## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-225-TP2.bam --OUTPUT ACR-225-TP2.md.bam --METRICS_FILE ACR-225-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 18:13:46 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	238	15277014	3934415	0	151	9503398	4061443	0.622072	7398194

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.118872	2232262	0	2915957
2.0	1.26077	1426137	916979	1611408
3.0	1.278766	855103	390864	729403
4.0	1.281048	494196	206705	291903
5.0	1.281338	284786	118382	113206
6.0	1.281374	168862	70399	45880
7.0	1.281379	102825	43189	21131
8.0	1.28138	64974	26340	11203
9.0	1.28138	42042	16147	6766
10.0	1.28138	28035	10199	4715
11.0	1.28138	18891	6374	3356
12.0	1.28138	13090	4132	2520
13.0	1.28138	9318	2575	2026
14.0	1.28138	6601	1717	1673
15.0	1.28138	4738	1157	1371
16.0	1.28138	3514	767	1157
17.0	1.28138	2607	546	947
18.0	1.28138	2054	375	805
19.0	1.28138	1619	253	660
20.0	1.28138	1233	212	597
21.0	1.28138	1061	144	538
22.0	1.28138	835	120	461
23.0	1.28138	704	114	447
24.0	1.28138	676	75	367
25.0	1.28138	505	57	313
26.0	1.28138	481	54	326
27.0	1.28138	418	50	287
28.0	1.28138	411	29	252
29.0	1.28138	346	34	237
30.0	1.28138	322	25	178
31.0	1.28138	284	23	186
32.0	1.28138	221	20	156
33.0	1.28138	236	20	143
34.0	1.28138	199	17	132
35.0	1.28138	178	24	148
36.0	1.28138	192	18	134
37.0	1.28138	183	17	103
38.0	1.28138	175	12	104
39.0	1.28138	147	14	91
40.0	1.28138	135	10	101
41.0	1.28138	121	6	87
42.0	1.28138	105	14	93
43.0	1.28138	96	10	59
44.0	1.28138	98	7	74
45.0	1.28138	108	7	73
46.0	1.28138	95	10	72
47.0	1.28138	76	10	60
48.0	1.28138	81	9	56
49.0	1.28138	87	8	65
50.0	1.28138	60	5	65
51.0	1.28138	66	5	51
52.0	1.28138	64	7	52
53.0	1.28138	65	5	45
54.0	1.28138	60	4	47
55.0	1.28138	60	4	33
56.0	1.28138	53	6	38
57.0	1.28138	38	4	31
58.0	1.28138	53	6	33
59.0	1.28138	42	5	28
60.0	1.28138	53	2	32
61.0	1.28138	58	4	18
62.0	1.28138	38	2	25
63.0	1.28138	32	3	33
64.0	1.28138	34	4	35
65.0	1.28138	31	3	36
66.0	1.28138	29	2	22
67.0	1.28138	35	1	31
68.0	1.28138	25	5	22
69.0	1.28138	33	0	15
70.0	1.28138	26	3	30
71.0	1.28138	31	0	25
72.0	1.28138	44	2	18
73.0	1.28138	26	2	16
74.0	1.28138	27	0	17
75.0	1.28138	18	3	24
76.0	1.28138	25	1	22
77.0	1.28138	32	0	13
78.0	1.28138	26	2	13
79.0	1.28138	14	4	18
80.0	1.28138	29	0	21
81.0	1.28138	25	0	13
82.0	1.28138	17	0	12
83.0	1.28138	18	0	11
84.0	1.28138	14	2	14
85.0	1.28138	31	0	11
86.0	1.28138	27	1	7
87.0	1.28138	12	3	14
88.0	1.28138	22	2	17
89.0	1.28138	11	3	11
90.0	1.28138	9	0	7
91.0	1.28138	12	0	10
92.0	1.28138	11	0	9
93.0	1.28138	9	1	12
94.0	1.28138	14	0	5
95.0	1.28138	9	3	9
96.0	1.28138	10	0	6
97.0	1.28138	14	1	9
98.0	1.28138	12	1	11
99.0	1.28138	13	1	10
100.0	1.28138	15	0	12
101.0	0	10	1	12
102.0	0	11	0	1
103.0	0	7	0	11
104.0	0	13	0	10
105.0	0	11	0	5
106.0	0	7	0	9
107.0	0	7	0	2
108.0	0	12	1	4
109.0	0	6	2	6
110.0	0	5	1	5
111.0	0	7	1	6
112.0	0	7	0	8
113.0	0	2	2	5
114.0	0	5	0	7
115.0	0	4	1	3
116.0	0	11	0	3
117.0	0	8	1	6
118.0	0	11	0	8
119.0	0	6	0	6
120.0	0	11	0	6
121.0	0	12	0	3
122.0	0	10	0	5
123.0	0	6	0	5
124.0	0	5	0	4
125.0	0	5	0	4
126.0	0	6	0	6
127.0	0	4	0	6
128.0	0	7	1	5
129.0	0	5	0	4
130.0	0	6	1	5
131.0	0	5	0	6
132.0	0	3	0	5
133.0	0	4	0	2
134.0	0	4	1	3
135.0	0	12	0	2
136.0	0	3	1	3
137.0	0	5	1	1
138.0	0	3	0	4
139.0	0	8	0	4
140.0	0	3	0	6
141.0	0	5	0	3
142.0	0	7	0	6
143.0	0	3	0	4
144.0	0	4	0	2
145.0	0	7	1	4
146.0	0	1	0	2
147.0	0	3	0	2
148.0	0	2	1	4
149.0	0	5	0	1
150.0	0	2	0	2
151.0	0	3	0	2
152.0	0	3	0	3
153.0	0	2	0	5
154.0	0	4	0	2
155.0	0	3	0	1
156.0	0	2	0	5
157.0	0	3	0	2
158.0	0	1	1	0
159.0	0	1	0	4
160.0	0	5	0	0
161.0	0	3	0	3
162.0	0	1	0	2
163.0	0	3	0	1
164.0	0	1	0	2
165.0	0	5	0	2
166.0	0	4	0	3
167.0	0	3	0	4
168.0	0	1	0	4
169.0	0	2	0	1
170.0	0	2	0	2
171.0	0	3	1	5
172.0	0	6	0	2
173.0	0	3	0	2
174.0	0	4	0	1
175.0	0	0	0	4
176.0	0	2	0	3
177.0	0	3	0	0
178.0	0	4	0	2
179.0	0	1	0	2
180.0	0	5	1	1
181.0	0	2	0	2
182.0	0	1	0	2
184.0	0	3	0	2
185.0	0	5	0	3
186.0	0	3	0	2
187.0	0	3	0	2
188.0	0	4	0	0
189.0	0	1	0	2
190.0	0	2	0	1
191.0	0	1	0	1
192.0	0	1	0	1
193.0	0	2	0	2
194.0	0	5	0	3
195.0	0	2	0	1
196.0	0	0	0	2
197.0	0	1	0	2
198.0	0	4	1	3
199.0	0	1	0	1
200.0	0	1	1	1
201.0	0	1	0	3
202.0	0	4	0	2
204.0	0	2	0	1
205.0	0	2	0	1
206.0	0	2	0	1
207.0	0	4	0	2
208.0	0	0	0	1
209.0	0	2	1	0
210.0	0	3	0	3
211.0	0	2	0	2
212.0	0	2	1	2
213.0	0	0	0	1
214.0	0	1	0	0
215.0	0	3	0	1
216.0	0	0	0	1
217.0	0	1	0	0
218.0	0	1	0	0
219.0	0	0	0	1
220.0	0	1	0	1
221.0	0	2	0	1
222.0	0	1	0	1
223.0	0	1	0	0
224.0	0	3	0	1
225.0	0	1	0	1
226.0	0	1	0	1
227.0	0	1	0	1
228.0	0	2	0	1
229.0	0	1	0	0
231.0	0	1	0	2
232.0	0	1	0	2
233.0	0	1	0	0
234.0	0	1	0	1
235.0	0	1	0	0
236.0	0	0	1	2
237.0	0	1	0	2
238.0	0	1	0	2
239.0	0	1	0	0
240.0	0	0	0	1
241.0	0	2	0	0
242.0	0	3	0	2
244.0	0	1	0	0
245.0	0	2	0	0
246.0	0	1	0	0
247.0	0	1	0	0
248.0	0	2	0	1
249.0	0	0	0	3
250.0	0	2	0	0
252.0	0	0	0	1
253.0	0	0	0	1
254.0	0	1	0	3
255.0	0	2	1	1
256.0	0	1	0	0
257.0	0	2	0	0
258.0	0	1	0	3
259.0	0	1	0	0
261.0	0	1	0	0
262.0	0	1	0	0
263.0	0	1	0	1
265.0	0	2	0	0
267.0	0	2	0	0
268.0	0	2	0	2
271.0	0	1	0	0
272.0	0	1	0	2
273.0	0	0	0	2
274.0	0	0	0	2
277.0	0	0	0	1
279.0	0	1	0	0
280.0	0	0	0	2
281.0	0	0	0	3
283.0	0	2	0	0
284.0	0	1	0	2
285.0	0	2	0	1
289.0	0	1	0	0
290.0	0	0	0	2
291.0	0	1	0	0
293.0	0	2	0	1
296.0	0	1	0	0
298.0	0	1	0	0
299.0	0	1	0	0
300.0	0	2	0	1
301.0	0	1	0	1
304.0	0	1	0	0
305.0	0	0	0	1
306.0	0	0	0	1
307.0	0	0	1	0
308.0	0	1	0	0
309.0	0	1	0	0
310.0	0	0	0	1
311.0	0	2	0	0
312.0	0	2	0	1
313.0	0	1	0	1
314.0	0	1	0	0
315.0	0	0	0	1
317.0	0	1	0	1
320.0	0	1	0	1
321.0	0	2	0	0
322.0	0	1	0	0
323.0	0	2	0	0
325.0	0	0	0	1
326.0	0	1	0	1
330.0	0	1	0	1
331.0	0	2	0	0
332.0	0	2	0	0
336.0	0	0	0	1
339.0	0	1	0	0
341.0	0	0	0	1
343.0	0	0	0	2
345.0	0	2	0	1
346.0	0	1	0	0
347.0	0	1	0	0
348.0	0	1	0	2
350.0	0	1	0	0
352.0	0	0	0	1
353.0	0	1	0	0
355.0	0	2	0	2
356.0	0	1	0	0
357.0	0	0	0	1
360.0	0	1	0	1
362.0	0	1	0	1
363.0	0	1	0	0
367.0	0	1	0	0
368.0	0	1	0	0
369.0	0	1	0	0
371.0	0	1	1	0
373.0	0	1	0	0
380.0	0	0	0	1
383.0	0	0	0	1
386.0	0	1	0	0
389.0	0	0	0	1
390.0	0	1	0	0
393.0	0	0	0	1
395.0	0	1	0	1
398.0	0	1	0	0
399.0	0	1	0	0
402.0	0	1	0	0
403.0	0	1	0	0
404.0	0	0	0	1
405.0	0	0	1	0
409.0	0	0	0	1
419.0	0	1	0	0
420.0	0	1	0	0
423.0	0	1	0	0
426.0	0	2	0	0
431.0	0	1	0	0
436.0	0	0	0	1
442.0	0	0	0	1
444.0	0	0	0	1
446.0	0	1	0	0
451.0	0	1	0	0
452.0	0	0	0	1
453.0	0	1	0	0
473.0	0	0	0	1
479.0	0	1	1	0
491.0	0	0	0	1
496.0	0	0	0	1
498.0	0	0	0	1
501.0	0	2	0	0
507.0	0	1	0	0
508.0	0	1	0	0
514.0	0	1	0	0
531.0	0	0	0	1
540.0	0	0	0	1
553.0	0	0	1	0
561.0	0	1	0	0
581.0	0	1	0	0
605.0	0	1	0	0
634.0	0	0	0	1
635.0	0	1	0	0
640.0	0	0	0	1
658.0	0	1	0	0
687.0	0	0	0	1
705.0	0	1	0	0
713.0	0	1	0	0
720.0	0	0	0	1
764.0	0	0	0	1
771.0	0	1	0	0
788.0	0	1	0	0
798.0	0	1	0	0
827.0	0	0	0	1
878.0	0	1	0	0
997.0	0	1	0	0
1015.0	0	0	0	1
1077.0	0	0	0	1
1087.0	0	1	0	0
1181.0	0	0	0	1
1183.0	0	0	0	1
1213.0	0	1	0	0
1259.0	0	1	0	0
1447.0	0	1	0	0