## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT DE-4.sorted.bam --OUTPUT DE-4.markdup.sorted.bam --METRICS_FILE DE-4.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: Fri Jul 18 00:10:27 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	84088	93895752	20710656	0	46763	29081203	912619	0.309828	120588205

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.006488	49376032	0	49832172
2.0	1.468492	11123533	818153	10887834
3.0	1.680564	2801700	22836	2666416
4.0	1.777911	796708	3615	745502
5.0	1.822596	279288	1622	261214
6.0	1.843107	126075	911	119459
7.0	1.852522	70461	582	67539
8.0	1.856844	45226	410	43692
9.0	1.858828	31481	288	30274
10.0	1.859739	23021	182	22483
11.0	1.860157	17839	138	17262
12.0	1.860349	13627	109	13325
13.0	1.860437	11232	97	10822
14.0	1.860477	9130	77	8883
15.0	1.860496	7506	72	7300
16.0	1.860504	6267	58	6140
17.0	1.860508	5581	53	5373
18.0	1.86051	4700	46	4633
19.0	1.860511	3987	22	3926
20.0	1.860511	3552	17	3486
21.0	1.860511	3113	17	3049
22.0	1.860511	2919	21	2820
23.0	1.860511	2511	13	2438
24.0	1.860511	2209	21	2228
25.0	1.860511	2040	12	1992
26.0	1.860511	1908	11	1867
27.0	1.860511	1693	9	1675
28.0	1.860511	1564	11	1585
29.0	1.860511	1466	15	1424
30.0	1.860511	1395	5	1316
31.0	1.860511	1234	4	1271
32.0	1.860511	1151	12	1135
33.0	1.860511	1080	6	1045
34.0	1.860511	1055	8	1021
35.0	1.860511	883	4	896
36.0	1.860511	870	4	877
37.0	1.860511	817	4	816
38.0	1.860511	816	6	783
39.0	1.860511	712	2	703
40.0	1.860511	740	4	697
41.0	1.860511	665	4	656
42.0	1.860511	593	1	615
43.0	1.860511	621	4	616
44.0	1.860511	591	1	582
45.0	1.860511	542	2	562
46.0	1.860511	500	4	472
47.0	1.860511	494	3	472
48.0	1.860511	455	1	447
49.0	1.860511	431	3	431
50.0	1.860511	407	1	410
51.0	1.860511	403	4	395
52.0	1.860511	434	2	427
53.0	1.860511	372	1	358
54.0	1.860511	358	0	357
55.0	1.860511	357	4	383
56.0	1.860511	362	0	348
57.0	1.860511	337	0	316
58.0	1.860511	316	1	320
59.0	1.860511	319	1	306
60.0	1.860511	286	1	298
61.0	1.860511	289	1	266
62.0	1.860511	248	1	262
63.0	1.860511	262	1	275
64.0	1.860511	278	1	265
65.0	1.860511	276	1	263
66.0	1.860511	227	0	242
67.0	1.860511	247	0	216
68.0	1.860511	208	0	206
69.0	1.860511	209	0	201
70.0	1.860511	201	0	205
71.0	1.860511	207	0	227
72.0	1.860511	200	0	209
73.0	1.860511	221	0	217
74.0	1.860511	201	0	178
75.0	1.860511	170	0	170
76.0	1.860511	188	0	178
77.0	1.860511	186	0	184
78.0	1.860511	166	0	203
79.0	1.860511	191	1	165
80.0	1.860511	163	0	167
81.0	1.860511	175	0	158
82.0	1.860511	159	0	177
83.0	1.860511	154	0	151
84.0	1.860511	182	0	178
85.0	1.860511	147	1	123
86.0	1.860511	132	0	133
87.0	1.860511	140	0	150
88.0	1.860511	152	0	171
89.0	1.860511	136	0	125
90.0	1.860511	138	1	116
91.0	1.860511	135	0	149
92.0	1.860511	124	0	129
93.0	1.860511	127	0	125
94.0	1.860511	136	0	119
95.0	1.860511	145	0	135
96.0	1.860511	106	0	120
97.0	1.860511	125	0	131
98.0	1.860511	116	0	102
99.0	1.860511	105	0	118
100.0	1.860511	125	0	113
101.0	0	97	1	106
102.0	0	109	0	118
103.0	0	106	0	96
104.0	0	108	0	99
105.0	0	88	0	90
106.0	0	96	0	86
107.0	0	86	0	82
108.0	0	88	0	90
109.0	0	78	0	81
110.0	0	88	0	80
111.0	0	93	0	103
112.0	0	89	0	87
113.0	0	78	0	87
114.0	0	91	0	69
115.0	0	74	0	73
116.0	0	80	0	80
117.0	0	81	0	77
118.0	0	75	0	88
119.0	0	69	0	71
120.0	0	71	0	70
121.0	0	80	0	104
122.0	0	81	0	64
123.0	0	87	0	72
124.0	0	69	0	73
125.0	0	66	0	84
126.0	0	70	0	62
127.0	0	79	0	77
128.0	0	75	0	70
129.0	0	82	0	68
130.0	0	57	0	72
131.0	0	70	0	73
132.0	0	67	0	72
133.0	0	67	0	67
134.0	0	68	0	73
135.0	0	77	0	56
136.0	0	72	0	79
137.0	0	70	0	64
138.0	0	69	1	64
139.0	0	52	0	58
140.0	0	74	0	64
141.0	0	58	0	55
142.0	0	43	0	52
143.0	0	63	0	70
144.0	0	70	0	68
145.0	0	66	0	76
146.0	0	56	0	46
147.0	0	53	0	70
148.0	0	62	0	50
149.0	0	59	0	46
150.0	0	42	0	46
151.0	0	46	0	49
152.0	0	56	0	48
153.0	0	55	0	48
154.0	0	38	0	43
155.0	0	55	0	56
156.0	0	46	0	43
157.0	0	50	0	48
158.0	0	37	0	42
159.0	0	63	0	57
160.0	0	38	0	40
161.0	0	50	0	49
162.0	0	46	0	48
163.0	0	50	0	51
164.0	0	53	0	54
165.0	0	43	0	39
166.0	0	45	0	29
167.0	0	37	0	46
168.0	0	38	0	46
169.0	0	47	0	48
170.0	0	36	0	37
171.0	0	48	0	49
172.0	0	44	0	37
173.0	0	45	0	42
174.0	0	44	0	29
175.0	0	25	0	36
176.0	0	36	0	30
177.0	0	32	0	40
178.0	0	39	0	32
179.0	0	31	0	39
180.0	0	39	0	36
181.0	0	32	0	42
182.0	0	34	0	41
183.0	0	41	0	28
184.0	0	38	0	39
185.0	0	41	0	32
186.0	0	39	0	27
187.0	0	25	0	32
188.0	0	30	0	35
189.0	0	29	0	26
190.0	0	26	0	35
191.0	0	34	0	30
192.0	0	20	0	24
193.0	0	38	0	33
194.0	0	38	0	39
195.0	0	28	0	25
196.0	0	17	0	19
197.0	0	34	0	28
198.0	0	27	0	25
199.0	0	31	0	31
200.0	0	22	0	32
201.0	0	29	0	34
202.0	0	29	0	18
203.0	0	31	0	24
204.0	0	31	0	33
205.0	0	20	0	30
206.0	0	24	0	36
207.0	0	35	0	28
208.0	0	30	0	25
209.0	0	24	0	27
210.0	0	41	0	27
211.0	0	23	0	29
212.0	0	29	0	30
213.0	0	20	0	19
214.0	0	29	0	38
215.0	0	24	0	26
216.0	0	36	0	31
217.0	0	24	0	28
218.0	0	32	0	30
219.0	0	24	0	29
220.0	0	33	0	33
221.0	0	30	0	28
222.0	0	29	0	31
223.0	0	31	0	30
224.0	0	28	0	26
225.0	0	33	0	21
226.0	0	24	0	28
227.0	0	31	0	20
228.0	0	18	0	22
229.0	0	24	0	31
230.0	0	26	0	15
231.0	0	21	0	29
232.0	0	25	0	26
233.0	0	28	0	21
234.0	0	21	0	17
235.0	0	18	0	17
236.0	0	22	0	17
237.0	0	18	0	25
238.0	0	18	0	23
239.0	0	21	0	25
240.0	0	18	0	23
241.0	0	17	0	16
242.0	0	30	0	26
243.0	0	20	0	24
244.0	0	18	0	18
245.0	0	22	0	18
246.0	0	21	0	24
247.0	0	22	0	16
248.0	0	22	0	16
249.0	0	23	0	19
250.0	0	15	0	16
251.0	0	14	0	19
252.0	0	19	0	23
253.0	0	15	0	15
254.0	0	26	0	17
255.0	0	18	0	20
256.0	0	15	0	13
257.0	0	12	0	25
258.0	0	17	0	13
259.0	0	23	0	15
260.0	0	21	0	11
261.0	0	12	0	13
262.0	0	11	0	24
263.0	0	20	0	16
264.0	0	14	0	13
265.0	0	17	0	22
266.0	0	20	0	19
267.0	0	13	0	19
268.0	0	22	0	14
269.0	0	11	0	24
270.0	0	20	0	15
271.0	0	24	0	18
272.0	0	20	0	20
273.0	0	15	0	9
274.0	0	22	0	11
275.0	0	11	0	23
276.0	0	14	0	19
277.0	0	17	0	13
278.0	0	14	0	8
279.0	0	19	0	9
280.0	0	10	0	17
281.0	0	9	0	12
282.0	0	9	0	6
283.0	0	9	0	13
284.0	0	11	0	10
285.0	0	17	0	18
286.0	0	14	0	15
287.0	0	9	0	15
288.0	0	14	0	10
289.0	0	14	0	14
290.0	0	16	0	21
291.0	0	13	0	13
292.0	0	14	0	15
293.0	0	15	0	18
294.0	0	13	0	13
295.0	0	23	0	16
296.0	0	14	0	19
297.0	0	16	0	15
298.0	0	15	0	19
299.0	0	14	0	11
300.0	0	16	0	13
301.0	0	15	0	17
302.0	0	11	0	10
303.0	0	16	0	15
304.0	0	13	0	16
305.0	0	17	0	22
306.0	0	10	0	14
307.0	0	22	0	13
308.0	0	19	0	12
309.0	0	15	0	16
310.0	0	11	0	12
311.0	0	13	0	5
312.0	0	12	0	16
313.0	0	11	0	10
314.0	0	12	0	11
315.0	0	14	0	8
316.0	0	7	0	11
317.0	0	8	0	17
318.0	0	9	0	14
319.0	0	19	0	19
320.0	0	8	0	10
321.0	0	13	0	18
322.0	0	12	0	15
323.0	0	21	0	8
324.0	0	13	0	10
325.0	0	21	0	12
326.0	0	11	0	14
327.0	0	11	0	17
328.0	0	8	0	9
329.0	0	13	0	24
330.0	0	17	0	13
331.0	0	11	0	7
332.0	0	14	0	14
333.0	0	16	0	9
334.0	0	10	0	15
335.0	0	10	0	14
336.0	0	19	0	14
337.0	0	8	0	12
338.0	0	14	0	9
339.0	0	10	0	12
340.0	0	15	0	7
341.0	0	12	0	16
342.0	0	13	0	15
343.0	0	10	0	10
344.0	0	13	0	13
345.0	0	8	0	7
346.0	0	11	0	9
347.0	0	12	0	12
348.0	0	15	0	11
349.0	0	7	0	14
350.0	0	6	0	9
351.0	0	12	0	12
352.0	0	14	0	12
353.0	0	16	0	9
354.0	0	13	0	6
355.0	0	9	0	10
356.0	0	7	0	9
357.0	0	8	0	14
358.0	0	17	0	16
359.0	0	8	0	17
360.0	0	14	0	6
361.0	0	12	0	10
362.0	0	9	0	9
363.0	0	11	0	10
364.0	0	9	0	9
365.0	0	6	0	14
366.0	0	12	0	11
367.0	0	12	0	16
368.0	0	11	0	12
369.0	0	8	0	7
370.0	0	13	0	6
371.0	0	11	0	13
372.0	0	10	0	11
373.0	0	13	0	4
374.0	0	14	0	15
375.0	0	5	0	7
376.0	0	10	0	3
377.0	0	7	0	3
378.0	0	9	0	13
379.0	0	12	0	10
380.0	0	9	0	8
381.0	0	3	0	9
382.0	0	9	0	8
383.0	0	6	0	4
384.0	0	8	0	4
385.0	0	5	0	7
386.0	0	9	0	7
387.0	0	7	0	12
388.0	0	6	0	8
389.0	0	4	0	6
390.0	0	11	0	8
391.0	0	6	0	3
392.0	0	8	0	12
393.0	0	5	0	7
394.0	0	6	0	13
395.0	0	8	0	7
396.0	0	11	0	10
397.0	0	5	0	6
398.0	0	13	0	13
399.0	0	9	0	6
400.0	0	11	0	8
401.0	0	6	0	11
402.0	0	9	0	8
403.0	0	13	0	13
404.0	0	14	0	9
405.0	0	8	0	7
406.0	0	13	0	3
407.0	0	3	0	10
408.0	0	10	0	17
409.0	0	5	0	7
410.0	0	3	0	14
411.0	0	13	0	13
412.0	0	11	0	10
413.0	0	13	0	6
414.0	0	8	0	5
415.0	0	12	0	7
416.0	0	12	0	12
417.0	0	7	0	7
418.0	0	8	0	8
419.0	0	8	0	6
420.0	0	5	0	6
421.0	0	6	0	6
422.0	0	7	0	12
423.0	0	9	0	9
424.0	0	11	0	6
425.0	0	9	0	10
426.0	0	5	0	4
427.0	0	7	0	7
428.0	0	11	0	10
429.0	0	6	0	10
430.0	0	7	0	8
431.0	0	12	0	5
432.0	0	9	0	4
433.0	0	7	0	9
434.0	0	10	0	7
435.0	0	6	0	7
436.0	0	4	0	5
437.0	0	9	0	3
438.0	0	4	0	5
439.0	0	2	0	11
440.0	0	8	0	11
441.0	0	6	0	6
442.0	0	11	0	14
443.0	0	7	0	5
444.0	0	8	0	3
445.0	0	6	0	6
446.0	0	7	0	3
447.0	0	3	0	2
448.0	0	5	0	6
449.0	0	7	0	6
450.0	0	9	0	7
451.0	0	4	0	10
452.0	0	4	0	4
453.0	0	6	0	10
454.0	0	9	0	3
455.0	0	5	0	8
456.0	0	6	0	11
457.0	0	4	0	6
458.0	0	4	0	4
459.0	0	8	0	3
460.0	0	8	0	0
461.0	0	7	0	6
462.0	0	3	0	7
463.0	0	3	0	5
464.0	0	5	0	11
465.0	0	5	0	6
466.0	0	5	0	3
467.0	0	9	0	7
468.0	0	12	0	8
469.0	0	7	0	7
470.0	0	1	0	7
471.0	0	7	0	10
472.0	0	6	0	3
473.0	0	6	0	9
474.0	0	9	0	7
475.0	0	7	0	8
476.0	0	7	0	2
477.0	0	7	0	5
478.0	0	6	0	4
479.0	0	6	0	9
480.0	0	3	0	10
481.0	0	8	0	0
482.0	0	8	0	6
483.0	0	5	0	5
484.0	0	5	0	4
485.0	0	8	0	8
486.0	0	4	0	4
487.0	0	6	0	6
488.0	0	6	0	6
489.0	0	5	0	5
490.0	0	4	0	3
491.0	0	4	0	5
492.0	0	9	0	3
493.0	0	4	0	6
494.0	0	5	0	3
495.0	0	4	0	7
496.0	0	3	0	8
497.0	0	3	0	3
498.0	0	5	0	5
499.0	0	2	0	2
500.0	0	4	0	6
501.0	0	3	0	7
502.0	0	10	0	8
503.0	0	8	0	8
504.0	0	3	0	7
505.0	0	5	0	8
506.0	0	4	0	5
507.0	0	8	0	5
508.0	0	10	0	7
509.0	0	5	0	4
510.0	0	6	0	10
511.0	0	4	0	6
512.0	0	3	0	3
513.0	0	6	0	5
514.0	0	8	0	4
515.0	0	6	0	5
516.0	0	10	0	5
517.0	0	5	0	5
518.0	0	4	0	8
519.0	0	5	0	8
520.0	0	4	0	5
521.0	0	6	0	8
522.0	0	8	0	6
523.0	0	3	0	5
524.0	0	6	0	2
525.0	0	8	0	4
526.0	0	9	0	2
527.0	0	10	0	5
528.0	0	5	0	4
529.0	0	4	0	1
530.0	0	1	0	3
531.0	0	3	0	6
532.0	0	2	0	2
533.0	0	2	0	4
534.0	0	4	0	3
535.0	0	5	0	3
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