## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-265-TP2.bam --OUTPUT ACR-265-TP2.md.bam --METRICS_FILE ACR-265-TP2.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 18:15:02 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	196	16879639	3769456	0	131	10557255	4078755	0.625443	7869361

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.098967	2364908	0	3035888
2.0	1.227624	1582825	1037425	1787457
3.0	1.242685	967540	412548	850402
4.0	1.244449	560229	205906	355331
5.0	1.244655	322060	114239	143256
6.0	1.244679	188229	65925	61299
7.0	1.244682	112867	39035	28712
8.0	1.244682	69819	23687	15580
9.0	1.244683	44900	14809	9317
10.0	1.244683	29735	9159	6362
11.0	1.244683	19648	5563	4596
12.0	1.244683	13661	3540	3452
13.0	1.244683	9439	2278	2594
14.0	1.244683	6783	1468	2209
15.0	1.244683	5027	971	1792
16.0	1.244683	3797	589	1524
17.0	1.244683	2814	441	1238
18.0	1.244683	2264	329	1043
19.0	1.244683	1776	253	962
20.0	1.244683	1441	162	773
21.0	1.244683	1207	131	688
22.0	1.244683	1044	87	622
23.0	1.244683	838	69	542
24.0	1.244683	732	66	455
25.0	1.244683	634	46	444
26.0	1.244683	575	43	350
27.0	1.244683	488	34	350
28.0	1.244683	436	49	328
29.0	1.244683	397	29	267
30.0	1.244683	410	19	288
31.0	1.244683	354	21	251
32.0	1.244683	328	17	203
33.0	1.244683	281	25	185
34.0	1.244683	266	26	187
35.0	1.244683	247	12	173
36.0	1.244683	207	17	150
37.0	1.244683	198	6	156
38.0	1.244683	178	14	107
39.0	1.244683	180	8	120
40.0	1.244683	155	13	101
41.0	1.244683	138	18	108
42.0	1.244683	138	8	97
43.0	1.244683	123	10	84
44.0	1.244683	111	7	95
45.0	1.244683	111	3	95
46.0	1.244683	111	9	89
47.0	1.244683	103	4	75
48.0	1.244683	92	6	92
49.0	1.244683	90	4	78
50.0	1.244683	90	1	58
51.0	1.244683	82	8	57
52.0	1.244683	76	5	47
53.0	1.244683	80	1	61
54.0	1.244683	71	5	64
55.0	1.244683	75	1	55
56.0	1.244683	58	1	58
57.0	1.244683	77	2	49
58.0	1.244683	59	2	48
59.0	1.244683	67	4	48
60.0	1.244683	53	2	40
61.0	1.244683	47	4	44
62.0	1.244683	50	0	26
63.0	1.244683	45	2	42
64.0	1.244683	54	1	28
65.0	1.244683	50	1	26
66.0	1.244683	36	2	38
67.0	1.244683	36	1	34
68.0	1.244683	37	2	21
69.0	1.244683	34	5	24
70.0	1.244683	35	0	29
71.0	1.244683	33	1	20
72.0	1.244683	25	1	21
73.0	1.244683	33	0	23
74.0	1.244683	23	1	23
75.0	1.244683	35	2	27
76.0	1.244683	34	2	21
77.0	1.244683	22	2	27
78.0	1.244683	29	0	24
79.0	1.244683	27	0	20
80.0	1.244683	27	0	14
81.0	1.244683	26	1	20
82.0	1.244683	20	0	11
83.0	1.244683	11	0	20
84.0	1.244683	24	0	14
85.0	1.244683	28	1	10
86.0	1.244683	14	0	10
87.0	1.244683	24	0	15
88.0	1.244683	27	1	20
89.0	1.244683	20	0	13
90.0	1.244683	16	1	11
91.0	1.244683	13	0	9
92.0	1.244683	14	0	7
93.0	1.244683	15	1	12
94.0	1.244683	11	0	9
95.0	1.244683	14	1	13
96.0	1.244683	13	1	9
97.0	1.244683	15	1	13
98.0	1.244683	19	0	7
99.0	1.244683	12	0	7
100.0	1.244683	19	0	9
101.0	0	10	0	8
102.0	0	10	0	5
103.0	0	8	0	8
104.0	0	6	2	8
105.0	0	12	0	8
106.0	0	11	0	8
107.0	0	10	0	2
108.0	0	12	1	13
109.0	0	6	2	6
110.0	0	10	0	5
111.0	0	7	0	9
112.0	0	9	0	8
113.0	0	10	0	5
114.0	0	9	0	9
115.0	0	14	1	6
116.0	0	5	1	11
117.0	0	6	0	11
118.0	0	2	0	2
119.0	0	7	0	4
120.0	0	10	0	6
121.0	0	9	0	8
122.0	0	4	0	11
123.0	0	7	0	6
124.0	0	13	0	5
125.0	0	8	0	3
126.0	0	7	0	4
127.0	0	4	0	3
128.0	0	7	0	1
129.0	0	12	0	3
130.0	0	7	0	4
131.0	0	3	0	1
132.0	0	3	0	2
133.0	0	6	0	1
134.0	0	6	0	1
135.0	0	2	0	4
136.0	0	3	0	3
137.0	0	3	0	3
138.0	0	0	0	7
139.0	0	3	0	7
140.0	0	4	1	6
141.0	0	8	0	2
142.0	0	5	0	2
143.0	0	6	0	4
144.0	0	6	0	8
145.0	0	3	0	3
146.0	0	10	0	2
147.0	0	1	1	2
148.0	0	4	0	3
149.0	0	4	1	2
150.0	0	4	0	0
152.0	0	4	0	1
153.0	0	4	0	4
154.0	0	5	0	3
155.0	0	2	0	4
156.0	0	1	0	3
157.0	0	6	1	3
158.0	0	4	0	2
159.0	0	0	0	3
160.0	0	1	1	3
161.0	0	4	0	3
162.0	0	3	0	0
163.0	0	3	0	4
164.0	0	1	0	0
165.0	0	3	0	5
166.0	0	2	0	2
167.0	0	3	0	1
168.0	0	3	0	0
169.0	0	1	0	2
170.0	0	1	0	1
171.0	0	1	0	4
172.0	0	1	0	3
173.0	0	4	0	1
174.0	0	3	0	0
175.0	0	2	0	1
176.0	0	3	0	2
177.0	0	2	0	0
178.0	0	2	0	0
179.0	0	2	0	2
180.0	0	2	0	1
181.0	0	2	0	2
182.0	0	1	0	2
183.0	0	1	0	2
184.0	0	0	0	2
185.0	0	0	0	2
186.0	0	4	0	2
187.0	0	4	0	0
188.0	0	0	0	2
189.0	0	2	0	1
190.0	0	1	0	2
191.0	0	1	0	4
192.0	0	4	0	1
193.0	0	1	0	0
194.0	0	1	0	3
195.0	0	1	0	3
196.0	0	2	0	2
198.0	0	3	0	1
199.0	0	1	0	2
200.0	0	4	0	0
201.0	0	3	0	1
202.0	0	1	0	3
203.0	0	2	0	1
204.0	0	3	0	2
206.0	0	2	0	0
207.0	0	1	0	1
208.0	0	3	0	1
209.0	0	1	0	2
210.0	0	0	0	4
211.0	0	3	0	1
212.0	0	3	0	1
213.0	0	5	0	0
215.0	0	0	0	2
216.0	0	0	0	1
217.0	0	0	0	2
218.0	0	2	0	4
219.0	0	1	0	1
220.0	0	2	0	0
221.0	0	2	0	1
222.0	0	1	0	1
223.0	0	1	0	1
224.0	0	1	0	0
225.0	0	1	0	2
226.0	0	0	0	1
227.0	0	2	0	0
228.0	0	4	0	2
229.0	0	1	0	1
230.0	0	3	0	1
232.0	0	0	0	1
233.0	0	2	0	0
234.0	0	1	0	0
235.0	0	2	0	0
236.0	0	2	0	0
237.0	0	0	0	1
238.0	0	3	0	0
239.0	0	1	0	0
240.0	0	1	0	0
241.0	0	1	0	0
244.0	0	2	0	0
245.0	0	2	0	1
246.0	0	1	0	1
247.0	0	2	0	2
248.0	0	0	0	1
252.0	0	1	0	1
254.0	0	1	0	0
257.0	0	0	0	1
259.0	0	2	0	2
265.0	0	1	0	0
266.0	0	0	0	2
267.0	0	2	0	1
269.0	0	1	0	0
271.0	0	1	0	1
272.0	0	1	0	1
274.0	0	0	0	1
275.0	0	2	0	1
276.0	0	3	0	0
278.0	0	0	0	1
279.0	0	0	0	1
280.0	0	1	0	1
281.0	0	0	0	1
282.0	0	0	0	1
284.0	0	1	0	0
287.0	0	0	0	2
288.0	0	0	0	1
289.0	0	1	0	1
292.0	0	1	0	1
293.0	0	0	0	1
294.0	0	1	0	0
295.0	0	1	0	1
296.0	0	0	0	1
297.0	0	0	0	1
298.0	0	0	0	1
299.0	0	1	0	0
300.0	0	2	0	0
302.0	0	0	0	1
304.0	0	2	0	0
305.0	0	1	0	0
308.0	0	1	0	0
310.0	0	1	0	0
312.0	0	2	0	0
313.0	0	1	0	1
314.0	0	0	0	1
316.0	0	0	0	1
319.0	0	0	0	1
323.0	0	1	0	0
324.0	0	0	0	1
326.0	0	1	0	0
328.0	0	0	0	1
332.0	0	2	0	0
335.0	0	2	0	0
336.0	0	1	0	0
338.0	0	0	0	1
339.0	0	1	0	0
340.0	0	1	0	0
347.0	0	1	0	0
353.0	0	1	0	0
356.0	0	0	0	3
357.0	0	0	0	1
359.0	0	1	0	0
360.0	0	1	0	0
361.0	0	1	0	0
362.0	0	0	0	2
368.0	0	1	0	1
370.0	0	1	0	1
374.0	0	1	0	0
377.0	0	1	0	0
378.0	0	1	0	0
379.0	0	1	0	0
381.0	0	0	0	1
389.0	0	0	0	1
392.0	0	0	0	1
397.0	0	2	0	0
401.0	0	0	0	1
402.0	0	1	0	2
408.0	0	0	0	1
410.0	0	1	0	0
411.0	0	0	0	1
413.0	0	0	0	1
415.0	0	1	0	0
421.0	0	0	0	1
427.0	0	1	0	0
428.0	0	1	0	0
437.0	0	1	0	0
445.0	0	0	0	1
448.0	0	1	0	0
458.0	0	1	0	0
469.0	0	1	0	0
470.0	0	1	0	0
481.0	0	0	0	2
483.0	0	0	0	1
486.0	0	1	0	0
491.0	0	0	0	1
499.0	0	1	0	1
500.0	0	1	0	0
516.0	0	1	0	0
525.0	0	1	0	0
542.0	0	0	0	1
554.0	0	1	0	0
558.0	0	0	0	1
562.0	0	0	0	1
565.0	0	0	0	1
581.0	0	1	0	0
597.0	0	1	0	0
629.0	0	1	0	0
667.0	0	0	0	1
670.0	0	1	0	0
696.0	0	0	0	1
707.0	0	0	0	1
716.0	0	0	0	1
730.0	0	0	0	1
735.0	0	1	0	0
737.0	0	1	0	0
741.0	0	1	0	0
748.0	0	1	0	0
754.0	0	0	0	1
780.0	0	1	0	0
862.0	0	1	0	0
1125.0	0	0	0	1
1162.0	0	1	0	0
1217.0	0	0	0	1
1279.0	0	1	0	0
1378.0	0	0	0	1
1432.0	0	0	0	1
1474.0	0	1	0	0
1546.0	0	1	0	0
1676.0	0	0	0	1
1723.0	0	1	0	0