## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT DE-2.sorted.bam --OUTPUT DE-2.markdup.sorted.bam --METRICS_FILE DE-2.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 23:05:21 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	80763	83017779	14991510	0	44202	24010724	850336	0.289349	116839755

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.007107	45047461	0	45486175
2.0	1.501985	10182840	774360	9957209
3.0	1.74516	2543061	20798	2412341
4.0	1.864653	699805	2952	648888
5.0	1.92337	230684	1273	213283
6.0	1.952223	96730	696	90424
7.0	1.966401	50601	455	47925
8.0	1.973367	31105	274	29590
9.0	1.976791	20891	184	20058
10.0	1.978473	15048	149	14560
11.0	1.979299	11469	105	11075
12.0	1.979706	8783	89	8401
13.0	1.979905	6886	59	6643
14.0	1.980003	5471	45	5334
15.0	1.980051	4650	43	4496
16.0	1.980075	3836	49	3715
17.0	1.980087	3284	24	3200
18.0	1.980093	2796	21	2663
19.0	1.980095	2433	14	2391
20.0	1.980097	2114	19	2052
21.0	1.980097	1944	17	1935
22.0	1.980098	1692	14	1654
23.0	1.980098	1558	12	1519
24.0	1.980098	1353	11	1339
25.0	1.980098	1264	8	1216
26.0	1.980098	1121	6	1118
27.0	1.980098	1081	7	1070
28.0	1.980098	1004	2	956
29.0	1.980098	869	5	879
30.0	1.980098	803	2	794
31.0	1.980098	750	5	749
32.0	1.980098	706	4	668
33.0	1.980098	641	4	646
34.0	1.980098	642	2	654
35.0	1.980098	572	5	566
36.0	1.980098	512	2	532
37.0	1.980098	589	2	544
38.0	1.980098	492	0	480
39.0	1.980098	468	1	446
40.0	1.980098	421	3	416
41.0	1.980098	404	0	381
42.0	1.980098	355	1	373
43.0	1.980098	368	1	366
44.0	1.980098	386	1	387
45.0	1.980098	357	0	369
46.0	1.980098	357	0	317
47.0	1.980098	294	0	323
48.0	1.980098	300	1	272
49.0	1.980098	261	1	266
50.0	1.980098	247	1	250
51.0	1.980098	292	0	281
52.0	1.980098	247	1	216
53.0	1.980098	233	0	249
54.0	1.980098	235	1	235
55.0	1.980098	204	0	219
56.0	1.980098	220	0	235
57.0	1.980098	244	0	222
58.0	1.980098	209	0	202
59.0	1.980098	204	0	205
60.0	1.980098	195	0	189
61.0	1.980098	194	0	202
62.0	1.980098	200	0	184
63.0	1.980098	152	0	164
64.0	1.980098	201	1	179
65.0	1.980098	160	0	154
66.0	1.980098	141	0	147
67.0	1.980098	152	0	154
68.0	1.980098	149	0	157
69.0	1.980098	153	0	164
70.0	1.980098	151	0	138
71.0	1.980098	157	0	168
72.0	1.980098	153	0	142
73.0	1.980098	138	0	136
74.0	1.980098	141	0	131
75.0	1.980098	120	1	121
76.0	1.980098	134	0	137
77.0	1.980098	131	0	135
78.0	1.980098	114	0	103
79.0	1.980098	118	0	122
80.0	1.980098	120	0	116
81.0	1.980098	107	0	116
82.0	1.980098	125	0	127
83.0	1.980098	103	0	79
84.0	1.980098	97	0	102
85.0	1.980098	99	0	124
86.0	1.980098	108	0	102
87.0	1.980098	93	0	79
88.0	1.980098	112	0	101
89.0	1.980098	98	0	104
90.0	1.980098	75	0	77
91.0	1.980098	94	0	114
92.0	1.980098	106	0	86
93.0	1.980098	92	0	99
94.0	1.980098	89	0	89
95.0	1.980098	89	0	76
96.0	1.980098	79	0	93
97.0	1.980098	81	0	75
98.0	1.980098	91	0	94
99.0	1.980098	82	0	88
100.0	1.980098	82	0	70
101.0	0	68	0	67
102.0	0	74	0	63
103.0	0	76	0	83
104.0	0	72	0	70
105.0	0	68	0	60
106.0	0	68	1	77
107.0	0	70	0	68
108.0	0	79	0	70
109.0	0	74	0	62
110.0	0	58	0	66
111.0	0	49	0	46
112.0	0	49	0	56
113.0	0	76	0	84
114.0	0	65	0	55
115.0	0	57	0	52
116.0	0	58	0	64
117.0	0	53	0	53
118.0	0	56	0	56
119.0	0	65	0	57
120.0	0	52	0	56
121.0	0	59	0	57
122.0	0	56	0	56
123.0	0	47	0	54
124.0	0	55	0	63
125.0	0	50	0	55
126.0	0	65	0	58
127.0	0	57	0	60
128.0	0	54	0	48
129.0	0	65	0	54
130.0	0	54	0	52
131.0	0	44	0	65
132.0	0	61	0	45
133.0	0	51	0	52
134.0	0	35	0	39
135.0	0	49	0	52
136.0	0	52	0	56
137.0	0	54	0	27
138.0	0	44	0	43
139.0	0	28	0	39
140.0	0	48	0	47
141.0	0	49	0	56
142.0	0	41	0	42
143.0	0	46	0	51
144.0	0	45	0	46
145.0	0	45	0	41
146.0	0	39	0	43
147.0	0	51	0	45
148.0	0	37	0	34
149.0	0	39	0	31
150.0	0	41	0	42
151.0	0	45	0	47
152.0	0	33	0	40
153.0	0	45	0	30
154.0	0	37	0	46
155.0	0	36	0	31
156.0	0	31	0	36
157.0	0	38	0	26
158.0	0	24	0	35
159.0	0	35	0	24
160.0	0	33	0	24
161.0	0	24	0	35
162.0	0	28	0	37
163.0	0	38	0	42
164.0	0	32	0	30
165.0	0	35	0	28
166.0	0	26	0	28
167.0	0	35	0	29
168.0	0	30	0	39
169.0	0	30	0	28
170.0	0	30	0	28
171.0	0	34	0	34
172.0	0	25	0	26
173.0	0	29	0	28
174.0	0	20	0	19
175.0	0	28	0	35
176.0	0	35	0	28
177.0	0	35	0	29
178.0	0	28	0	32
179.0	0	36	0	26
180.0	0	20	0	28
181.0	0	23	0	23
182.0	0	29	0	29
183.0	0	33	0	32
184.0	0	20	0	38
185.0	0	37	0	33
186.0	0	37	0	38
187.0	0	29	0	28
188.0	0	32	0	29
189.0	0	29	0	22
190.0	0	28	0	34
191.0	0	28	0	19
192.0	0	26	0	19
193.0	0	21	0	18
194.0	0	19	0	24
195.0	0	22	0	20
196.0	0	28	0	24
197.0	0	16	0	22
198.0	0	24	0	13
199.0	0	24	0	24
200.0	0	14	0	23
201.0	0	21	0	25
202.0	0	18	0	15
203.0	0	22	0	18
204.0	0	14	0	30
205.0	0	21	0	16
206.0	0	27	0	26
207.0	0	18	0	17
208.0	0	25	0	16
209.0	0	18	0	16
210.0	0	20	0	12
211.0	0	13	0	29
212.0	0	16	0	20
213.0	0	20	0	11
214.0	0	19	0	18
215.0	0	26	0	21
216.0	0	22	0	27
217.0	0	13	0	19
218.0	0	12	0	11
219.0	0	17	0	16
220.0	0	20	0	19
221.0	0	21	0	18
222.0	0	21	0	13
223.0	0	14	0	18
224.0	0	16	0	20
225.0	0	18	0	16
226.0	0	18	0	16
227.0	0	17	0	16
228.0	0	13	0	15
229.0	0	18	0	18
230.0	0	18	0	17
231.0	0	16	0	13
232.0	0	6	0	14
233.0	0	21	0	15
234.0	0	14	0	15
235.0	0	17	0	14
236.0	0	16	0	16
237.0	0	17	0	24
238.0	0	9	0	14
239.0	0	24	0	18
240.0	0	14	0	23
241.0	0	19	0	9
242.0	0	18	0	11
243.0	0	13	0	15
244.0	0	14	0	14
245.0	0	10	0	11
246.0	0	21	0	22
247.0	0	18	0	21
248.0	0	15	0	11
249.0	0	15	0	16
250.0	0	14	0	18
251.0	0	13	0	9
252.0	0	17	0	14
253.0	0	15	0	16
254.0	0	14	0	14
255.0	0	7	0	14
256.0	0	11	0	14
257.0	0	16	0	12
258.0	0	11	0	13
259.0	0	11	0	7
260.0	0	11	0	18
261.0	0	16	0	18
262.0	0	13	0	11
263.0	0	18	0	18
264.0	0	18	0	11
265.0	0	9	0	19
266.0	0	16	0	10
267.0	0	14	0	10
268.0	0	12	0	8
269.0	0	16	0	21
270.0	0	13	0	14
271.0	0	12	0	12
272.0	0	11	0	6
273.0	0	13	0	15
274.0	0	14	0	14
275.0	0	13	0	13
276.0	0	12	0	17
277.0	0	16	0	8
278.0	0	10	0	9
279.0	0	10	0	6
280.0	0	13	0	12
281.0	0	4	0	9
282.0	0	14	0	21
283.0	0	11	0	9
284.0	0	14	0	9
285.0	0	16	0	8
286.0	0	11	0	17
287.0	0	7	0	11
288.0	0	12	0	16
289.0	0	7	0	7
290.0	0	9	0	10
291.0	0	9	0	4
292.0	0	11	0	6
293.0	0	17	0	9
294.0	0	8	0	8
295.0	0	8	0	13
296.0	0	7	0	10
297.0	0	7	0	9
298.0	0	9	0	6
299.0	0	11	0	8
300.0	0	11	0	10
301.0	0	11	0	12
302.0	0	7	0	5
303.0	0	3	0	14
304.0	0	6	0	7
305.0	0	8	0	17
306.0	0	18	0	6
307.0	0	13	0	9
308.0	0	10	0	14
309.0	0	11	0	7
310.0	0	6	0	8
311.0	0	12	0	14
312.0	0	9	0	9
313.0	0	12	0	11
314.0	0	9	0	12
315.0	0	11	0	15
316.0	0	12	0	13
317.0	0	12	0	4
318.0	0	10	0	8
319.0	0	8	0	19
320.0	0	8	0	10
321.0	0	13	0	9
322.0	0	15	0	14
323.0	0	6	0	12
324.0	0	14	0	6
325.0	0	10	0	3
326.0	0	10	0	8
327.0	0	9	0	8
328.0	0	5	0	11
329.0	0	4	0	9
330.0	0	13	0	6
331.0	0	9	0	8
332.0	0	8	0	10
333.0	0	7	0	8
334.0	0	8	0	10
335.0	0	7	0	11
336.0	0	14	0	11
337.0	0	7	0	7
338.0	0	6	0	5
339.0	0	13	0	11
340.0	0	7	0	5
341.0	0	10	0	6
342.0	0	5	0	14
343.0	0	9	0	8
344.0	0	6	0	7
345.0	0	10	0	10
346.0	0	8	0	6
347.0	0	11	0	5
348.0	0	8	0	8
349.0	0	6	0	6
350.0	0	5	0	12
351.0	0	10	0	11
352.0	0	8	0	5
353.0	0	7	0	9
354.0	0	7	0	6
355.0	0	14	0	7
356.0	0	9	0	6
357.0	0	7	0	9
358.0	0	7	0	9
359.0	0	3	0	9
360.0	0	6	0	7
361.0	0	12	0	6
362.0	0	6	0	6
363.0	0	7	0	10
364.0	0	9	0	9
365.0	0	10	0	11
366.0	0	6	0	2
367.0	0	5	0	9
368.0	0	6	0	7
369.0	0	9	0	9
370.0	0	9	0	5
371.0	0	5	0	7
372.0	0	5	0	9
373.0	0	9	0	7
374.0	0	11	0	8
375.0	0	10	0	10
376.0	0	5	0	4
377.0	0	3	0	9
378.0	0	15	0	8
379.0	0	6	0	6
380.0	0	4	0	4
381.0	0	4	0	11
382.0	0	11	0	3
383.0	0	11	0	8
384.0	0	4	0	7
385.0	0	5	0	9
386.0	0	7	0	2
387.0	0	12	0	7
388.0	0	6	0	7
389.0	0	6	0	5
390.0	0	2	0	4
391.0	0	4	0	8
392.0	0	3	0	8
393.0	0	7	0	5
394.0	0	6	0	5
395.0	0	5	0	6
396.0	0	9	0	8
397.0	0	6	0	6
398.0	0	5	0	5
399.0	0	6	0	7
400.0	0	5	0	6
401.0	0	6	0	3
402.0	0	5	0	6
403.0	0	7	0	2
404.0	0	8	0	8
405.0	0	8	0	8
406.0	0	5	0	1
407.0	0	4	0	9
408.0	0	6	0	7
409.0	0	1	0	5
410.0	0	6	0	3
411.0	0	8	0	4
412.0	0	9	0	4
413.0	0	3	0	5
414.0	0	4	0	2
415.0	0	5	0	6
416.0	0	4	0	7
417.0	0	2	0	9
418.0	0	6	0	4
419.0	0	5	0	3
420.0	0	6	0	8
421.0	0	7	0	4
422.0	0	6	0	6
423.0	0	8	0	3
424.0	0	7	0	12
425.0	0	6	0	7
426.0	0	4	0	4
427.0	0	6	0	5
428.0	0	2	0	4
429.0	0	3	0	6
430.0	0	8	0	4
431.0	0	4	0	5
432.0	0	5	0	7
433.0	0	8	0	5
434.0	0	7	0	3
435.0	0	4	0	7
436.0	0	3	0	9
437.0	0	3	0	1
438.0	0	9	0	7
439.0	0	4	0	3
440.0	0	8	0	6
441.0	0	5	0	6
442.0	0	6	0	3
443.0	0	4	0	2
444.0	0	5	0	8
445.0	0	2	0	3
446.0	0	5	0	5
447.0	0	4	0	4
448.0	0	4	0	2
449.0	0	8	0	5
450.0	0	7	0	6
451.0	0	2	0	3
452.0	0	1	0	3
453.0	0	2	0	6
454.0	0	5	0	3
455.0	0	6	0	4
456.0	0	4	0	6
457.0	0	3	0	4
458.0	0	7	0	5
459.0	0	4	0	4
460.0	0	3	0	0
461.0	0	2	0	3
462.0	0	1	0	1
463.0	0	2	0	7
464.0	0	5	0	2
465.0	0	5	0	1
466.0	0	4	0	5
467.0	0	0	0	4
468.0	0	6	0	5
469.0	0	7	0	3
470.0	0	3	0	3
471.0	0	2	0	3
472.0	0	2	0	6
473.0	0	4	0	1
474.0	0	5	0	5
475.0	0	2	0	2
476.0	0	1	0	5
477.0	0	3	0	2
478.0	0	5	0	7
479.0	0	3	0	5
480.0	0	4	0	7
481.0	0	5	0	3
482.0	0	5	0	2
483.0	0	1	0	8
484.0	0	6	0	13
485.0	0	6	0	3
486.0	0	5	0	3
487.0	0	5	0	4
488.0	0	13	0	5
489.0	0	4	0	4
490.0	0	5	0	4
491.0	0	7	0	8
492.0	0	5	0	4
493.0	0	5	0	2
494.0	0	5	0	1
495.0	0	6	0	2
496.0	0	4	0	5
497.0	0	0	0	3
498.0	0	3	0	3
499.0	0	2	0	5
500.0	0	4	0	1
501.0	0	1	0	3
502.0	0	3	0	4
503.0	0	2	0	4
504.0	0	3	0	2
505.0	0	7	0	7
506.0	0	3	0	2
507.0	0	2	0	0
508.0	0	5	0	0
509.0	0	2	0	3
510.0	0	2	0	5
511.0	0	3	0	2
512.0	0	3	0	3
513.0	0	2	0	3
514.0	0	1	0	1
515.0	0	4	0	3
516.0	0	4	0	4
517.0	0	1	0	5
518.0	0	1	0	0
519.0	0	6	0	0
520.0	0	0	0	2
521.0	0	2	0	4
522.0	0	2	0	3
523.0	0	2	0	4
524.0	0	5	0	3
525.0	0	4	0	0
526.0	0	0	0	2
527.0	0	4	0	2
528.0	0	2	0	6
529.0	0	3	0	5
530.0	0	2	0	2
531.0	0	3	0	2
532.0	0	2	0	4
533.0	0	2	0	4
534.0	0	5	0	4
535.0	0	1	0	4
536.0	0	6	0	6
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