## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-260-TP2.bam --OUTPUT POR-260-TP2.md.bam --METRICS_FILE POR-260-TP2.md.MarkDuplicates.metrics.txt --ASSUME_SORTED true --VALIDATION_STRINGENCY LENIENT --REFERENCE_SEQUENCE Porites_evermanni_v1.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_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_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 --REMOVE_DUPLICATES false --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: Tue Jul 22 18:15:11 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	3030	14920847	9481642	0	2943	11645512	3353650	0.780505	3386611

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.021353	1892317	0	2371928
2.0	1.03382	574359	455919	408600
3.0	1.033972	242136	184634	126312
4.0	1.033974	129870	94215	67954
5.0	1.033974	79546	53558	45297
6.0	1.033974	53685	32356	33316
7.0	1.033974	38640	20988	25603
8.0	1.033974	29147	14526	20233
9.0	1.033974	23024	10634	16437
10.0	1.033974	18561	8004	13822
11.0	1.033974	15576	6245	11658
12.0	1.033974	13324	5101	10073
13.0	1.033974	11600	4190	8662
14.0	1.033974	10225	3591	7463
15.0	1.033974	8919	2908	6782
16.0	1.033974	7927	2535	6025
17.0	1.033974	7157	2201	5422
18.0	1.033974	6308	1849	4832
19.0	1.033974	5924	1795	4473
20.0	1.033974	5254	1506	3937
21.0	1.033974	4843	1333	3637
22.0	1.033974	4323	1232	3297
23.0	1.033974	4062	1156	3094
24.0	1.033974	3734	1042	2841
25.0	1.033974	3397	893	2552
26.0	1.033974	3202	887	2490
27.0	1.033974	3085	773	2240
28.0	1.033974	2836	670	2097
29.0	1.033974	2533	716	2054
30.0	1.033974	2462	579	1882
31.0	1.033974	2323	554	1780
32.0	1.033974	2174	469	1640
33.0	1.033974	2041	513	1566
34.0	1.033974	1894	431	1438
35.0	1.033974	1767	420	1336
36.0	1.033974	1743	390	1371
37.0	1.033974	1637	345	1198
38.0	1.033974	1594	365	1210
39.0	1.033974	1433	313	1119
40.0	1.033974	1369	310	1058
41.0	1.033974	1317	288	1039
42.0	1.033974	1330	288	904
43.0	1.033974	1256	236	895
44.0	1.033974	1169	238	909
45.0	1.033974	1140	231	820
46.0	1.033974	1085	194	834
47.0	1.033974	1045	216	770
48.0	1.033974	1021	192	760
49.0	1.033974	915	182	713
50.0	1.033974	888	179	668
51.0	1.033974	869	177	647
52.0	1.033974	884	156	610
53.0	1.033974	812	111	617
54.0	1.033974	752	141	569
55.0	1.033974	793	140	627
56.0	1.033974	671	133	520
57.0	1.033974	750	134	531
58.0	1.033974	690	117	561
59.0	1.033974	611	120	510
60.0	1.033974	631	132	464
61.0	1.033974	614	118	462
62.0	1.033974	560	102	419
63.0	1.033974	596	87	431
64.0	1.033974	599	101	441
65.0	1.033974	532	85	414
66.0	1.033974	545	95	367
67.0	1.033974	514	84	369
68.0	1.033974	457	89	355
69.0	1.033974	479	71	366
70.0	1.033974	464	92	330
71.0	1.033974	451	78	318
72.0	1.033974	443	68	328
73.0	1.033974	409	66	325
74.0	1.033974	414	63	298
75.0	1.033974	412	57	283
76.0	1.033974	408	62	275
77.0	1.033974	402	57	284
78.0	1.033974	396	47	236
79.0	1.033974	331	59	267
80.0	1.033974	347	50	222
81.0	1.033974	336	41	244
82.0	1.033974	326	58	229
83.0	1.033974	310	52	248
84.0	1.033974	272	50	251
85.0	1.033974	309	45	237
86.0	1.033974	276	46	237
87.0	1.033974	280	48	224
88.0	1.033974	304	46	203
89.0	1.033974	290	33	204
90.0	1.033974	245	37	221
91.0	1.033974	257	38	212
92.0	1.033974	249	44	196
93.0	1.033974	266	33	154
94.0	1.033974	248	35	173
95.0	1.033974	233	32	175
96.0	1.033974	256	30	173
97.0	1.033974	245	28	171
98.0	1.033974	225	26	154
99.0	1.033974	207	33	166
100.0	1.033974	191	33	165
101.0	0	209	26	154
102.0	0	206	32	158
103.0	0	194	23	156
104.0	0	184	26	151
105.0	0	222	30	128
106.0	0	190	25	126
107.0	0	188	24	130
108.0	0	187	24	145
109.0	0	207	28	124
110.0	0	165	31	128
111.0	0	165	26	120
112.0	0	160	19	136
113.0	0	171	17	119
114.0	0	141	18	127
115.0	0	156	17	98
116.0	0	154	16	134
117.0	0	145	16	135
118.0	0	152	21	109
119.0	0	160	14	96
120.0	0	151	26	83
121.0	0	144	20	93
122.0	0	143	12	79
123.0	0	110	10	112
124.0	0	127	16	91
125.0	0	111	14	86
126.0	0	148	12	83
127.0	0	122	20	86
128.0	0	103	22	78
129.0	0	128	18	82
130.0	0	105	18	69
131.0	0	104	7	77
132.0	0	103	18	97
133.0	0	116	13	87
134.0	0	90	13	89
135.0	0	99	15	94
136.0	0	115	18	94
137.0	0	100	14	71
138.0	0	102	11	72
139.0	0	95	10	88
140.0	0	111	15	65
141.0	0	103	11	73
142.0	0	92	14	74
143.0	0	86	13	70
144.0	0	104	13	76
145.0	0	92	6	54
146.0	0	93	16	59
147.0	0	89	9	58
148.0	0	93	11	78
149.0	0	105	13	75
150.0	0	99	9	60
151.0	0	93	10	56
152.0	0	83	8	64
153.0	0	95	9	58
154.0	0	76	15	53
155.0	0	84	10	68
156.0	0	67	14	55
157.0	0	68	9	60
158.0	0	71	13	64
159.0	0	87	9	53
160.0	0	70	8	50
161.0	0	81	6	61
162.0	0	75	7	62
163.0	0	71	15	51
164.0	0	67	7	52
165.0	0	75	8	49
166.0	0	73	11	63
167.0	0	75	12	41
168.0	0	66	5	55
169.0	0	78	10	46
170.0	0	59	9	58
171.0	0	62	5	47
172.0	0	66	10	46
173.0	0	57	7	44
174.0	0	68	2	39
175.0	0	56	5	37
176.0	0	69	7	49
177.0	0	64	4	45
178.0	0	50	4	46
179.0	0	56	8	38
180.0	0	65	9	37
181.0	0	52	11	49
182.0	0	55	9	27
183.0	0	63	5	57
184.0	0	58	5	34
185.0	0	45	4	36
186.0	0	46	0	39
187.0	0	56	9	47
188.0	0	61	4	41
189.0	0	62	7	53
190.0	0	50	3	36
191.0	0	45	9	42
192.0	0	48	6	33
193.0	0	61	7	32
194.0	0	53	6	48
195.0	0	61	10	30
196.0	0	43	3	37
197.0	0	48	6	28
198.0	0	31	5	31
199.0	0	35	5	23
200.0	0	44	6	33
201.0	0	56	7	33
202.0	0	38	5	34
203.0	0	46	1	40
204.0	0	40	3	34
205.0	0	42	3	30
206.0	0	38	7	26
207.0	0	45	7	26
208.0	0	31	4	34
209.0	0	27	8	34
210.0	0	37	5	31
211.0	0	47	4	28
212.0	0	35	4	31
213.0	0	43	2	32
214.0	0	49	6	30
215.0	0	43	2	29
216.0	0	37	7	30
217.0	0	32	3	27
218.0	0	32	2	22
219.0	0	47	4	29
220.0	0	37	5	23
221.0	0	40	3	38
222.0	0	39	4	23
223.0	0	42	5	28
224.0	0	33	3	38
225.0	0	38	6	26
226.0	0	39	1	24
227.0	0	41	4	27
228.0	0	32	7	16
229.0	0	32	3	32
230.0	0	25	1	29
231.0	0	37	2	14
232.0	0	25	5	26
233.0	0	25	6	15
234.0	0	21	2	37
235.0	0	33	9	26
236.0	0	27	5	20
237.0	0	27	3	21
238.0	0	25	3	21
239.0	0	32	2	34
240.0	0	31	1	20
241.0	0	27	4	24
242.0	0	28	2	26
243.0	0	27	2	18
244.0	0	28	5	17
245.0	0	23	4	15
246.0	0	14	0	20
247.0	0	23	2	18
248.0	0	34	5	13
249.0	0	30	3	10
250.0	0	30	3	27
251.0	0	26	4	7
252.0	0	24	5	21
253.0	0	19	2	14
254.0	0	26	5	17
255.0	0	21	4	17
256.0	0	26	3	25
257.0	0	25	1	10
258.0	0	17	4	18
259.0	0	21	4	18
260.0	0	22	2	19
261.0	0	31	3	18
262.0	0	23	2	17
263.0	0	31	4	14
264.0	0	16	1	21
265.0	0	15	2	12
266.0	0	20	3	20
267.0	0	20	2	23
268.0	0	23	4	15
269.0	0	29	2	23
270.0	0	31	0	22
271.0	0	15	2	17
272.0	0	17	4	15
273.0	0	18	1	18
274.0	0	22	3	19
275.0	0	17	4	16
276.0	0	23	2	11
277.0	0	22	1	18
278.0	0	21	3	16
279.0	0	26	3	19
280.0	0	24	2	10
281.0	0	22	1	14
282.0	0	22	4	21
283.0	0	26	3	24
284.0	0	24	2	14
285.0	0	14	1	15
286.0	0	20	0	14
287.0	0	15	2	19
288.0	0	27	1	11
289.0	0	22	1	18
290.0	0	19	2	10
291.0	0	19	4	12
292.0	0	26	2	14
293.0	0	16	0	12
294.0	0	22	2	17
295.0	0	15	3	17
296.0	0	18	2	17
297.0	0	16	0	13
298.0	0	18	1	19
299.0	0	14	1	11
300.0	0	16	0	23
301.0	0	28	1	19
302.0	0	21	2	16
303.0	0	20	4	8
304.0	0	14	2	13
305.0	0	29	2	14
306.0	0	10	3	16
307.0	0	16	3	12
308.0	0	18	3	6
309.0	0	16	1	9
310.0	0	16	2	6
311.0	0	25	1	25
312.0	0	7	2	19
313.0	0	24	2	14
314.0	0	12	1	17
315.0	0	13	1	5
316.0	0	11	0	12
317.0	0	14	2	10
318.0	0	20	1	9
319.0	0	18	3	11
320.0	0	15	0	13
321.0	0	18	1	11
322.0	0	15	1	13
323.0	0	17	1	8
324.0	0	18	1	13
325.0	0	8	2	13
326.0	0	21	2	4
327.0	0	16	0	16
328.0	0	13	0	18
329.0	0	20	4	10
330.0	0	10	0	9
331.0	0	17	0	9
332.0	0	20	4	9
333.0	0	12	2	11
334.0	0	6	4	6
335.0	0	17	1	15
336.0	0	14	1	14
337.0	0	13	1	8
338.0	0	12	0	6
339.0	0	15	1	9
340.0	0	14	0	15
341.0	0	13	1	10
342.0	0	11	0	16
343.0	0	13	1	14
344.0	0	11	1	13
345.0	0	13	4	10
346.0	0	11	0	6
347.0	0	15	0	9
348.0	0	14	0	12
349.0	0	17	1	6
350.0	0	6	2	5
351.0	0	15	3	4
352.0	0	7	0	6
353.0	0	12	3	6
354.0	0	5	3	4
355.0	0	13	0	12
356.0	0	17	1	9
357.0	0	9	0	9
358.0	0	17	2	14
359.0	0	10	0	16
360.0	0	11	1	8
361.0	0	9	1	7
362.0	0	11	0	10
363.0	0	7	0	10
364.0	0	16	1	7
365.0	0	14	1	6
366.0	0	13	0	9
367.0	0	7	2	11
368.0	0	11	1	6
369.0	0	10	0	10
370.0	0	10	2	12
371.0	0	11	0	7
372.0	0	8	0	6
373.0	0	18	0	9
374.0	0	11	2	12
375.0	0	10	0	4
376.0	0	10	0	6
377.0	0	5	1	2
378.0	0	11	1	9
379.0	0	9	0	11
380.0	0	7	3	6
381.0	0	15	1	6
382.0	0	10	1	7
383.0	0	12	1	8
384.0	0	10	2	8
385.0	0	9	1	10
386.0	0	4	0	10
387.0	0	14	0	4
388.0	0	10	2	6
389.0	0	12	0	5
390.0	0	12	1	10
391.0	0	18	1	9
392.0	0	8	0	6
393.0	0	12	4	9
394.0	0	9	0	5
395.0	0	9	1	6
396.0	0	8	1	7
397.0	0	5	0	8
398.0	0	5	1	4
399.0	0	10	2	8
400.0	0	6	0	4
401.0	0	10	2	14
402.0	0	11	0	7
403.0	0	10	0	3
404.0	0	13	1	12
405.0	0	12	1	3
406.0	0	7	0	7
407.0	0	10	1	4
408.0	0	8	0	8
409.0	0	5	0	2
410.0	0	5	2	7
411.0	0	9	1	8
412.0	0	8	0	5
413.0	0	7	1	8
414.0	0	9	0	4
415.0	0	10	1	5
416.0	0	10	0	4
417.0	0	11	2	7
418.0	0	9	2	5
419.0	0	11	2	2
420.0	0	3	0	5
421.0	0	12	0	6
422.0	0	5	1	5
423.0	0	10	0	4
424.0	0	4	1	5
425.0	0	7	1	3
426.0	0	9	0	2
427.0	0	8	0	5
428.0	0	12	1	8
429.0	0	6	1	8
430.0	0	6	0	3
431.0	0	8	0	1
432.0	0	5	0	4
433.0	0	11	1	7
434.0	0	5	1	6
435.0	0	7	1	5
436.0	0	10	0	4
437.0	0	6	1	6
438.0	0	12	0	5
439.0	0	6	0	5
440.0	0	8	0	6
441.0	0	2	0	10
442.0	0	12	0	2
443.0	0	9	4	7
444.0	0	6	0	2
445.0	0	8	0	5
446.0	0	4	2	4
447.0	0	6	0	3
448.0	0	7	0	4
449.0	0	6	2	2
450.0	0	4	0	4
451.0	0	5	0	5
452.0	0	4	0	5
453.0	0	10	0	10
454.0	0	8	0	1
455.0	0	8	1	3
456.0	0	7	1	4
457.0	0	7	0	4
458.0	0	6	0	2
459.0	0	3	0	6
460.0	0	8	0	1
461.0	0	7	1	9
462.0	0	5	1	7
463.0	0	3	0	8
464.0	0	7	1	3
465.0	0	5	0	3
466.0	0	6	2	4
467.0	0	7	0	5
468.0	0	4	0	5
469.0	0	6	0	7
470.0	0	3	0	5
471.0	0	5	0	2
472.0	0	5	1	6
473.0	0	2	0	8
474.0	0	4	0	5
475.0	0	6	1	7
476.0	0	3	3	3
477.0	0	3	0	1
478.0	0	4	1	4
479.0	0	2	0	5
480.0	0	2	2	5
481.0	0	10	0	4
482.0	0	2	1	3
483.0	0	10	1	4
484.0	0	6	0	6
485.0	0	10	0	2
486.0	0	2	0	3
487.0	0	6	0	3
488.0	0	4	1	3
489.0	0	2	1	6
490.0	0	10	0	5
491.0	0	4	1	6
492.0	0	9	0	4
493.0	0	5	1	6
494.0	0	4	0	2
495.0	0	4	0	4
496.0	0	6	0	3
497.0	0	4	0	5
498.0	0	4	0	2
499.0	0	3	0	1
500.0	0	1	0	1
501.0	0	6	1	4
502.0	0	5	0	1
503.0	0	4	0	8
504.0	0	6	0	5
505.0	0	1	0	2
506.0	0	6	0	2
507.0	0	1	0	1
508.0	0	3	0	7
509.0	0	5	0	9
510.0	0	8	2	1
511.0	0	1	0	1
512.0	0	5	0	5
513.0	0	6	1	3
514.0	0	7	0	2
515.0	0	4	2	2
516.0	0	4	1	2
517.0	0	5	1	2
518.0	0	4	1	2
519.0	0	4	1	2
520.0	0	3	0	2
521.0	0	5	1	4
522.0	0	8	1	1
523.0	0	7	0	1
524.0	0	3	1	5
525.0	0	4	0	4
526.0	0	5	0	5
527.0	0	4	1	1
528.0	0	3	0	2
529.0	0	3	0	3
530.0	0	3	0	4
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