## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-229-TP4.bam --OUTPUT ACR-229-TP4.md.bam --METRICS_FILE ACR-229-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 18:15:10 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	635	14106665	3627457	0	485	12149750	1961350	0.861275	1960919

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.001293	180288	0	193878
2.0	1.002046	112465	372914	131358
3.0	1.002046	133151	156963	165771
4.0	1.002046	163898	80827	206705
5.0	1.002046	187099	48412	229971
6.0	1.002046	195679	32161	228478
7.0	1.002046	188998	21808	206202
8.0	1.002046	169559	15567	169862
9.0	1.002046	143954	11118	128583
10.0	1.002046	115014	8155	91774
11.0	1.002046	89478	5933	62444
12.0	1.002046	67607	4403	41454
13.0	1.002046	49747	3079	27091
14.0	1.002046	37142	2296	18335
15.0	1.002046	27725	1606	12639
16.0	1.002046	20507	1211	8837
17.0	1.002046	15675	882	6500
18.0	1.002046	11969	653	4953
19.0	1.002046	9183	462	3744
20.0	1.002046	7099	337	2883
21.0	1.002046	5594	214	2329
22.0	1.002046	4388	182	1861
23.0	1.002046	3382	122	1445
24.0	1.002046	2712	73	1149
25.0	1.002046	2176	70	956
26.0	1.002046	1737	50	798
27.0	1.002046	1366	39	692
28.0	1.002046	1118	29	564
29.0	1.002046	955	18	521
30.0	1.002046	751	14	398
31.0	1.002046	694	6	416
32.0	1.002046	533	9	305
33.0	1.002046	484	8	280
34.0	1.002046	406	4	283
35.0	1.002046	337	4	234
36.0	1.002046	301	4	213
37.0	1.002046	254	1	190
38.0	1.002046	271	2	176
39.0	1.002046	192	2	145
40.0	1.002046	190	1	131
41.0	1.002046	169	1	136
42.0	1.002046	131	2	126
43.0	1.002046	140	0	96
44.0	1.002046	135	3	121
45.0	1.002046	134	0	90
46.0	1.002046	97	0	94
47.0	1.002046	93	0	68
48.0	1.002046	79	1	70
49.0	1.002046	80	1	71
50.0	1.002046	102	1	68
51.0	1.002046	75	0	68
52.0	1.002046	69	1	50
53.0	1.002046	75	0	56
54.0	1.002046	52	0	38
55.0	1.002046	55	0	41
56.0	1.002046	50	1	47
57.0	1.002046	42	0	31
58.0	1.002046	42	0	52
59.0	1.002046	44	1	34
60.0	1.002046	42	1	35
61.0	1.002046	44	1	30
62.0	1.002046	36	0	29
63.0	1.002046	44	0	40
64.0	1.002046	35	0	25
65.0	1.002046	28	1	23
66.0	1.002046	29	0	34
67.0	1.002046	38	0	30
68.0	1.002046	22	0	14
69.0	1.002046	25	0	29
70.0	1.002046	20	0	24
71.0	1.002046	32	0	28
72.0	1.002046	24	0	15
73.0	1.002046	27	0	23
74.0	1.002046	22	0	18
75.0	1.002046	18	0	18
76.0	1.002046	17	0	16
77.0	1.002046	23	0	17
78.0	1.002046	13	0	13
79.0	1.002046	22	0	13
80.0	1.002046	23	0	18
81.0	1.002046	16	0	13
82.0	1.002046	12	0	19
83.0	1.002046	18	0	9
84.0	1.002046	14	0	10
85.0	1.002046	8	0	14
86.0	1.002046	14	0	9
87.0	1.002046	14	0	10
88.0	1.002046	17	0	10
89.0	1.002046	10	1	6
90.0	1.002046	11	0	10
91.0	1.002046	6	0	7
92.0	1.002046	5	0	11
93.0	1.002046	11	0	11
94.0	1.002046	13	0	5
95.0	1.002046	6	0	6
96.0	1.002046	10	0	6
97.0	1.002046	10	0	10
98.0	1.002046	9	0	6
99.0	1.002046	6	0	7
100.0	1.002046	11	0	4
101.0	0	1	0	7
102.0	0	9	0	8
103.0	0	6	0	7
104.0	0	10	0	10
105.0	0	8	0	8
106.0	0	10	0	5
107.0	0	9	0	4
108.0	0	8	0	4
109.0	0	2	0	7
110.0	0	4	0	3
111.0	0	3	0	3
112.0	0	7	0	6
113.0	0	2	0	4
114.0	0	3	0	5
115.0	0	6	0	3
116.0	0	4	0	6
117.0	0	7	0	3
118.0	0	5	0	3
119.0	0	2	0	3
120.0	0	8	0	8
121.0	0	2	0	5
122.0	0	7	0	4
123.0	0	4	0	5
124.0	0	4	0	6
125.0	0	5	0	6
126.0	0	4	0	1
127.0	0	1	0	1
128.0	0	4	0	5
129.0	0	3	0	5
130.0	0	3	0	3
131.0	0	2	0	3
132.0	0	4	0	3
133.0	0	3	0	0
134.0	0	9	0	4
135.0	0	3	0	3
136.0	0	2	0	2
137.0	0	3	0	5
138.0	0	3	0	3
139.0	0	7	0	2
140.0	0	3	0	1
141.0	0	2	0	3
142.0	0	2	0	2
143.0	0	1	0	5
144.0	0	3	0	3
145.0	0	2	0	1
146.0	0	1	0	3
147.0	0	5	0	1
148.0	0	0	0	5
149.0	0	1	0	4
150.0	0	3	0	1
151.0	0	9	0	0
152.0	0	1	0	3
153.0	0	4	0	0
154.0	0	0	0	2
155.0	0	2	0	4
156.0	0	2	0	2
157.0	0	3	0	3
158.0	0	3	0	4
160.0	0	0	0	1
161.0	0	2	0	0
162.0	0	1	0	0
163.0	0	2	0	2
164.0	0	2	0	0
165.0	0	2	0	1
166.0	0	1	0	0
167.0	0	2	0	1
168.0	0	1	0	1
169.0	0	3	0	0
170.0	0	0	0	3
171.0	0	1	0	3
172.0	0	1	0	1
173.0	0	1	0	1
174.0	0	2	0	0
175.0	0	1	0	1
176.0	0	2	0	2
177.0	0	0	0	2
178.0	0	1	0	3
179.0	0	3	0	0
180.0	0	2	0	1
181.0	0	1	0	2
182.0	0	1	0	0
183.0	0	3	0	0
184.0	0	1	0	1
185.0	0	0	0	3
186.0	0	0	0	2
187.0	0	0	0	1
189.0	0	1	0	0
190.0	0	2	0	0
191.0	0	2	0	1
192.0	0	2	0	1
193.0	0	1	0	2
194.0	0	1	0	0
196.0	0	2	0	0
198.0	0	1	0	2
199.0	0	0	0	1
200.0	0	1	0	0
201.0	0	0	0	1
202.0	0	0	0	1
204.0	0	1	0	0
205.0	0	1	0	1
206.0	0	1	0	0
207.0	0	0	0	1
208.0	0	1	0	0
209.0	0	1	0	0
210.0	0	0	0	1
211.0	0	0	0	1
213.0	0	2	0	0
214.0	0	1	0	1
215.0	0	0	0	2
216.0	0	1	0	1
217.0	0	2	0	1
219.0	0	1	0	0
220.0	0	1	0	1
221.0	0	1	0	0
222.0	0	0	0	2
223.0	0	1	0	2
224.0	0	0	0	2
225.0	0	0	0	1
226.0	0	0	0	1
227.0	0	1	0	1
228.0	0	1	0	0
229.0	0	1	0	1
230.0	0	0	0	1
231.0	0	2	0	0
233.0	0	1	0	0
234.0	0	0	0	1
236.0	0	1	0	0
237.0	0	0	0	2
238.0	0	1	0	1
239.0	0	0	0	1
240.0	0	2	0	0
241.0	0	2	0	0
242.0	0	1	0	0
244.0	0	0	0	1
245.0	0	1	0	0
246.0	0	2	0	0
247.0	0	1	0	0
249.0	0	2	0	0
251.0	0	1	0	2
254.0	0	0	0	1
255.0	0	1	0	0
256.0	0	1	0	0
258.0	0	0	0	1
259.0	0	1	0	0
261.0	0	0	0	1
262.0	0	0	0	1
264.0	0	1	0	1
267.0	0	1	0	0
268.0	0	0	0	1
270.0	0	2	0	0
271.0	0	1	0	1
276.0	0	0	0	1
279.0	0	2	0	1
283.0	0	0	0	1
284.0	0	0	0	1
286.0	0	1	0	0
289.0	0	1	0	1
293.0	0	0	0	2
294.0	0	1	0	1
296.0	0	2	0	0
299.0	0	1	0	1
301.0	0	1	0	0
302.0	0	1	0	0
305.0	0	0	0	1
307.0	0	1	0	1
311.0	0	1	0	0
313.0	0	1	0	0
315.0	0	1	0	1
318.0	0	1	0	0
319.0	0	1	0	0
320.0	0	0	0	1
329.0	0	1	0	0
330.0	0	0	0	1
335.0	0	0	0	1
344.0	0	1	0	0
345.0	0	1	0	1
358.0	0	0	0	1
363.0	0	1	0	0
369.0	0	0	0	1
374.0	0	1	0	0
390.0	0	0	0	1
393.0	0	0	0	1
402.0	0	1	0	0
403.0	0	0	0	1
409.0	0	1	0	0
410.0	0	0	0	1
412.0	0	1	0	0
415.0	0	1	0	0
441.0	0	0	0	1
446.0	0	0	0	1
456.0	0	1	0	0
471.0	0	1	0	0
474.0	0	1	0	0
519.0	0	0	0	1
533.0	0	0	0	1
542.0	0	0	0	1
549.0	0	1	0	0
562.0	0	0	0	1
573.0	0	1	0	0
583.0	0	1	0	0
596.0	0	0	0	1
597.0	0	1	0	0
619.0	0	0	0	1
620.0	0	1	0	0
622.0	0	0	0	1
633.0	0	1	0	0
637.0	0	1	0	0
649.0	0	0	0	1
652.0	0	0	0	1
667.0	0	0	0	1
674.0	0	1	0	0
681.0	0	1	0	0
724.0	0	0	0	1
755.0	0	1	0	0
775.0	0	1	0	0
831.0	0	0	0	1
834.0	0	0	0	1
855.0	0	1	0	0
890.0	0	1	0	0
897.0	0	0	0	1
936.0	0	1	0	0