## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-237-TP4.bam --OUTPUT ACR-237-TP4.md.bam --METRICS_FILE ACR-237-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 18:15:56 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	344	17423319	3736839	0	253	12876766	3055562	0.739054	4783939

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.024646	896304	0	1064127
2.0	1.05149	886779	787104	1073065
3.0	1.052193	796359	304370	910014
4.0	1.052212	625805	149143	633577
5.0	1.052212	448548	82690	383694
6.0	1.052212	300253	48649	210372
7.0	1.052212	196127	29817	110815
8.0	1.052212	126697	18437	58146
9.0	1.052212	81470	11929	31816
10.0	1.052212	53756	7368	18553
11.0	1.052212	36132	4863	11860
12.0	1.052212	24581	3010	7902
13.0	1.052212	17082	1971	5627
14.0	1.052212	12200	1307	4131
15.0	1.052212	8819	810	3152
16.0	1.052212	6362	521	2605
17.0	1.052212	5042	391	2109
18.0	1.052212	3766	214	1682
19.0	1.052212	2812	172	1384
20.0	1.052212	2291	121	1171
21.0	1.052212	1724	85	951
22.0	1.052212	1463	67	874
23.0	1.052212	1208	45	775
24.0	1.052212	1016	35	682
25.0	1.052212	930	32	607
26.0	1.052212	751	23	555
27.0	1.052212	654	32	461
28.0	1.052212	587	14	376
29.0	1.052212	483	12	368
30.0	1.052212	447	9	351
31.0	1.052212	413	5	299
32.0	1.052212	361	5	268
33.0	1.052212	359	8	265
34.0	1.052212	305	8	229
35.0	1.052212	276	8	212
36.0	1.052212	268	5	190
37.0	1.052212	242	5	196
38.0	1.052212	198	4	160
39.0	1.052212	200	5	156
40.0	1.052212	179	2	145
41.0	1.052212	151	3	118
42.0	1.052212	144	2	105
43.0	1.052212	143	1	122
44.0	1.052212	145	2	93
45.0	1.052212	136	2	95
46.0	1.052212	123	2	103
47.0	1.052212	95	0	87
48.0	1.052212	106	3	72
49.0	1.052212	97	0	78
50.0	1.052212	90	3	84
51.0	1.052212	86	1	63
52.0	1.052212	69	2	56
53.0	1.052212	76	0	45
54.0	1.052212	69	0	56
55.0	1.052212	56	1	54
56.0	1.052212	66	0	38
57.0	1.052212	58	1	37
58.0	1.052212	54	0	47
59.0	1.052212	44	0	36
60.0	1.052212	41	0	28
61.0	1.052212	42	1	26
62.0	1.052212	43	0	37
63.0	1.052212	44	1	34
64.0	1.052212	34	1	23
65.0	1.052212	31	0	29
66.0	1.052212	31	3	37
67.0	1.052212	42	1	44
68.0	1.052212	31	0	32
69.0	1.052212	26	0	28
70.0	1.052212	44	0	34
71.0	1.052212	23	0	34
72.0	1.052212	40	1	20
73.0	1.052212	31	0	28
74.0	1.052212	29	1	20
75.0	1.052212	32	0	26
76.0	1.052212	23	0	11
77.0	1.052212	26	0	14
78.0	1.052212	18	0	17
79.0	1.052212	23	0	26
80.0	1.052212	17	0	25
81.0	1.052212	25	0	15
82.0	1.052212	27	0	14
83.0	1.052212	15	0	19
84.0	1.052212	16	1	9
85.0	1.052212	20	0	13
86.0	1.052212	14	0	10
87.0	1.052212	18	0	9
88.0	1.052212	18	0	10
89.0	1.052212	10	0	10
90.0	1.052212	12	0	15
91.0	1.052212	12	0	11
92.0	1.052212	15	0	16
93.0	1.052212	7	0	7
94.0	1.052212	11	0	9
95.0	1.052212	14	0	10
96.0	1.052212	20	0	15
97.0	1.052212	12	0	9
98.0	1.052212	13	0	13
99.0	1.052212	11	0	6
100.0	1.052212	11	0	6
101.0	0	19	0	7
102.0	0	6	1	12
103.0	0	9	0	6
104.0	0	10	0	13
105.0	0	7	0	3
106.0	0	5	0	10
107.0	0	12	0	10
108.0	0	11	0	5
109.0	0	14	0	9
110.0	0	11	0	7
111.0	0	5	0	4
112.0	0	5	0	6
113.0	0	9	0	10
114.0	0	7	0	4
115.0	0	6	0	3
116.0	0	6	0	6
117.0	0	10	0	2
118.0	0	5	0	8
119.0	0	9	0	2
120.0	0	6	0	3
121.0	0	4	0	3
122.0	0	6	0	2
123.0	0	5	0	2
124.0	0	4	0	2
125.0	0	5	0	3
126.0	0	2	0	6
127.0	0	3	0	3
128.0	0	5	0	5
129.0	0	5	0	7
130.0	0	2	0	4
131.0	0	5	0	3
132.0	0	3	0	4
133.0	0	2	0	5
134.0	0	1	0	4
135.0	0	4	0	5
136.0	0	8	0	7
137.0	0	7	0	4
138.0	0	3	0	4
139.0	0	6	0	2
140.0	0	1	0	0
142.0	0	6	0	4
143.0	0	3	0	3
144.0	0	2	0	3
145.0	0	5	0	2
146.0	0	4	0	2
147.0	0	0	0	1
148.0	0	2	0	5
149.0	0	1	0	4
150.0	0	7	0	2
151.0	0	4	0	3
152.0	0	1	0	1
153.0	0	5	0	2
154.0	0	1	0	4
155.0	0	0	0	3
156.0	0	4	0	3
157.0	0	4	0	4
158.0	0	4	0	3
159.0	0	1	0	3
160.0	0	3	0	1
161.0	0	6	0	2
162.0	0	2	0	2
163.0	0	2	0	0
164.0	0	3	0	5
165.0	0	1	0	5
166.0	0	3	0	1
167.0	0	5	0	2
168.0	0	3	0	0
169.0	0	3	0	1
170.0	0	2	0	1
171.0	0	0	0	1
172.0	0	3	0	2
173.0	0	0	0	3
174.0	0	0	0	1
175.0	0	2	0	1
176.0	0	3	0	2
177.0	0	2	0	0
178.0	0	2	0	3
179.0	0	0	0	1
180.0	0	5	0	2
181.0	0	1	0	1
182.0	0	2	0	0
183.0	0	0	0	4
184.0	0	2	0	0
186.0	0	2	0	2
187.0	0	1	0	0
188.0	0	1	0	4
189.0	0	1	0	0
190.0	0	1	0	2
191.0	0	1	0	1
192.0	0	3	0	1
193.0	0	3	0	1
194.0	0	1	0	1
195.0	0	0	0	1
197.0	0	2	0	3
198.0	0	1	0	0
199.0	0	1	0	1
200.0	0	1	0	3
201.0	0	0	0	3
202.0	0	3	0	0
203.0	0	2	0	0
204.0	0	1	0	0
206.0	0	1	0	2
207.0	0	1	0	1
208.0	0	0	0	1
209.0	0	2	0	0
210.0	0	1	0	1
211.0	0	2	0	1
212.0	0	0	0	1
213.0	0	1	0	0
214.0	0	1	0	1
215.0	0	2	0	1
216.0	0	1	0	2
218.0	0	0	0	2
219.0	0	2	0	1
220.0	0	1	0	0
221.0	0	1	0	1
222.0	0	1	0	2
223.0	0	0	0	1
224.0	0	1	0	2
225.0	0	1	0	0
226.0	0	1	0	3
227.0	0	2	0	0
228.0	0	0	0	1
230.0	0	0	0	1
231.0	0	1	0	1
232.0	0	1	0	0
233.0	0	1	0	0
234.0	0	0	0	2
235.0	0	1	0	2
236.0	0	1	0	2
237.0	0	0	0	2
238.0	0	1	0	1
240.0	0	3	0	0
241.0	0	2	0	1
242.0	0	0	0	3
243.0	0	2	0	1
245.0	0	3	0	0
246.0	0	0	0	1
247.0	0	1	0	2
248.0	0	2	0	0
249.0	0	1	0	2
251.0	0	2	0	0
252.0	0	1	0	0
253.0	0	2	0	0
254.0	0	1	0	0
255.0	0	1	0	2
257.0	0	1	0	1
258.0	0	1	0	0
259.0	0	4	0	0
261.0	0	0	0	1
262.0	0	1	0	0
263.0	0	1	0	1
264.0	0	1	0	0
268.0	0	0	0	2
269.0	0	0	0	1
270.0	0	1	0	0
271.0	0	1	0	0
273.0	0	1	0	1
274.0	0	0	0	1
275.0	0	1	0	0
277.0	0	1	0	2
278.0	0	1	0	1
279.0	0	1	0	0
280.0	0	1	0	0
283.0	0	1	0	0
287.0	0	0	0	1
288.0	0	1	0	1
289.0	0	1	0	1
291.0	0	1	0	1
293.0	0	1	0	0
294.0	0	0	0	1
296.0	0	0	0	1
298.0	0	2	0	0
302.0	0	1	0	0
304.0	0	0	0	1
305.0	0	0	0	1
307.0	0	0	0	1
308.0	0	0	0	2
309.0	0	1	0	0
310.0	0	1	0	0
311.0	0	0	0	1
315.0	0	1	0	1
317.0	0	1	0	0
324.0	0	1	0	2
325.0	0	0	0	1
326.0	0	0	0	1
328.0	0	2	0	0
333.0	0	2	0	0
334.0	0	2	0	0
336.0	0	2	0	0
338.0	0	0	0	1
340.0	0	1	0	0
341.0	0	0	0	1
344.0	0	0	0	1
347.0	0	1	0	0
348.0	0	1	0	1
349.0	0	0	0	1
352.0	0	1	0	0
354.0	0	1	0	0
356.0	0	0	0	2
363.0	0	1	0	1
365.0	0	0	0	1
370.0	0	1	0	0
371.0	0	0	0	1
374.0	0	1	0	0
375.0	0	0	0	1
376.0	0	1	0	0
377.0	0	1	0	0
378.0	0	1	0	0
379.0	0	1	0	0
383.0	0	0	0	1
385.0	0	1	0	0
390.0	0	0	0	1
391.0	0	1	0	0
395.0	0	0	0	1
406.0	0	1	0	0
411.0	0	1	0	0
412.0	0	0	0	1
422.0	0	0	0	1
424.0	0	0	0	1
427.0	0	1	0	0
434.0	0	0	0	1
435.0	0	1	0	0
445.0	0	1	0	0
446.0	0	1	0	0
447.0	0	0	0	1
453.0	0	1	0	0
485.0	0	0	0	2
498.0	0	1	0	0
502.0	0	1	0	1
514.0	0	1	0	0
530.0	0	1	0	0
531.0	0	0	0	1
552.0	0	0	0	1
553.0	0	1	0	0
560.0	0	0	0	1
562.0	0	1	0	0
570.0	0	0	0	1
573.0	0	1	0	0
582.0	0	0	0	1
594.0	0	0	0	1
605.0	0	1	0	0
611.0	0	0	0	1
617.0	0	1	0	0
625.0	0	0	0	1
636.0	0	1	0	0
646.0	0	1	0	0
649.0	0	0	0	1
658.0	0	1	0	0
669.0	0	0	0	1
687.0	0	1	0	0
714.0	0	0	0	1
719.0	0	1	0	0
736.0	0	0	0	1
762.0	0	1	0	0
763.0	0	1	0	0
771.0	0	0	0	1
786.0	0	0	0	1
793.0	0	0	0	1
808.0	0	1	0	0
820.0	0	1	0	0
829.0	0	1	0	0
847.0	0	0	0	1
873.0	0	1	0	0
881.0	0	0	0	1
891.0	0	1	0	0
913.0	0	0	0	1
950.0	0	1	0	1
965.0	0	0	0	1
974.0	0	1	0	0
983.0	0	0	0	1
1009.0	0	1	0	0
1016.0	0	1	0	0
1035.0	0	0	0	1
1052.0	0	0	0	1
1084.0	0	1	0	0
1099.0	0	1	0	0
1260.0	0	0	0	1
1323.0	0	1	0	0
1515.0	0	0	0	1
1598.0	0	1	0	0