## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT DE-5.sorted.bam --OUTPUT DE-5.markdup.sorted.bam --METRICS_FILE DE-5.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 23:02:40 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	81461	79463438	20290672	0	44722	26669252	749847	0.335726	91516597

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.005985	39892820	0	40249823
2.0	1.428163	9177954	660486	8997730
3.0	1.605337	2360316	19154	2254070
4.0	1.679691	691306	3269	649025
5.0	1.710895	249880	1469	235326
6.0	1.72399	116029	873	110378
7.0	1.729486	66182	577	63702
8.0	1.731792	42997	392	41593
9.0	1.73276	29924	301	28986
10.0	1.733166	22262	183	21712
11.0	1.733336	17180	138	16704
12.0	1.733408	13598	132	13282
13.0	1.733438	10993	80	10634
14.0	1.733451	8957	84	8812
15.0	1.733456	7686	70	7508
16.0	1.733458	6458	57	6356
17.0	1.733459	5433	38	5357
18.0	1.733459	4722	33	4610
19.0	1.73346	4236	37	4157
20.0	1.73346	3725	28	3682
21.0	1.73346	3390	26	3299
22.0	1.73346	2870	26	2804
23.0	1.73346	2660	20	2657
24.0	1.73346	2332	25	2274
25.0	1.73346	2191	16	2173
26.0	1.73346	1959	20	1903
27.0	1.73346	1837	17	1808
28.0	1.73346	1668	22	1643
29.0	1.73346	1518	6	1520
30.0	1.73346	1406	16	1374
31.0	1.73346	1316	12	1339
32.0	1.73346	1236	14	1154
33.0	1.73346	1201	9	1206
34.0	1.73346	1103	14	1099
35.0	1.73346	1047	5	1015
36.0	1.73346	894	6	861
37.0	1.73346	841	2	877
38.0	1.73346	810	2	796
39.0	1.73346	806	5	823
40.0	1.73346	763	2	709
41.0	1.73346	709	3	714
42.0	1.73346	696	6	687
43.0	1.73346	636	4	623
44.0	1.73346	599	2	604
45.0	1.73346	607	3	606
46.0	1.73346	551	3	515
47.0	1.73346	521	6	562
48.0	1.73346	556	2	498
49.0	1.73346	435	1	447
50.0	1.73346	484	1	508
51.0	1.73346	473	6	445
52.0	1.73346	419	4	425
53.0	1.73346	401	1	383
54.0	1.73346	390	2	367
55.0	1.73346	369	1	384
56.0	1.73346	363	2	369
57.0	1.73346	345	2	354
58.0	1.73346	354	2	330
59.0	1.73346	342	3	343
60.0	1.73346	346	1	355
61.0	1.73346	312	3	296
62.0	1.73346	302	1	284
63.0	1.73346	259	3	274
64.0	1.73346	299	1	288
65.0	1.73346	265	1	253
66.0	1.73346	267	1	279
67.0	1.73346	230	1	227
68.0	1.73346	264	1	270
69.0	1.73346	246	0	212
70.0	1.73346	234	0	265
71.0	1.73346	246	2	240
72.0	1.73346	220	0	203
73.0	1.73346	205	1	220
74.0	1.73346	208	0	208
75.0	1.73346	206	0	191
76.0	1.73346	194	0	183
77.0	1.73346	202	0	179
78.0	1.73346	176	1	186
79.0	1.73346	182	1	187
80.0	1.73346	161	0	167
81.0	1.73346	166	1	173
82.0	1.73346	192	0	171
83.0	1.73346	159	2	176
84.0	1.73346	166	1	172
85.0	1.73346	158	0	150
86.0	1.73346	152	0	151
87.0	1.73346	154	0	147
88.0	1.73346	146	1	150
89.0	1.73346	141	1	117
90.0	1.73346	142	0	144
91.0	1.73346	146	0	142
92.0	1.73346	125	0	152
93.0	1.73346	150	1	134
94.0	1.73346	144	0	135
95.0	1.73346	135	0	143
96.0	1.73346	116	1	112
97.0	1.73346	128	0	132
98.0	1.73346	122	0	116
99.0	1.73346	115	0	113
100.0	1.73346	119	0	115
101.0	0	102	0	116
102.0	0	115	0	111
103.0	0	109	0	95
104.0	0	98	0	116
105.0	0	117	0	127
106.0	0	115	0	116
107.0	0	119	0	93
108.0	0	108	0	118
109.0	0	108	0	105
110.0	0	98	0	93
111.0	0	93	1	81
112.0	0	93	0	102
113.0	0	97	0	100
114.0	0	84	0	86
115.0	0	90	0	99
116.0	0	89	0	63
117.0	0	80	0	86
118.0	0	94	0	94
119.0	0	85	0	83
120.0	0	90	0	85
121.0	0	70	0	73
122.0	0	73	0	83
123.0	0	73	0	79
124.0	0	85	0	87
125.0	0	85	0	83
126.0	0	86	0	73
127.0	0	75	0	75
128.0	0	79	0	83
129.0	0	68	0	85
130.0	0	87	0	55
131.0	0	68	1	68
132.0	0	63	0	80
133.0	0	74	0	47
134.0	0	62	0	57
135.0	0	54	0	57
136.0	0	51	0	71
137.0	0	77	0	62
138.0	0	57	0	56
139.0	0	62	0	59
140.0	0	55	0	48
141.0	0	50	0	83
142.0	0	65	0	67
143.0	0	65	0	63
144.0	0	66	0	71
145.0	0	59	0	60
146.0	0	67	0	68
147.0	0	60	0	51
148.0	0	57	0	54
149.0	0	66	0	58
150.0	0	58	0	40
151.0	0	50	0	52
152.0	0	45	0	61
153.0	0	67	0	64
154.0	0	54	0	57
155.0	0	62	0	59
156.0	0	50	0	51
157.0	0	54	0	49
158.0	0	56	0	56
159.0	0	48	0	48
160.0	0	51	0	56
161.0	0	53	0	46
162.0	0	41	0	42
163.0	0	59	0	48
164.0	0	48	0	52
165.0	0	44	0	48
166.0	0	47	0	45
167.0	0	47	0	39
168.0	0	40	0	36
169.0	0	41	0	45
170.0	0	29	0	37
171.0	0	34	0	46
172.0	0	50	0	26
173.0	0	35	0	53
174.0	0	36	0	38
175.0	0	39	0	35
176.0	0	58	0	53
177.0	0	46	0	45
178.0	0	40	0	41
179.0	0	30	0	35
180.0	0	44	0	32
181.0	0	37	0	49
182.0	0	48	0	38
183.0	0	26	0	41
184.0	0	49	0	46
185.0	0	38	0	32
186.0	0	41	0	29
187.0	0	30	0	29
188.0	0	29	0	48
189.0	0	39	0	43
190.0	0	28	0	27
191.0	0	44	0	42
192.0	0	40	0	38
193.0	0	36	0	29
194.0	0	32	0	29
195.0	0	23	0	34
196.0	0	35	0	36
197.0	0	43	0	33
198.0	0	30	0	40
199.0	0	37	0	41
200.0	0	41	0	36
201.0	0	43	0	25
202.0	0	29	0	32
203.0	0	23	0	25
204.0	0	30	0	28
205.0	0	33	0	23
206.0	0	30	0	26
207.0	0	18	0	29
208.0	0	24	0	29
209.0	0	34	0	26
210.0	0	31	0	21
211.0	0	27	0	33
212.0	0	26	0	38
213.0	0	23	0	17
214.0	0	25	0	27
215.0	0	31	0	31
216.0	0	31	0	28
217.0	0	27	0	34
218.0	0	26	0	28
219.0	0	30	0	27
220.0	0	28	0	29
221.0	0	33	0	29
222.0	0	21	0	22
223.0	0	27	0	26
224.0	0	23	0	24
225.0	0	24	0	28
226.0	0	33	0	25
227.0	0	31	0	25
228.0	0	19	0	27
229.0	0	32	0	32
230.0	0	24	0	22
231.0	0	28	0	28
232.0	0	23	0	33
233.0	0	25	0	32
234.0	0	29	0	31
235.0	0	32	0	23
236.0	0	34	0	34
237.0	0	27	0	24
238.0	0	28	0	28
239.0	0	22	0	18
240.0	0	33	0	31
241.0	0	24	0	26
242.0	0	22	0	22
243.0	0	22	0	25
244.0	0	27	0	20
245.0	0	31	0	26
246.0	0	17	0	22
247.0	0	24	0	13
248.0	0	18	0	14
249.0	0	15	0	20
250.0	0	16	0	20
251.0	0	30	0	30
252.0	0	14	0	20
253.0	0	14	0	15
254.0	0	26	0	22
255.0	0	21	0	20
256.0	0	21	0	19
257.0	0	17	0	14
258.0	0	14	0	12
259.0	0	17	0	19
260.0	0	18	0	14
261.0	0	21	0	18
262.0	0	15	0	14
263.0	0	19	0	25
264.0	0	9	0	16
265.0	0	17	0	31
266.0	0	21	0	21
267.0	0	20	0	21
268.0	0	25	0	10
269.0	0	25	0	18
270.0	0	19	0	18
271.0	0	14	0	18
272.0	0	13	0	9
273.0	0	15	0	9
274.0	0	19	0	14
275.0	0	16	0	13
276.0	0	15	0	11
277.0	0	12	0	20
278.0	0	6	0	17
279.0	0	18	0	16
280.0	0	12	0	11
281.0	0	15	0	12
282.0	0	12	0	27
283.0	0	16	0	23
284.0	0	22	0	18
285.0	0	20	0	18
286.0	0	24	0	20
287.0	0	20	0	17
288.0	0	17	0	14
289.0	0	19	0	16
290.0	0	11	0	14
291.0	0	18	0	22
292.0	0	17	0	15
293.0	0	20	0	17
294.0	0	11	0	15
295.0	0	14	0	18
296.0	0	17	0	13
297.0	0	14	0	17
298.0	0	17	0	14
299.0	0	14	0	13
300.0	0	11	0	22
301.0	0	19	0	13
302.0	0	22	0	18
303.0	0	16	0	22
304.0	0	20	0	17
305.0	0	13	0	13
306.0	0	18	0	12
307.0	0	17	0	11
308.0	0	11	0	14
309.0	0	12	0	11
310.0	0	21	0	15
311.0	0	8	0	7
312.0	0	15	0	13
313.0	0	14	0	18
314.0	0	10	0	12
315.0	0	14	0	10
316.0	0	14	0	15
317.0	0	16	0	19
318.0	0	6	0	12
319.0	0	13	0	16
320.0	0	9	0	7
321.0	0	11	0	14
322.0	0	17	0	14
323.0	0	18	0	14
324.0	0	13	0	9
325.0	0	13	0	18
326.0	0	12	0	10
327.0	0	13	0	10
328.0	0	12	0	12
329.0	0	15	0	8
330.0	0	9	0	9
331.0	0	5	0	11
332.0	0	8	0	13
333.0	0	9	0	15
334.0	0	18	0	11
335.0	0	13	0	10
336.0	0	8	0	10
337.0	0	18	0	11
338.0	0	20	0	9
339.0	0	8	0	13
340.0	0	5	0	9
341.0	0	6	0	8
342.0	0	8	0	12
343.0	0	8	0	14
344.0	0	8	0	11
345.0	0	9	0	13
346.0	0	11	0	15
347.0	0	19	0	12
348.0	0	8	0	11
349.0	0	13	0	8
350.0	0	13	0	10
351.0	0	11	0	14
352.0	0	17	0	8
353.0	0	11	0	13
354.0	0	9	0	11
355.0	0	10	0	11
356.0	0	15	0	11
357.0	0	13	0	10
358.0	0	8	0	10
359.0	0	8	0	7
360.0	0	13	0	13
361.0	0	10	0	9
362.0	0	3	0	5
363.0	0	9	0	10
364.0	0	10	0	13
365.0	0	9	0	11
366.0	0	12	0	5
367.0	0	10	0	8
368.0	0	11	0	11
369.0	0	11	0	11
370.0	0	7	0	8
371.0	0	13	0	14
372.0	0	7	0	14
373.0	0	13	0	9
374.0	0	11	0	6
375.0	0	10	0	18
376.0	0	8	0	12
377.0	0	7	0	11
378.0	0	12	0	12
379.0	0	11	0	11
380.0	0	16	0	1
381.0	0	15	0	12
382.0	0	4	0	13
383.0	0	8	0	14
384.0	0	9	0	6
385.0	0	8	0	1
386.0	0	8	0	9
387.0	0	11	0	10
388.0	0	14	0	10
389.0	0	5	0	10
390.0	0	12	0	10
391.0	0	8	0	8
392.0	0	11	0	10
393.0	0	9	0	13
394.0	0	14	0	6
395.0	0	9	0	9
396.0	0	8	0	12
397.0	0	9	0	10
398.0	0	6	0	11
399.0	0	9	0	8
400.0	0	7	0	2
401.0	0	5	0	10
402.0	0	15	0	13
403.0	0	7	0	11
404.0	0	6	0	8
405.0	0	15	0	5
406.0	0	4	0	6
407.0	0	9	0	2
408.0	0	10	0	13
409.0	0	9	0	5
410.0	0	5	0	11
411.0	0	8	0	7
412.0	0	5	0	15
413.0	0	5	0	6
414.0	0	5	0	8
415.0	0	16	0	12
416.0	0	8	0	10
417.0	0	13	0	8
418.0	0	7	0	5
419.0	0	8	0	4
420.0	0	7	0	13
421.0	0	8	0	4
422.0	0	6	0	16
423.0	0	10	0	11
424.0	0	7	0	7
425.0	0	14	0	6
426.0	0	12	0	9
427.0	0	8	0	7
428.0	0	11	0	5
429.0	0	7	0	3
430.0	0	9	0	12
431.0	0	7	0	6
432.0	0	2	0	4
433.0	0	4	0	12
434.0	0	5	0	5
435.0	0	8	0	7
436.0	0	7	0	5
437.0	0	12	0	6
438.0	0	7	0	7
439.0	0	7	0	11
440.0	0	10	0	4
441.0	0	2	0	14
442.0	0	5	0	8
443.0	0	6	0	6
444.0	0	10	0	4
445.0	0	11	0	6
446.0	0	7	0	12
447.0	0	7	0	8
448.0	0	12	0	6
449.0	0	6	0	7
450.0	0	2	0	10
451.0	0	10	0	5
452.0	0	5	0	8
453.0	0	4	0	6
454.0	0	8	0	3
455.0	0	5	0	8
456.0	0	11	0	7
457.0	0	9	0	7
458.0	0	9	0	3
459.0	0	7	0	4
460.0	0	4	0	9
461.0	0	4	0	4
462.0	0	4	0	10
463.0	0	10	0	10
464.0	0	5	0	7
465.0	0	8	0	8
466.0	0	11	0	9
467.0	0	6	0	8
468.0	0	8	0	8
469.0	0	6	0	4
470.0	0	7	0	5
471.0	0	4	0	3
472.0	0	10	0	9
473.0	0	10	0	6
474.0	0	3	0	7
475.0	0	2	0	7
476.0	0	5	0	4
477.0	0	6	0	9
478.0	0	5	0	3
479.0	0	5	0	5
480.0	0	13	0	3
481.0	0	4	0	7
482.0	0	6	0	5
483.0	0	4	0	2
484.0	0	5	0	7
485.0	0	6	0	1
486.0	0	1	0	12
487.0	0	5	0	9
488.0	0	7	0	3
489.0	0	5	0	4
490.0	0	7	0	8
491.0	0	6	0	6
492.0	0	5	0	6
493.0	0	8	0	11
494.0	0	6	0	5
495.0	0	8	0	9
496.0	0	4	0	5
497.0	0	12	0	6
498.0	0	4	0	6
499.0	0	9	0	7
500.0	0	5	0	2
501.0	0	9	0	8
502.0	0	6	0	5
503.0	0	6	0	4
504.0	0	2	0	7
505.0	0	6	0	5
506.0	0	8	0	5
507.0	0	3	0	1
508.0	0	5	0	7
509.0	0	7	0	8
510.0	0	2	0	4
511.0	0	4	0	8
512.0	0	6	0	2
513.0	0	4	0	4
514.0	0	5	0	2
515.0	0	5	0	5
516.0	0	3	0	1
517.0	0	5	0	5
518.0	0	8	0	4
519.0	0	3	0	5
520.0	0	2	0	8
521.0	0	3	0	4
522.0	0	3	0	7
523.0	0	4	0	10
524.0	0	4	0	6
525.0	0	7	0	5
526.0	0	7	0	9
527.0	0	9	0	3
528.0	0	8	0	7
529.0	0	3	0	3
530.0	0	5	0	3
531.0	0	6	0	3
532.0	0	6	0	7
533.0	0	6	0	6
534.0	0	4	0	11
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