## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-216-TP3.bam --OUTPUT POR-216-TP3.md.bam --METRICS_FILE POR-216-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 18:06:11 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	2136	13689121	8521215	0	1994	10707949	3124837	0.782235	3081082

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.021358	1388649	0	1759115
2.0	1.033371	645084	445455	620805
3.0	1.033512	314054	184104	217044
4.0	1.033514	168022	96303	92095
5.0	1.033514	98878	56029	51040
6.0	1.033514	63688	34437	34137
7.0	1.033514	44357	22255	25205
8.0	1.033514	32370	15383	19810
9.0	1.033514	24887	10931	16110
10.0	1.033514	19934	8299	13257
11.0	1.033514	16104	6365	11280
12.0	1.033514	13528	4898	9534
13.0	1.033514	11467	4017	8210
14.0	1.033514	9765	3284	7177
15.0	1.033514	8662	2694	6324
16.0	1.033514	7509	2410	5596
17.0	1.033514	6721	2054	4920
18.0	1.033514	5993	1830	4485
19.0	1.033514	5479	1562	4051
20.0	1.033514	4975	1373	3683
21.0	1.033514	4468	1237	3431
22.0	1.033514	4203	1154	3163
23.0	1.033514	3853	933	2870
24.0	1.033514	3479	877	2635
25.0	1.033514	3272	801	2406
26.0	1.033514	3090	729	2116
27.0	1.033514	2796	637	2073
28.0	1.033514	2633	585	1920
29.0	1.033514	2366	545	1813
30.0	1.033514	2305	501	1678
31.0	1.033514	2154	480	1630
32.0	1.033514	1998	427	1518
33.0	1.033514	1867	432	1400
34.0	1.033514	1818	382	1357
35.0	1.033514	1632	360	1249
36.0	1.033514	1590	332	1118
37.0	1.033514	1523	279	1075
38.0	1.033514	1416	281	1068
39.0	1.033514	1378	264	1043
40.0	1.033514	1270	247	918
41.0	1.033514	1236	230	884
42.0	1.033514	1175	209	869
43.0	1.033514	1094	199	792
44.0	1.033514	1042	205	786
45.0	1.033514	951	198	756
46.0	1.033514	940	168	714
47.0	1.033514	926	170	661
48.0	1.033514	904	144	641
49.0	1.033514	874	149	639
50.0	1.033514	770	136	641
51.0	1.033514	780	143	540
52.0	1.033514	721	132	510
53.0	1.033514	682	118	513
54.0	1.033514	690	119	502
55.0	1.033514	629	116	467
56.0	1.033514	646	108	497
57.0	1.033514	622	105	508
58.0	1.033514	603	93	437
59.0	1.033514	583	91	442
60.0	1.033514	515	102	397
61.0	1.033514	525	98	416
62.0	1.033514	546	84	372
63.0	1.033514	540	75	367
64.0	1.033514	454	60	365
65.0	1.033514	443	90	344
66.0	1.033514	463	66	319
67.0	1.033514	430	68	330
68.0	1.033514	445	63	299
69.0	1.033514	441	62	307
70.0	1.033514	386	62	296
71.0	1.033514	367	65	313
72.0	1.033514	376	49	260
73.0	1.033514	360	57	239
74.0	1.033514	314	62	260
75.0	1.033514	359	61	264
76.0	1.033514	327	39	226
77.0	1.033514	330	48	251
78.0	1.033514	319	53	260
79.0	1.033514	283	53	226
80.0	1.033514	299	41	229
81.0	1.033514	309	38	227
82.0	1.033514	293	38	218
83.0	1.033514	256	46	197
84.0	1.033514	268	41	199
85.0	1.033514	255	42	204
86.0	1.033514	272	36	178
87.0	1.033514	252	29	177
88.0	1.033514	250	27	152
89.0	1.033514	221	28	165
90.0	1.033514	240	47	166
91.0	1.033514	242	33	162
92.0	1.033514	218	28	165
93.0	1.033514	244	32	174
94.0	1.033514	183	24	155
95.0	1.033514	204	24	129
96.0	1.033514	215	29	145
97.0	1.033514	204	23	120
98.0	1.033514	208	25	164
99.0	1.033514	186	28	140
100.0	1.033514	186	36	125
101.0	0	173	22	131
102.0	0	175	18	130
103.0	0	165	23	138
104.0	0	143	26	114
105.0	0	170	21	128
106.0	0	159	23	103
107.0	0	170	18	105
108.0	0	170	13	121
109.0	0	169	22	108
110.0	0	126	16	103
111.0	0	137	21	104
112.0	0	140	17	109
113.0	0	119	14	82
114.0	0	136	18	103
115.0	0	121	17	100
116.0	0	147	18	89
117.0	0	120	13	90
118.0	0	112	11	86
119.0	0	119	24	92
120.0	0	134	21	76
121.0	0	118	13	87
122.0	0	121	20	81
123.0	0	114	13	89
124.0	0	115	13	81
125.0	0	117	16	88
126.0	0	96	13	65
127.0	0	97	9	75
128.0	0	91	11	75
129.0	0	105	3	68
130.0	0	106	8	79
131.0	0	110	9	66
132.0	0	90	11	83
133.0	0	88	9	69
134.0	0	93	13	66
135.0	0	119	10	67
136.0	0	93	10	64
137.0	0	82	9	73
138.0	0	87	4	53
139.0	0	90	13	60
140.0	0	78	12	67
141.0	0	94	10	53
142.0	0	88	5	56
143.0	0	82	11	44
144.0	0	82	5	56
145.0	0	67	4	62
146.0	0	66	4	50
147.0	0	73	7	46
148.0	0	80	8	48
149.0	0	65	13	64
150.0	0	70	4	66
151.0	0	68	5	45
152.0	0	76	9	53
153.0	0	60	4	58
154.0	0	57	5	59
155.0	0	56	13	38
156.0	0	62	1	46
157.0	0	61	5	47
158.0	0	58	6	46
159.0	0	80	5	46
160.0	0	65	7	33
161.0	0	67	5	53
162.0	0	66	7	40
163.0	0	66	5	42
164.0	0	58	6	43
165.0	0	60	7	46
166.0	0	56	10	51
167.0	0	59	5	33
168.0	0	57	4	40
169.0	0	50	4	45
170.0	0	64	8	37
171.0	0	46	4	46
172.0	0	57	5	33
173.0	0	51	7	43
174.0	0	50	8	32
175.0	0	42	4	33
176.0	0	42	2	27
177.0	0	51	5	25
178.0	0	65	5	38
179.0	0	47	7	37
180.0	0	40	7	33
181.0	0	48	1	32
182.0	0	45	4	37
183.0	0	44	8	32
184.0	0	37	6	37
185.0	0	37	1	41
186.0	0	48	5	32
187.0	0	37	6	32
188.0	0	47	3	28
189.0	0	51	3	37
190.0	0	47	4	30
191.0	0	42	7	24
192.0	0	36	3	25
193.0	0	42	1	40
194.0	0	35	7	34
195.0	0	33	5	22
196.0	0	32	5	34
197.0	0	26	2	32
198.0	0	31	2	26
199.0	0	34	3	18
200.0	0	39	6	22
201.0	0	42	2	16
202.0	0	38	9	22
203.0	0	36	4	23
204.0	0	31	2	31
205.0	0	34	6	27
206.0	0	33	4	35
207.0	0	31	3	23
208.0	0	28	4	25
209.0	0	37	6	19
210.0	0	34	3	30
211.0	0	28	3	20
212.0	0	30	0	22
213.0	0	33	2	23
214.0	0	49	3	20
215.0	0	24	7	14
216.0	0	20	3	26
217.0	0	29	2	27
218.0	0	22	2	19
219.0	0	31	3	25
220.0	0	31	0	25
221.0	0	21	5	19
222.0	0	32	4	21
223.0	0	30	1	18
224.0	0	27	2	20
225.0	0	29	1	22
226.0	0	29	0	18
227.0	0	22	1	23
228.0	0	23	2	22
229.0	0	28	3	21
230.0	0	24	4	15
231.0	0	26	4	20
232.0	0	35	1	19
233.0	0	22	4	10
234.0	0	26	5	13
235.0	0	25	3	17
236.0	0	30	1	23
237.0	0	24	1	17
238.0	0	25	2	23
239.0	0	26	3	10
240.0	0	20	2	16
241.0	0	15	2	19
242.0	0	21	3	18
243.0	0	23	3	18
244.0	0	21	4	14
245.0	0	18	0	18
246.0	0	16	0	13
247.0	0	20	1	14
248.0	0	20	2	20
249.0	0	28	2	17
250.0	0	13	1	15
251.0	0	20	1	16
252.0	0	30	0	5
253.0	0	23	0	11
254.0	0	19	1	15
255.0	0	17	1	15
256.0	0	22	2	20
257.0	0	15	5	14
258.0	0	15	1	16
259.0	0	17	1	16
260.0	0	10	0	16
261.0	0	22	1	20
262.0	0	28	2	12
263.0	0	15	1	13
264.0	0	18	4	13
265.0	0	19	1	17
266.0	0	22	0	11
267.0	0	17	2	16
268.0	0	13	1	11
269.0	0	13	0	10
270.0	0	17	0	11
271.0	0	20	2	15
272.0	0	28	2	17
273.0	0	20	2	14
274.0	0	22	0	13
275.0	0	19	1	16
276.0	0	19	1	13
277.0	0	19	5	18
278.0	0	17	1	7
279.0	0	18	4	10
280.0	0	13	2	10
281.0	0	18	0	16
282.0	0	10	2	12
283.0	0	14	1	12
284.0	0	13	3	8
285.0	0	13	0	20
286.0	0	16	1	10
287.0	0	14	0	16
288.0	0	21	1	16
289.0	0	14	0	11
290.0	0	16	0	10
291.0	0	18	0	15
292.0	0	10	1	11
293.0	0	11	2	11
294.0	0	12	1	16
295.0	0	20	1	10
296.0	0	14	0	9
297.0	0	11	3	12
298.0	0	15	1	7
299.0	0	13	1	16
300.0	0	17	2	6
301.0	0	19	1	9
302.0	0	18	1	6
303.0	0	21	1	8
304.0	0	13	3	10
305.0	0	10	2	12
306.0	0	28	0	8
307.0	0	16	0	10
308.0	0	10	0	12
309.0	0	14	0	6
310.0	0	14	0	14
311.0	0	12	0	3
312.0	0	18	2	8
313.0	0	14	0	4
314.0	0	8	2	5
315.0	0	9	2	8
316.0	0	15	3	8
317.0	0	16	0	11
318.0	0	11	1	9
319.0	0	12	5	3
320.0	0	7	0	9
321.0	0	13	2	10
322.0	0	13	2	2
323.0	0	9	0	4
324.0	0	15	1	7
325.0	0	13	0	9
326.0	0	7	0	13
327.0	0	8	2	8
328.0	0	7	0	6
329.0	0	5	0	13
330.0	0	15	0	11
331.0	0	11	2	5
332.0	0	6	2	13
333.0	0	10	1	4
334.0	0	6	1	6
335.0	0	8	2	7
336.0	0	11	0	4
337.0	0	10	0	8
338.0	0	13	1	9
339.0	0	9	0	7
340.0	0	8	0	10
341.0	0	8	0	8
342.0	0	5	0	9
343.0	0	15	0	12
344.0	0	5	1	4
345.0	0	9	0	2
346.0	0	8	0	9
347.0	0	11	1	10
348.0	0	11	2	11
349.0	0	5	0	2
350.0	0	12	1	8
351.0	0	8	0	6
352.0	0	9	1	10
353.0	0	7	2	10
354.0	0	8	0	7
355.0	0	11	1	8
356.0	0	9	1	6
357.0	0	6	0	6
358.0	0	8	0	7
359.0	0	9	3	3
360.0	0	11	1	7
361.0	0	11	0	7
362.0	0	11	0	8
363.0	0	10	1	7
364.0	0	12	0	3
365.0	0	12	1	4
366.0	0	8	1	2
367.0	0	3	0	3
368.0	0	6	0	3
369.0	0	13	0	3
370.0	0	12	1	10
371.0	0	4	0	6
372.0	0	7	0	9
373.0	0	6	1	9
374.0	0	12	0	6
375.0	0	7	1	8
376.0	0	4	1	6
377.0	0	7	1	5
378.0	0	6	0	4
379.0	0	9	0	5
380.0	0	5	0	5
381.0	0	10	1	4
382.0	0	7	2	3
383.0	0	8	0	5
384.0	0	3	0	8
385.0	0	4	1	4
386.0	0	6	1	2
387.0	0	9	0	9
388.0	0	7	0	6
389.0	0	8	1	2
390.0	0	7	1	6
391.0	0	9	1	3
392.0	0	4	0	2
393.0	0	1	1	7
394.0	0	10	1	5
395.0	0	7	1	5
396.0	0	5	0	4
397.0	0	11	0	4
398.0	0	9	0	6
399.0	0	6	0	2
400.0	0	5	0	7
401.0	0	4	0	6
402.0	0	7	1	6
403.0	0	8	0	5
404.0	0	3	0	7
405.0	0	5	1	3
406.0	0	4	0	3
407.0	0	3	0	7
408.0	0	4	0	2
409.0	0	5	0	5
410.0	0	4	0	4
411.0	0	5	0	3
412.0	0	10	0	4
413.0	0	1	0	5
414.0	0	10	0	3
415.0	0	8	0	3
416.0	0	10	0	4
417.0	0	8	0	3
418.0	0	8	0	3
419.0	0	5	0	4
420.0	0	8	1	2
421.0	0	8	0	7
422.0	0	4	0	7
423.0	0	11	0	2
424.0	0	8	0	4
425.0	0	5	0	9
426.0	0	7	0	4
427.0	0	7	0	5
428.0	0	9	0	4
429.0	0	5	1	7
430.0	0	4	0	5
431.0	0	11	0	4
432.0	0	5	0	7
433.0	0	6	0	3
434.0	0	4	0	3
435.0	0	5	1	3
436.0	0	6	0	4
437.0	0	7	0	4
438.0	0	13	1	3
439.0	0	5	0	4
440.0	0	1	0	6
441.0	0	5	1	3
442.0	0	6	0	6
443.0	0	3	2	6
444.0	0	8	0	2
445.0	0	2	0	8
446.0	0	6	0	4
447.0	0	9	1	3
448.0	0	7	0	1
449.0	0	7	1	3
450.0	0	4	0	3
451.0	0	4	0	5
452.0	0	3	0	3
453.0	0	3	0	4
454.0	0	5	1	5
455.0	0	4	0	2
456.0	0	10	0	2
457.0	0	5	0	4
458.0	0	4	0	2
459.0	0	4	0	3
460.0	0	4	0	3
461.0	0	6	0	4
462.0	0	4	0	3
463.0	0	4	0	4
464.0	0	4	0	4
465.0	0	3	0	3
466.0	0	8	1	1
467.0	0	4	1	4
468.0	0	4	0	5
469.0	0	3	0	4
470.0	0	4	0	3
471.0	0	5	0	2
472.0	0	2	1	3
473.0	0	3	0	2
474.0	0	4	0	1
475.0	0	1	0	4
476.0	0	5	0	2
477.0	0	4	0	5
478.0	0	6	0	4
479.0	0	3	0	4
480.0	0	8	1	0
481.0	0	5	0	3
482.0	0	9	0	4
483.0	0	0	1	2
484.0	0	2	0	4
485.0	0	3	0	3
486.0	0	5	0	2
487.0	0	6	0	2
488.0	0	8	0	4
489.0	0	2	0	3
490.0	0	4	0	3
491.0	0	0	1	2
492.0	0	1	0	1
493.0	0	4	1	4
494.0	0	4	0	5
495.0	0	6	0	2
496.0	0	2	0	1
497.0	0	3	1	1
498.0	0	1	0	4
499.0	0	3	0	4
500.0	0	3	0	0
501.0	0	2	0	0
502.0	0	4	0	0
503.0	0	5	0	3
504.0	0	1	0	3
505.0	0	2	0	1
506.0	0	7	0	0
507.0	0	0	1	0
508.0	0	3	0	2
509.0	0	4	0	4
510.0	0	2	0	2
511.0	0	2	0	0
512.0	0	5	0	1
513.0	0	6	0	2
514.0	0	6	0	3
515.0	0	3	1	2
516.0	0	2	0	5
517.0	0	5	0	4
518.0	0	6	0	2
519.0	0	5	0	2
520.0	0	0	1	2
521.0	0	3	1	4
522.0	0	5	0	2
523.0	0	4	0	3
524.0	0	4	0	4
525.0	0	1	0	1
526.0	0	2	0	2
527.0	0	3	0	2
528.0	0	1	0	1
529.0	0	3	0	1
530.0	0	3	0	1
531.0	0	0	0	1
532.0	0	5	1	4
533.0	0	1	0	3
534.0	0	3	0	2
535.0	0	3	0	2
536.0	0	3	0	1
537.0	0	6	0	2
538.0	0	2	0	3
539.0	0	3	0	2
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