## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-265-TP1.bam --OUTPUT ACR-265-TP1.md.bam --METRICS_FILE ACR-265-TP1.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 18:18:03 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	485	19586511	4855936	0	363	16538027	2652927	0.844357	3060588

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.002302	287758	0	317320
2.0	1.003968	223120	611880	271590
3.0	1.00397	273390	260730	344128
4.0	1.00397	321102	130737	396983
5.0	1.00397	341554	74611	399560
6.0	1.00397	330212	44616	356358
7.0	1.00397	293657	27511	287203
8.0	1.00397	242336	17398	211340
9.0	1.00397	190857	11224	147319
10.0	1.00397	144430	7145	98160
11.0	1.00397	106178	4506	64537
12.0	1.00397	76750	3111	41480
13.0	1.00397	54426	1950	28149
14.0	1.00397	39629	1231	19379
15.0	1.00397	29071	818	13902
16.0	1.00397	21234	588	10356
17.0	1.00397	15515	370	7765
18.0	1.00397	11575	225	5806
19.0	1.00397	8815	165	4325
20.0	1.00397	6605	96	3430
21.0	1.00397	4963	96	2624
22.0	1.00397	3887	58	2053
23.0	1.00397	2920	48	1640
24.0	1.00397	2389	35	1359
25.0	1.00397	1912	20	1130
26.0	1.00397	1586	19	972
27.0	1.00397	1289	13	878
28.0	1.00397	1054	11	678
29.0	1.00397	891	16	637
30.0	1.00397	777	9	566
31.0	1.00397	685	8	451
32.0	1.00397	560	7	418
33.0	1.00397	525	6	430
34.0	1.00397	475	6	362
35.0	1.00397	422	4	309
36.0	1.00397	405	3	286
37.0	1.00397	324	6	271
38.0	1.00397	317	3	252
39.0	1.00397	263	4	206
40.0	1.00397	247	3	223
41.0	1.00397	242	1	191
42.0	1.00397	220	2	183
43.0	1.00397	216	3	186
44.0	1.00397	186	0	132
45.0	1.00397	177	2	148
46.0	1.00397	154	2	129
47.0	1.00397	152	4	117
48.0	1.00397	119	0	102
49.0	1.00397	110	0	94
50.0	1.00397	123	1	91
51.0	1.00397	105	0	96
52.0	1.00397	77	1	82
53.0	1.00397	87	3	75
54.0	1.00397	108	0	89
55.0	1.00397	87	0	65
56.0	1.00397	77	1	50
57.0	1.00397	77	1	68
58.0	1.00397	71	1	59
59.0	1.00397	64	2	63
60.0	1.00397	63	2	58
61.0	1.00397	70	1	55
62.0	1.00397	60	3	32
63.0	1.00397	54	0	49
64.0	1.00397	55	0	56
65.0	1.00397	51	0	53
66.0	1.00397	67	0	45
67.0	1.00397	44	1	35
68.0	1.00397	56	0	39
69.0	1.00397	34	0	30
70.0	1.00397	41	0	29
71.0	1.00397	37	0	38
72.0	1.00397	38	1	41
73.0	1.00397	35	2	33
74.0	1.00397	40	0	24
75.0	1.00397	24	0	28
76.0	1.00397	34	1	31
77.0	1.00397	36	0	15
78.0	1.00397	30	0	24
79.0	1.00397	26	0	21
80.0	1.00397	26	0	21
81.0	1.00397	20	1	21
82.0	1.00397	21	0	20
83.0	1.00397	23	0	26
84.0	1.00397	24	0	26
85.0	1.00397	20	1	14
86.0	1.00397	17	0	10
87.0	1.00397	16	1	17
88.0	1.00397	16	0	18
89.0	1.00397	22	1	15
90.0	1.00397	22	0	22
91.0	1.00397	18	0	15
92.0	1.00397	16	0	12
93.0	1.00397	23	0	9
94.0	1.00397	12	0	14
95.0	1.00397	18	0	14
96.0	1.00397	11	0	10
97.0	1.00397	17	0	11
98.0	1.00397	11	0	7
99.0	1.00397	15	0	7
100.0	1.00397	9	0	8
101.0	0	20	0	12
102.0	0	7	0	12
103.0	0	10	0	13
104.0	0	11	1	7
105.0	0	9	0	14
106.0	0	17	0	5
107.0	0	13	0	13
108.0	0	11	0	9
109.0	0	11	0	9
110.0	0	12	0	10
111.0	0	8	0	8
112.0	0	10	0	4
113.0	0	6	0	4
114.0	0	3	0	12
115.0	0	8	0	14
116.0	0	8	0	5
117.0	0	9	0	3
118.0	0	9	0	4
119.0	0	7	1	7
120.0	0	7	0	8
121.0	0	10	0	4
122.0	0	4	0	4
123.0	0	3	0	6
124.0	0	8	0	7
125.0	0	5	0	8
126.0	0	6	0	6
127.0	0	8	0	7
128.0	0	8	0	4
129.0	0	7	0	5
130.0	0	4	0	5
131.0	0	5	0	12
132.0	0	9	0	4
133.0	0	8	0	9
134.0	0	6	0	4
135.0	0	8	0	3
136.0	0	7	0	4
137.0	0	3	0	6
138.0	0	10	0	4
139.0	0	6	0	1
140.0	0	3	0	5
141.0	0	7	0	2
142.0	0	4	0	5
143.0	0	1	0	8
144.0	0	3	0	3
145.0	0	2	0	2
146.0	0	3	0	4
147.0	0	5	0	4
148.0	0	3	0	1
149.0	0	6	0	4
150.0	0	2	0	6
151.0	0	3	0	4
152.0	0	3	0	1
153.0	0	4	0	1
154.0	0	1	0	2
155.0	0	1	0	1
156.0	0	7	0	2
157.0	0	1	0	2
158.0	0	4	0	4
159.0	0	3	0	3
160.0	0	5	0	3
161.0	0	1	0	3
162.0	0	1	0	2
163.0	0	4	0	1
164.0	0	3	0	4
165.0	0	1	0	1
166.0	0	2	0	4
167.0	0	2	0	4
168.0	0	2	0	1
169.0	0	1	0	1
170.0	0	6	0	4
171.0	0	3	0	1
172.0	0	3	0	3
173.0	0	2	0	4
174.0	0	2	0	4
175.0	0	2	0	4
176.0	0	1	0	3
177.0	0	2	0	1
178.0	0	3	0	0
179.0	0	2	0	3
180.0	0	3	0	3
181.0	0	3	0	3
182.0	0	1	0	0
183.0	0	4	0	0
184.0	0	4	0	1
185.0	0	1	0	3
186.0	0	1	0	1
187.0	0	2	0	3
188.0	0	1	0	2
189.0	0	3	0	4
190.0	0	2	0	2
191.0	0	1	0	1
192.0	0	1	0	0
193.0	0	1	0	1
194.0	0	1	0	4
195.0	0	3	0	1
196.0	0	1	0	0
197.0	0	2	0	0
198.0	0	1	0	3
199.0	0	1	0	2
200.0	0	3	0	0
201.0	0	1	0	0
202.0	0	2	0	0
203.0	0	1	0	2
204.0	0	2	0	2
205.0	0	4	0	1
206.0	0	1	0	1
207.0	0	2	0	0
208.0	0	5	0	0
209.0	0	1	0	0
210.0	0	0	0	3
211.0	0	0	0	2
212.0	0	2	0	2
213.0	0	3	0	0
214.0	0	1	0	4
215.0	0	1	0	2
217.0	0	1	0	0
218.0	0	1	0	0
219.0	0	1	0	1
220.0	0	1	0	1
221.0	0	1	0	1
222.0	0	4	0	2
223.0	0	3	0	0
224.0	0	1	0	0
225.0	0	3	0	2
226.0	0	2	0	4
227.0	0	1	0	2
228.0	0	1	0	0
229.0	0	0	0	2
230.0	0	2	0	0
231.0	0	1	0	2
232.0	0	2	0	1
233.0	0	0	0	1
234.0	0	0	0	1
236.0	0	1	0	2
237.0	0	1	0	2
238.0	0	1	0	1
239.0	0	0	0	1
240.0	0	2	0	1
241.0	0	1	0	0
242.0	0	2	0	0
244.0	0	0	0	1
245.0	0	1	0	0
246.0	0	2	0	0
247.0	0	0	0	1
248.0	0	0	0	1
249.0	0	0	0	1
251.0	0	1	0	0
252.0	0	2	0	1
253.0	0	1	0	0
255.0	0	1	0	2
257.0	0	2	0	3
258.0	0	0	0	1
259.0	0	1	0	0
260.0	0	3	0	0
261.0	0	1	0	0
262.0	0	1	0	0
263.0	0	2	0	0
264.0	0	1	0	2
267.0	0	0	0	1
268.0	0	1	0	1
269.0	0	0	0	1
271.0	0	0	0	1
272.0	0	1	0	1
273.0	0	0	0	2
274.0	0	1	0	0
275.0	0	1	0	1
276.0	0	0	0	1
277.0	0	4	0	0
279.0	0	1	0	1
280.0	0	1	0	1
281.0	0	1	0	2
284.0	0	1	0	1
285.0	0	0	0	1
287.0	0	2	0	1
288.0	0	2	0	0
289.0	0	1	0	0
290.0	0	0	0	4
291.0	0	1	0	0
292.0	0	2	0	0
293.0	0	0	0	1
295.0	0	1	0	0
296.0	0	0	0	1
297.0	0	0	0	1
300.0	0	2	0	0
301.0	0	1	0	0
303.0	0	1	0	0
304.0	0	1	0	1
305.0	0	1	0	3
306.0	0	1	0	2
307.0	0	1	0	2
308.0	0	0	0	2
310.0	0	1	0	0
314.0	0	1	0	0
315.0	0	0	0	1
316.0	0	2	0	0
317.0	0	1	0	0
319.0	0	0	0	1
321.0	0	2	0	0
322.0	0	1	0	0
325.0	0	0	0	2
328.0	0	1	0	0
329.0	0	1	0	1
330.0	0	1	0	0
332.0	0	1	0	0
333.0	0	1	0	0
335.0	0	0	0	1
336.0	0	0	0	1
337.0	0	1	0	0
338.0	0	0	0	1
341.0	0	1	0	0
342.0	0	0	0	1
343.0	0	2	0	0
351.0	0	1	0	0
352.0	0	0	0	1
355.0	0	2	0	0
360.0	0	1	0	1
361.0	0	1	0	0
367.0	0	0	0	1
371.0	0	1	0	0
372.0	0	0	0	1
373.0	0	0	0	2
376.0	0	1	0	0
377.0	0	1	0	0
379.0	0	0	0	1
380.0	0	0	0	1
387.0	0	0	0	1
390.0	0	1	0	0
393.0	0	0	0	1
395.0	0	0	0	1
397.0	0	0	0	1
398.0	0	1	0	0
399.0	0	1	0	0
400.0	0	1	0	0
401.0	0	1	0	0
402.0	0	1	0	1
405.0	0	1	0	0
407.0	0	0	0	1
409.0	0	0	0	1
413.0	0	2	0	0
415.0	0	1	0	0
416.0	0	0	0	1
423.0	0	0	0	1
428.0	0	1	0	0
430.0	0	0	0	1
433.0	0	0	0	1
439.0	0	0	0	1
440.0	0	1	0	0
442.0	0	0	0	1
443.0	0	1	0	0
444.0	0	1	0	0
448.0	0	1	0	0
450.0	0	1	0	0
453.0	0	1	0	0
458.0	0	0	0	1
459.0	0	0	0	1
462.0	0	0	0	1
467.0	0	1	0	0
469.0	0	1	0	1
470.0	0	1	0	0
477.0	0	1	0	0
479.0	0	0	0	1
486.0	0	1	0	0
489.0	0	0	0	1
493.0	0	1	0	0
494.0	0	0	0	1
503.0	0	0	0	1
505.0	0	0	0	1
510.0	0	1	0	0
511.0	0	1	0	0
513.0	0	0	0	1
519.0	0	0	0	1
520.0	0	1	0	0
522.0	0	1	0	0
528.0	0	1	0	0
535.0	0	1	0	0
536.0	0	0	0	1
548.0	0	1	0	0
555.0	0	1	0	0
556.0	0	0	0	1
582.0	0	0	0	1
604.0	0	1	0	0
631.0	0	1	0	0
645.0	0	0	0	1
686.0	0	0	0	1
711.0	0	0	0	1
728.0	0	0	0	1
748.0	0	1	0	0
756.0	0	1	0	0
772.0	0	1	0	0
774.0	0	1	0	0
848.0	0	0	0	1
907.0	0	1	0	0
913.0	0	0	0	1
946.0	0	1	0	0
971.0	0	0	0	1
974.0	0	0	0	1
1019.0	0	0	0	1
1028.0	0	1	0	0
1046.0	0	0	0	1
1074.0	0	1	0	0
1075.0	0	1	0	0
1085.0	0	0	0	1
1092.0	0	1	0	0
1105.0	0	1	0	0
1171.0	0	0	0	1
1232.0	0	1	0	0
1314.0	0	0	0	1
1391.0	0	0	0	1
1400.0	0	1	0	0
1449.0	0	1	0	0
1648.0	0	0	0	1
1683.0	0	1	0	0