## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-186-TP3.bam --OUTPUT ACR-186-TP3.md.bam --METRICS_FILE ACR-186-TP3.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 18:11:12 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	206	11931822	2316330	0	154	8087490	2493319	0.677809	4336097

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.05594	1115192	0	1379183
2.0	1.123326	912665	609596	1079960
3.0	1.127626	656220	238406	674120
4.0	1.127901	429639	120101	357008
5.0	1.127918	266304	69188	171234
6.0	1.127919	162279	41524	80404
7.0	1.127919	100857	25701	39061
8.0	1.127919	63230	16229	20205
9.0	1.127919	40858	10223	11644
10.0	1.127919	26906	6517	7121
11.0	1.127919	18151	4357	4830
12.0	1.127919	12601	2729	3308
13.0	1.127919	8947	1773	2502
14.0	1.127919	6291	1167	1878
15.0	1.127919	4764	798	1511
16.0	1.127919	3468	490	1290
17.0	1.127919	2584	378	1062
18.0	1.127919	2033	216	879
19.0	1.127919	1573	182	735
20.0	1.127919	1220	111	603
21.0	1.127919	957	88	514
22.0	1.127919	855	43	478
23.0	1.127919	666	47	408
24.0	1.127919	598	31	319
25.0	1.127919	438	17	321
26.0	1.127919	408	20	286
27.0	1.127919	384	19	241
28.0	1.127919	348	11	243
29.0	1.127919	273	10	198
30.0	1.127919	250	14	176
31.0	1.127919	208	10	176
32.0	1.127919	210	9	139
33.0	1.127919	177	8	146
34.0	1.127919	177	6	106
35.0	1.127919	137	1	118
36.0	1.127919	131	3	88
37.0	1.127919	148	2	88
38.0	1.127919	105	2	77
39.0	1.127919	86	2	69
40.0	1.127919	91	3	73
41.0	1.127919	103	1	73
42.0	1.127919	76	0	66
43.0	1.127919	71	2	58
44.0	1.127919	68	2	55
45.0	1.127919	58	0	46
46.0	1.127919	60	1	44
47.0	1.127919	65	0	35
48.0	1.127919	50	0	36
49.0	1.127919	54	0	43
50.0	1.127919	54	3	44
51.0	1.127919	43	1	39
52.0	1.127919	39	1	29
53.0	1.127919	40	2	32
54.0	1.127919	48	3	34
55.0	1.127919	42	2	30
56.0	1.127919	30	1	31
57.0	1.127919	39	0	31
58.0	1.127919	35	1	27
59.0	1.127919	35	2	23
60.0	1.127919	27	0	35
61.0	1.127919	26	0	25
62.0	1.127919	29	0	16
63.0	1.127919	22	0	17
64.0	1.127919	12	0	17
65.0	1.127919	21	0	12
66.0	1.127919	24	2	20
67.0	1.127919	20	0	18
68.0	1.127919	17	1	19
69.0	1.127919	27	1	11
70.0	1.127919	14	1	13
71.0	1.127919	16	0	21
72.0	1.127919	23	0	14
73.0	1.127919	14	0	9
74.0	1.127919	17	0	19
75.0	1.127919	19	0	10
76.0	1.127919	12	1	11
77.0	1.127919	9	1	9
78.0	1.127919	9	0	12
79.0	1.127919	15	1	9
80.0	1.127919	13	0	12
81.0	1.127919	9	0	5
82.0	1.127919	12	0	9
83.0	1.127919	11	0	7
84.0	1.127919	12	0	7
85.0	1.127919	6	0	10
86.0	1.127919	5	0	11
87.0	1.127919	12	1	11
88.0	1.127919	16	1	6
89.0	1.127919	9	0	10
90.0	1.127919	10	0	8
91.0	1.127919	6	1	7
92.0	1.127919	7	0	8
93.0	1.127919	5	0	7
94.0	1.127919	9	1	7
95.0	1.127919	7	0	9
96.0	1.127919	7	0	6
97.0	1.127919	9	0	6
98.0	1.127919	6	0	5
99.0	1.127919	13	0	7
100.0	1.127919	9	0	4
101.0	0	8	0	5
102.0	0	6	0	6
103.0	0	3	0	11
104.0	0	6	0	4
105.0	0	6	0	0
106.0	0	9	0	2
107.0	0	5	0	4
108.0	0	4	0	4
109.0	0	5	0	3
110.0	0	1	0	8
111.0	0	4	0	0
112.0	0	5	0	4
113.0	0	2	0	3
114.0	0	4	0	3
115.0	0	4	0	6
116.0	0	2	0	2
117.0	0	5	0	2
118.0	0	5	0	4
119.0	0	3	0	4
120.0	0	2	0	2
121.0	0	4	0	0
122.0	0	5	0	4
123.0	0	4	0	5
124.0	0	3	0	2
125.0	0	3	0	4
126.0	0	2	0	4
127.0	0	4	0	5
128.0	0	4	0	3
129.0	0	3	0	2
130.0	0	4	0	2
131.0	0	5	0	4
132.0	0	3	0	3
133.0	0	2	0	0
134.0	0	0	0	2
135.0	0	2	0	2
136.0	0	3	0	0
137.0	0	3	0	1
138.0	0	5	0	1
139.0	0	2	0	2
140.0	0	3	0	2
141.0	0	1	0	4
142.0	0	1	0	3
143.0	0	3	0	0
144.0	0	3	0	0
145.0	0	2	0	1
146.0	0	2	0	3
147.0	0	3	0	0
148.0	0	2	0	1
149.0	0	2	0	1
150.0	0	1	0	1
151.0	0	4	0	0
152.0	0	2	0	0
153.0	0	0	0	1
154.0	0	3	0	1
155.0	0	1	0	1
156.0	0	1	0	3
157.0	0	2	0	1
158.0	0	0	0	1
159.0	0	0	0	2
160.0	0	1	0	1
161.0	0	2	0	0
162.0	0	4	0	2
163.0	0	1	0	3
165.0	0	0	0	1
167.0	0	1	0	0
168.0	0	1	0	0
169.0	0	1	0	0
170.0	0	1	0	0
171.0	0	0	0	1
172.0	0	2	0	3
173.0	0	1	0	2
174.0	0	1	0	2
175.0	0	1	0	1
176.0	0	1	0	0
177.0	0	1	0	3
178.0	0	0	0	1
179.0	0	3	0	2
180.0	0	2	0	0
181.0	0	1	0	2
182.0	0	1	0	0
183.0	0	1	0	1
184.0	0	0	0	3
185.0	0	1	0	3
186.0	0	3	0	0
187.0	0	0	0	1
188.0	0	3	0	1
189.0	0	2	0	1
191.0	0	1	0	0
192.0	0	1	0	0
194.0	0	1	0	0
195.0	0	2	0	0
196.0	0	1	0	0
197.0	0	0	0	3
198.0	0	1	0	1
199.0	0	3	0	0
200.0	0	1	0	0
202.0	0	0	0	3
203.0	0	1	0	1
204.0	0	0	0	1
205.0	0	0	0	1
206.0	0	0	0	3
207.0	0	3	0	0
209.0	0	0	0	1
210.0	0	3	0	0
212.0	0	1	0	1
213.0	0	1	0	0
215.0	0	1	0	1
216.0	0	0	0	1
217.0	0	1	0	0
218.0	0	0	0	1
219.0	0	2	0	1
220.0	0	1	0	1
221.0	0	0	0	1
223.0	0	2	0	0
224.0	0	0	0	1
228.0	0	2	0	1
229.0	0	0	0	1
230.0	0	1	0	2
231.0	0	1	0	0
234.0	0	0	0	1
235.0	0	0	0	1
236.0	0	0	0	1
237.0	0	1	0	0
238.0	0	0	0	1
240.0	0	0	0	3
241.0	0	0	0	1
242.0	0	1	0	2
245.0	0	0	0	1
246.0	0	1	0	1
247.0	0	1	0	0
248.0	0	4	0	0
249.0	0	2	0	2
250.0	0	1	0	1
251.0	0	1	0	1
252.0	0	3	0	1
253.0	0	3	0	0
254.0	0	0	0	1
256.0	0	2	0	1
258.0	0	1	0	0
260.0	0	2	0	0
262.0	0	0	0	1
263.0	0	0	0	1
264.0	0	0	0	1
265.0	0	0	0	2
266.0	0	0	0	1
267.0	0	0	0	1
268.0	0	1	0	1
271.0	0	1	0	0
272.0	0	2	0	0
276.0	0	1	0	0
278.0	0	1	0	1
280.0	0	0	0	1
284.0	0	1	0	1
286.0	0	0	0	1
287.0	0	0	0	1
288.0	0	2	0	0
289.0	0	1	0	1
291.0	0	1	0	0
293.0	0	1	0	0
297.0	0	0	0	1
300.0	0	1	0	0
302.0	0	1	0	0
304.0	0	1	0	2
306.0	0	1	0	0
309.0	0	0	0	1
312.0	0	0	0	1
313.0	0	1	0	0
316.0	0	1	0	0
318.0	0	0	0	1
319.0	0	1	0	0
320.0	0	0	0	1
322.0	0	1	0	0
323.0	0	1	0	0
324.0	0	1	0	0
327.0	0	0	0	1
328.0	0	0	0	1
334.0	0	1	0	0
341.0	0	0	0	1
346.0	0	1	0	0
347.0	0	1	0	0
349.0	0	0	0	1
350.0	0	0	0	1
357.0	0	1	0	0
360.0	0	1	0	0
367.0	0	1	0	0
372.0	0	2	0	1
376.0	0	1	0	1
387.0	0	1	0	0
395.0	0	0	0	1
398.0	0	0	0	1
409.0	0	1	0	0
410.0	0	1	0	0
427.0	0	0	0	1
434.0	0	0	0	1
443.0	0	0	0	1
446.0	0	0	0	1
462.0	0	1	0	0
468.0	0	0	0	1
472.0	0	1	0	0
474.0	0	1	0	0
485.0	0	1	0	0
488.0	0	1	0	0
496.0	0	0	0	1
507.0	0	0	0	1
516.0	0	0	0	1
531.0	0	1	0	0
534.0	0	1	0	0
574.0	0	1	0	0
599.0	0	0	0	1
630.0	0	0	0	1
660.0	0	0	0	1
665.0	0	1	0	0
668.0	0	1	0	0
697.0	0	1	0	0
790.0	0	0	0	1
866.0	0	1	0	0
898.0	0	0	0	1
917.0	0	0	0	1
926.0	0	1	0	0
947.0	0	0	0	1
970.0	0	1	0	0
975.0	0	1	0	0
1244.0	0	0	0	1
1331.0	0	1	0	0
1457.0	0	0	0	1
1485.0	0	1	0	0