## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT DE-3.sorted.bam --OUTPUT DE-3.markdup.sorted.bam --METRICS_FILE DE-3.markdup.sorted.MarkDuplicates.metrics.txt --REMOVE_DUPLICATES false --ASSUME_SORTED true --TMP_DIR tmp --VALIDATION_STRINGENCY LENIENT --REFERENCE_SEQUENCE 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_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_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 --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: Thu Jul 17 23:07:37 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	84168	80767510	17417642	0	46325	24627638	848089	0.305048	106074413

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.007083	42680450	0	43106356
2.0	1.477392	9747172	761188	9530001
3.0	1.697027	2467009	21585	2340035
4.0	1.799597	689584	3337	639771
5.0	1.847497	231440	1460	213863
6.0	1.869867	97906	841	91503
7.0	1.880314	52389	532	49657
8.0	1.885192	32547	384	31191
9.0	1.88747	22455	252	21521
10.0	1.888534	16400	191	15844
11.0	1.889031	12387	147	12039
12.0	1.889263	9907	102	9480
13.0	1.889372	7763	73	7481
14.0	1.889422	6302	70	6113
15.0	1.889446	5168	55	5007
16.0	1.889457	4241	45	4151
17.0	1.889462	3845	38	3738
18.0	1.889464	3243	38	3180
19.0	1.889466	2887	32	2799
20.0	1.889466	2494	25	2456
21.0	1.889466	2246	12	2151
22.0	1.889466	1952	28	1952
23.0	1.889467	1841	9	1807
24.0	1.889467	1598	16	1540
25.0	1.889467	1385	12	1382
26.0	1.889467	1294	15	1282
27.0	1.889467	1297	13	1249
28.0	1.889467	1110	8	1110
29.0	1.889467	1027	10	974
30.0	1.889467	911	7	964
31.0	1.889467	929	6	898
32.0	1.889467	871	8	842
33.0	1.889467	760	3	736
34.0	1.889467	684	3	701
35.0	1.889467	710	6	674
36.0	1.889467	640	3	669
37.0	1.889467	663	4	644
38.0	1.889467	577	1	565
39.0	1.889467	576	2	562
40.0	1.889467	536	2	504
41.0	1.889467	483	1	483
42.0	1.889467	452	2	491
43.0	1.889467	470	3	467
44.0	1.889467	465	2	454
45.0	1.889467	456	0	443
46.0	1.889467	406	2	403
47.0	1.889467	405	2	387
48.0	1.889467	321	2	298
49.0	1.889467	321	4	322
50.0	1.889467	352	0	349
51.0	1.889467	300	2	310
52.0	1.889467	294	0	299
53.0	1.889467	305	3	321
54.0	1.889467	315	0	282
55.0	1.889467	265	0	270
56.0	1.889467	276	1	260
57.0	1.889467	219	0	237
58.0	1.889467	235	0	220
59.0	1.889467	244	2	244
60.0	1.889467	234	0	227
61.0	1.889467	242	0	267
62.0	1.889467	224	0	177
63.0	1.889467	185	0	212
64.0	1.889467	226	1	214
65.0	1.889467	180	0	191
66.0	1.889467	196	0	190
67.0	1.889467	198	0	198
68.0	1.889467	184	1	195
69.0	1.889467	202	0	183
70.0	1.889467	178	0	179
71.0	1.889467	170	0	168
72.0	1.889467	187	0	180
73.0	1.889467	155	0	164
74.0	1.889467	176	0	155
75.0	1.889467	152	0	145
76.0	1.889467	150	0	171
77.0	1.889467	160	0	151
78.0	1.889467	155	0	157
79.0	1.889467	154	0	145
80.0	1.889467	152	0	145
81.0	1.889467	136	0	125
82.0	1.889467	126	0	132
83.0	1.889467	111	0	113
84.0	1.889467	124	0	139
85.0	1.889467	123	0	130
86.0	1.889467	108	0	118
87.0	1.889467	144	0	122
88.0	1.889467	117	0	114
89.0	1.889467	116	0	112
90.0	1.889467	99	0	100
91.0	1.889467	113	0	87
92.0	1.889467	93	1	97
93.0	1.889467	91	0	104
94.0	1.889467	96	0	96
95.0	1.889467	88	0	102
96.0	1.889467	91	0	107
97.0	1.889467	122	0	115
98.0	1.889467	109	0	106
99.0	1.889467	108	0	92
100.0	1.889467	98	0	93
101.0	0	81	0	81
102.0	0	85	0	86
103.0	0	85	0	86
104.0	0	86	0	88
105.0	0	87	0	92
106.0	0	103	0	96
107.0	0	95	0	77
108.0	0	72	0	85
109.0	0	75	0	89
110.0	0	95	0	68
111.0	0	69	0	75
112.0	0	71	0	74
113.0	0	77	0	56
114.0	0	59	0	77
115.0	0	74	0	69
116.0	0	63	0	46
117.0	0	61	0	63
118.0	0	53	0	63
119.0	0	58	0	73
120.0	0	78	0	75
121.0	0	62	0	62
122.0	0	66	1	64
123.0	0	71	0	67
124.0	0	63	0	59
125.0	0	55	0	46
126.0	0	48	0	56
127.0	0	54	0	57
128.0	0	54	0	57
129.0	0	57	0	61
130.0	0	56	0	63
131.0	0	58	0	50
132.0	0	57	0	40
133.0	0	56	0	63
134.0	0	47	0	46
135.0	0	64	0	70
136.0	0	50	0	62
137.0	0	69	0	65
138.0	0	72	0	51
139.0	0	41	0	53
140.0	0	53	0	55
141.0	0	58	0	47
142.0	0	45	0	48
143.0	0	49	0	60
144.0	0	52	0	51
145.0	0	68	0	56
146.0	0	46	0	57
147.0	0	51	0	47
148.0	0	54	0	50
149.0	0	42	0	61
150.0	0	50	0	38
151.0	0	52	0	47
152.0	0	46	0	44
153.0	0	37	0	49
154.0	0	53	0	42
155.0	0	49	0	47
156.0	0	43	0	42
157.0	0	50	0	41
158.0	0	44	0	41
159.0	0	34	0	45
160.0	0	44	0	32
161.0	0	35	0	41
162.0	0	38	0	53
163.0	0	46	0	51
164.0	0	54	0	37
165.0	0	40	0	36
166.0	0	46	0	40
167.0	0	31	0	46
168.0	0	34	0	35
169.0	0	39	0	39
170.0	0	42	0	35
171.0	0	34	0	34
172.0	0	37	0	35
173.0	0	33	0	22
174.0	0	33	0	35
175.0	0	34	0	35
176.0	0	31	0	33
177.0	0	31	0	35
178.0	0	32	0	34
179.0	0	41	0	30
180.0	0	30	0	29
181.0	0	38	0	37
182.0	0	28	0	33
183.0	0	24	0	33
184.0	0	41	0	35
185.0	0	22	0	26
186.0	0	42	0	37
187.0	0	24	0	33
188.0	0	41	0	28
189.0	0	26	0	32
190.0	0	28	0	29
191.0	0	31	0	29
192.0	0	27	0	31
193.0	0	38	0	26
194.0	0	20	0	24
195.0	0	28	0	18
196.0	0	21	0	31
197.0	0	30	0	32
198.0	0	21	0	28
199.0	0	32	0	30
200.0	0	34	0	27
201.0	0	31	0	20
202.0	0	21	0	31
203.0	0	29	0	23
204.0	0	24	0	21
205.0	0	24	0	32
206.0	0	22	0	21
207.0	0	21	0	25
208.0	0	27	0	30
209.0	0	25	0	27
210.0	0	32	0	20
211.0	0	20	0	24
212.0	0	25	0	21
213.0	0	21	0	24
214.0	0	26	0	21
215.0	0	26	0	16
216.0	0	17	0	24
217.0	0	20	0	24
218.0	0	19	0	21
219.0	0	30	0	29
220.0	0	20	0	21
221.0	0	24	0	19
222.0	0	22	0	28
223.0	0	28	0	17
224.0	0	13	0	22
225.0	0	23	0	19
226.0	0	18	0	26
227.0	0	23	0	17
228.0	0	19	0	23
229.0	0	13	0	20
230.0	0	24	0	16
231.0	0	20	0	17
232.0	0	22	0	22
233.0	0	26	0	22
234.0	0	21	0	15
235.0	0	16	0	19
236.0	0	22	0	17
237.0	0	12	0	22
238.0	0	19	0	21
239.0	0	24	0	22
240.0	0	23	0	12
241.0	0	15	0	25
242.0	0	19	0	24
243.0	0	17	0	19
244.0	0	21	0	14
245.0	0	17	0	19
246.0	0	23	0	17
247.0	0	20	0	13
248.0	0	18	0	20
249.0	0	20	0	18
250.0	0	15	0	27
251.0	0	19	0	16
252.0	0	11	0	12
253.0	0	13	0	17
254.0	0	16	0	22
255.0	0	21	0	12
256.0	0	9	0	19
257.0	0	26	0	14
258.0	0	18	0	9
259.0	0	13	0	11
260.0	0	15	0	16
261.0	0	13	0	13
262.0	0	14	0	13
263.0	0	8	0	20
264.0	0	18	0	16
265.0	0	18	0	16
266.0	0	14	0	15
267.0	0	23	0	13
268.0	0	9	0	22
269.0	0	11	0	9
270.0	0	16	0	15
271.0	0	12	0	11
272.0	0	11	0	18
273.0	0	20	0	13
274.0	0	17	0	11
275.0	0	11	0	13
276.0	0	15	0	16
277.0	0	14	0	20
278.0	0	17	0	20
279.0	0	17	0	11
280.0	0	9	0	13
281.0	0	13	0	13
282.0	0	11	0	15
283.0	0	16	0	14
284.0	0	14	0	16
285.0	0	14	0	10
286.0	0	14	0	10
287.0	0	15	0	24
288.0	0	14	0	12
289.0	0	11	0	12
290.0	0	22	0	13
291.0	0	15	0	16
292.0	0	14	0	14
293.0	0	13	0	17
294.0	0	14	0	10
295.0	0	15	0	12
296.0	0	15	0	9
297.0	0	10	0	10
298.0	0	10	0	14
299.0	0	9	0	12
300.0	0	13	0	16
301.0	0	16	0	13
302.0	0	10	0	18
303.0	0	16	0	10
304.0	0	15	0	19
305.0	0	11	0	10
306.0	0	15	0	15
307.0	0	12	0	12
308.0	0	12	0	18
309.0	0	8	0	9
310.0	0	19	0	13
311.0	0	11	0	14
312.0	0	12	0	10
313.0	0	11	0	11
314.0	0	15	0	9
315.0	0	11	0	11
316.0	0	17	0	11
317.0	0	12	0	12
318.0	0	7	0	12
319.0	0	12	0	12
320.0	0	13	0	14
321.0	0	16	0	10
322.0	0	14	0	17
323.0	0	6	0	11
324.0	0	10	0	12
325.0	0	14	0	9
326.0	0	13	0	15
327.0	0	12	0	11
328.0	0	10	0	9
329.0	0	10	0	11
330.0	0	16	0	14
331.0	0	7	0	12
332.0	0	14	0	11
333.0	0	5	0	13
334.0	0	12	0	9
335.0	0	15	0	6
336.0	0	12	0	9
337.0	0	10	0	9
338.0	0	10	0	16
339.0	0	12	0	5
340.0	0	8	0	13
341.0	0	14	0	11
342.0	0	9	0	7
343.0	0	8	0	12
344.0	0	9	0	11
345.0	0	9	0	16
346.0	0	11	0	14
347.0	0	10	0	6
348.0	0	11	0	7
349.0	0	15	0	20
350.0	0	11	0	6
351.0	0	11	0	8
352.0	0	13	0	17
353.0	0	9	0	7
354.0	0	5	0	9
355.0	0	12	0	7
356.0	0	11	0	7
357.0	0	13	0	8
358.0	0	6	0	13
359.0	0	9	0	8
360.0	0	9	0	11
361.0	0	7	0	9
362.0	0	12	0	10
363.0	0	9	0	12
364.0	0	9	0	9
365.0	0	10	0	7
366.0	0	11	0	7
367.0	0	8	0	11
368.0	0	10	0	9
369.0	0	8	0	10
370.0	0	8	0	9
371.0	0	9	0	9
372.0	0	7	0	8
373.0	0	9	0	7
374.0	0	10	0	5
375.0	0	12	0	9
376.0	0	8	0	7
377.0	0	8	0	9
378.0	0	4	0	8
379.0	0	8	0	9
380.0	0	8	0	7
381.0	0	8	0	8
382.0	0	7	0	4
383.0	0	9	0	7
384.0	0	5	0	7
385.0	0	10	0	10
386.0	0	8	0	9
387.0	0	4	0	8
388.0	0	8	0	7
389.0	0	7	0	8
390.0	0	9	0	1
391.0	0	8	0	8
392.0	0	5	0	8
393.0	0	13	0	15
394.0	0	4	0	5
395.0	0	10	0	7
396.0	0	3	0	8
397.0	0	5	0	7
398.0	0	9	0	12
399.0	0	10	0	9
400.0	0	15	0	11
401.0	0	8	0	8
402.0	0	7	0	7
403.0	0	11	0	8
404.0	0	4	0	5
405.0	0	8	0	2
406.0	0	4	0	2
407.0	0	6	0	7
408.0	0	8	0	13
409.0	0	6	0	12
410.0	0	10	0	9
411.0	0	5	0	13
412.0	0	9	0	6
413.0	0	9	0	3
414.0	0	11	0	5
415.0	0	9	0	4
416.0	0	7	0	8
417.0	0	10	0	7
418.0	0	4	0	5
419.0	0	1	0	7
420.0	0	9	0	2
421.0	0	6	0	2
422.0	0	7	0	8
423.0	0	8	0	7
424.0	0	1	0	6
425.0	0	3	0	3
426.0	0	4	0	7
427.0	0	6	0	10
428.0	0	6	0	9
429.0	0	7	0	2
430.0	0	8	0	8
431.0	0	2	0	4
432.0	0	8	0	6
433.0	0	3	0	10
434.0	0	9	0	4
435.0	0	6	0	5
436.0	0	6	0	2
437.0	0	9	0	8
438.0	0	5	0	7
439.0	0	7	0	6
440.0	0	3	0	7
441.0	0	3	0	8
442.0	0	4	0	7
443.0	0	7	0	4
444.0	0	8	0	7
445.0	0	7	0	3
446.0	0	6	0	7
447.0	0	8	0	7
448.0	0	7	0	7
449.0	0	6	0	12
450.0	0	10	0	7
451.0	0	6	0	10
452.0	0	8	0	6
453.0	0	6	0	6
454.0	0	10	0	7
455.0	0	7	0	8
456.0	0	8	0	8
457.0	0	6	0	8
458.0	0	6	0	5
459.0	0	7	0	7
460.0	0	5	0	9
461.0	0	3	0	6
462.0	0	11	0	5
463.0	0	8	0	3
464.0	0	8	0	7
465.0	0	5	0	7
466.0	0	5	0	6
467.0	0	8	0	5
468.0	0	0	0	4
469.0	0	0	0	5
470.0	0	6	0	5
471.0	0	6	0	2
472.0	0	7	0	4
473.0	0	8	0	6
474.0	0	11	0	7
475.0	0	5	0	2
476.0	0	5	0	4
477.0	0	2	0	5
478.0	0	4	0	0
479.0	0	8	0	5
480.0	0	2	0	6
481.0	0	2	0	9
482.0	0	4	0	6
483.0	0	5	0	1
484.0	0	2	0	5
485.0	0	6	0	7
486.0	0	5	0	4
487.0	0	7	0	6
488.0	0	3	0	6
489.0	0	3	0	6
490.0	0	9	0	7
491.0	0	5	0	6
492.0	0	5	0	2
493.0	0	5	0	2
494.0	0	4	0	5
495.0	0	8	0	4
496.0	0	5	0	7
497.0	0	7	0	6
498.0	0	4	0	3
499.0	0	4	0	5
500.0	0	4	0	1
501.0	0	6	0	5
502.0	0	3	0	6
503.0	0	3	0	2
504.0	0	4	0	7
505.0	0	4	0	6
506.0	0	5	0	1
507.0	0	5	0	3
508.0	0	0	0	5
509.0	0	7	0	3
510.0	0	2	0	4
511.0	0	6	0	5
512.0	0	3	0	6
513.0	0	4	0	7
514.0	0	1	0	6
515.0	0	6	0	6
516.0	0	7	0	4
517.0	0	6	0	3
518.0	0	5	0	6
519.0	0	4	0	5
520.0	0	2	0	3
521.0	0	4	0	6
522.0	0	5	0	5
523.0	0	9	0	3
524.0	0	4	0	4
525.0	0	2	0	3
526.0	0	10	0	2
527.0	0	6	0	5
528.0	0	3	0	3
529.0	0	3	0	5
530.0	0	2	0	7
531.0	0	5	0	4
532.0	0	6	0	3
533.0	0	3	0	7
534.0	0	5	0	1
535.0	0	4	0	7
536.0	0	4	0	2
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