## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT DE-7.sorted.bam --OUTPUT DE-7.markdup.sorted.bam --METRICS_FILE DE-7.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 23:00:17 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	60476	68549432	16575291	0	32205	21402648	604254	0.312319	86940807

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.005846	36592175	0	36898392
2.0	1.463047	7707474	536722	7541240
3.0	1.670865	1836326	14907	1747527
4.0	1.765327	507053	2608	475633
5.0	1.808265	179793	1249	169510
6.0	1.827781	84005	667	80260
7.0	1.836653	49128	434	47267
8.0	1.840685	32261	288	31329
9.0	1.842518	23040	206	22486
10.0	1.843351	17280	144	16819
11.0	1.84373	13382	121	13078
12.0	1.843902	10768	94	10482
13.0	1.84398	8698	74	8553
14.0	1.844016	7269	65	7138
15.0	1.844032	6159	45	6088
16.0	1.844039	5213	46	5075
17.0	1.844043	4496	32	4427
18.0	1.844044	3930	30	3885
19.0	1.844045	3481	30	3357
20.0	1.844045	3100	26	3085
21.0	1.844045	2782	23	2677
22.0	1.844045	2322	15	2332
23.0	1.844045	2232	13	2173
24.0	1.844045	2010	12	2006
25.0	1.844045	1759	15	1705
26.0	1.844045	1690	21	1653
27.0	1.844045	1404	10	1408
28.0	1.844045	1408	11	1411
29.0	1.844045	1274	5	1240
30.0	1.844045	1218	2	1223
31.0	1.844045	1116	9	1108
32.0	1.844045	1010	5	987
33.0	1.844045	1003	7	1002
34.0	1.844045	899	3	886
35.0	1.844045	866	1	840
36.0	1.844045	782	3	793
37.0	1.844045	743	2	707
38.0	1.844045	704	1	713
39.0	1.844045	645	4	628
40.0	1.844045	637	6	646
41.0	1.844045	603	3	604
42.0	1.844045	566	5	550
43.0	1.844045	513	0	495
44.0	1.844045	534	2	525
45.0	1.844045	466	3	463
46.0	1.844045	421	4	452
47.0	1.844045	470	3	465
48.0	1.844045	459	4	430
49.0	1.844045	391	1	410
50.0	1.844045	407	2	376
51.0	1.844045	385	0	388
52.0	1.844045	386	1	360
53.0	1.844045	386	1	410
54.0	1.844045	348	0	333
55.0	1.844045	315	1	306
56.0	1.844045	301	3	281
57.0	1.844045	279	0	293
58.0	1.844045	281	1	265
59.0	1.844045	266	0	276
60.0	1.844045	262	0	270
61.0	1.844045	254	0	265
62.0	1.844045	258	1	232
63.0	1.844045	239	1	239
64.0	1.844045	236	1	256
65.0	1.844045	258	0	239
66.0	1.844045	235	0	231
67.0	1.844045	228	0	234
68.0	1.844045	204	0	208
69.0	1.844045	215	1	200
70.0	1.844045	203	0	186
71.0	1.844045	178	0	188
72.0	1.844045	183	0	183
73.0	1.844045	183	0	193
74.0	1.844045	181	1	175
75.0	1.844045	180	0	171
76.0	1.844045	162	0	158
77.0	1.844045	141	0	153
78.0	1.844045	190	0	150
79.0	1.844045	148	1	171
80.0	1.844045	141	0	140
81.0	1.844045	140	1	157
82.0	1.844045	152	0	135
83.0	1.844045	137	0	137
84.0	1.844045	135	0	147
85.0	1.844045	146	0	147
86.0	1.844045	132	0	120
87.0	1.844045	134	0	120
88.0	1.844045	119	0	131
89.0	1.844045	122	0	132
90.0	1.844045	132	0	136
91.0	1.844045	132	0	113
92.0	1.844045	121	0	121
93.0	1.844045	105	0	124
94.0	1.844045	133	0	123
95.0	1.844045	115	0	112
96.0	1.844045	115	0	121
97.0	1.844045	114	0	116
98.0	1.844045	118	0	107
99.0	1.844045	111	0	103
100.0	1.844045	96	0	101
101.0	0	100	0	92
102.0	0	105	0	101
103.0	0	90	0	86
104.0	0	77	0	94
105.0	0	92	0	86
106.0	0	96	0	103
107.0	0	96	0	85
108.0	0	84	1	92
109.0	0	88	0	76
110.0	0	76	0	86
111.0	0	94	0	83
112.0	0	82	0	80
113.0	0	82	0	67
114.0	0	67	0	80
115.0	0	69	0	64
116.0	0	66	0	76
117.0	0	81	0	67
118.0	0	76	0	82
119.0	0	70	0	73
120.0	0	63	0	62
121.0	0	68	0	68
122.0	0	61	1	58
123.0	0	70	0	65
124.0	0	70	0	65
125.0	0	53	0	69
126.0	0	83	0	72
127.0	0	57	0	69
128.0	0	66	0	57
129.0	0	66	0	63
130.0	0	64	0	65
131.0	0	69	0	73
132.0	0	63	0	62
133.0	0	55	0	58
134.0	0	61	0	61
135.0	0	64	0	52
136.0	0	49	0	67
137.0	0	62	0	52
138.0	0	48	0	57
139.0	0	59	0	56
140.0	0	58	0	62
141.0	0	58	0	47
142.0	0	66	0	62
143.0	0	61	0	64
144.0	0	45	0	49
145.0	0	65	0	50
146.0	0	39	0	36
147.0	0	47	0	48
148.0	0	47	0	43
149.0	0	44	0	55
150.0	0	52	0	46
151.0	0	44	0	54
152.0	0	40	0	38
153.0	0	40	0	34
154.0	0	42	0	55
155.0	0	50	0	40
156.0	0	47	0	52
157.0	0	50	0	41
158.0	0	36	0	44
159.0	0	52	0	42
160.0	0	44	0	42
161.0	0	39	0	36
162.0	0	32	0	28
163.0	0	35	0	37
164.0	0	35	0	52
165.0	0	48	0	37
166.0	0	43	0	48
167.0	0	50	0	48
168.0	0	38	0	29
169.0	0	35	0	46
170.0	0	39	0	36
171.0	0	38	0	37
172.0	0	36	0	33
173.0	0	33	0	37
174.0	0	37	0	33
175.0	0	38	0	40
176.0	0	39	0	35
177.0	0	36	0	28
178.0	0	28	0	34
179.0	0	32	0	36
180.0	0	26	0	32
181.0	0	35	0	30
182.0	0	33	0	24
183.0	0	27	0	26
184.0	0	24	0	30
185.0	0	39	0	37
186.0	0	31	0	29
187.0	0	29	0	19
188.0	0	31	0	46
189.0	0	36	0	28
190.0	0	23	0	38
191.0	0	39	0	21
192.0	0	29	0	31
193.0	0	27	0	33
194.0	0	26	0	33
195.0	0	31	0	36
196.0	0	37	0	29
197.0	0	30	0	27
198.0	0	23	0	15
199.0	0	32	0	31
200.0	0	15	0	29
201.0	0	31	0	31
202.0	0	36	0	33
203.0	0	29	0	26
204.0	0	29	0	35
205.0	0	34	0	22
206.0	0	25	0	33
207.0	0	22	0	25
208.0	0	31	0	33
209.0	0	23	0	28
210.0	0	29	0	24
211.0	0	32	0	18
212.0	0	23	0	20
213.0	0	22	0	21
214.0	0	16	0	17
215.0	0	23	0	29
216.0	0	21	0	20
217.0	0	29	0	30
218.0	0	29	0	25
219.0	0	23	0	26
220.0	0	18	0	26
221.0	0	24	0	16
222.0	0	24	0	25
223.0	0	28	0	23
224.0	0	14	0	18
225.0	0	22	0	25
226.0	0	22	0	23
227.0	0	20	0	23
228.0	0	31	0	19
229.0	0	19	0	18
230.0	0	17	0	19
231.0	0	15	0	19
232.0	0	16	0	13
233.0	0	23	0	22
234.0	0	24	0	20
235.0	0	17	0	23
236.0	0	22	0	16
237.0	0	14	0	12
238.0	0	16	0	14
239.0	0	18	0	23
240.0	0	15	0	18
241.0	0	16	0	21
242.0	0	22	0	26
243.0	0	23	0	26
244.0	0	24	0	20
245.0	0	25	0	23
246.0	0	19	0	21
247.0	0	20	0	16
248.0	0	17	0	17
249.0	0	16	0	14
250.0	0	21	0	24
251.0	0	16	0	17
252.0	0	20	0	22
253.0	0	18	0	14
254.0	0	20	0	14
255.0	0	17	0	24
256.0	0	23	0	16
257.0	0	11	0	25
258.0	0	25	0	15
259.0	0	19	0	10
260.0	0	25	0	22
261.0	0	13	0	11
262.0	0	18	0	19
263.0	0	13	0	19
264.0	0	12	0	17
265.0	0	16	0	18
266.0	0	17	0	16
267.0	0	16	0	21
268.0	0	22	0	22
269.0	0	15	0	16
270.0	0	13	0	9
271.0	0	16	0	14
272.0	0	16	0	10
273.0	0	14	0	19
274.0	0	18	0	21
275.0	0	17	0	10
276.0	0	21	0	8
277.0	0	6	0	18
278.0	0	12	0	15
279.0	0	19	0	23
280.0	0	14	0	5
281.0	0	19	0	15
282.0	0	11	0	15
283.0	0	9	0	10
284.0	0	14	0	12
285.0	0	8	0	12
286.0	0	11	0	15
287.0	0	16	0	15
288.0	0	18	0	11
289.0	0	14	0	15
290.0	0	18	0	13
291.0	0	13	0	17
292.0	0	13	0	13
293.0	0	15	0	12
294.0	0	7	0	14
295.0	0	15	0	10
296.0	0	7	0	15
297.0	0	11	0	18
298.0	0	17	0	16
299.0	0	17	0	13
300.0	0	14	0	11
301.0	0	18	0	12
302.0	0	16	0	15
303.0	0	9	0	13
304.0	0	9	0	14
305.0	0	16	0	16
306.0	0	14	0	16
307.0	0	22	0	16
308.0	0	10	0	16
309.0	0	21	0	12
310.0	0	7	0	13
311.0	0	12	0	12
312.0	0	11	0	20
313.0	0	14	0	13
314.0	0	15	0	13
315.0	0	19	0	10
316.0	0	14	0	18
317.0	0	13	0	9
318.0	0	9	0	13
319.0	0	11	0	10
320.0	0	10	0	12
321.0	0	10	0	8
322.0	0	17	0	12
323.0	0	12	0	11
324.0	0	14	0	8
325.0	0	10	0	11
326.0	0	12	0	15
327.0	0	10	0	10
328.0	0	13	0	13
329.0	0	10	0	7
330.0	0	10	0	7
331.0	0	6	0	10
332.0	0	13	0	12
333.0	0	11	0	10
334.0	0	10	0	12
335.0	0	10	0	6
336.0	0	11	0	7
337.0	0	12	0	15
338.0	0	6	0	7
339.0	0	15	0	14
340.0	0	7	0	13
341.0	0	6	0	9
342.0	0	5	0	4
343.0	0	6	0	17
344.0	0	13	0	12
345.0	0	16	0	10
346.0	0	13	0	10
347.0	0	13	0	17
348.0	0	11	0	8
349.0	0	9	0	8
350.0	0	15	0	9
351.0	0	10	0	6
352.0	0	11	0	8
353.0	0	6	0	11
354.0	0	9	0	12
355.0	0	9	0	13
356.0	0	8	0	10
357.0	0	8	0	14
358.0	0	11	0	13
359.0	0	11	0	7
360.0	0	8	0	10
361.0	0	16	0	12
362.0	0	9	0	10
363.0	0	8	0	15
364.0	0	14	0	7
365.0	0	13	0	11
366.0	0	17	0	13
367.0	0	6	0	8
368.0	0	12	0	11
369.0	0	11	0	7
370.0	0	8	0	6
371.0	0	6	0	13
372.0	0	12	0	14
373.0	0	8	0	8
374.0	0	10	0	5
375.0	0	5	0	11
376.0	0	13	0	7
377.0	0	11	0	7
378.0	0	6	0	8
379.0	0	12	0	7
380.0	0	5	0	5
381.0	0	5	0	8
382.0	0	5	0	9
383.0	0	5	0	12
384.0	0	13	0	13
385.0	0	14	0	6
386.0	0	7	0	6
387.0	0	5	0	3
388.0	0	10	0	12
389.0	0	10	0	9
390.0	0	5	0	9
391.0	0	7	0	12
392.0	0	11	0	8
393.0	0	6	0	5
394.0	0	13	0	12
395.0	0	6	0	9
396.0	0	9	0	5
397.0	0	5	0	5
398.0	0	8	0	8
399.0	0	9	0	9
400.0	0	7	0	7
401.0	0	6	0	4
402.0	0	10	0	10
403.0	0	9	0	9
404.0	0	12	0	6
405.0	0	3	0	10
406.0	0	9	0	5
407.0	0	7	0	6
408.0	0	6	0	4
409.0	0	8	0	11
410.0	0	3	0	8
411.0	0	8	0	8
412.0	0	7	0	8
413.0	0	7	0	8
414.0	0	9	0	10
415.0	0	6	0	7
416.0	0	12	0	8
417.0	0	7	0	4
418.0	0	6	0	7
419.0	0	5	0	4
420.0	0	9	0	2
421.0	0	6	0	4
422.0	0	10	0	8
423.0	0	3	0	9
424.0	0	5	0	7
425.0	0	4	0	10
426.0	0	7	0	10
427.0	0	3	0	3
428.0	0	11	0	10
429.0	0	9	0	8
430.0	0	8	0	8
431.0	0	10	0	4
432.0	0	3	0	4
433.0	0	7	0	6
434.0	0	6	0	8
435.0	0	7	0	6
436.0	0	8	0	9
437.0	0	5	0	8
438.0	0	10	0	9
439.0	0	5	0	3
440.0	0	12	0	10
441.0	0	5	0	8
442.0	0	6	0	8
443.0	0	6	0	4
444.0	0	9	0	4
445.0	0	7	0	5
446.0	0	7	0	5
447.0	0	7	0	8
448.0	0	3	0	10
449.0	0	3	0	8
450.0	0	7	0	4
451.0	0	7	0	5
452.0	0	8	0	8
453.0	0	4	0	4
454.0	0	8	0	2
455.0	0	8	0	5
456.0	0	5	0	6
457.0	0	2	0	2
458.0	0	5	0	5
459.0	0	6	0	4
460.0	0	5	0	8
461.0	0	3	0	7
462.0	0	8	0	7
463.0	0	4	0	3
464.0	0	4	0	8
465.0	0	8	0	4
466.0	0	7	0	5
467.0	0	6	0	5
468.0	0	3	0	1
469.0	0	4	0	8
470.0	0	4	0	12
471.0	0	10	0	5
472.0	0	5	0	4
473.0	0	5	0	6
474.0	0	4	0	6
475.0	0	9	0	5
476.0	0	10	0	5
477.0	0	1	0	2
478.0	0	3	0	3
479.0	0	6	0	4
480.0	0	2	0	4
481.0	0	9	0	6
482.0	0	2	0	8
483.0	0	3	0	7
484.0	0	5	0	6
485.0	0	3	0	3
486.0	0	8	0	8
487.0	0	4	0	7
488.0	0	9	0	5
489.0	0	7	0	6
490.0	0	4	0	7
491.0	0	3	0	8
492.0	0	8	0	8
493.0	0	9	0	5
494.0	0	4	0	2
495.0	0	6	0	7
496.0	0	12	0	4
497.0	0	3	0	5
498.0	0	2	0	4
499.0	0	10	0	9
500.0	0	5	0	9
501.0	0	2	0	5
502.0	0	5	0	6
503.0	0	6	0	5
504.0	0	6	0	4
505.0	0	10	0	5
506.0	0	7	0	8
507.0	0	8	0	3
508.0	0	1	0	6
509.0	0	3	0	5
510.0	0	7	0	4
511.0	0	4	0	1
512.0	0	3	0	6
513.0	0	6	0	4
514.0	0	7	0	7
515.0	0	2	0	6
516.0	0	3	0	3
517.0	0	3	0	3
518.0	0	5	0	5
519.0	0	9	0	7
520.0	0	5	0	3
521.0	0	6	0	11
522.0	0	5	0	4
523.0	0	5	0	3
524.0	0	7	0	12
525.0	0	6	0	2
526.0	0	5	0	3
527.0	0	4	0	6
528.0	0	6	0	5
529.0	0	4	0	3
530.0	0	3	0	10
531.0	0	10	0	3
532.0	0	3	0	6
533.0	0	8	0	2
534.0	0	3	0	7
535.0	0	3	0	2
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