0
171.0	0	2	0	1
172.0	0	0	0	1
173.0	0	1	0	2
174.0	0	1	0	1
175.0	0	2	0	0
176.0	0	0	0	2
177.0	0	3	0	0
178.0	0	4	0	1
179.0	0	2	0	0
180.0	0	0	0	2
181.0	0	0	0	1
183.0	0	2	0	2
184.0	0	1	0	1
185.0	0	0	0	1
186.0	0	3	0	0
187.0	0	2	0	1
188.0	0	0	0	2
189.0	0	2	0	0
190.0	0	2	0	0
191.0	0	0	0	1
192.0	0	0	0	1
193.0	0	1	0	0
195.0	0	0	0	2
197.0	0	0	0	2
198.0	0	1	0	0
199.0	0	1	0	0
201.0	0	1	0	1
202.0	0	2	0	0
203.0	0	3	0	0
204.0	0	1	0	0
205.0	0	1	0	1
208.0	0	4	0	0
210.0	0	0	0	2
212.0	0	0	0	1
213.0	0	0	0	2
214.0	0	0	0	2
215.0	0	1	0	0
217.0	0	0	0	1
218.0	0	3	0	1
219.0	0	0	0	2
220.0	0	1	0	0
221.0	0	0	0	1
222.0	0	3	0	0
223.0	0	1	0	1
227.0	0	0	0	1
228.0	0	2	0	1
229.0	0	1	0	2
230.0	0	1	0	0
235.0	0	1	0	0
236.0	0	0	0	3
237.0	0	2	0	1
239.0	0	1	0	1
240.0	0	1	0	0
241.0	0	2	0	0
242.0	0	1	0	0
243.0	0	1	0	0
244.0	0	0	0	1
246.0	0	0	0	1
248.0	0	2	0	0
249.0	0	1	0	0
250.0	0	1	0	0
253.0	0	1	0	0
254.0	0	1	0	0
255.0	0	2	0	0
259.0	0	1	0	1
264.0	0	0	0	1
268.0	0	0	0	1
270.0	0	0	0	1
272.0	0	0	0	2
274.0	0	1	0	1
275.0	0	0	0	2
276.0	0	1	0	0
277.0	0	0	0	1
279.0	0	0	0	1
281.0	0	1	0	0
282.0	0	1	0	0
287.0	0	0	0	1
289.0	0	2	0	0
291.0	0	1	0	1
294.0	0	0	0	1
296.0	0	1	0	0
297.0	0	1	0	1
298.0	0	1	0	0
299.0	0	1	0	0
302.0	0	1	0	1
303.0	0	0	0	1
306.0	0	0	0	1
309.0	0	1	0	0
310.0	0	1	0	0
315.0	0	0	0	1
318.0	0	2	0	1
320.0	0	1	0	0
321.0	0	0	0	1
322.0	0	0	0	1
329.0	0	1	0	0
333.0	0	1	0	0
335.0	0	0	0	1
338.0	0	1	0	0
339.0	0	1	0	0
340.0	0	0	0	1
341.0	0	1	0	0
348.0	0	1	0	0
359.0	0	0	0	1
362.0	0	0	0	1
363.0	0	1	0	0
368.0	0	0	0	1
378.0	0	1	0	0
394.0	0	1	0	0
398.0	0	0	0	1
404.0	0	0	0	1
416.0	0	0	0	1
418.0	0	0	0	1
422.0	0	1	0	0
432.0	0	1	0	0
438.0	0	0	0	1
453.0	0	1	0	0
456.0	0	1	0	0
462.0	0	1	0	0
466.0	0	0	0	1
474.0	0	1	0	0
551.0	0	0	0	1
558.0	0	1	0	0
559.0	0	0	0	1
584.0	0	1	0	0
617.0	0	1	0	1
636.0	0	0	0	1
641.0	0	0	0	1
642.0	0	1	0	0
674.0	0	1	0	0
715.0	0	1	0	0
777.0	0	0	0	2
794.0	0	1	0	0
837.0	0	1	0	0
875.0	0	0	0	1
887.0	0	0	0	1
899.0	0	1	0	0
948.0	0	1	0	0
1051.0	0	0	0	1
1077.0	0	1	0	0