## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-262-TP4.bam --OUTPUT POR-262-TP4.md.bam --METRICS_FILE POR-262-TP4.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 18:17:41 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	437	14864915	9058994	0	254	11191612	3275294	0.752885	3866246

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.030011	2155132	0	2676742
2.0	1.052044	666852	499848	493887
3.0	1.052515	272989	194755	141006
4.0	1.052526	140582	98804	69684
5.0	1.052526	84287	55147	44884
6.0	1.052526	55962	33397	32807
7.0	1.052526	39545	21425	25298
8.0	1.052526	29801	14560	19963
9.0	1.052526	23231	10519	16112
10.0	1.052526	18681	7866	13507
11.0	1.052526	15618	6018	11121
12.0	1.052526	13022	4784	9675
13.0	1.052526	11172	3986	8510
14.0	1.052526	9913	3298	7282
15.0	1.052526	8687	2773	6600
16.0	1.052526	7850	2376	5922
17.0	1.052526	6832	2034	5100
18.0	1.052526	6117	1786	4610
19.0	1.052526	5630	1617	4120
20.0	1.052526	4976	1355	3837
21.0	1.052526	4556	1287	3573
22.0	1.052526	4252	1129	3257
23.0	1.052526	4005	1075	3032
24.0	1.052526	3665	1013	2736
25.0	1.052526	3302	849	2483
26.0	1.052526	3016	802	2282
27.0	1.052526	3000	704	2203
28.0	1.052526	2682	644	2008
29.0	1.052526	2396	582	1912
30.0	1.052526	2304	541	1843
31.0	1.052526	2250	520	1684
32.0	1.052526	1988	446	1563
33.0	1.052526	2037	453	1496
34.0	1.052526	1821	412	1333
35.0	1.052526	1713	347	1285
36.0	1.052526	1627	345	1199
37.0	1.052526	1530	309	1194
38.0	1.052526	1482	319	1096
39.0	1.052526	1414	278	1046
40.0	1.052526	1365	287	1034
41.0	1.052526	1274	270	1000
42.0	1.052526	1209	237	924
43.0	1.052526	1164	193	896
44.0	1.052526	1142	224	870
45.0	1.052526	1064	203	815
46.0	1.052526	998	189	813
47.0	1.052526	995	176	711
48.0	1.052526	930	172	699
49.0	1.052526	871	168	710
50.0	1.052526	930	144	651
51.0	1.052526	824	167	610
52.0	1.052526	866	134	601
53.0	1.052526	797	128	569
54.0	1.052526	740	141	581
55.0	1.052526	678	123	491
56.0	1.052526	673	123	526
57.0	1.052526	645	120	462
58.0	1.052526	603	109	485
59.0	1.052526	641	82	459
60.0	1.052526	610	98	428
61.0	1.052526	573	83	408
62.0	1.052526	541	85	446
63.0	1.052526	552	77	404
64.0	1.052526	536	78	394
65.0	1.052526	490	77	360
66.0	1.052526	481	75	390
67.0	1.052526	438	74	355
68.0	1.052526	493	72	318
69.0	1.052526	466	64	361
70.0	1.052526	428	48	313
71.0	1.052526	392	65	341
72.0	1.052526	400	59	318
73.0	1.052526	359	59	282
74.0	1.052526	420	71	255
75.0	1.052526	383	42	278
76.0	1.052526	373	51	241
77.0	1.052526	340	68	246
78.0	1.052526	358	51	231
79.0	1.052526	343	54	252
80.0	1.052526	348	47	264
81.0	1.052526	316	53	227
82.0	1.052526	293	47	212
83.0	1.052526	313	37	227
84.0	1.052526	276	36	214
85.0	1.052526	303	49	237
86.0	1.052526	256	49	224
87.0	1.052526	280	48	175
88.0	1.052526	261	35	178
89.0	1.052526	278	38	200
90.0	1.052526	239	27	178
91.0	1.052526	226	34	191
92.0	1.052526	244	34	212
93.0	1.052526	248	25	156
94.0	1.052526	205	27	177
95.0	1.052526	198	32	160
96.0	1.052526	198	29	178
97.0	1.052526	220	30	136
98.0	1.052526	230	27	154
99.0	1.052526	210	33	155
100.0	1.052526	191	25	133
101.0	0	207	26	131
102.0	0	183	22	141
103.0	0	183	25	148
104.0	0	206	20	137
105.0	0	167	21	146
106.0	0	174	12	119
107.0	0	159	28	111
108.0	0	176	20	141
109.0	0	193	20	126
110.0	0	163	24	85
111.0	0	148	22	99
112.0	0	131	18	119
113.0	0	151	23	100
114.0	0	144	16	108
115.0	0	144	13	121
116.0	0	128	11	111
117.0	0	129	10	100
118.0	0	142	14	118
119.0	0	121	14	109
120.0	0	125	6	99
121.0	0	130	12	102
122.0	0	123	20	121
123.0	0	114	15	66
124.0	0	111	16	91
125.0	0	120	15	90
126.0	0	114	15	91
127.0	0	112	10	87
128.0	0	108	15	81
129.0	0	114	15	84
130.0	0	112	17	82
131.0	0	119	10	86
132.0	0	118	14	79
133.0	0	104	18	75
134.0	0	94	17	74
135.0	0	99	12	67
136.0	0	113	12	77
137.0	0	96	9	72
138.0	0	115	4	67
139.0	0	95	16	66
140.0	0	88	11	64
141.0	0	90	14	71
142.0	0	106	12	69
143.0	0	98	12	72
144.0	0	95	9	65
145.0	0	93	9	86
146.0	0	84	7	61
147.0	0	78	7	62
148.0	0	82	8	53
149.0	0	89	13	63
150.0	0	66	12	52
151.0	0	81	12	68
152.0	0	94	15	50
153.0	0	89	7	52
154.0	0	73	17	56
155.0	0	66	15	58
156.0	0	86	10	45
157.0	0	73	7	60
158.0	0	64	8	51
159.0	0	77	6	53
160.0	0	86	6	50
161.0	0	64	7	57
162.0	0	73	4	62
163.0	0	63	10	47
164.0	0	56	6	41
165.0	0	74	8	46
166.0	0	59	13	46
167.0	0	59	7	50
168.0	0	79	9	47
169.0	0	58	3	47
170.0	0	63	2	53
171.0	0	57	8	33
172.0	0	73	6	50
173.0	0	53	3	37
174.0	0	65	11	43
175.0	0	50	7	41
176.0	0	48	7	40
177.0	0	57	6	45
178.0	0	47	7	37
179.0	0	52	3	36
180.0	0	66	15	35
181.0	0	51	2	39
182.0	0	56	8	39
183.0	0	52	8	25
184.0	0	54	4	41
185.0	0	43	8	38
186.0	0	50	4	30
187.0	0	50	2	39
188.0	0	38	3	35
189.0	0	48	7	36
190.0	0	42	5	35
191.0	0	41	1	31
192.0	0	54	6	33
193.0	0	46	2	33
194.0	0	43	4	41
195.0	0	42	5	36
196.0	0	42	5	29
197.0	0	38	3	32
198.0	0	37	1	36
199.0	0	32	7	39
200.0	0	37	0	23
201.0	0	26	4	33
202.0	0	34	3	18
203.0	0	41	8	34
204.0	0	47	4	23
205.0	0	38	5	30
206.0	0	40	1	29
207.0	0	46	3	27
208.0	0	56	5	27
209.0	0	41	3	33
210.0	0	35	5	33
211.0	0	22	3	32
212.0	0	34	3	30
213.0	0	37	3	29
214.0	0	33	1	35
215.0	0	36	7	34
216.0	0	33	4	32
217.0	0	36	2	24
218.0	0	33	0	18
219.0	0	34	1	32
220.0	0	40	2	37
221.0	0	37	7	26
222.0	0	35	5	21
223.0	0	23	1	18
224.0	0	27	1	27
225.0	0	26	7	30
226.0	0	32	1	18
227.0	0	25	1	22
228.0	0	27	3	16
229.0	0	28	5	25
230.0	0	29	1	23
231.0	0	33	1	19
232.0	0	39	3	29
233.0	0	16	2	20
234.0	0	19	3	26
235.0	0	31	2	20
236.0	0	41	2	18
237.0	0	21	3	17
238.0	0	21	3	16
239.0	0	25	2	19
240.0	0	18	1	25
241.0	0	12	3	18
242.0	0	24	2	22
243.0	0	20	2	27
244.0	0	34	2	19
245.0	0	22	1	26
246.0	0	21	0	14
247.0	0	21	6	13
248.0	0	28	4	18
249.0	0	33	2	19
250.0	0	24	2	14
251.0	0	27	4	20
252.0	0	20	0	11
253.0	0	15	3	19
254.0	0	29	0	22
255.0	0	27	4	14
256.0	0	37	2	18
257.0	0	20	2	12
258.0	0	21	2	15
259.0	0	21	3	15
260.0	0	23	1	20
261.0	0	22	4	26
262.0	0	19	3	23
263.0	0	24	0	19
264.0	0	20	2	12
265.0	0	19	1	12
266.0	0	25	1	15
267.0	0	17	2	18
268.0	0	18	2	16
269.0	0	15	4	16
270.0	0	17	1	16
271.0	0	19	2	21
272.0	0	24	2	11
273.0	0	20	2	17
274.0	0	18	0	15
275.0	0	21	0	19
276.0	0	18	1	10
277.0	0	30	0	13
278.0	0	20	1	12
279.0	0	22	1	10
280.0	0	28	0	18
281.0	0	23	0	13
282.0	0	20	1	4
283.0	0	21	1	17
284.0	0	16	1	13
285.0	0	21	3	5
286.0	0	24	2	15
287.0	0	18	2	13
288.0	0	17	6	12
289.0	0	20	1	19
290.0	0	12	2	13
291.0	0	22	0	16
292.0	0	15	1	9
293.0	0	11	2	14
294.0	0	22	2	5
295.0	0	16	0	15
296.0	0	10	2	13
297.0	0	11	2	11
298.0	0	21	0	12
299.0	0	13	1	8
300.0	0	16	1	14
301.0	0	14	1	9
302.0	0	18	2	12
303.0	0	15	0	14
304.0	0	22	4	14
305.0	0	15	1	12
306.0	0	15	0	11
307.0	0	20	3	14
308.0	0	16	2	14
309.0	0	17	1	14
310.0	0	14	2	15
311.0	0	14	3	11
312.0	0	12	2	14
313.0	0	13	0	13
314.0	0	15	2	10
315.0	0	12	2	12
316.0	0	14	0	11
317.0	0	5	0	13
318.0	0	13	2	11
319.0	0	19	1	13
320.0	0	13	0	13
321.0	0	10	0	13
322.0	0	17	2	14
323.0	0	17	2	8
324.0	0	8	2	7
325.0	0	13	1	16
326.0	0	16	1	9
327.0	0	9	1	13
328.0	0	9	1	13
329.0	0	11	1	10
330.0	0	20	0	6
331.0	0	8	2	12
332.0	0	9	3	9
333.0	0	7	0	10
334.0	0	10	1	9
335.0	0	12	1	8
336.0	0	8	1	10
337.0	0	8	1	13
338.0	0	10	1	5
339.0	0	12	1	8
340.0	0	12	1	5
341.0	0	14	1	8
342.0	0	17	1	8
343.0	0	9	2	7
344.0	0	14	0	3
345.0	0	14	1	6
346.0	0	17	3	9
347.0	0	10	3	11
348.0	0	12	2	12
349.0	0	13	2	8
350.0	0	14	0	5
351.0	0	11	0	5
352.0	0	5	2	8
353.0	0	9	3	5
354.0	0	11	1	5
355.0	0	12	1	4
356.0	0	14	2	9
357.0	0	9	2	6
358.0	0	12	0	9
359.0	0	18	0	12
360.0	0	13	0	8
361.0	0	7	0	8
362.0	0	9	0	15
363.0	0	8	0	7
364.0	0	12	2	5
365.0	0	17	3	11
366.0	0	12	1	7
367.0	0	12	1	6
368.0	0	7	1	9
369.0	0	6	2	8
370.0	0	12	0	11
371.0	0	10	0	7
372.0	0	10	0	6
373.0	0	8	0	10
374.0	0	11	4	7
375.0	0	9	0	2
376.0	0	5	0	8
377.0	0	14	0	6
378.0	0	8	0	7
379.0	0	7	0	3
380.0	0	12	0	6
381.0	0	13	1	7
382.0	0	18	0	2
383.0	0	7	2	10
384.0	0	9	4	9
385.0	0	10	1	6
386.0	0	7	2	4
387.0	0	8	0	6
388.0	0	9	0	9
389.0	0	4	2	6
390.0	0	7	1	5
391.0	0	7	1	8
392.0	0	8	0	5
393.0	0	5	0	7
394.0	0	8	0	2
395.0	0	12	0	9
396.0	0	5	0	11
397.0	0	9	0	7
398.0	0	11	0	7
399.0	0	9	1	5
400.0	0	12	1	9
401.0	0	7	0	4
402.0	0	12	1	5
403.0	0	9	0	7
404.0	0	8	1	6
405.0	0	6	0	10
406.0	0	6	0	2
407.0	0	9	0	6
408.0	0	8	0	4
409.0	0	7	0	5
410.0	0	7	0	3
411.0	0	11	2	8
412.0	0	10	3	7
413.0	0	10	0	7
414.0	0	8	0	4
415.0	0	2	1	4
416.0	0	5	1	6
417.0	0	2	0	10
418.0	0	5	1	3
419.0	0	11	0	6
420.0	0	5	0	5
421.0	0	7	1	6
422.0	0	12	0	4
423.0	0	3	1	5
424.0	0	9	1	5
425.0	0	4	0	2
426.0	0	7	1	6
427.0	0	7	0	5
428.0	0	8	1	6
429.0	0	7	0	6
430.0	0	9	1	4
431.0	0	7	1	9
432.0	0	6	0	4
433.0	0	8	0	5
434.0	0	5	1	6
435.0	0	6	3	0
436.0	0	8	1	6
437.0	0	5	0	2
438.0	0	5	0	4
439.0	0	9	0	9
440.0	0	5	0	6
441.0	0	9	1	3
442.0	0	4	0	5
443.0	0	6	1	4
444.0	0	6	0	4
445.0	0	4	0	4
446.0	0	4	0	9
447.0	0	4	0	5
448.0	0	11	0	5
449.0	0	8	0	2
450.0	0	6	0	4
451.0	0	10	0	5
452.0	0	8	0	2
453.0	0	8	0	4
454.0	0	6	1	5
455.0	0	9	1	3
456.0	0	3	0	7
457.0	0	6	0	1
458.0	0	3	0	3
459.0	0	4	0	1
460.0	0	3	0	2
461.0	0	5	0	2
462.0	0	5	0	5
463.0	0	2	1	7
464.0	0	4	0	3
465.0	0	7	1	6
466.0	0	6	0	2
467.0	0	5	1	3
468.0	0	2	2	6
469.0	0	3	0	4
470.0	0	10	0	3
471.0	0	5	0	6
472.0	0	1	1	2
473.0	0	10	0	2
474.0	0	1	0	2
475.0	0	5	1	6
476.0	0	6	0	2
477.0	0	3	1	3
478.0	0	11	0	4
479.0	0	7	0	9
480.0	0	5	1	2
481.0	0	4	0	3
482.0	0	7	0	6
483.0	0	8	1	4
484.0	0	4	0	2
485.0	0	3	1	5
486.0	0	3	1	0
487.0	0	4	1	3
488.0	0	4	0	1
489.0	0	8	0	5
490.0	0	4	0	3
491.0	0	1	0	3
492.0	0	2	1	5
493.0	0	6	0	2
494.0	0	6	0	0
495.0	0	3	0	2
496.0	0	3	0	3
497.0	0	4	0	1
498.0	0	6	0	3
499.0	0	4	0	4
500.0	0	6	1	2
501.0	0	2	0	1
502.0	0	7	0	1
503.0	0	0	0	7
504.0	0	6	0	1
505.0	0	3	0	7
506.0	0	5	0	2
507.0	0	3	0	7
508.0	0	5	0	3
509.0	0	5	0	3
510.0	0	3	0	2
511.0	0	3	0	1
512.0	0	3	0	2
513.0	0	2	1	0
514.0	0	5	0	7
515.0	0	6	0	5
516.0	0	4	0	3
517.0	0	7	1	3
518.0	0	2	0	1
519.0	0	8	0	8
520.0	0	4	1	3
521.0	0	1	0	3
522.0	0	5	0	3
523.0	0	3	0	2
524.0	0	4	0	1
525.0	0	2	0	5
526.0	0	4	0	3
527.0	0	2	0	6
528.0	0	1	1	3
529.0	0	5	1	3
530.0	0	5	0	4
531.0	0	9	0	3
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1595.0	0	1	0	0
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1620.0	0	0	0	1
1630.0	0	0	0	1
1635.0	0	0	0	1
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1648.0	0	2	0	0
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1917.0	0	0	0	1
1928.0	0	1	0	0
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1956.0	0	1	0	0
1971.0	0	1	0	0
1974.0	0	1	0	0
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1979.0	0	1	0	0
1984.0	0	0	0	1
1986.0	0	1	0	0
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