## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-69-TP3.bam --OUTPUT POR-69-TP3.md.bam --METRICS_FILE POR-69-TP3.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 18:18:40 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	3935	18042023	12329735	0	3825	14667095	3519801	0.812958	3424211

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.009379	1928466	0	2336564
2.0	1.014576	587736	450212	450859
3.0	1.014603	242020	172654	144064
4.0	1.014603	126964	87419	77078
5.0	1.014603	79539	50458	51806
6.0	1.014603	54755	31444	38232
7.0	1.014603	40686	21320	29724
8.0	1.014603	31549	15084	23917
9.0	1.014603	25331	11343	19449
10.0	1.014603	21051	8669	16641
11.0	1.014603	17830	6945	14010
12.0	1.014603	15329	5721	12083
13.0	1.014603	13280	4587	10712
14.0	1.014603	11947	3989	9312
15.0	1.014603	10498	3333	8314
16.0	1.014603	9168	2837	7286
17.0	1.014603	8388	2404	6670
18.0	1.014603	7682	2185	5940
19.0	1.014603	6897	1972	5551
20.0	1.014603	6353	1731	5023
21.0	1.014603	5812	1620	4552
22.0	1.014603	5333	1386	4169
23.0	1.014603	4815	1250	3868
24.0	1.014603	4495	1121	3526
25.0	1.014603	4118	1042	3338
26.0	1.014603	3987	1021	3230
27.0	1.014603	3644	884	2761
28.0	1.014603	3432	780	2752
29.0	1.014603	3247	724	2549
30.0	1.014603	3035	665	2331
31.0	1.014603	2862	613	2252
32.0	1.014603	2684	629	2125
33.0	1.014603	2606	562	2048
34.0	1.014603	2329	518	1806
35.0	1.014603	2207	480	1770
36.0	1.014603	2173	448	1700
37.0	1.014603	2008	435	1567
38.0	1.014603	1981	417	1554
39.0	1.014603	1875	387	1473
40.0	1.014603	1773	372	1394
41.0	1.014603	1624	321	1326
42.0	1.014603	1725	302	1270
43.0	1.014603	1526	271	1282
44.0	1.014603	1430	287	1162
45.0	1.014603	1462	279	1180
46.0	1.014603	1352	251	1088
47.0	1.014603	1287	252	1018
48.0	1.014603	1252	214	1044
49.0	1.014603	1240	196	970
50.0	1.014603	1171	186	910
51.0	1.014603	1111	170	938
52.0	1.014603	1055	195	857
53.0	1.014603	1082	188	828
54.0	1.014603	961	164	824
55.0	1.014603	947	163	778
56.0	1.014603	875	164	672
57.0	1.014603	949	135	680
58.0	1.014603	863	121	691
59.0	1.014603	821	148	623
60.0	1.014603	807	142	590
61.0	1.014603	780	142	639
62.0	1.014603	766	119	566
63.0	1.014603	757	132	582
64.0	1.014603	712	109	568
65.0	1.014603	682	97	564
66.0	1.014603	631	91	532
67.0	1.014603	678	95	519
68.0	1.014603	593	91	494
69.0	1.014603	596	94	466
70.0	1.014603	574	97	506
71.0	1.014603	603	72	461
72.0	1.014603	589	76	437
73.0	1.014603	509	72	455
74.0	1.014603	560	73	398
75.0	1.014603	497	72	435
76.0	1.014603	549	65	367
77.0	1.014603	487	84	389
78.0	1.014603	468	75	389
79.0	1.014603	472	75	355
80.0	1.014603	500	59	347
81.0	1.014603	452	55	334
82.0	1.014603	480	54	366
83.0	1.014603	454	59	305
84.0	1.014603	365	59	335
85.0	1.014603	388	62	320
86.0	1.014603	419	54	294
87.0	1.014603	378	52	282
88.0	1.014603	377	42	288
89.0	1.014603	384	46	301
90.0	1.014603	370	45	289
91.0	1.014603	348	41	267
92.0	1.014603	359	37	280
93.0	1.014603	308	43	270
94.0	1.014603	319	34	237
95.0	1.014603	314	37	215
96.0	1.014603	340	38	257
97.0	1.014603	312	28	250
98.0	1.014603	317	32	239
99.0	1.014603	290	42	214
100.0	1.014603	284	28	229
101.0	0	300	41	220
102.0	0	276	38	213
103.0	0	253	28	218
104.0	0	288	37	194
105.0	0	257	33	191
106.0	0	260	32	218
107.0	0	275	29	186
108.0	0	259	41	184
109.0	0	236	29	161
110.0	0	230	23	170
111.0	0	242	25	190
112.0	0	213	31	189
113.0	0	226	30	157
114.0	0	214	28	152
115.0	0	228	17	154
116.0	0	199	26	159
117.0	0	201	29	155
118.0	0	206	14	147
119.0	0	186	18	156
120.0	0	175	24	118
121.0	0	168	19	158
122.0	0	180	14	156
123.0	0	179	20	150
124.0	0	170	17	146
125.0	0	143	13	145
126.0	0	193	21	133
127.0	0	180	14	131
128.0	0	162	12	132
129.0	0	182	22	130
130.0	0	176	12	123
131.0	0	174	20	111
132.0	0	136	13	135
133.0	0	167	10	117
134.0	0	150	12	130
135.0	0	132	17	113
136.0	0	139	13	110
137.0	0	154	16	111
138.0	0	128	12	109
139.0	0	142	15	102
140.0	0	153	18	107
141.0	0	131	21	107
142.0	0	132	10	89
143.0	0	126	11	80
144.0	0	118	17	97
145.0	0	132	13	94
146.0	0	146	16	118
147.0	0	123	19	85
148.0	0	101	5	106
149.0	0	112	17	112
150.0	0	117	7	83
151.0	0	102	15	78
152.0	0	115	22	73
153.0	0	86	16	100
154.0	0	105	9	82
155.0	0	113	7	70
156.0	0	111	11	101
157.0	0	112	11	84
158.0	0	118	16	87
159.0	0	111	14	87
160.0	0	115	7	81
161.0	0	95	13	82
162.0	0	106	8	74
163.0	0	106	9	73
164.0	0	93	8	77
165.0	0	99	17	78
166.0	0	92	6	61
167.0	0	95	16	83
168.0	0	109	15	100
169.0	0	77	9	72
170.0	0	84	7	69
171.0	0	103	7	63
172.0	0	100	13	67
173.0	0	96	10	60
174.0	0	75	5	53
175.0	0	80	6	51
176.0	0	83	9	51
177.0	0	75	7	56
178.0	0	88	4	63
179.0	0	83	6	50
180.0	0	57	9	50
181.0	0	75	6	62
182.0	0	77	7	57
183.0	0	69	6	49
184.0	0	74	8	51
185.0	0	74	5	57
186.0	0	92	12	61
187.0	0	77	9	48
188.0	0	62	15	63
189.0	0	65	8	47
190.0	0	71	7	68
191.0	0	59	10	60
192.0	0	58	6	51
193.0	0	52	5	43
194.0	0	51	5	49
195.0	0	56	7	55
196.0	0	67	5	45
197.0	0	59	7	52
198.0	0	57	4	50
199.0	0	70	7	51
200.0	0	55	6	44
201.0	0	65	4	45
202.0	0	51	6	42
203.0	0	63	7	51
204.0	0	63	10	36
205.0	0	62	5	54
206.0	0	71	2	54
207.0	0	62	4	43
208.0	0	54	4	41
209.0	0	62	7	48
210.0	0	61	2	38
211.0	0	55	6	40
212.0	0	50	4	30
213.0	0	59	5	46
214.0	0	59	8	37
215.0	0	47	3	41
216.0	0	51	7	44
217.0	0	53	4	39
218.0	0	64	3	40
219.0	0	56	4	45
220.0	0	52	6	41
221.0	0	41	8	31
222.0	0	43	3	49
223.0	0	37	3	44
224.0	0	50	6	46
225.0	0	43	3	38
226.0	0	55	4	38
227.0	0	53	6	38
228.0	0	46	6	28
229.0	0	48	2	33
230.0	0	39	1	40
231.0	0	37	1	31
232.0	0	32	5	38
233.0	0	44	4	32
234.0	0	52	1	28
235.0	0	42	5	24
236.0	0	53	3	34
237.0	0	39	8	14
238.0	0	43	4	34
239.0	0	41	3	42
240.0	0	42	6	45
241.0	0	33	5	38
242.0	0	34	0	22
243.0	0	51	1	30
244.0	0	49	3	32
245.0	0	48	3	45
246.0	0	45	5	27
247.0	0	38	1	42
248.0	0	43	4	30
249.0	0	44	1	27
250.0	0	48	2	32
251.0	0	30	1	36
252.0	0	41	2	30
253.0	0	39	4	33
254.0	0	25	3	36
255.0	0	35	4	21
256.0	0	39	3	16
257.0	0	34	0	36
258.0	0	32	1	36
259.0	0	30	2	24
260.0	0	36	5	19
261.0	0	32	3	30
262.0	0	30	5	17
263.0	0	27	5	15
264.0	0	30	8	27
265.0	0	29	4	22
266.0	0	34	3	30
267.0	0	37	5	26
268.0	0	32	1	29
269.0	0	42	3	18
270.0	0	31	3	25
271.0	0	22	2	29
272.0	0	27	1	27
273.0	0	30	4	19
274.0	0	33	2	19
275.0	0	25	4	26
276.0	0	25	0	28
277.0	0	30	0	38
278.0	0	34	2	19
279.0	0	25	1	24
280.0	0	33	2	23
281.0	0	20	5	31
282.0	0	30	1	30
283.0	0	27	2	25
284.0	0	30	2	25
285.0	0	34	2	13
286.0	0	22	1	20
287.0	0	29	4	30
288.0	0	28	1	15
289.0	0	27	0	25
290.0	0	34	2	27
291.0	0	21	1	31
292.0	0	24	4	22
293.0	0	30	1	30
294.0	0	20	1	19
295.0	0	26	0	22
296.0	0	31	6	13
297.0	0	24	2	20
298.0	0	42	1	14
299.0	0	32	5	13
300.0	0	25	2	22
301.0	0	20	4	19
302.0	0	20	0	16
303.0	0	21	3	14
304.0	0	26	0	22
305.0	0	25	0	15
306.0	0	23	3	22
307.0	0	27	1	18
308.0	0	18	2	19
309.0	0	34	2	16
310.0	0	19	4	19
311.0	0	18	1	18
312.0	0	20	2	26
313.0	0	24	1	15
314.0	0	21	3	7
315.0	0	21	1	20
316.0	0	27	3	12
317.0	0	30	1	25
318.0	0	32	1	16
319.0	0	17	0	16
320.0	0	19	2	16
321.0	0	26	3	12
322.0	0	14	2	13
323.0	0	20	3	18
324.0	0	15	2	15
325.0	0	18	1	21
326.0	0	12	0	12
327.0	0	23	2	23
328.0	0	23	1	16
329.0	0	19	2	13
330.0	0	17	1	17
331.0	0	28	4	15
332.0	0	16	2	14
333.0	0	20	1	15
334.0	0	12	2	14
335.0	0	11	1	10
336.0	0	21	1	11
337.0	0	20	1	12
338.0	0	17	1	13
339.0	0	22	1	12
340.0	0	9	2	11
341.0	0	17	4	11
342.0	0	21	0	16
343.0	0	24	0	11
344.0	0	16	1	16
345.0	0	19	1	13
346.0	0	13	1	15
347.0	0	15	1	8
348.0	0	15	0	15
349.0	0	14	0	14
350.0	0	15	1	14
351.0	0	12	2	11
352.0	0	18	0	10
353.0	0	20	1	14
354.0	0	20	1	7
355.0	0	14	0	16
356.0	0	13	0	14
357.0	0	13	1	9
358.0	0	16	1	9
359.0	0	17	0	13
360.0	0	18	0	11
361.0	0	16	3	18
362.0	0	20	0	16
363.0	0	19	0	15
364.0	0	14	3	7
365.0	0	17	0	15
366.0	0	16	2	9
367.0	0	11	2	12
368.0	0	17	2	11
369.0	0	12	0	14
370.0	0	14	1	13
371.0	0	14	1	12
372.0	0	16	2	9
373.0	0	10	0	12
374.0	0	14	1	9
375.0	0	16	1	8
376.0	0	7	0	16
377.0	0	14	1	19
378.0	0	12	1	12
379.0	0	12	1	10
380.0	0	14	0	9
381.0	0	23	1	17
382.0	0	8	1	13
383.0	0	14	1	17
384.0	0	19	1	9
385.0	0	13	2	7
386.0	0	10	1	7
387.0	0	10	3	15
388.0	0	12	1	14
389.0	0	12	0	11
390.0	0	9	1	6
391.0	0	16	1	7
392.0	0	11	0	8
393.0	0	15	1	9
394.0	0	10	0	14
395.0	0	11	0	8
396.0	0	18	2	8
397.0	0	16	0	6
398.0	0	10	1	9
399.0	0	13	2	17
400.0	0	8	0	7
401.0	0	9	3	9
402.0	0	15	1	11
403.0	0	14	0	11
404.0	0	8	4	12
405.0	0	12	0	8
406.0	0	10	0	8
407.0	0	11	0	14
408.0	0	17	0	8
409.0	0	11	1	2
410.0	0	11	0	8
411.0	0	15	3	13
412.0	0	11	0	3
413.0	0	9	1	6
414.0	0	8	1	8
415.0	0	13	2	11
416.0	0	15	0	12
417.0	0	13	0	6
418.0	0	17	1	9
419.0	0	9	2	10
420.0	0	13	0	13
421.0	0	10	1	7
422.0	0	14	2	11
423.0	0	10	0	17
424.0	0	6	2	15
425.0	0	14	2	11
426.0	0	12	1	10
427.0	0	12	0	10
428.0	0	9	0	14
429.0	0	15	1	10
430.0	0	9	0	10
431.0	0	9	2	7
432.0	0	14	0	9
433.0	0	14	1	8
434.0	0	16	0	7
435.0	0	10	1	10
436.0	0	12	1	5
437.0	0	11	1	7
438.0	0	10	1	9
439.0	0	14	2	7
440.0	0	11	1	9
441.0	0	12	0	13
442.0	0	5	0	8
443.0	0	12	1	6
444.0	0	6	1	8
445.0	0	8	2	5
446.0	0	11	0	12
447.0	0	16	2	11
448.0	0	14	1	6
449.0	0	13	2	12
450.0	0	16	1	13
451.0	0	7	0	2
452.0	0	9	0	6
453.0	0	15	2	12
454.0	0	4	3	7
455.0	0	10	0	6
456.0	0	11	0	10
457.0	0	5	1	7
458.0	0	9	0	5
459.0	0	7	2	4
460.0	0	12	0	9
461.0	0	4	0	13
462.0	0	13	0	8
463.0	0	10	2	5
464.0	0	10	0	5
465.0	0	9	1	1
466.0	0	9	0	6
467.0	0	7	0	6
468.0	0	4	0	6
469.0	0	9	0	5
470.0	0	10	0	7
471.0	0	6	0	9
472.0	0	2	1	7
473.0	0	12	1	5
474.0	0	8	1	8
475.0	0	8	1	5
476.0	0	11	0	9
477.0	0	9	1	4
478.0	0	10	0	8
479.0	0	7	0	9
480.0	0	10	2	1
481.0	0	11	0	6
482.0	0	9	0	10
483.0	0	12	0	8
484.0	0	11	1	6
485.0	0	12	5	2
486.0	0	8	1	1
487.0	0	7	0	3
488.0	0	10	0	7
489.0	0	11	0	4
490.0	0	6	0	7
491.0	0	4	0	7
492.0	0	7	1	2
493.0	0	3	0	4
494.0	0	11	1	5
495.0	0	9	0	3
496.0	0	9	0	4
497.0	0	11	2	8
498.0	0	3	1	4
499.0	0	11	1	7
500.0	0	5	0	6
501.0	0	8	0	3
502.0	0	5	0	7
503.0	0	8	0	14
504.0	0	7	0	3
505.0	0	6	0	8
506.0	0	8	1	3
507.0	0	8	0	6
508.0	0	9	0	6
509.0	0	9	2	4
510.0	0	3	0	5
511.0	0	8	0	6
512.0	0	8	0	8
513.0	0	9	1	7
514.0	0	12	0	2
515.0	0	9	2	8
516.0	0	9	0	4
517.0	0	5	1	7
518.0	0	9	1	10
519.0	0	9	3	8
520.0	0	7	1	1
521.0	0	5	2	4
522.0	0	10	0	3
523.0	0	7	0	5
524.0	0	5	0	6
525.0	0	6	0	9
526.0	0	9	0	5
527.0	0	8	1	4
528.0	0	8	1	3
529.0	0	5	0	4
530.0	0	5	0	11
531.0	0	8	1	2
532.0	0	6	0	7
533.0	0	7	1	5
534.0	0	8	0	5
535.0	0	4	0	8
536.0	0	8	1	1
537.0	0	2	0	6
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