## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-244-TP4.bam --OUTPUT ACR-244-TP4.md.bam --METRICS_FILE ACR-244-TP4.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 18:15:56 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	409	14855742	3885846	0	303	11030671	2566748	0.742519	4012752

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.023185	792580	0	939990
2.0	1.048428	750533	650319	905231
3.0	1.04905	655911	246121	739585
4.0	1.049066	505964	119313	504526
5.0	1.049066	360025	66510	304669
6.0	1.049066	244600	39880	172510
7.0	1.049066	161941	25229	95837
8.0	1.049066	106376	16269	54043
9.0	1.049066	70493	10497	31650
10.0	1.049066	47535	6984	19435
11.0	1.049066	32188	4663	12329
12.0	1.049066	22341	3154	8482
13.0	1.049066	15948	2104	6078
14.0	1.049066	11343	1483	4386
15.0	1.049066	8634	1003	3510
16.0	1.049066	6233	688	2751
17.0	1.049066	5001	439	2275
18.0	1.049066	3713	332	1852
19.0	1.049066	3032	215	1608
20.0	1.049066	2417	179	1298
21.0	1.049066	1958	143	1134
22.0	1.049066	1649	104	988
23.0	1.049066	1327	62	817
24.0	1.049066	1122	51	761
25.0	1.049066	1012	36	669
26.0	1.049066	863	36	610
27.0	1.049066	780	25	564
28.0	1.049066	682	17	502
29.0	1.049066	637	21	457
30.0	1.049066	544	15	394
31.0	1.049066	495	13	329
32.0	1.049066	389	9	337
33.0	1.049066	403	15	289
34.0	1.049066	375	12	297
35.0	1.049066	331	7	255
36.0	1.049066	281	5	243
37.0	1.049066	273	11	203
38.0	1.049066	248	7	183
39.0	1.049066	248	6	177
40.0	1.049066	225	5	178
41.0	1.049066	177	8	161
42.0	1.049066	183	7	129
43.0	1.049066	156	5	144
44.0	1.049066	159	1	112
45.0	1.049066	138	2	113
46.0	1.049066	140	5	107
47.0	1.049066	122	3	111
48.0	1.049066	140	2	123
49.0	1.049066	120	1	103
50.0	1.049066	138	1	106
51.0	1.049066	110	0	79
52.0	1.049066	116	1	80
53.0	1.049066	88	2	83
54.0	1.049066	88	2	87
55.0	1.049066	90	0	81
56.0	1.049066	106	6	59
57.0	1.049066	81	3	54
58.0	1.049066	61	1	60
59.0	1.049066	74	0	67
60.0	1.049066	70	0	62
61.0	1.049066	63	1	38
62.0	1.049066	57	1	61
63.0	1.049066	55	1	59
64.0	1.049066	57	1	54
65.0	1.049066	65	0	44
66.0	1.049066	53	0	48
67.0	1.049066	55	1	44
68.0	1.049066	42	0	30
69.0	1.049066	46	0	49
70.0	1.049066	50	1	39
71.0	1.049066	39	0	32
72.0	1.049066	42	1	32
73.0	1.049066	40	0	30
74.0	1.049066	43	2	26
75.0	1.049066	34	0	30
76.0	1.049066	33	1	23
77.0	1.049066	30	0	30
78.0	1.049066	35	1	26
79.0	1.049066	30	0	34
80.0	1.049066	28	0	19
81.0	1.049066	28	0	21
82.0	1.049066	33	0	20
83.0	1.049066	30	1	26
84.0	1.049066	25	0	24
85.0	1.049066	32	0	16
86.0	1.049066	22	1	17
87.0	1.049066	28	0	24
88.0	1.049066	15	0	19
89.0	1.049066	17	0	14
90.0	1.049066	28	0	19
91.0	1.049066	15	1	14
92.0	1.049066	20	0	16
93.0	1.049066	17	0	12
94.0	1.049066	22	0	11
95.0	1.049066	20	0	11
96.0	1.049066	13	0	16
97.0	1.049066	14	0	15
98.0	1.049066	18	1	6
99.0	1.049066	11	0	14
100.0	1.049066	20	0	12
101.0	0	9	1	15
102.0	0	10	0	10
103.0	0	19	1	7
104.0	0	13	0	14
105.0	0	6	0	9
106.0	0	13	0	8
107.0	0	7	0	7
108.0	0	11	0	9
109.0	0	7	0	12
110.0	0	13	0	7
111.0	0	13	0	9
112.0	0	9	0	9
113.0	0	14	0	5
114.0	0	6	1	4
115.0	0	6	0	15
116.0	0	10	0	12
117.0	0	8	0	7
118.0	0	9	0	11
119.0	0	10	0	6
120.0	0	9	0	6
121.0	0	12	0	8
122.0	0	12	0	6
123.0	0	10	0	3
124.0	0	9	0	6
125.0	0	8	0	14
126.0	0	4	0	4
127.0	0	4	0	7
128.0	0	9	0	3
129.0	0	9	1	5
130.0	0	6	0	8
131.0	0	9	0	5
132.0	0	3	0	7
133.0	0	3	0	12
134.0	0	6	0	6
135.0	0	8	0	6
136.0	0	3	0	4
137.0	0	3	0	2
138.0	0	6	0	6
139.0	0	5	0	7
140.0	0	11	0	7
141.0	0	5	0	3
142.0	0	4	0	6
143.0	0	4	0	2
144.0	0	0	0	3
145.0	0	5	0	2
146.0	0	7	0	3
147.0	0	7	0	5
148.0	0	6	0	2
149.0	0	6	0	6
150.0	0	4	0	4
151.0	0	4	0	2
152.0	0	5	0	9
153.0	0	4	0	4
154.0	0	9	0	1
155.0	0	6	0	5
156.0	0	4	0	3
157.0	0	1	0	4
158.0	0	1	0	6
159.0	0	4	0	6
160.0	0	8	0	2
161.0	0	3	0	4
162.0	0	3	0	8
163.0	0	3	0	3
164.0	0	2	0	4
165.0	0	6	0	1
166.0	0	5	0	3
167.0	0	6	0	3
168.0	0	1	0	1
169.0	0	3	0	3
170.0	0	7	0	1
171.0	0	4	0	0
172.0	0	2	0	0
173.0	0	1	0	0
174.0	0	2	0	2
175.0	0	4	0	4
176.0	0	2	0	2
177.0	0	2	0	2
178.0	0	0	0	3
179.0	0	3	0	4
180.0	0	5	0	1
181.0	0	4	0	1
182.0	0	3	0	2
183.0	0	2	0	3
184.0	0	1	0	4
185.0	0	2	0	1
186.0	0	0	0	1
187.0	0	2	0	6
188.0	0	6	0	3
189.0	0	3	0	1
190.0	0	1	1	1
191.0	0	0	0	2
192.0	0	3	0	2
193.0	0	3	0	3
194.0	0	1	0	1
195.0	0	1	0	2
196.0	0	2	0	1
197.0	0	2	0	0
198.0	0	4	0	0
199.0	0	4	0	2
200.0	0	1	0	4
201.0	0	1	0	1
202.0	0	1	0	2
203.0	0	0	0	1
204.0	0	0	0	2
205.0	0	2	0	0
206.0	0	1	0	2
207.0	0	2	0	1
208.0	0	2	0	0
209.0	0	1	0	3
210.0	0	0	0	2
211.0	0	3	0	3
212.0	0	2	0	3
213.0	0	1	0	1
214.0	0	2	0	0
215.0	0	4	0	1
216.0	0	0	0	2
217.0	0	1	0	1
218.0	0	2	0	2
219.0	0	0	0	4
220.0	0	1	0	0
221.0	0	1	0	2
222.0	0	1	0	0
223.0	0	1	0	0
224.0	0	1	0	2
225.0	0	2	0	0
226.0	0	2	0	0
227.0	0	2	0	2
228.0	0	5	0	2
229.0	0	1	0	0
230.0	0	2	0	1
231.0	0	1	0	0
232.0	0	1	0	2
233.0	0	0	0	1
234.0	0	4	0	2
235.0	0	2	0	1
236.0	0	0	0	1
237.0	0	1	0	3
238.0	0	1	0	1
239.0	0	2	0	1
240.0	0	3	0	1
241.0	0	3	0	1
242.0	0	2	0	2
244.0	0	1	0	2
245.0	0	1	0	2
246.0	0	1	0	2
247.0	0	1	0	0
249.0	0	3	0	0
252.0	0	4	0	2
253.0	0	1	0	1
254.0	0	2	0	1
255.0	0	1	0	0
256.0	0	2	0	0
258.0	0	0	0	1
260.0	0	1	0	0
261.0	0	0	0	4
262.0	0	1	0	0
263.0	0	3	0	0
264.0	0	0	0	2
265.0	0	0	0	1
266.0	0	2	0	0
267.0	0	1	0	1
268.0	0	2	0	1
269.0	0	1	0	0
271.0	0	1	0	0
272.0	0	0	0	2
274.0	0	1	0	0
276.0	0	1	0	0
277.0	0	1	0	2
278.0	0	1	0	2
280.0	0	1	0	2
282.0	0	1	0	1
283.0	0	1	0	0
284.0	0	1	0	0
285.0	0	1	0	0
286.0	0	0	0	3
287.0	0	1	0	1
289.0	0	2	0	2
290.0	0	0	0	2
291.0	0	1	0	1
292.0	0	2	0	1
297.0	0	2	0	0
298.0	0	0	0	2
299.0	0	1	0	1
302.0	0	1	0	0
303.0	0	2	0	1
304.0	0	1	0	0
307.0	0	0	0	1
308.0	0	2	0	0
309.0	0	0	0	1
310.0	0	1	0	0
315.0	0	0	0	1
316.0	0	3	0	0
317.0	0	1	0	1
318.0	0	1	0	1
320.0	0	0	0	1
321.0	0	0	0	1
323.0	0	1	0	0
326.0	0	1	0	1
329.0	0	1	0	0
331.0	0	1	0	0
332.0	0	1	0	2
333.0	0	0	0	2
334.0	0	0	0	1
335.0	0	1	0	0
337.0	0	0	0	1
338.0	0	1	0	0
340.0	0	0	0	1
342.0	0	1	0	0
345.0	0	1	0	0
346.0	0	2	0	0
348.0	0	1	0	0
351.0	0	1	0	0
354.0	0	0	0	1
356.0	0	1	0	2
360.0	0	1	0	0
362.0	0	0	0	1
364.0	0	1	0	0
367.0	0	1	0	0
368.0	0	1	0	0
378.0	0	0	0	1
380.0	0	1	0	0
381.0	0	1	0	1
383.0	0	0	0	1
384.0	0	0	0	1
385.0	0	0	0	1
388.0	0	1	0	1
390.0	0	0	0	1
394.0	0	3	0	0
399.0	0	0	0	1
400.0	0	1	0	1
402.0	0	1	0	0
406.0	0	1	0	0
407.0	0	1	0	0
408.0	0	0	0	1
415.0	0	0	0	1
422.0	0	1	0	0
428.0	0	1	0	0
430.0	0	0	0	1
435.0	0	0	0	1
436.0	0	0	0	2
438.0	0	0	0	1
442.0	0	1	0	0
444.0	0	1	0	0
447.0	0	0	0	1
448.0	0	1	0	0
452.0	0	0	0	1
455.0	0	0	0	2
456.0	0	1	0	0
457.0	0	1	0	0
460.0	0	0	0	1
462.0	0	0	0	1
468.0	0	1	0	0
473.0	0	1	0	0
476.0	0	1	0	0
480.0	0	1	0	0
490.0	0	1	0	0
491.0	0	1	0	0
496.0	0	0	0	1
502.0	0	0	0	1
513.0	0	1	0	0
521.0	0	2	0	0
525.0	0	0	0	1
537.0	0	0	0	1
538.0	0	1	0	0
555.0	0	1	0	0
560.0	0	1	0	0
566.0	0	0	0	1
600.0	0	1	0	0
612.0	0	0	0	1
617.0	0	0	0	1
683.0	0	1	0	0
691.0	0	0	0	1
695.0	0	0	0	1
699.0	0	0	0	1
703.0	0	1	0	0
709.0	0	1	0	0
715.0	0	0	0	1
718.0	0	0	0	1
721.0	0	0	0	1
722.0	0	1	0	0
723.0	0	0	0	1
725.0	0	0	0	1
734.0	0	1	0	0
739.0	0	1	0	0
748.0	0	0	0	1
757.0	0	1	0	0
761.0	0	1	0	0
770.0	0	0	0	1
777.0	0	0	0	1
780.0	0	1	0	0
793.0	0	1	0	0
800.0	0	0	0	1
814.0	0	1	0	0
826.0	0	1	0	0
836.0	0	1	0	0
843.0	0	1	0	0
850.0	0	0	0	2
881.0	0	1	0	0
887.0	0	0	0	1
890.0	0	1	0	0
1064.0	0	0	0	1
1076.0	0	1	0	0
1102.0	0	0	0	1
1117.0	0	1	0	0
1130.0	0	1	0	0
1131.0	0	0	0	1
1204.0	0	1	0	0
1299.0	0	0	0	1
1331.0	0	1	0	0
1383.0	0	0	0	1
1454.0	0	1	0	0
2031.0	0	0	0	1
2144.0	0	1	0	0