## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-145-TP3.bam --OUTPUT ACR-145-TP3.md.bam --METRICS_FILE ACR-145-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 18:14:27 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	266	16005279	3269383	0	209	13263332	2865475	0.828684	2765859

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.005626	263979	0	313928
2.0	1.008711	261005	549278	342774
3.0	1.008721	316613	239234	414258
4.0	1.008721	344016	127247	423481
5.0	1.008721	334499	77245	370940
6.0	1.008721	292716	49160	288521
7.0	1.008721	239283	32910	203964
8.0	1.008721	183740	22743	133143
9.0	1.008721	135677	15409	83553
10.0	1.008721	97864	10843	51429
11.0	1.008721	70072	7572	32476
12.0	1.008721	50450	5305	21180
13.0	1.008721	36534	3656	14384
14.0	1.008721	26375	2702	9995
15.0	1.008721	19670	1920	7330
16.0	1.008721	14345	1244	5374
17.0	1.008721	11009	922	4045
18.0	1.008721	8251	680	3114
19.0	1.008721	6287	445	2370
20.0	1.008721	4755	326	1906
21.0	1.008721	3833	233	1578
22.0	1.008721	3040	171	1205
23.0	1.008721	2395	123	1086
24.0	1.008721	1909	89	958
25.0	1.008721	1553	50	758
26.0	1.008721	1297	50	682
27.0	1.008721	1088	51	584
28.0	1.008721	893	23	505
29.0	1.008721	743	25	447
30.0	1.008721	644	24	434
31.0	1.008721	590	11	378
32.0	1.008721	505	11	311
33.0	1.008721	436	14	293
34.0	1.008721	418	9	281
35.0	1.008721	358	4	250
36.0	1.008721	295	8	214
37.0	1.008721	282	6	216
38.0	1.008721	247	5	222
39.0	1.008721	249	4	178
40.0	1.008721	225	8	161
41.0	1.008721	190	2	142
42.0	1.008721	185	3	143
43.0	1.008721	166	2	129
44.0	1.008721	139	2	118
45.0	1.008721	145	2	118
46.0	1.008721	126	3	106
47.0	1.008721	124	2	81
48.0	1.008721	112	0	88
49.0	1.008721	122	2	82
50.0	1.008721	114	1	105
51.0	1.008721	108	4	87
52.0	1.008721	93	0	94
53.0	1.008721	83	0	62
54.0	1.008721	86	1	76
55.0	1.008721	65	2	73
56.0	1.008721	78	2	62
57.0	1.008721	75	0	53
58.0	1.008721	76	2	46
59.0	1.008721	70	0	43
60.0	1.008721	54	3	42
61.0	1.008721	53	1	37
62.0	1.008721	55	0	39
63.0	1.008721	40	2	43
64.0	1.008721	52	0	41
65.0	1.008721	49	0	41
66.0	1.008721	45	0	39
67.0	1.008721	48	2	32
68.0	1.008721	43	1	32
69.0	1.008721	39	0	31
70.0	1.008721	34	1	29
71.0	1.008721	33	0	22
72.0	1.008721	27	1	24
73.0	1.008721	29	0	31
74.0	1.008721	38	0	27
75.0	1.008721	25	0	29
76.0	1.008721	22	0	25
77.0	1.008721	24	0	21
78.0	1.008721	29	0	17
79.0	1.008721	28	2	18
80.0	1.008721	24	0	14
81.0	1.008721	29	0	14
82.0	1.008721	22	0	18
83.0	1.008721	20	1	15
84.0	1.008721	12	0	17
85.0	1.008721	17	0	15
86.0	1.008721	25	0	19
87.0	1.008721	12	0	11
88.0	1.008721	26	1	14
89.0	1.008721	18	0	12
90.0	1.008721	9	0	12
91.0	1.008721	13	1	10
92.0	1.008721	11	0	9
93.0	1.008721	14	0	16
94.0	1.008721	17	0	10
95.0	1.008721	10	0	11
96.0	1.008721	9	0	6
97.0	1.008721	12	0	12
98.0	1.008721	10	0	9
99.0	1.008721	16	0	9
100.0	1.008721	6	1	8
101.0	0	14	0	11
102.0	0	11	0	18
103.0	0	10	0	8
104.0	0	18	0	9
105.0	0	14	0	5
106.0	0	9	0	11
107.0	0	7	0	5
108.0	0	11	0	9
109.0	0	10	0	11
110.0	0	6	0	6
111.0	0	4	0	0
112.0	0	10	0	5
113.0	0	12	0	3
114.0	0	10	0	8
115.0	0	8	0	7
116.0	0	5	0	1
117.0	0	7	0	5
118.0	0	10	0	4
119.0	0	3	0	2
120.0	0	13	0	9
121.0	0	5	1	3
122.0	0	4	0	3
123.0	0	0	0	6
124.0	0	9	0	11
125.0	0	4	0	5
126.0	0	6	0	4
127.0	0	3	0	6
128.0	0	5	1	5
129.0	0	8	0	4
130.0	0	4	0	2
131.0	0	1	0	2
132.0	0	5	0	4
133.0	0	5	0	4
134.0	0	5	0	5
135.0	0	7	0	3
136.0	0	2	0	3
137.0	0	2	0	2
138.0	0	3	0	2
139.0	0	6	0	3
140.0	0	3	0	3
141.0	0	3	0	7
142.0	0	2	0	4
143.0	0	3	0	2
144.0	0	3	0	3
145.0	0	1	0	2
146.0	0	5	0	4
147.0	0	4	0	2
148.0	0	3	0	5
149.0	0	3	0	5
150.0	0	4	0	3
151.0	0	3	0	0
152.0	0	0	0	2
153.0	0	2	0	5
154.0	0	7	0	1
155.0	0	5	0	4
156.0	0	0	0	2
157.0	0	3	0	4
158.0	0	3	0	2
159.0	0	3	0	2
160.0	0	1	0	6
161.0	0	2	0	2
162.0	0	4	0	2
163.0	0	3	0	1
164.0	0	5	0	4
165.0	0	5	0	2
166.0	0	4	0	3
167.0	0	3	0	1
168.0	0	3	0	1
169.0	0	2	0	5
170.0	0	3	0	5
171.0	0	0	0	2
172.0	0	1	0	2
173.0	0	2	0	0
174.0	0	2	0	0
175.0	0	2	0	2
176.0	0	1	0	3
177.0	0	3	0	2
178.0	0	2	0	0
179.0	0	2	0	0
180.0	0	3	0	4
181.0	0	3	0	1
182.0	0	3	0	0
183.0	0	1	0	1
184.0	0	2	0	2
185.0	0	0	0	1
186.0	0	5	0	0
187.0	0	0	1	1
188.0	0	1	0	1
189.0	0	1	0	5
190.0	0	0	0	2
191.0	0	2	0	2
192.0	0	2	0	3
193.0	0	2	0	2
194.0	0	4	0	2
195.0	0	2	0	3
196.0	0	0	0	2
197.0	0	1	0	3
198.0	0	2	0	2
199.0	0	3	0	3
200.0	0	2	0	0
201.0	0	1	0	2
202.0	0	2	0	0
203.0	0	3	0	2
204.0	0	1	0	2
205.0	0	2	0	0
206.0	0	4	0	1
207.0	0	2	0	1
208.0	0	4	0	0
209.0	0	3	0	0
210.0	0	2	0	0
211.0	0	2	0	1
212.0	0	0	0	1
213.0	0	0	0	1
214.0	0	2	0	2
215.0	0	1	0	1
216.0	0	1	0	1
217.0	0	1	0	0
218.0	0	0	0	2
219.0	0	1	0	1
220.0	0	2	0	1
221.0	0	3	0	1
223.0	0	1	0	1
224.0	0	1	0	0
225.0	0	0	0	1
226.0	0	2	0	0
227.0	0	1	0	1
228.0	0	2	0	0
229.0	0	1	0	0
230.0	0	1	0	0
232.0	0	2	0	0
233.0	0	0	0	1
234.0	0	2	0	1
236.0	0	0	0	2
237.0	0	0	0	1
238.0	0	1	0	0
239.0	0	0	0	2
240.0	0	1	0	2
242.0	0	1	0	0
243.0	0	1	0	2
245.0	0	3	0	0
246.0	0	0	0	2
247.0	0	1	0	1
248.0	0	2	0	1
250.0	0	1	0	0
251.0	0	1	0	1
253.0	0	1	0	0
256.0	0	1	0	0
257.0	0	1	0	0
258.0	0	1	0	1
259.0	0	0	0	1
261.0	0	2	0	0
262.0	0	0	0	1
263.0	0	1	0	1
264.0	0	1	0	0
267.0	0	0	0	1
268.0	0	1	0	1
269.0	0	1	0	0
270.0	0	1	0	0
271.0	0	0	0	1
273.0	0	1	0	2
278.0	0	1	0	1
281.0	0	2	0	0
282.0	0	0	0	1
286.0	0	0	0	1
287.0	0	1	0	1
288.0	0	1	0	0
289.0	0	1	0	0
291.0	0	1	0	0
295.0	0	1	0	1
298.0	0	0	0	1
301.0	0	1	0	0
302.0	0	1	0	0
303.0	0	1	0	0
307.0	0	0	0	1
308.0	0	0	0	1
311.0	0	0	0	1
313.0	0	1	0	0
319.0	0	0	0	2
328.0	0	1	0	0
330.0	0	1	0	0
331.0	0	0	0	1
334.0	0	1	0	0
338.0	0	1	0	0
339.0	0	1	0	0
341.0	0	0	0	1
343.0	0	0	0	1
344.0	0	1	0	0
346.0	0	1	0	0
351.0	0	0	0	1
352.0	0	1	0	0
353.0	0	0	0	1
354.0	0	0	0	1
360.0	0	1	0	0
363.0	0	1	0	0
364.0	0	1	0	1
365.0	0	0	0	1
368.0	0	1	0	0
374.0	0	0	0	1
379.0	0	0	0	1
383.0	0	0	0	1
384.0	0	1	0	0
390.0	0	1	0	0
394.0	0	1	0	0
397.0	0	0	0	1
398.0	0	0	0	1
402.0	0	0	0	1
407.0	0	0	0	1
409.0	0	0	0	1
410.0	0	1	0	0
411.0	0	1	0	0
412.0	0	1	0	0
423.0	0	0	0	1
424.0	0	1	0	0
426.0	0	1	0	0
437.0	0	0	0	1
445.0	0	0	0	1
456.0	0	1	0	0
461.0	0	1	0	0
463.0	0	0	0	1
467.0	0	1	0	0
471.0	0	1	0	0
472.0	0	0	0	2
475.0	0	0	0	1
479.0	0	1	0	0
481.0	0	1	0	0
489.0	0	1	0	0
490.0	0	0	0	1
493.0	0	1	0	0
507.0	0	1	0	0
550.0	0	0	0	1
558.0	0	0	0	1
560.0	0	0	0	1
577.0	0	1	0	0
581.0	0	0	0	1
583.0	0	1	0	0
597.0	0	1	0	0
677.0	0	1	0	0
679.0	0	0	0	1
767.0	0	1	0	0
769.0	0	1	0	0
929.0	0	0	0	1
961.0	0	0	0	1
965.0	0	0	0	1
973.0	0	1	0	0
995.0	0	1	0	0
1006.0	0	1	0	0
1011.0	0	0	0	1
1065.0	0	1	0	0
1494.0	0	0	0	1
1537.0	0	1	0	0