## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-244-TP2.bam --OUTPUT ACR-244-TP2.md.bam --METRICS_FILE ACR-244-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 18:16:45 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	163	16180049	3543844	0	99	10331504	3627870	0.638533	7025402

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.081159	2017993	0	2547143
2.0	1.189222	1461664	957870	1683640
3.0	1.200023	949268	378186	889306
4.0	1.201102	569257	186127	399639
5.0	1.20121	330602	101782	167196
6.0	1.201221	192408	57786	70740
7.0	1.201222	114077	33522	32061
8.0	1.201222	69749	19841	16603
9.0	1.201222	43755	11925	9605
10.0	1.201222	28173	7068	6130
11.0	1.201222	18255	4386	4312
12.0	1.201222	12684	2667	3262
13.0	1.201222	8519	1641	2483
14.0	1.201222	6211	1048	2042
15.0	1.201222	4412	630	1629
16.0	1.201222	3266	490	1314
17.0	1.201222	2500	297	1110
18.0	1.201222	1933	194	950
19.0	1.201222	1490	166	807
20.0	1.201222	1234	122	759
21.0	1.201222	1061	90	663
22.0	1.201222	840	72	531
23.0	1.201222	782	49	483
24.0	1.201222	632	47	437
25.0	1.201222	566	42	400
26.0	1.201222	458	32	349
27.0	1.201222	468	35	316
28.0	1.201222	446	28	295
29.0	1.201222	357	18	263
30.0	1.201222	373	19	262
31.0	1.201222	327	12	193
32.0	1.201222	263	18	191
33.0	1.201222	239	17	180
34.0	1.201222	219	11	177
35.0	1.201222	180	11	126
36.0	1.201222	198	12	136
37.0	1.201222	156	13	142
38.0	1.201222	170	7	124
39.0	1.201222	154	5	101
40.0	1.201222	143	11	105
41.0	1.201222	133	4	96
42.0	1.201222	105	3	99
43.0	1.201222	122	5	78
44.0	1.201222	103	7	79
45.0	1.201222	91	5	82
46.0	1.201222	101	1	64
47.0	1.201222	105	5	69
48.0	1.201222	80	5	69
49.0	1.201222	89	4	75
50.0	1.201222	66	3	63
51.0	1.201222	68	7	56
52.0	1.201222	63	4	49
53.0	1.201222	62	4	55
54.0	1.201222	76	3	36
55.0	1.201222	62	2	49
56.0	1.201222	59	6	37
57.0	1.201222	50	7	49
58.0	1.201222	50	3	44
59.0	1.201222	47	2	37
60.0	1.201222	52	1	32
61.0	1.201222	50	3	34
62.0	1.201222	49	6	26
63.0	1.201222	41	2	36
64.0	1.201222	35	1	24
65.0	1.201222	29	1	26
66.0	1.201222	31	1	25
67.0	1.201222	36	2	26
68.0	1.201222	34	0	22
69.0	1.201222	30	1	12
70.0	1.201222	29	0	17
71.0	1.201222	26	0	28
72.0	1.201222	28	1	25
73.0	1.201222	33	1	20
74.0	1.201222	26	0	15
75.0	1.201222	35	1	19
76.0	1.201222	22	0	12
77.0	1.201222	17	1	10
78.0	1.201222	13	0	14
79.0	1.201222	17	0	18
80.0	1.201222	19	0	8
81.0	1.201222	20	0	12
82.0	1.201222	20	0	22
83.0	1.201222	14	1	14
84.0	1.201222	20	0	11
85.0	1.201222	15	0	11
86.0	1.201222	10	2	9
87.0	1.201222	19	0	12
88.0	1.201222	10	1	8
89.0	1.201222	10	0	10
90.0	1.201222	9	2	6
91.0	1.201222	8	1	13
92.0	1.201222	8	0	7
93.0	1.201222	7	0	7
94.0	1.201222	15	1	16
95.0	1.201222	13	0	10
96.0	1.201222	12	0	12
97.0	1.201222	9	1	13
98.0	1.201222	17	0	9
99.0	1.201222	10	1	8
100.0	1.201222	11	0	10
101.0	0	8	0	10
102.0	0	15	1	10
103.0	0	8	0	8
104.0	0	12	0	6
105.0	0	10	0	9
106.0	0	13	0	4
107.0	0	8	0	8
108.0	0	6	0	6
109.0	0	9	0	6
110.0	0	8	1	6
111.0	0	8	1	4
112.0	0	10	0	8
113.0	0	6	1	11
114.0	0	10	0	8
115.0	0	5	0	3
116.0	0	11	0	8
117.0	0	8	0	6
118.0	0	11	2	5
119.0	0	9	1	7
120.0	0	6	0	3
121.0	0	2	0	6
122.0	0	7	0	1
123.0	0	7	0	2
124.0	0	8	0	8
125.0	0	7	0	3
126.0	0	8	0	4
127.0	0	4	0	4
128.0	0	6	0	3
129.0	0	7	0	4
130.0	0	4	2	2
131.0	0	5	0	5
132.0	0	4	0	4
133.0	0	1	0	5
134.0	0	9	0	3
135.0	0	7	0	9
136.0	0	3	0	4
137.0	0	5	0	5
138.0	0	4	0	4
139.0	0	4	0	5
140.0	0	4	0	4
141.0	0	6	0	3
142.0	0	4	0	5
143.0	0	5	0	2
144.0	0	3	0	4
145.0	0	4	0	4
146.0	0	4	0	3
147.0	0	3	1	1
148.0	0	2	0	6
149.0	0	3	0	4
150.0	0	3	0	1
151.0	0	5	1	2
152.0	0	2	0	2
153.0	0	4	0	3
154.0	0	5	0	2
155.0	0	3	0	3
156.0	0	2	0	1
157.0	0	3	0	4
158.0	0	4	0	0
159.0	0	1	0	2
160.0	0	2	0	3
161.0	0	1	0	2
162.0	0	0	0	6
163.0	0	5	0	1
164.0	0	6	0	1
165.0	0	4	0	1
166.0	0	4	0	7
167.0	0	1	0	2
168.0	0	3	0	1
169.0	0	1	0	2
170.0	0	2	0	4
171.0	0	2	0	2
172.0	0	4	0	1
173.0	0	8	0	1
174.0	0	5	0	5
175.0	0	1	0	2
176.0	0	2	0	0
177.0	0	3	1	2
178.0	0	1	0	1
179.0	0	1	0	5
180.0	0	2	0	4
181.0	0	2	0	1
182.0	0	4	1	2
183.0	0	3	0	0
184.0	0	1	0	1
185.0	0	1	0	1
186.0	0	0	1	3
187.0	0	1	0	0
188.0	0	2	0	2
189.0	0	2	0	5
190.0	0	3	0	2
191.0	0	2	0	1
192.0	0	4	0	1
193.0	0	1	0	0
194.0	0	0	0	1
195.0	0	2	0	2
196.0	0	2	1	1
197.0	0	2	0	3
198.0	0	4	0	2
199.0	0	3	0	1
200.0	0	1	0	1
201.0	0	0	0	3
202.0	0	1	1	5
203.0	0	1	0	2
204.0	0	1	0	1
205.0	0	3	0	2
206.0	0	3	0	1
207.0	0	3	0	2
208.0	0	3	0	0
209.0	0	2	0	0
210.0	0	2	0	0
211.0	0	1	0	1
212.0	0	1	0	6
213.0	0	1	1	1
214.0	0	0	0	1
215.0	0	2	0	1
216.0	0	3	0	0
217.0	0	0	0	1
218.0	0	3	0	2
219.0	0	1	0	0
220.0	0	0	0	1
221.0	0	1	0	1
222.0	0	2	0	3
223.0	0	1	0	2
224.0	0	0	0	1
225.0	0	1	0	1
226.0	0	1	0	1
227.0	0	3	0	0
228.0	0	2	0	0
229.0	0	3	0	1
230.0	0	2	0	0
231.0	0	3	0	0
232.0	0	2	0	0
234.0	0	2	0	1
235.0	0	1	0	2
237.0	0	1	0	0
238.0	0	2	0	2
240.0	0	2	0	2
241.0	0	0	0	1
242.0	0	1	0	0
244.0	0	3	0	1
245.0	0	1	0	2
246.0	0	2	0	2
247.0	0	2	0	1
249.0	0	2	0	0
252.0	0	2	0	2
253.0	0	0	0	2
255.0	0	2	0	2
256.0	0	1	0	1
257.0	0	1	0	1
259.0	0	1	1	0
260.0	0	1	0	1
261.0	0	2	0	0
263.0	0	1	0	0
264.0	0	3	0	1
266.0	0	2	0	2
267.0	0	2	1	0
269.0	0	0	0	3
270.0	0	0	0	2
271.0	0	1	0	0
272.0	0	0	0	2
273.0	0	0	0	1
274.0	0	0	0	1
275.0	0	0	0	1
276.0	0	3	0	0
277.0	0	2	0	1
278.0	0	2	1	1
279.0	0	1	0	0
281.0	0	0	0	1
283.0	0	1	0	1
284.0	0	3	0	0
286.0	0	0	0	1
287.0	0	1	0	0
288.0	0	0	1	0
289.0	0	1	0	0
290.0	0	1	0	0
292.0	0	1	0	1
293.0	0	0	0	1
294.0	0	0	0	1
295.0	0	1	0	1
296.0	0	1	0	1
297.0	0	0	0	1
298.0	0	1	0	0
299.0	0	0	0	1
301.0	0	3	0	0
302.0	0	1	0	0
303.0	0	0	0	1
305.0	0	0	0	1
306.0	0	1	0	0
311.0	0	0	0	2
313.0	0	2	0	1
314.0	0	0	0	1
316.0	0	1	0	1
317.0	0	1	0	0
318.0	0	1	0	0
321.0	0	2	0	0
322.0	0	1	0	0
324.0	0	1	0	0
326.0	0	0	0	1
327.0	0	0	0	1
329.0	0	0	0	1
330.0	0	1	0	0
334.0	0	1	0	0
336.0	0	1	0	0
337.0	0	1	0	1
342.0	0	1	0	0
344.0	0	1	0	0
350.0	0	1	0	0
351.0	0	2	0	2
352.0	0	0	0	1
358.0	0	1	0	0
361.0	0	1	0	0
364.0	0	1	0	0
370.0	0	1	1	0
374.0	0	0	0	1
376.0	0	0	0	1
380.0	0	0	0	1
383.0	0	1	0	0
384.0	0	0	0	1
391.0	0	1	0	1
394.0	0	0	0	1
395.0	0	0	0	1
397.0	0	1	0	0
398.0	0	2	0	0
400.0	0	0	0	1
401.0	0	1	0	0
404.0	0	1	0	0
405.0	0	1	0	0
408.0	0	1	0	0
411.0	0	0	0	1
417.0	0	1	0	0
422.0	0	1	0	0
430.0	0	0	0	1
436.0	0	1	0	0
437.0	0	0	0	1
460.0	0	1	0	0
463.0	0	1	0	0
465.0	0	1	0	0
476.0	0	0	0	1
477.0	0	0	0	1
478.0	0	0	0	1
482.0	0	1	0	0
489.0	0	1	0	0
501.0	0	1	0	0
505.0	0	0	0	1
506.0	0	0	0	1
517.0	0	1	0	0
521.0	0	0	0	1
523.0	0	1	0	0
533.0	0	1	0	0
536.0	0	1	0	0
541.0	0	1	0	0
544.0	0	1	0	0
553.0	0	0	0	1
554.0	0	0	0	1
555.0	0	0	0	1
559.0	0	0	0	1
563.0	0	2	0	0
576.0	0	0	0	1
591.0	0	1	0	0
610.0	0	1	0	0
620.0	0	1	0	0
666.0	0	0	0	1
697.0	0	1	0	0
698.0	0	1	0	0
738.0	0	0	0	1
750.0	0	1	0	0
861.0	0	0	0	1
917.0	0	1	0	0
921.0	0	0	0	1
971.0	0	1	0	0
1064.0	0	0	0	1
1351.0	0	1	0	0