## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-69-TP2.bam --OUTPUT POR-69-TP2.md.bam --METRICS_FILE POR-69-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 18:18:37 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	4283	17507513	10455569	0	4161	13622891	3927615	0.778141	4022063

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.022056	1985354	0	2514524
2.0	1.035209	815661	569509	722003
3.0	1.035379	368664	231171	220640
4.0	1.035381	188735	117654	92195
5.0	1.035381	109550	66462	53331
6.0	1.035381	70073	39958	36783
7.0	1.035381	47833	25491	27601
8.0	1.035381	35316	17158	21926
9.0	1.035381	26926	12287	18085
10.0	1.035381	21639	9196	15221
11.0	1.035381	17761	7086	12909
12.0	1.035381	14924	5682	10911
13.0	1.035381	12813	4653	9609
14.0	1.035381	11071	3827	8479
15.0	1.035381	9808	3304	7554
16.0	1.035381	8834	2812	6570
17.0	1.035381	7768	2383	5888
18.0	1.035381	6912	2090	5307
19.0	1.035381	6173	1883	4822
20.0	1.035381	5589	1720	4429
21.0	1.035381	5235	1476	4038
22.0	1.035381	4796	1300	3751
23.0	1.035381	4548	1174	3460
24.0	1.035381	4237	1059	3123
25.0	1.035381	3867	961	2882
26.0	1.035381	3542	980	2675
27.0	1.035381	3332	782	2626
28.0	1.035381	3026	752	2309
29.0	1.035381	2913	753	2284
30.0	1.035381	2832	651	2193
31.0	1.035381	2578	604	2066
32.0	1.035381	2397	560	1825
33.0	1.035381	2291	548	1729
34.0	1.035381	2127	477	1560
35.0	1.035381	1973	437	1551
36.0	1.035381	1825	396	1446
37.0	1.035381	1832	384	1416
38.0	1.035381	1768	321	1345
39.0	1.035381	1619	373	1239
40.0	1.035381	1532	339	1244
41.0	1.035381	1445	306	1146
42.0	1.035381	1438	288	1046
43.0	1.035381	1453	277	982
44.0	1.035381	1375	258	969
45.0	1.035381	1204	241	886
46.0	1.035381	1203	234	897
47.0	1.035381	1125	226	847
48.0	1.035381	1073	197	845
49.0	1.035381	1075	219	782
50.0	1.035381	1017	178	803
51.0	1.035381	980	177	719
52.0	1.035381	897	176	715
53.0	1.035381	858	183	648
54.0	1.035381	833	159	595
55.0	1.035381	833	139	617
56.0	1.035381	796	141	592
57.0	1.035381	774	153	609
58.0	1.035381	803	133	586
59.0	1.035381	756	121	554
60.0	1.035381	675	119	536
61.0	1.035381	684	105	498
62.0	1.035381	691	132	506
63.0	1.035381	615	117	501
64.0	1.035381	625	107	450
65.0	1.035381	570	88	446
66.0	1.035381	557	117	420
67.0	1.035381	549	94	430
68.0	1.035381	540	105	463
69.0	1.035381	516	86	360
70.0	1.035381	491	95	367
71.0	1.035381	494	88	364
72.0	1.035381	509	73	351
73.0	1.035381	449	79	375
74.0	1.035381	429	82	363
75.0	1.035381	469	77	340
76.0	1.035381	416	72	332
77.0	1.035381	405	60	315
78.0	1.035381	387	52	334
79.0	1.035381	397	82	305
80.0	1.035381	360	67	300
81.0	1.035381	358	54	324
82.0	1.035381	401	62	255
83.0	1.035381	372	54	277
84.0	1.035381	364	66	253
85.0	1.035381	354	53	276
86.0	1.035381	321	41	259
87.0	1.035381	301	49	248
88.0	1.035381	299	46	244
89.0	1.035381	295	53	226
90.0	1.035381	323	42	227
91.0	1.035381	297	37	238
92.0	1.035381	320	36	221
93.0	1.035381	292	32	224
94.0	1.035381	245	49	201
95.0	1.035381	265	31	214
96.0	1.035381	258	31	183
97.0	1.035381	267	33	222
98.0	1.035381	262	28	179
99.0	1.035381	265	32	193
100.0	1.035381	260	29	172
101.0	0	251	36	189
102.0	0	246	23	185
103.0	0	245	25	165
104.0	0	265	36	195
105.0	0	224	31	146
106.0	0	203	21	174
107.0	0	198	29	138
108.0	0	220	37	160
109.0	0	190	20	120
110.0	0	190	23	146
111.0	0	164	27	124
112.0	0	206	26	134
113.0	0	171	38	120
114.0	0	162	32	134
115.0	0	175	23	137
116.0	0	165	24	139
117.0	0	184	26	127
118.0	0	164	20	114
119.0	0	202	24	99
120.0	0	152	23	109
121.0	0	172	10	116
122.0	0	160	21	107
123.0	0	120	11	116
124.0	0	171	22	117
125.0	0	132	10	109
126.0	0	145	24	87
127.0	0	131	14	97
128.0	0	141	18	99
129.0	0	134	18	111
130.0	0	126	17	78
131.0	0	128	22	105
132.0	0	101	13	84
133.0	0	140	15	108
134.0	0	135	11	93
135.0	0	141	16	86
136.0	0	126	15	93
137.0	0	121	18	94
138.0	0	97	21	85
139.0	0	116	22	97
140.0	0	89	14	95
141.0	0	103	17	102
142.0	0	130	9	78
143.0	0	103	22	64
144.0	0	118	8	95
145.0	0	114	16	85
146.0	0	108	17	66
147.0	0	93	12	77
148.0	0	94	11	76
149.0	0	133	17	75
150.0	0	91	11	67
151.0	0	85	5	76
152.0	0	106	8	75
153.0	0	105	12	63
154.0	0	78	12	68
155.0	0	97	8	67
156.0	0	83	5	54
157.0	0	94	10	69
158.0	0	92	5	69
159.0	0	94	7	50
160.0	0	90	12	69
161.0	0	78	9	78
162.0	0	90	9	61
163.0	0	62	8	53
164.0	0	81	6	64
165.0	0	85	9	45
166.0	0	94	11	51
167.0	0	76	10	60
168.0	0	69	13	62
169.0	0	68	7	53
170.0	0	74	12	35
171.0	0	68	6	53
172.0	0	77	6	52
173.0	0	77	7	63
174.0	0	58	11	42
175.0	0	66	5	55
176.0	0	76	8	52
177.0	0	66	5	45
178.0	0	65	7	45
179.0	0	64	10	54
180.0	0	63	9	45
181.0	0	65	12	57
182.0	0	58	5	56
183.0	0	67	5	46
184.0	0	55	6	54
185.0	0	44	6	50
186.0	0	60	4	48
187.0	0	55	14	51
188.0	0	61	4	51
189.0	0	43	9	48
190.0	0	53	7	31
191.0	0	69	9	39
192.0	0	53	5	46
193.0	0	67	4	48
194.0	0	51	11	47
195.0	0	51	6	50
196.0	0	54	7	33
197.0	0	66	4	37
198.0	0	51	3	41
199.0	0	59	1	35
200.0	0	50	2	44
201.0	0	51	7	41
202.0	0	53	3	31
203.0	0	53	9	41
204.0	0	52	5	32
205.0	0	48	5	34
206.0	0	45	2	38
207.0	0	49	5	30
208.0	0	41	2	22
209.0	0	52	6	36
210.0	0	62	5	27
211.0	0	44	4	38
212.0	0	49	6	27
213.0	0	52	1	19
214.0	0	47	7	27
215.0	0	46	3	33
216.0	0	40	4	35
217.0	0	47	8	30
218.0	0	36	5	25
219.0	0	39	6	32
220.0	0	36	3	23
221.0	0	40	7	26
222.0	0	38	6	31
223.0	0	33	3	30
224.0	0	43	3	31
225.0	0	37	2	25
226.0	0	36	2	25
227.0	0	41	3	34
228.0	0	38	3	27
229.0	0	39	3	28
230.0	0	39	3	25
231.0	0	31	5	31
232.0	0	41	3	23
233.0	0	33	1	13
234.0	0	28	8	33
235.0	0	32	4	16
236.0	0	27	3	18
237.0	0	40	1	27
238.0	0	21	3	33
239.0	0	31	2	24
240.0	0	18	7	22
241.0	0	34	3	24
242.0	0	30	6	26
243.0	0	49	1	21
244.0	0	33	2	27
245.0	0	23	2	20
246.0	0	40	1	28
247.0	0	24	1	23
248.0	0	36	6	23
249.0	0	24	3	18
250.0	0	42	2	20
251.0	0	21	4	25
252.0	0	35	3	27
253.0	0	26	4	21
254.0	0	25	5	22
255.0	0	28	3	25
256.0	0	18	4	19
257.0	0	30	3	26
258.0	0	29	1	19
259.0	0	23	2	14
260.0	0	21	2	22
261.0	0	23	6	18
262.0	0	25	1	17
263.0	0	38	2	22
264.0	0	23	2	25
265.0	0	30	3	23
266.0	0	25	1	20
267.0	0	20	5	20
268.0	0	19	2	23
269.0	0	25	3	14
270.0	0	27	0	19
271.0	0	17	1	18
272.0	0	28	3	18
273.0	0	24	1	14
274.0	0	16	4	23
275.0	0	23	5	16
276.0	0	22	5	20
277.0	0	18	6	8
278.0	0	23	2	17
279.0	0	37	1	8
280.0	0	34	1	19
281.0	0	23	2	21
282.0	0	18	3	19
283.0	0	22	3	21
284.0	0	30	2	20
285.0	0	20	1	17
286.0	0	23	1	9
287.0	0	13	3	16
288.0	0	21	5	23
289.0	0	15	0	22
290.0	0	24	2	12
291.0	0	26	2	16
292.0	0	26	3	7
293.0	0	16	2	12
294.0	0	17	1	10
295.0	0	23	0	8
296.0	0	18	1	12
297.0	0	25	0	16
298.0	0	28	4	23
299.0	0	27	0	22
300.0	0	19	1	17
301.0	0	17	2	22
302.0	0	18	1	11
303.0	0	14	1	9
304.0	0	19	4	11
305.0	0	18	2	15
306.0	0	22	1	15
307.0	0	21	1	9
308.0	0	16	2	9
309.0	0	22	0	16
310.0	0	21	3	11
311.0	0	14	1	10
312.0	0	25	3	13
313.0	0	27	0	15
314.0	0	14	4	16
315.0	0	16	1	11
316.0	0	23	4	11
317.0	0	14	1	13
318.0	0	16	1	15
319.0	0	14	0	20
320.0	0	16	0	18
321.0	0	18	2	7
322.0	0	21	1	14
323.0	0	10	3	15
324.0	0	18	2	11
325.0	0	13	2	10
326.0	0	22	1	9
327.0	0	13	0	12
328.0	0	23	1	14
329.0	0	16	1	10
330.0	0	19	2	13
331.0	0	21	0	16
332.0	0	18	0	3
333.0	0	15	0	7
334.0	0	5	2	13
335.0	0	18	1	14
336.0	0	12	2	13
337.0	0	14	0	22
338.0	0	13	5	11
339.0	0	18	1	12
340.0	0	17	2	8
341.0	0	12	1	8
342.0	0	15	4	13
343.0	0	8	1	9
344.0	0	9	2	13
345.0	0	20	1	8
346.0	0	17	1	13
347.0	0	10	0	15
348.0	0	16	1	12
349.0	0	16	0	15
350.0	0	10	2	13
351.0	0	15	0	5
352.0	0	6	0	6
353.0	0	15	2	5
354.0	0	15	2	15
355.0	0	10	0	9
356.0	0	16	3	6
357.0	0	17	0	9
358.0	0	13	3	14
359.0	0	16	1	14
360.0	0	14	0	12
361.0	0	12	1	7
362.0	0	10	1	13
363.0	0	9	0	7
364.0	0	9	4	7
365.0	0	10	1	7
366.0	0	10	1	9
367.0	0	12	3	8
368.0	0	19	0	15
369.0	0	10	0	6
370.0	0	10	0	8
371.0	0	14	1	13
372.0	0	16	1	7
373.0	0	12	1	6
374.0	0	12	3	6
375.0	0	10	2	6
376.0	0	11	2	4
377.0	0	14	1	7
378.0	0	13	0	5
379.0	0	5	1	9
380.0	0	12	1	8
381.0	0	11	0	7
382.0	0	11	0	6
383.0	0	13	0	5
384.0	0	11	3	8
385.0	0	15	0	6
386.0	0	9	1	12
387.0	0	4	0	10
388.0	0	10	1	4
389.0	0	12	0	9
390.0	0	7	0	7
391.0	0	4	0	9
392.0	0	8	1	9
393.0	0	5	1	9
394.0	0	11	2	8
395.0	0	11	1	7
396.0	0	10	1	5
397.0	0	7	1	6
398.0	0	7	1	10
399.0	0	14	1	9
400.0	0	8	1	8
401.0	0	11	0	10
402.0	0	7	0	9
403.0	0	13	4	10
404.0	0	6	2	9
405.0	0	9	0	7
406.0	0	10	0	4
407.0	0	11	0	11
408.0	0	14	1	5
409.0	0	6	0	7
410.0	0	4	2	8
411.0	0	6	0	12
412.0	0	12	0	8
413.0	0	13	1	8
414.0	0	4	0	9
415.0	0	4	4	12
416.0	0	11	0	7
417.0	0	6	1	4
418.0	0	10	2	3
419.0	0	8	0	1
420.0	0	6	0	6
421.0	0	7	0	8
422.0	0	13	1	5
423.0	0	12	2	6
424.0	0	12	0	4
425.0	0	8	0	2
426.0	0	8	0	11
427.0	0	7	2	10
428.0	0	8	1	6
429.0	0	11	0	10
430.0	0	6	1	2
431.0	0	4	1	7
432.0	0	10	1	5
433.0	0	10	0	6
434.0	0	8	3	3
435.0	0	4	0	4
436.0	0	11	0	9
437.0	0	12	0	4
438.0	0	9	0	6
439.0	0	6	0	7
440.0	0	6	1	3
441.0	0	8	1	8
442.0	0	4	1	7
443.0	0	12	1	2
444.0	0	3	2	3
445.0	0	2	0	5
446.0	0	6	1	5
447.0	0	5	0	4
448.0	0	9	0	2
449.0	0	12	1	6
450.0	0	8	1	5
451.0	0	2	1	7
452.0	0	6	1	6
453.0	0	7	0	4
454.0	0	16	0	4
455.0	0	14	2	3
456.0	0	12	0	5
457.0	0	9	0	6
458.0	0	6	1	8
459.0	0	9	0	8
460.0	0	7	0	5
461.0	0	3	0	4
462.0	0	9	0	5
463.0	0	9	0	5
464.0	0	8	2	1
465.0	0	9	1	2
466.0	0	5	0	4
467.0	0	5	1	6
468.0	0	11	0	4
469.0	0	7	0	6
470.0	0	4	0	5
471.0	0	10	1	3
472.0	0	2	0	5
473.0	0	2	0	7
474.0	0	5	0	6
475.0	0	5	0	10
476.0	0	9	1	3
477.0	0	9	0	4
478.0	0	4	0	4
479.0	0	7	0	3
480.0	0	4	0	6
481.0	0	4	1	3
482.0	0	5	1	4
483.0	0	3	1	3
484.0	0	9	0	3
485.0	0	4	1	7
486.0	0	9	0	3
487.0	0	9	1	5
488.0	0	3	2	3
489.0	0	5	1	4
490.0	0	3	0	7
491.0	0	6	0	5
492.0	0	6	0	4
493.0	0	2	0	7
494.0	0	9	0	3
495.0	0	6	1	6
496.0	0	8	0	4
497.0	0	10	0	4
498.0	0	3	2	3
499.0	0	5	0	2
500.0	0	1	0	5
501.0	0	4	0	4
502.0	0	3	0	7
503.0	0	4	0	3
504.0	0	2	1	2
505.0	0	11	0	2
506.0	0	2	0	4
507.0	0	6	0	1
508.0	0	5	0	2
509.0	0	7	0	3
510.0	0	9	0	7
511.0	0	3	0	2
512.0	0	5	0	2
513.0	0	1	0	7
514.0	0	6	0	8
515.0	0	9	0	3
516.0	0	6	0	1
517.0	0	0	0	4
518.0	0	5	0	4
519.0	0	5	0	6
520.0	0	2	1	2
521.0	0	7	0	3
522.0	0	6	1	5
523.0	0	4	1	6
524.0	0	6	1	2
525.0	0	9	0	4
526.0	0	5	0	5
527.0	0	7	0	5
528.0	0	6	2	6
529.0	0	5	0	1
530.0	0	4	0	3
531.0	0	5	0	3
532.0	0	7	1	3
533.0	0	5	2	5
534.0	0	2	1	3
535.0	0	4	1	2
536.0	0	5	0	1
537.0	0	0	0	2
538.0	0	3	0	6
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