## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-245-TP1.bam --OUTPUT POR-245-TP1.md.bam --METRICS_FILE POR-245-TP1.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 18:15:38 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	556	16389463	8578473	0	343	11643091	3818916	0.710399	5214342

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.051195	2463366	0	3148233
2.0	1.09655	1041077	699476	932629
3.0	1.098507	472177	281604	273228
4.0	1.098591	237410	141337	101626
5.0	1.098595	133406	78328	52872
6.0	1.098595	81615	45586	34445
7.0	1.098595	53571	27809	25714
8.0	1.098595	38099	17692	19984
9.0	1.098595	27730	12222	15927
10.0	1.098595	20922	8580	13230
11.0	1.098595	16768	6320	10712
12.0	1.098595	13641	4747	9401
13.0	1.098595	11503	3897	8140
14.0	1.098595	9674	3082	7039
15.0	1.098595	8591	2575	6214
16.0	1.098595	7446	2183	5417
17.0	1.098595	6556	1935	4923
18.0	1.098595	5864	1619	4386
19.0	1.098595	5264	1436	3971
20.0	1.098595	4860	1278	3610
21.0	1.098595	4506	1069	3342
22.0	1.098595	3953	967	2983
23.0	1.098595	3661	926	2749
24.0	1.098595	3368	792	2445
25.0	1.098595	3126	718	2289
26.0	1.098595	2862	666	2127
27.0	1.098595	2662	607	2026
28.0	1.098595	2537	544	1892
29.0	1.098595	2357	491	1710
30.0	1.098595	2173	439	1619
31.0	1.098595	2052	424	1521
32.0	1.098595	1962	375	1393
33.0	1.098595	1821	380	1422
34.0	1.098595	1578	326	1310
35.0	1.098595	1632	312	1186
36.0	1.098595	1497	285	1151
37.0	1.098595	1431	290	1012
38.0	1.098595	1320	265	956
39.0	1.098595	1291	258	949
40.0	1.098595	1204	230	929
41.0	1.098595	1153	215	918
42.0	1.098595	1134	170	845
43.0	1.098595	1022	201	830
44.0	1.098595	1038	197	729
45.0	1.098595	971	159	775
46.0	1.098595	952	158	666
47.0	1.098595	857	170	643
48.0	1.098595	802	130	651
49.0	1.098595	785	133	578
50.0	1.098595	796	126	577
51.0	1.098595	722	132	544
52.0	1.098595	746	107	541
53.0	1.098595	662	110	497
54.0	1.098595	659	114	506
55.0	1.098595	625	114	471
56.0	1.098595	595	109	436
57.0	1.098595	551	92	461
58.0	1.098595	553	90	426
59.0	1.098595	608	82	431
60.0	1.098595	505	75	405
61.0	1.098595	514	81	352
62.0	1.098595	498	84	382
63.0	1.098595	480	73	337
64.0	1.098595	447	71	326
65.0	1.098595	411	59	329
66.0	1.098595	422	65	307
67.0	1.098595	416	60	318
68.0	1.098595	430	54	275
69.0	1.098595	394	70	287
70.0	1.098595	360	47	253
71.0	1.098595	380	49	276
72.0	1.098595	342	55	277
73.0	1.098595	341	49	264
74.0	1.098595	328	55	276
75.0	1.098595	322	51	236
76.0	1.098595	316	48	234
77.0	1.098595	311	39	248
78.0	1.098595	300	46	186
79.0	1.098595	269	37	206
80.0	1.098595	274	38	192
81.0	1.098595	293	35	196
82.0	1.098595	280	25	207
83.0	1.098595	255	36	205
84.0	1.098595	263	33	158
85.0	1.098595	234	29	165
86.0	1.098595	232	32	163
87.0	1.098595	215	25	179
88.0	1.098595	240	29	170
89.0	1.098595	234	30	154
90.0	1.098595	223	28	177
91.0	1.098595	191	31	151
92.0	1.098595	194	20	140
93.0	1.098595	178	26	146
94.0	1.098595	203	25	135
95.0	1.098595	193	26	151
96.0	1.098595	183	30	161
97.0	1.098595	193	24	150
98.0	1.098595	209	24	153
99.0	1.098595	180	19	134
100.0	1.098595	151	23	120
101.0	0	170	24	126
102.0	0	170	24	142
103.0	0	161	21	115
104.0	0	166	22	116
105.0	0	166	16	117
106.0	0	169	12	111
107.0	0	134	13	108
108.0	0	136	13	99
109.0	0	140	18	108
110.0	0	130	20	103
111.0	0	147	9	103
112.0	0	141	19	95
113.0	0	143	19	94
114.0	0	117	13	100
115.0	0	129	16	97
116.0	0	121	12	91
117.0	0	96	20	84
118.0	0	108	20	91
119.0	0	112	8	82
120.0	0	102	14	93
121.0	0	105	15	107
122.0	0	131	14	75
123.0	0	91	13	81
124.0	0	107	18	80
125.0	0	107	12	90
126.0	0	110	8	69
127.0	0	89	10	68
128.0	0	96	8	78
129.0	0	121	12	79
130.0	0	93	18	71
131.0	0	93	20	63
132.0	0	95	4	66
133.0	0	100	15	74
134.0	0	74	16	68
135.0	0	97	8	58
136.0	0	82	10	59
137.0	0	118	10	76
138.0	0	79	9	75
139.0	0	79	11	64
140.0	0	78	4	53
141.0	0	67	3	60
142.0	0	69	6	51
143.0	0	76	6	58
144.0	0	67	7	41
145.0	0	75	7	59
146.0	0	72	7	42
147.0	0	78	3	46
148.0	0	68	9	48
149.0	0	83	12	51
150.0	0	67	2	39
151.0	0	60	7	48
152.0	0	79	3	44
153.0	0	54	10	46
154.0	0	78	7	51
155.0	0	75	4	45
156.0	0	62	6	50
157.0	0	58	9	44
158.0	0	59	8	49
159.0	0	56	7	48
160.0	0	52	7	49
161.0	0	64	9	44
162.0	0	48	4	33
163.0	0	67	6	38
164.0	0	52	5	48
165.0	0	69	8	40
166.0	0	59	5	34
167.0	0	49	8	34
168.0	0	50	1	31
169.0	0	48	3	31
170.0	0	54	5	44
171.0	0	47	6	38
172.0	0	59	6	29
173.0	0	51	3	42
174.0	0	37	3	33
175.0	0	43	5	34
176.0	0	45	1	34
177.0	0	55	3	39
178.0	0	45	0	30
179.0	0	32	3	26
180.0	0	62	3	28
181.0	0	38	1	30
182.0	0	46	5	42
183.0	0	39	3	29
184.0	0	31	4	31
185.0	0	42	5	26
186.0	0	35	3	26
187.0	0	44	4	36
188.0	0	40	5	35
189.0	0	35	4	29
190.0	0	38	5	31
191.0	0	32	5	22
192.0	0	47	5	27
193.0	0	37	1	32
194.0	0	54	6	19
195.0	0	38	0	21
196.0	0	38	2	22
197.0	0	43	2	20
198.0	0	43	5	22
199.0	0	30	5	34
200.0	0	29	3	27
201.0	0	38	4	36
202.0	0	30	5	28
203.0	0	38	3	28
204.0	0	35	4	20
205.0	0	38	3	23
206.0	0	44	6	31
207.0	0	29	3	14
208.0	0	31	1	31
209.0	0	30	3	28
210.0	0	33	2	16
211.0	0	26	5	24
212.0	0	26	4	20
213.0	0	30	1	23
214.0	0	30	2	19
215.0	0	31	2	23
216.0	0	24	8	19
217.0	0	28	4	19
218.0	0	30	1	20
219.0	0	34	1	26
220.0	0	15	5	24
221.0	0	22	2	20
222.0	0	15	4	18
223.0	0	24	1	18
224.0	0	35	0	21
225.0	0	17	1	14
226.0	0	28	3	18
227.0	0	19	0	21
228.0	0	30	1	15
229.0	0	30	1	18
230.0	0	18	2	13
231.0	0	26	2	17
232.0	0	26	1	16
233.0	0	26	1	14
234.0	0	18	1	15
235.0	0	20	6	14
236.0	0	21	3	22
237.0	0	20	0	16
238.0	0	23	1	11
239.0	0	23	1	10
240.0	0	22	1	16
241.0	0	23	3	9
242.0	0	29	0	16
243.0	0	17	0	17
244.0	0	20	0	23
245.0	0	20	1	23
246.0	0	23	3	23
247.0	0	20	3	15
248.0	0	25	4	13
249.0	0	14	0	15
250.0	0	15	3	13
251.0	0	16	5	10
252.0	0	24	0	10
253.0	0	21	2	16
254.0	0	24	1	22
255.0	0	22	2	10
256.0	0	10	2	17
257.0	0	19	2	14
258.0	0	19	1	10
259.0	0	15	3	14
260.0	0	20	1	12
261.0	0	19	2	11
262.0	0	19	1	11
263.0	0	16	1	14
264.0	0	21	1	5
265.0	0	15	1	10
266.0	0	22	4	14
267.0	0	19	1	18
268.0	0	20	1	16
269.0	0	18	0	17
270.0	0	6	1	12
271.0	0	20	2	14
272.0	0	12	2	8
273.0	0	13	2	11
274.0	0	11	2	13
275.0	0	15	0	13
276.0	0	17	2	10
277.0	0	12	0	15
278.0	0	17	0	13
279.0	0	12	1	13
280.0	0	14	1	18
281.0	0	18	2	13
282.0	0	10	2	11
283.0	0	5	4	8
284.0	0	13	0	12
285.0	0	19	0	8
286.0	0	16	0	13
287.0	0	9	2	9
288.0	0	22	2	15
289.0	0	15	2	12
290.0	0	13	2	11
291.0	0	21	0	12
292.0	0	14	2	10
293.0	0	15	0	7
294.0	0	13	0	11
295.0	0	17	0	5
296.0	0	11	1	10
297.0	0	18	2	10
298.0	0	13	4	14
299.0	0	14	2	13
300.0	0	11	2	10
301.0	0	15	2	15
302.0	0	12	3	8
303.0	0	10	0	16
304.0	0	11	2	19
305.0	0	18	1	8
306.0	0	10	0	11
307.0	0	15	1	6
308.0	0	6	2	12
309.0	0	11	1	10
310.0	0	9	1	9
311.0	0	16	0	9
312.0	0	11	0	7
313.0	0	10	0	11
314.0	0	11	2	6
315.0	0	18	2	3
316.0	0	9	1	13
317.0	0	8	0	8
318.0	0	15	1	9
319.0	0	9	0	8
320.0	0	10	1	6
321.0	0	12	0	5
322.0	0	5	1	9
323.0	0	4	0	9
324.0	0	11	2	6
325.0	0	11	2	10
326.0	0	7	0	9
327.0	0	12	0	3
328.0	0	7	0	7
329.0	0	7	0	8
330.0	0	12	0	7
331.0	0	12	2	10
332.0	0	8	1	6
333.0	0	5	0	7
334.0	0	14	0	8
335.0	0	4	1	5
336.0	0	8	0	2
337.0	0	13	1	6
338.0	0	7	0	5
339.0	0	12	0	7
340.0	0	10	1	4
341.0	0	14	2	6
342.0	0	7	1	8
343.0	0	13	1	8
344.0	0	7	0	10
345.0	0	9	1	4
346.0	0	6	0	6
347.0	0	9	0	9
348.0	0	12	0	4
349.0	0	10	0	10
350.0	0	9	0	1
351.0	0	9	0	3
352.0	0	8	0	3
353.0	0	6	0	7
354.0	0	5	1	7
355.0	0	11	1	5
356.0	0	8	0	2
357.0	0	12	1	2
358.0	0	9	1	6
359.0	0	3	0	9
360.0	0	7	1	11
361.0	0	10	0	7
362.0	0	8	0	7
363.0	0	10	0	5
364.0	0	4	0	1
365.0	0	7	1	3
366.0	0	6	0	8
367.0	0	7	0	3
368.0	0	11	0	8
369.0	0	8	0	8
370.0	0	7	2	1
371.0	0	12	0	3
372.0	0	7	0	9
373.0	0	4	0	3
374.0	0	7	0	8
375.0	0	5	2	4
376.0	0	9	1	4
377.0	0	6	0	3
378.0	0	3	0	4
379.0	0	7	1	9
380.0	0	10	0	4
381.0	0	11	0	9
382.0	0	4	1	6
383.0	0	6	0	7
384.0	0	4	0	4
385.0	0	4	1	2
386.0	0	5	1	1
387.0	0	7	2	12
388.0	0	5	0	9
389.0	0	8	0	4
390.0	0	11	0	5
391.0	0	6	0	7
392.0	0	12	0	7
393.0	0	7	0	4
394.0	0	9	0	5
395.0	0	9	1	4
396.0	0	7	0	5
397.0	0	7	1	7
398.0	0	5	0	3
399.0	0	4	0	9
400.0	0	7	0	8
401.0	0	6	1	2
402.0	0	7	1	6
403.0	0	8	0	5
404.0	0	5	0	6
405.0	0	11	0	3
406.0	0	5	0	6
407.0	0	7	0	5
408.0	0	12	0	4
409.0	0	6	0	5
410.0	0	1	0	5
411.0	0	2	1	7
412.0	0	6	0	5
413.0	0	2	0	6
414.0	0	5	1	9
415.0	0	12	0	2
416.0	0	6	0	4
417.0	0	4	0	2
418.0	0	6	0	3
419.0	0	9	0	1
420.0	0	8	0	4
421.0	0	10	0	2
422.0	0	4	1	3
423.0	0	3	0	7
424.0	0	3	0	5
425.0	0	4	0	5
426.0	0	7	1	6
427.0	0	7	0	5
428.0	0	4	1	5
429.0	0	6	0	2
430.0	0	10	1	4
431.0	0	10	0	5
432.0	0	4	0	3
433.0	0	4	0	3
434.0	0	4	0	1
435.0	0	6	1	1
436.0	0	3	0	3
437.0	0	8	0	8
438.0	0	5	0	1
439.0	0	7	0	7
440.0	0	6	0	5
441.0	0	4	0	2
442.0	0	7	0	3
443.0	0	5	0	5
444.0	0	2	0	0
445.0	0	1	0	3
446.0	0	6	1	2
447.0	0	9	0	3
448.0	0	10	0	6
449.0	0	3	0	2
450.0	0	4	0	4
451.0	0	2	1	3
452.0	0	3	1	4
453.0	0	2	0	2
454.0	0	4	0	7
455.0	0	5	0	3
456.0	0	6	0	3
457.0	0	8	1	10
458.0	0	6	0	3
459.0	0	5	0	2
460.0	0	5	0	2
461.0	0	4	0	5
462.0	0	3	0	1
463.0	0	5	0	5
464.0	0	2	1	5
465.0	0	2	0	3
466.0	0	5	1	6
467.0	0	3	0	6
468.0	0	4	0	2
469.0	0	6	0	2
470.0	0	4	0	7
471.0	0	6	0	4
472.0	0	2	0	3
473.0	0	6	0	5
474.0	0	2	0	3
475.0	0	5	0	2
476.0	0	6	0	5
477.0	0	3	0	3
478.0	0	6	0	1
479.0	0	1	0	2
480.0	0	6	0	1
481.0	0	4	0	0
482.0	0	1	0	3
483.0	0	8	1	2
484.0	0	0	0	4
485.0	0	3	1	4
486.0	0	1	0	4
487.0	0	4	1	2
488.0	0	3	0	2
489.0	0	5	0	6
490.0	0	3	1	1
491.0	0	7	1	1
492.0	0	8	0	0
493.0	0	1	0	2
494.0	0	4	1	2
495.0	0	4	0	4
496.0	0	5	0	4
497.0	0	5	0	1
498.0	0	3	1	2
499.0	0	3	0	2
500.0	0	1	0	3
501.0	0	3	1	3
502.0	0	2	0	1
503.0	0	0	1	5
504.0	0	2	0	0
505.0	0	1	0	3
506.0	0	4	0	0
507.0	0	4	1	1
508.0	0	3	0	3
509.0	0	2	1	1
510.0	0	2	1	2
511.0	0	1	0	2
512.0	0	2	1	3
513.0	0	3	0	3
514.0	0	9	1	0
515.0	0	3	0	0
516.0	0	6	1	3
517.0	0	7	0	2
518.0	0	3	1	1
519.0	0	5	0	0
520.0	0	8	0	2
521.0	0	5	0	1
522.0	0	2	1	2
523.0	0	5	0	0
524.0	0	2	0	5
525.0	0	3	0	4
526.0	0	0	1	1
527.0	0	4	0	1
528.0	0	3	1	0
529.0	0	1	1	0
530.0	0	0	0	2
531.0	0	2	0	2
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