## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT HB.sorted.bam --OUTPUT HB.markdup.sorted.bam --METRICS_FILE HB.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 23:00:23 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	78212	75319060	21268179	0	44034	25674091	781980	0.340986	85049044

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.006527	37126306	0	37492137
2.0	1.421688	8893372	683801	8716154
3.0	1.592928	2340761	20767	2228167
4.0	1.66356	679924	3511	634403
5.0	1.692693	235728	1633	219512
6.0	1.704709	103896	912	97663
7.0	1.709666	56759	643	54200
8.0	1.71171	36334	408	35034
9.0	1.712553	25706	306	24754
10.0	1.712901	18843	253	18203
11.0	1.713045	14392	166	13885
12.0	1.713104	11414	151	11174
13.0	1.713128	9492	102	9260
14.0	1.713138	7731	99	7521
15.0	1.713142	6367	68	6166
16.0	1.713144	5599	71	5438
17.0	1.713145	4711	49	4583
18.0	1.713145	4065	58	4029
19.0	1.713145	3780	48	3745
20.0	1.713145	3237	49	3057
21.0	1.713145	2841	31	2827
22.0	1.713145	2585	25	2542
23.0	1.713145	2326	16	2283
24.0	1.713145	2029	28	2017
25.0	1.713145	1953	24	1901
26.0	1.713145	1677	15	1690
27.0	1.713145	1615	11	1581
28.0	1.713145	1546	14	1490
29.0	1.713145	1409	11	1351
30.0	1.713145	1190	17	1213
31.0	1.713145	1181	10	1176
32.0	1.713145	1092	7	1087
33.0	1.713145	1082	6	1055
34.0	1.713145	919	8	918
35.0	1.713145	914	13	893
36.0	1.713145	911	7	887
37.0	1.713145	795	6	832
38.0	1.713145	808	8	792
39.0	1.713145	742	6	747
40.0	1.713145	700	4	661
41.0	1.713145	637	6	638
42.0	1.713145	652	3	610
43.0	1.713145	572	3	584
44.0	1.713145	547	2	551
45.0	1.713145	517	4	506
46.0	1.713145	488	5	464
47.0	1.713145	458	2	475
48.0	1.713145	486	2	440
49.0	1.713145	418	1	427
50.0	1.713145	429	4	414
51.0	1.713145	363	3	395
52.0	1.713145	432	4	399
53.0	1.713145	379	2	376
54.0	1.713145	350	4	383
55.0	1.713145	376	3	336
56.0	1.713145	307	5	341
57.0	1.713145	347	2	341
58.0	1.713145	328	2	314
59.0	1.713145	325	1	304
60.0	1.713145	277	0	317
61.0	1.713145	315	1	288
62.0	1.713145	267	3	262
63.0	1.713145	281	2	279
64.0	1.713145	264	0	244
65.0	1.713145	239	1	268
66.0	1.713145	257	0	243
67.0	1.713145	267	1	237
68.0	1.713145	196	0	217
69.0	1.713145	234	1	227
70.0	1.713145	226	2	222
71.0	1.713145	211	0	203
72.0	1.713145	205	2	218
73.0	1.713145	216	0	212
74.0	1.713145	183	0	170
75.0	1.713145	177	0	180
76.0	1.713145	187	0	155
77.0	1.713145	180	3	189
78.0	1.713145	162	2	160
79.0	1.713145	160	0	185
80.0	1.713145	185	0	172
81.0	1.713145	176	0	182
82.0	1.713145	160	0	148
83.0	1.713145	170	0	161
84.0	1.713145	148	1	168
85.0	1.713145	159	1	154
86.0	1.713145	150	2	136
87.0	1.713145	128	0	140
88.0	1.713145	160	0	152
89.0	1.713145	123	0	125
90.0	1.713145	140	0	116
91.0	1.713145	116	1	112
92.0	1.713145	117	1	131
93.0	1.713145	127	0	133
94.0	1.713145	118	0	141
95.0	1.713145	152	0	127
96.0	1.713145	120	0	126
97.0	1.713145	124	0	122
98.0	1.713145	129	0	107
99.0	1.713145	96	0	92
100.0	1.713145	89	0	104
101.0	0	116	0	123
102.0	0	109	0	105
103.0	0	102	0	100
104.0	0	96	1	94
105.0	0	120	0	122
106.0	0	108	0	117
107.0	0	114	0	108
108.0	0	92	0	101
109.0	0	116	0	95
110.0	0	87	0	98
111.0	0	102	0	98
112.0	0	103	0	89
113.0	0	78	0	85
114.0	0	80	0	82
115.0	0	99	0	100
116.0	0	96	0	86
117.0	0	86	0	85
118.0	0	98	0	84
119.0	0	81	1	71
120.0	0	67	0	90
121.0	0	71	1	83
122.0	0	90	0	63
123.0	0	86	0	95
124.0	0	73	0	79
125.0	0	64	0	61
126.0	0	71	0	68
127.0	0	83	0	82
128.0	0	64	0	56
129.0	0	70	0	63
130.0	0	61	0	77
131.0	0	74	0	67
132.0	0	67	0	57
133.0	0	57	0	68
134.0	0	70	0	67
135.0	0	57	0	73
136.0	0	73	0	76
137.0	0	63	0	58
138.0	0	66	0	63
139.0	0	75	0	63
140.0	0	59	0	68
141.0	0	58	0	59
142.0	0	65	0	76
143.0	0	66	0	57
144.0	0	61	0	59
145.0	0	65	0	50
146.0	0	53	0	51
147.0	0	37	0	56
148.0	0	62	0	53
149.0	0	49	0	56
150.0	0	59	0	53
151.0	0	58	0	46
152.0	0	54	0	38
153.0	0	35	0	45
154.0	0	42	0	61
155.0	0	55	0	34
156.0	0	36	0	46
157.0	0	44	0	46
158.0	0	57	0	51
159.0	0	47	0	34
160.0	0	37	0	50
161.0	0	43	0	39
162.0	0	42	0	44
163.0	0	40	0	46
164.0	0	48	0	49
165.0	0	42	0	42
166.0	0	47	0	35
167.0	0	44	0	43
168.0	0	35	0	50
169.0	0	37	0	37
170.0	0	52	0	51
171.0	0	31	0	38
172.0	0	55	1	43
173.0	0	39	0	46
174.0	0	38	0	37
175.0	0	41	0	42
176.0	0	46	0	42
177.0	0	42	0	36
178.0	0	42	0	48
179.0	0	39	0	36
180.0	0	42	0	42
181.0	0	43	0	34
182.0	0	42	0	49
183.0	0	42	0	41
184.0	0	34	0	37
185.0	0	36	0	32
186.0	0	35	0	35
187.0	0	37	0	39
188.0	0	41	0	36
189.0	0	31	0	34
190.0	0	31	0	39
191.0	0	36	0	32
192.0	0	36	0	38
193.0	0	36	0	41
194.0	0	34	0	28
195.0	0	37	0	26
196.0	0	33	0	32
197.0	0	28	0	36
198.0	0	36	0	28
199.0	0	33	0	42
200.0	0	31	0	29
201.0	0	36	0	39
202.0	0	35	0	43
203.0	0	34	0	22
204.0	0	33	0	21
205.0	0	31	0	26
206.0	0	27	0	31
207.0	0	26	0	26
208.0	0	31	0	35
209.0	0	33	0	33
210.0	0	19	0	32
211.0	0	29	0	30
212.0	0	33	0	27
213.0	0	35	0	28
214.0	0	26	0	21
215.0	0	22	0	30
216.0	0	26	0	27
217.0	0	32	0	24
218.0	0	30	0	25
219.0	0	24	0	23
220.0	0	23	0	20
221.0	0	23	0	21
222.0	0	21	0	33
223.0	0	26	0	21
224.0	0	30	0	25
225.0	0	26	0	20
226.0	0	19	0	21
227.0	0	25	0	25
228.0	0	15	0	15
229.0	0	17	0	27
230.0	0	24	0	31
231.0	0	27	0	16
232.0	0	22	0	25
233.0	0	16	0	28
234.0	0	27	0	24
235.0	0	30	0	38
236.0	0	25	0	15
237.0	0	25	0	31
238.0	0	33	0	26
239.0	0	30	0	17
240.0	0	23	0	23
241.0	0	17	0	24
242.0	0	19	0	24
243.0	0	29	0	27
244.0	0	14	0	26
245.0	0	28	0	26
246.0	0	14	0	22
247.0	0	29	0	28
248.0	0	37	0	23
249.0	0	26	0	15
250.0	0	18	0	18
251.0	0	18	0	20
252.0	0	28	0	19
253.0	0	19	0	20
254.0	0	7	0	20
255.0	0	25	0	28
256.0	0	19	0	16
257.0	0	27	0	28
258.0	0	28	0	19
259.0	0	20	0	18
260.0	0	21	0	19
261.0	0	17	0	20
262.0	0	17	0	18
263.0	0	13	0	15
264.0	0	24	0	23
265.0	0	16	0	19
266.0	0	18	0	19
267.0	0	17	0	19
268.0	0	20	0	19
269.0	0	23	0	28
270.0	0	24	0	15
271.0	0	21	0	21
272.0	0	15	0	16
273.0	0	15	0	17
274.0	0	19	0	17
275.0	0	22	0	20
276.0	0	17	0	20
277.0	0	19	0	13
278.0	0	22	0	19
279.0	0	10	0	18
280.0	0	16	0	25
281.0	0	17	0	9
282.0	0	18	0	12
283.0	0	15	0	14
284.0	0	16	0	11
285.0	0	15	0	16
286.0	0	12	0	9
287.0	0	15	0	14
288.0	0	10	0	13
289.0	0	16	0	26
290.0	0	19	0	15
291.0	0	11	0	15
292.0	0	21	0	17
293.0	0	18	0	19
294.0	0	16	0	10
295.0	0	12	0	13
296.0	0	13	0	25
297.0	0	15	0	16
298.0	0	21	0	16
299.0	0	10	0	15
300.0	0	17	0	15
301.0	0	17	0	10
302.0	0	16	0	17
303.0	0	16	0	12
304.0	0	13	0	17
305.0	0	14	0	17
306.0	0	11	0	10
307.0	0	11	0	11
308.0	0	13	0	15
309.0	0	16	0	14
310.0	0	23	0	11
311.0	0	11	0	14
312.0	0	10	0	19
313.0	0	7	0	11
314.0	0	19	0	12
315.0	0	17	0	17
316.0	0	19	0	14
317.0	0	9	0	11
318.0	0	12	0	18
319.0	0	13	0	14
320.0	0	14	0	16
321.0	0	21	0	10
322.0	0	14	0	18
323.0	0	10	0	13
324.0	0	11	0	9
325.0	0	15	0	15
326.0	0	20	0	13
327.0	0	5	0	15
328.0	0	12	0	12
329.0	0	16	0	21
330.0	0	11	0	14
331.0	0	16	0	11
332.0	0	12	0	17
333.0	0	22	0	7
334.0	0	10	0	11
335.0	0	15	0	12
336.0	0	14	0	14
337.0	0	14	0	12
338.0	0	12	0	11
339.0	0	9	0	17
340.0	0	9	0	12
341.0	0	14	0	11
342.0	0	18	0	9
343.0	0	13	0	16
344.0	0	8	0	10
345.0	0	7	0	15
346.0	0	14	0	14
347.0	0	13	0	13
348.0	0	12	0	11
349.0	0	13	0	19
350.0	0	15	0	6
351.0	0	13	0	12
352.0	0	12	0	8
353.0	0	14	0	15
354.0	0	7	0	14
355.0	0	14	0	15
356.0	0	11	0	13
357.0	0	9	0	10
358.0	0	18	0	3
359.0	0	11	0	5
360.0	0	8	0	11
361.0	0	7	0	10
362.0	0	10	0	13
363.0	0	16	0	15
364.0	0	6	0	12
365.0	0	9	0	12
366.0	0	12	0	13
367.0	0	14	0	5
368.0	0	12	0	6
369.0	0	8	0	13
370.0	0	10	0	7
371.0	0	10	0	9
372.0	0	8	0	5
373.0	0	8	0	13
374.0	0	9	0	13
375.0	0	8	0	8
376.0	0	17	0	13
377.0	0	5	0	11
378.0	0	11	0	12
379.0	0	8	0	7
380.0	0	9	0	8
381.0	0	12	0	7
382.0	0	9	0	8
383.0	0	7	0	10
384.0	0	8	0	12
385.0	0	13	0	11
386.0	0	12	0	13
387.0	0	12	0	7
388.0	0	7	0	16
389.0	0	8	0	8
390.0	0	10	0	6
391.0	0	16	0	13
392.0	0	10	0	7
393.0	0	14	0	12
394.0	0	9	0	9
395.0	0	5	0	15
396.0	0	13	0	11
397.0	0	7	0	16
398.0	0	11	0	10
399.0	0	8	0	5
400.0	0	10	0	15
401.0	0	11	0	7
402.0	0	14	0	8
403.0	0	11	0	7
404.0	0	11	0	9
405.0	0	11	0	11
406.0	0	9	0	9
407.0	0	7	0	8
408.0	0	13	0	9
409.0	0	5	0	12
410.0	0	13	0	11
411.0	0	3	0	9
412.0	0	9	0	1
413.0	0	9	0	6
414.0	0	6	0	13
415.0	0	13	0	8
416.0	0	3	0	9
417.0	0	10	0	5
418.0	0	8	0	5
419.0	0	5	0	9
420.0	0	13	0	8
421.0	0	5	0	6
422.0	0	11	0	5
423.0	0	3	0	6
424.0	0	6	0	9
425.0	0	8	0	10
426.0	0	10	0	5
427.0	0	7	0	10
428.0	0	3	0	8
429.0	0	7	0	7
430.0	0	7	0	4
431.0	0	9	0	10
432.0	0	6	0	10
433.0	0	5	0	5
434.0	0	8	0	10
435.0	0	11	0	9
436.0	0	11	0	6
437.0	0	10	0	8
438.0	0	10	0	6
439.0	0	9	0	8
440.0	0	5	0	6
441.0	0	6	0	5
442.0	0	3	0	10
443.0	0	4	0	4
444.0	0	11	0	10
445.0	0	5	0	3
446.0	0	5	0	8
447.0	0	9	0	8
448.0	0	9	0	3
449.0	0	3	0	11
450.0	0	4	0	6
451.0	0	15	0	9
452.0	0	4	0	5
453.0	0	8	0	7
454.0	0	11	0	13
455.0	0	5	0	11
456.0	0	7	0	3
457.0	0	7	0	6
458.0	0	8	0	7
459.0	0	6	0	3
460.0	0	9	0	11
461.0	0	8	0	12
462.0	0	8	0	3
463.0	0	7	0	6
464.0	0	5	0	8
465.0	0	6	0	10
466.0	0	5	0	7
467.0	0	9	0	8
468.0	0	6	0	3
469.0	0	8	0	10
470.0	0	5	0	6
471.0	0	11	0	8
472.0	0	8	0	6
473.0	0	4	0	4
474.0	0	9	0	5
475.0	0	6	0	7
476.0	0	8	0	5
477.0	0	6	0	2
478.0	0	6	0	2
479.0	0	7	0	6
480.0	0	5	0	9
481.0	0	4	0	4
482.0	0	3	0	12
483.0	0	5	0	1
484.0	0	6	0	2
485.0	0	5	0	10
486.0	0	7	0	3
487.0	0	5	0	3
488.0	0	6	0	7
489.0	0	4	0	6
490.0	0	5	0	10
491.0	0	9	0	5
492.0	0	7	0	4
493.0	0	6	0	4
494.0	0	3	0	6
495.0	0	2	0	8
496.0	0	5	0	5
497.0	0	3	0	5
498.0	0	7	0	6
499.0	0	5	0	7
500.0	0	7	0	2
501.0	0	5	0	8
502.0	0	5	0	4
503.0	0	3	0	3
504.0	0	13	0	9
505.0	0	6	0	4
506.0	0	2	0	11
507.0	0	5	0	7
508.0	0	8	0	4
509.0	0	5	0	8
510.0	0	6	0	3
511.0	0	9	0	8
512.0	0	5	0	7
513.0	0	6	0	4
514.0	0	5	0	11
515.0	0	10	0	5
516.0	0	6	0	3
517.0	0	8	0	4
518.0	0	4	0	5
519.0	0	3	0	2
520.0	0	5	0	6
521.0	0	4	0	4
522.0	0	7	0	6
523.0	0	5	0	7
524.0	0	8	0	11
525.0	0	3	0	9
526.0	0	7	0	3
527.0	0	5	0	2
528.0	0	4	0	2
529.0	0	3	0	2
530.0	0	6	0	6
531.0	0	4	0	8
532.0	0	6	0	3
533.0	0	6	0	7
534.0	0	5	0	9
535.0	0	4	0	6
536.0	0	2	0	4
537.0	0	5	0	4
538.0	0	7	0	7
539.0	0	3	0	9
540.0	0	8	0	1
541.0	0	8	0	7
542.0	0	6	0	6
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