## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-265-TP4.bam --OUTPUT ACR-265-TP4.md.bam --METRICS_FILE ACR-265-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	308	16581499	3357259	0	230	13515188	2715463	0.815076	3101807

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.006753	342219	0	393962
2.0	1.011553	338464	569705	421414
3.0	1.011576	393925	237635	491069
4.0	1.011576	407243	123840	483386
5.0	1.011576	375905	73222	407897
6.0	1.011576	313597	46583	302712
7.0	1.011576	244425	30448	205485
8.0	1.011576	182312	20312	129188
9.0	1.011576	130316	13847	78535
10.0	1.011576	92412	9318	47903
11.0	1.011576	64447	6404	29736
12.0	1.011576	45955	4327	18785
13.0	1.011576	32931	2879	12875
14.0	1.011576	23869	1992	8922
15.0	1.011576	17244	1408	6181
16.0	1.011576	12677	973	4667
17.0	1.011576	9602	669	3572
18.0	1.011576	7143	465	2766
19.0	1.011576	5335	349	2139
20.0	1.011576	4077	236	1731
21.0	1.011576	3205	158	1431
22.0	1.011576	2528	118	1216
23.0	1.011576	2044	81	1002
24.0	1.011576	1611	50	832
25.0	1.011576	1333	39	758
26.0	1.011576	1130	32	665
27.0	1.011576	1002	35	647
28.0	1.011576	826	26	504
29.0	1.011576	702	16	488
30.0	1.011576	633	13	399
31.0	1.011576	556	11	364
32.0	1.011576	485	14	336
33.0	1.011576	447	11	285
34.0	1.011576	375	7	262
35.0	1.011576	343	5	236
36.0	1.011576	319	9	237
37.0	1.011576	280	5	212
38.0	1.011576	238	3	183
39.0	1.011576	236	8	164
40.0	1.011576	205	2	163
41.0	1.011576	178	3	141
42.0	1.011576	179	5	160
43.0	1.011576	164	3	137
44.0	1.011576	172	1	118
45.0	1.011576	146	5	121
46.0	1.011576	119	1	101
47.0	1.011576	134	3	105
48.0	1.011576	110	2	73
49.0	1.011576	104	0	91
50.0	1.011576	99	2	80
51.0	1.011576	95	0	66
52.0	1.011576	67	0	63
53.0	1.011576	75	1	79
54.0	1.011576	67	2	64
55.0	1.011576	84	3	51
56.0	1.011576	74	1	53
57.0	1.011576	61	1	62
58.0	1.011576	67	0	46
59.0	1.011576	73	0	44
60.0	1.011576	53	1	32
61.0	1.011576	58	3	49
62.0	1.011576	41	0	40
63.0	1.011576	51	2	46
64.0	1.011576	52	0	41
65.0	1.011576	48	0	35
66.0	1.011576	34	0	37
67.0	1.011576	38	0	28
68.0	1.011576	41	0	43
69.0	1.011576	39	0	30
70.0	1.011576	42	0	40
71.0	1.011576	29	0	23
72.0	1.011576	36	0	23
73.0	1.011576	41	1	23
74.0	1.011576	34	1	23
75.0	1.011576	26	1	16
76.0	1.011576	23	0	19
77.0	1.011576	29	0	18
78.0	1.011576	19	1	21
79.0	1.011576	26	1	19
80.0	1.011576	20	0	21
81.0	1.011576	24	0	19
82.0	1.011576	11	0	22
83.0	1.011576	34	0	20
84.0	1.011576	23	0	14
85.0	1.011576	19	0	13
86.0	1.011576	12	0	12
87.0	1.011576	19	1	20
88.0	1.011576	21	1	13
89.0	1.011576	15	0	10
90.0	1.011576	22	0	8
91.0	1.011576	9	0	12
92.0	1.011576	13	0	13
93.0	1.011576	11	0	10
94.0	1.011576	20	0	11
95.0	1.011576	12	0	14
96.0	1.011576	12	0	10
97.0	1.011576	12	0	10
98.0	1.011576	12	0	5
99.0	1.011576	8	0	8
100.0	1.011576	9	0	4
101.0	0	10	1	7
102.0	0	4	0	9
103.0	0	6	0	13
104.0	0	9	0	7
105.0	0	13	0	4
106.0	0	9	0	7
107.0	0	11	0	8
108.0	0	10	0	9
109.0	0	14	0	7
110.0	0	3	0	6
111.0	0	5	0	6
112.0	0	13	0	10
113.0	0	7	0	6
114.0	0	10	0	2
115.0	0	5	1	5
116.0	0	3	0	7
117.0	0	9	0	5
118.0	0	8	0	4
119.0	0	9	0	3
120.0	0	5	0	3
121.0	0	4	0	10
122.0	0	4	0	4
123.0	0	5	0	2
124.0	0	6	0	11
125.0	0	6	0	5
126.0	0	5	0	6
127.0	0	7	0	2
128.0	0	5	0	0
129.0	0	6	0	7
130.0	0	10	0	4
131.0	0	4	0	8
132.0	0	4	0	10
133.0	0	4	0	3
134.0	0	2	0	4
135.0	0	5	0	4
136.0	0	6	0	3
137.0	0	5	0	3
138.0	0	6	0	4
139.0	0	1	0	5
140.0	0	8	0	2
141.0	0	3	0	5
142.0	0	5	0	0
143.0	0	3	0	9
144.0	0	5	0	2
145.0	0	3	0	4
146.0	0	5	0	1
147.0	0	1	0	5
148.0	0	2	0	4
149.0	0	7	0	3
150.0	0	2	0	2
151.0	0	4	0	5
152.0	0	4	0	3
153.0	0	4	0	2
154.0	0	2	0	3
155.0	0	2	0	3
156.0	0	2	0	2
157.0	0	3	0	1
158.0	0	2	0	4
159.0	0	1	0	2
160.0	0	4	0	2
161.0	0	4	0	3
162.0	0	3	0	4
163.0	0	3	0	3
164.0	0	2	0	1
165.0	0	2	0	0
166.0	0	2	0	3
167.0	0	2	0	1
168.0	0	1	0	1
169.0	0	1	0	4
170.0	0	3	0	3
171.0	0	1	0	1
172.0	0	4	0	5
173.0	0	1	0	1
174.0	0	3	0	1
175.0	0	5	0	3
176.0	0	5	0	4
177.0	0	2	0	1
178.0	0	4	0	2
179.0	0	3	0	0
180.0	0	1	0	3
181.0	0	2	0	3
182.0	0	5	0	4
183.0	0	2	0	1
184.0	0	2	0	2
185.0	0	1	0	0
186.0	0	2	0	2
187.0	0	0	0	3
188.0	0	0	0	2
189.0	0	1	0	2
190.0	0	0	0	3
191.0	0	5	0	0
192.0	0	3	0	2
193.0	0	2	0	2
194.0	0	3	0	0
195.0	0	1	0	0
196.0	0	0	0	2
197.0	0	4	0	1
198.0	0	3	0	1
200.0	0	1	0	5
201.0	0	0	0	1
202.0	0	3	0	1
203.0	0	1	0	1
204.0	0	4	0	0
206.0	0	2	0	0
207.0	0	4	0	0
209.0	0	0	0	2
211.0	0	1	0	1
213.0	0	1	0	1
214.0	0	2	0	0
215.0	0	3	0	1
216.0	0	0	0	1
218.0	0	2	0	2
219.0	0	1	0	0
220.0	0	1	0	1
221.0	0	1	0	3
222.0	0	3	0	1
223.0	0	0	0	1
224.0	0	0	0	2
226.0	0	0	0	1
227.0	0	2	0	1
229.0	0	0	0	1
231.0	0	0	0	3
232.0	0	1	0	0
234.0	0	0	0	1
235.0	0	2	0	1
236.0	0	0	0	1
237.0	0	1	0	1
238.0	0	1	0	0
239.0	0	2	0	0
241.0	0	0	0	1
242.0	0	1	0	1
243.0	0	3	0	1
246.0	0	1	0	1
248.0	0	1	0	0
249.0	0	1	0	0
252.0	0	2	0	0
253.0	0	0	0	2
254.0	0	1	0	0
255.0	0	0	0	2
256.0	0	1	0	0
258.0	0	1	0	1
259.0	0	2	0	1
260.0	0	0	0	2
261.0	0	1	0	0
263.0	0	2	0	1
264.0	0	1	0	0
268.0	0	3	0	2
269.0	0	0	0	1
270.0	0	1	0	0
271.0	0	0	0	1
273.0	0	1	0	0
275.0	0	1	0	2
278.0	0	1	0	1
280.0	0	1	0	0
282.0	0	1	0	1
285.0	0	1	0	0
286.0	0	1	0	1
289.0	0	1	0	0
290.0	0	0	0	2
292.0	0	0	0	1
293.0	0	0	0	1
296.0	0	0	0	1
298.0	0	0	0	1
299.0	0	1	0	0
300.0	0	1	0	0
301.0	0	1	0	2
302.0	0	1	0	0
303.0	0	1	0	1
304.0	0	1	0	0
305.0	0	1	0	0
306.0	0	1	0	0
307.0	0	2	0	0
308.0	0	0	0	2
309.0	0	1	0	0
312.0	0	0	0	1
313.0	0	1	0	0
314.0	0	2	0	1
315.0	0	1	0	1
316.0	0	0	0	1
320.0	0	1	0	0
321.0	0	1	0	0
323.0	0	0	0	1
327.0	0	0	0	1
328.0	0	1	0	0
329.0	0	1	0	0
332.0	0	0	0	1
334.0	0	1	0	0
336.0	0	0	0	1
341.0	0	0	0	2
342.0	0	1	0	0
343.0	0	0	0	2
348.0	0	1	0	0
349.0	0	0	0	1
350.0	0	2	0	0
351.0	0	1	0	1
355.0	0	1	0	0
361.0	0	1	0	0
363.0	0	0	0	3
364.0	0	1	0	0
365.0	0	0	0	1
368.0	0	2	0	1
371.0	0	1	0	0
373.0	0	1	0	0
377.0	0	1	0	1
378.0	0	0	0	1
380.0	0	1	0	0
381.0	0	1	0	0
384.0	0	1	0	0
387.0	0	1	0	0
393.0	0	1	0	0
395.0	0	0	0	1
406.0	0	1	0	0
407.0	0	1	0	0
424.0	0	0	0	1
426.0	0	0	0	1
437.0	0	1	0	0
439.0	0	0	0	1
442.0	0	0	0	1
452.0	0	1	0	0
460.0	0	1	0	0
464.0	0	1	0	0
465.0	0	0	0	1
475.0	0	1	0	0
549.0	0	0	0	1
582.0	0	0	0	1
602.0	0	0	0	1
606.0	0	0	0	1
612.0	0	1	0	0
615.0	0	0	0	1
622.0	0	1	0	0
629.0	0	0	0	1
637.0	0	1	0	0
640.0	0	1	0	0
682.0	0	1	0	0
698.0	0	0	0	1
706.0	0	1	0	0
710.0	0	0	0	1
726.0	0	1	0	0
750.0	0	0	0	1
758.0	0	0	0	1
797.0	0	2	0	0
802.0	0	0	0	1
807.0	0	0	0	1
827.0	0	1	0	0
831.0	0	1	0	0
840.0	0	1	0	0
851.0	0	0	0	1
852.0	0	0	0	1
870.0	0	1	0	0
896.0	0	1	0	0
935.0	0	0	0	1
994.0	0	1	0	0
1090.0	0	0	0	1
1134.0	0	1	0	0
1180.0	0	0	0	1
1199.0	0	1	0	0