## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-260-TP3.bam --OUTPUT POR-260-TP3.md.bam --METRICS_FILE POR-260-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 18:17:33 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	2321	14747591	8970013	0	2175	11042397	3106665	0.748774	3902914

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.029289	1932590	0	2399509
2.0	1.052813	781876	520144	701791
3.0	1.05335	346646	203800	215844
4.0	1.053363	175261	103095	88749
5.0	1.053363	100557	58039	50033
6.0	1.053363	64378	34432	34812
7.0	1.053363	44309	21782	25811
8.0	1.053363	32150	14778	20176
9.0	1.053363	24890	10214	16499
10.0	1.053363	19245	7560	13522
11.0	1.053363	16051	5794	11632
12.0	1.053363	13606	4516	9967
13.0	1.053363	11261	3716	8374
14.0	1.053363	10049	2947	7538
15.0	1.053363	8571	2472	6659
16.0	1.053363	7714	2095	5829
17.0	1.053363	6767	1913	5286
18.0	1.053363	6137	1603	4685
19.0	1.053363	5591	1407	4220
20.0	1.053363	5086	1238	3860
21.0	1.053363	4517	1112	3521
22.0	1.053363	4264	1016	3204
23.0	1.053363	3828	862	2887
24.0	1.053363	3566	804	2753
25.0	1.053363	3339	684	2608
26.0	1.053363	3044	696	2347
27.0	1.053363	2873	592	2093
28.0	1.053363	2691	517	2052
29.0	1.053363	2518	499	1873
30.0	1.053363	2303	457	1778
31.0	1.053363	2127	422	1604
32.0	1.053363	2013	417	1498
33.0	1.053363	1930	353	1444
34.0	1.053363	1719	326	1356
35.0	1.053363	1698	334	1305
36.0	1.053363	1639	311	1249
37.0	1.053363	1525	254	1147
38.0	1.053363	1482	222	1069
39.0	1.053363	1378	245	1023
40.0	1.053363	1299	219	988
41.0	1.053363	1213	203	1024
42.0	1.053363	1234	209	916
43.0	1.053363	1047	191	825
44.0	1.053363	1045	156	840
45.0	1.053363	1008	154	774
46.0	1.053363	948	160	765
47.0	1.053363	955	151	728
48.0	1.053363	884	156	683
49.0	1.053363	900	170	595
50.0	1.053363	858	122	631
51.0	1.053363	760	129	598
52.0	1.053363	797	122	584
53.0	1.053363	713	106	550
54.0	1.053363	680	119	551
55.0	1.053363	671	95	539
56.0	1.053363	656	96	523
57.0	1.053363	610	102	487
58.0	1.053363	612	82	455
59.0	1.053363	567	103	456
60.0	1.053363	541	76	433
61.0	1.053363	537	70	400
62.0	1.053363	492	69	399
63.0	1.053363	518	92	397
64.0	1.053363	540	62	397
65.0	1.053363	481	67	354
66.0	1.053363	484	53	361
67.0	1.053363	445	63	388
68.0	1.053363	446	55	336
69.0	1.053363	408	63	305
70.0	1.053363	402	58	312
71.0	1.053363	360	51	268
72.0	1.053363	353	57	271
73.0	1.053363	360	39	271
74.0	1.053363	364	52	283
75.0	1.053363	352	47	257
76.0	1.053363	373	34	280
77.0	1.053363	302	47	260
78.0	1.053363	322	39	253
79.0	1.053363	325	43	236
80.0	1.053363	265	37	233
81.0	1.053363	303	34	226
82.0	1.053363	304	37	227
83.0	1.053363	293	34	209
84.0	1.053363	279	30	183
85.0	1.053363	270	35	195
86.0	1.053363	280	30	195
87.0	1.053363	245	23	190
88.0	1.053363	234	27	180
89.0	1.053363	245	24	169
90.0	1.053363	233	23	148
91.0	1.053363	228	37	188
92.0	1.053363	220	24	171
93.0	1.053363	214	21	162
94.0	1.053363	208	21	167
95.0	1.053363	189	16	147
96.0	1.053363	194	18	136
97.0	1.053363	195	22	153
98.0	1.053363	206	28	146
99.0	1.053363	189	25	135
100.0	1.053363	155	24	157
101.0	0	183	18	136
102.0	0	169	13	129
103.0	0	182	22	106
104.0	0	157	15	124
105.0	0	147	16	115
106.0	0	172	19	136
107.0	0	159	21	143
108.0	0	131	14	122
109.0	0	150	15	121
110.0	0	176	15	105
111.0	0	149	22	118
112.0	0	141	14	116
113.0	0	139	8	92
114.0	0	132	18	110
115.0	0	130	12	96
116.0	0	152	11	92
117.0	0	142	18	97
118.0	0	144	7	89
119.0	0	131	11	79
120.0	0	129	24	88
121.0	0	124	13	74
122.0	0	134	7	88
123.0	0	98	6	83
124.0	0	87	13	78
125.0	0	115	5	87
126.0	0	106	10	98
127.0	0	112	12	89
128.0	0	89	16	82
129.0	0	113	5	82
130.0	0	108	4	79
131.0	0	95	12	74
132.0	0	93	7	88
133.0	0	97	9	78
134.0	0	106	8	64
135.0	0	101	14	79
136.0	0	96	10	47
137.0	0	89	8	67
138.0	0	83	12	57
139.0	0	88	5	76
140.0	0	69	12	70
141.0	0	84	6	75
142.0	0	69	13	76
143.0	0	99	8	55
144.0	0	71	10	50
145.0	0	95	6	51
146.0	0	67	11	65
147.0	0	82	8	66
148.0	0	77	5	57
149.0	0	79	3	64
150.0	0	82	3	51
151.0	0	80	5	54
152.0	0	62	11	53
153.0	0	68	7	46
154.0	0	78	10	54
155.0	0	60	8	59
156.0	0	57	5	59
157.0	0	72	7	41
158.0	0	82	6	48
159.0	0	64	8	55
160.0	0	73	2	51
161.0	0	69	4	41
162.0	0	56	9	38
163.0	0	59	2	33
164.0	0	65	4	48
165.0	0	66	1	48
166.0	0	69	6	53
167.0	0	72	2	41
168.0	0	50	3	45
169.0	0	52	2	47
170.0	0	59	6	32
171.0	0	51	5	48
172.0	0	52	4	37
173.0	0	51	11	41
174.0	0	54	8	62
175.0	0	48	2	46
176.0	0	52	4	38
177.0	0	39	7	36
178.0	0	42	3	37
179.0	0	55	6	28
180.0	0	48	5	30
181.0	0	44	5	35
182.0	0	42	3	38
183.0	0	42	2	40
184.0	0	50	0	36
185.0	0	55	2	37
186.0	0	50	3	23
187.0	0	39	0	34
188.0	0	42	2	21
189.0	0	59	3	38
190.0	0	50	5	31
191.0	0	29	4	36
192.0	0	40	7	30
193.0	0	42	4	26
194.0	0	35	3	42
195.0	0	41	3	32
196.0	0	45	5	28
197.0	0	32	0	33
198.0	0	32	4	39
199.0	0	44	3	26
200.0	0	34	2	28
201.0	0	35	3	25
202.0	0	31	2	38
203.0	0	40	5	31
204.0	0	30	0	30
205.0	0	40	2	21
206.0	0	40	2	28
207.0	0	33	5	30
208.0	0	28	4	27
209.0	0	39	2	15
210.0	0	31	4	26
211.0	0	38	4	32
212.0	0	39	5	25
213.0	0	32	4	20
214.0	0	37	3	22
215.0	0	25	2	25
216.0	0	31	2	25
217.0	0	41	2	13
218.0	0	33	1	23
219.0	0	34	3	18
220.0	0	24	2	18
221.0	0	20	3	21
222.0	0	30	1	18
223.0	0	25	1	18
224.0	0	26	2	26
225.0	0	30	0	14
226.0	0	25	1	18
227.0	0	27	1	29
228.0	0	23	1	21
229.0	0	30	2	21
230.0	0	23	1	23
231.0	0	21	1	16
232.0	0	30	0	20
233.0	0	24	0	20
234.0	0	25	2	29
235.0	0	29	2	23
236.0	0	17	2	24
237.0	0	39	0	15
238.0	0	25	3	22
239.0	0	25	2	21
240.0	0	31	0	21
241.0	0	32	2	18
242.0	0	28	1	8
243.0	0	29	3	20
244.0	0	14	2	10
245.0	0	24	2	15
246.0	0	17	2	17
247.0	0	23	0	15
248.0	0	20	1	8
249.0	0	19	3	8
250.0	0	24	1	24
251.0	0	20	2	20
252.0	0	25	2	20
253.0	0	25	1	13
254.0	0	17	3	13
255.0	0	24	2	21
256.0	0	24	2	18
257.0	0	18	0	7
258.0	0	16	1	17
259.0	0	18	2	8
260.0	0	20	2	17
261.0	0	21	4	14
262.0	0	22	2	11
263.0	0	17	2	12
264.0	0	22	1	18
265.0	0	22	1	19
266.0	0	26	2	11
267.0	0	14	1	7
268.0	0	17	2	16
269.0	0	19	2	8
270.0	0	17	2	15
271.0	0	13	1	19
272.0	0	11	3	14
273.0	0	15	1	9
274.0	0	15	2	14
275.0	0	19	2	17
276.0	0	17	1	18
277.0	0	24	1	15
278.0	0	14	1	12
279.0	0	17	2	13
280.0	0	9	0	9
281.0	0	17	0	11
282.0	0	7	1	18
283.0	0	17	2	13
284.0	0	16	1	17
285.0	0	18	0	14
286.0	0	17	2	9
287.0	0	15	1	8
288.0	0	14	1	15
289.0	0	11	1	12
290.0	0	15	2	12
291.0	0	15	2	12
292.0	0	11	0	11
293.0	0	15	0	10
294.0	0	11	1	12
295.0	0	20	1	10
296.0	0	15	0	11
297.0	0	7	1	10
298.0	0	13	0	15
299.0	0	16	0	14
300.0	0	14	0	13
301.0	0	13	1	7
302.0	0	16	1	11
303.0	0	7	3	9
304.0	0	10	1	6
305.0	0	14	1	11
306.0	0	14	1	7
307.0	0	10	0	13
308.0	0	10	2	14
309.0	0	9	1	9
310.0	0	15	1	12
311.0	0	15	0	7
312.0	0	11	2	10
313.0	0	13	0	11
314.0	0	16	0	8
315.0	0	13	1	8
316.0	0	13	0	11
317.0	0	5	2	11
318.0	0	12	0	9
319.0	0	14	0	9
320.0	0	18	0	7
321.0	0	9	0	12
322.0	0	11	0	9
323.0	0	8	0	8
324.0	0	10	0	12
325.0	0	12	0	6
326.0	0	18	0	12
327.0	0	8	1	7
328.0	0	9	0	9
329.0	0	7	0	10
330.0	0	12	1	6
331.0	0	13	0	5
332.0	0	11	0	10
333.0	0	11	2	10
334.0	0	11	1	4
335.0	0	12	0	8
336.0	0	10	1	2
337.0	0	12	3	11
338.0	0	10	0	9
339.0	0	11	0	10
340.0	0	11	0	8
341.0	0	12	0	8
342.0	0	13	1	7
343.0	0	8	1	6
344.0	0	10	0	11
345.0	0	10	0	7
346.0	0	13	0	2
347.0	0	7	0	8
348.0	0	7	0	11
349.0	0	11	0	9
350.0	0	15	1	5
351.0	0	10	0	2
352.0	0	9	0	8
353.0	0	6	1	10
354.0	0	10	0	8
355.0	0	10	0	5
356.0	0	15	1	10
357.0	0	9	0	3
358.0	0	14	2	9
359.0	0	9	0	9
360.0	0	10	0	8
361.0	0	8	1	3
362.0	0	9	1	6
363.0	0	5	1	1
364.0	0	4	1	10
365.0	0	7	0	9
366.0	0	7	0	5
367.0	0	1	1	6
368.0	0	7	0	4
369.0	0	10	1	6
370.0	0	9	0	8
371.0	0	8	1	8
372.0	0	9	0	7
373.0	0	14	0	10
374.0	0	10	0	6
375.0	0	7	2	7
376.0	0	5	1	9
377.0	0	9	0	5
378.0	0	7	0	8
379.0	0	6	0	4
380.0	0	7	1	4
381.0	0	9	0	7
382.0	0	6	0	9
383.0	0	6	0	3
384.0	0	11	0	4
385.0	0	7	0	5
386.0	0	4	0	5
387.0	0	8	0	1
388.0	0	3	0	7
389.0	0	9	0	9
390.0	0	5	1	3
391.0	0	13	1	4
392.0	0	13	0	4
393.0	0	3	0	8
394.0	0	5	0	4
395.0	0	4	0	4
396.0	0	8	0	10
397.0	0	11	0	7
398.0	0	8	1	7
399.0	0	3	0	3
400.0	0	7	1	6
401.0	0	9	0	5
402.0	0	8	0	7
403.0	0	3	0	6
404.0	0	9	0	6
405.0	0	3	1	5
406.0	0	7	0	2
407.0	0	11	1	5
408.0	0	6	0	4
409.0	0	1	1	7
410.0	0	6	0	8
411.0	0	11	1	6
412.0	0	9	0	8
413.0	0	5	0	6
414.0	0	5	0	5
415.0	0	9	0	2
416.0	0	5	0	3
417.0	0	10	0	5
418.0	0	5	1	2
419.0	0	8	0	5
420.0	0	7	0	10
421.0	0	5	0	3
422.0	0	7	0	1
423.0	0	6	1	3
424.0	0	6	0	4
425.0	0	5	0	4
426.0	0	7	0	5
427.0	0	7	0	5
428.0	0	4	0	2
429.0	0	5	0	6
430.0	0	7	0	6
431.0	0	8	0	8
432.0	0	5	0	5
433.0	0	7	0	5
434.0	0	8	0	5
435.0	0	6	0	6
436.0	0	2	1	3
437.0	0	4	0	5
438.0	0	8	0	2
439.0	0	4	1	3
440.0	0	4	1	3
441.0	0	7	0	4
442.0	0	3	0	5
443.0	0	3	0	6
444.0	0	5	0	6
445.0	0	8	0	5
446.0	0	7	1	8
447.0	0	0	1	4
448.0	0	8	0	2
449.0	0	3	1	7
450.0	0	6	0	2
451.0	0	3	0	6
452.0	0	7	0	4
453.0	0	6	0	1
454.0	0	7	0	5
455.0	0	4	0	8
456.0	0	3	1	5
457.0	0	4	0	4
458.0	0	6	1	5
459.0	0	3	0	3
460.0	0	3	0	1
461.0	0	3	1	0
462.0	0	3	0	5
463.0	0	7	0	2
464.0	0	8	0	3
465.0	0	6	0	2
466.0	0	4	0	5
467.0	0	6	1	2
468.0	0	5	0	0
469.0	0	6	0	6
470.0	0	4	2	3
471.0	0	3	1	1
472.0	0	2	0	3
473.0	0	7	0	4
474.0	0	5	0	3
475.0	0	4	0	3
476.0	0	3	0	4
477.0	0	7	1	3
478.0	0	5	0	0
479.0	0	3	0	1
480.0	0	5	0	3
481.0	0	6	0	5
482.0	0	4	0	5
483.0	0	5	1	5
484.0	0	2	0	3
485.0	0	2	0	1
486.0	0	3	1	3
487.0	0	3	0	3
488.0	0	6	0	2
489.0	0	4	0	4
490.0	0	2	0	4
491.0	0	1	0	0
492.0	0	7	0	5
493.0	0	4	0	10
494.0	0	5	1	4
495.0	0	3	0	0
496.0	0	5	1	2
497.0	0	7	0	4
498.0	0	4	0	0
499.0	0	4	0	2
500.0	0	5	0	2
501.0	0	7	0	1
502.0	0	6	1	1
503.0	0	5	0	3
504.0	0	4	0	3
505.0	0	5	0	5
506.0	0	3	0	6
507.0	0	7	0	0
508.0	0	0	0	2
509.0	0	2	0	3
510.0	0	4	0	5
511.0	0	1	0	1
512.0	0	5	0	2
513.0	0	3	0	2
514.0	0	4	1	3
515.0	0	2	0	3
516.0	0	2	0	3
517.0	0	2	0	0
518.0	0	4	0	3
519.0	0	4	1	4
520.0	0	3	1	2
521.0	0	3	0	3
522.0	0	2	0	3
523.0	0	7	0	3
524.0	0	2	0	1
525.0	0	2	1	0
526.0	0	4	0	2
527.0	0	4	0	2
528.0	0	2	0	1
529.0	0	2	0	2
530.0	0	2	0	2
531.0	0	5	0	0
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1716.0	0	2	0	0
1728.0	0	1	0	0
1734.0	0	0	0	1
1745.0	0	0	0	1
1746.0	0	1	0	0
1750.0	0	1	0	0
1768.0	0	1	0	0
1776.0	0	1	0	0
1790.0	0	1	0	1
1806.0	0	0	0	1
1812.0	0	0	0	1
1814.0	0	0	0	1
1823.0	0	1	0	0
1826.0	0	1	0	0
1831.0	0	0	0	1
1839.0	0	1	0	0
1844.0	0	1	0	0
1849.0	0	1	0	0
1862.0	0	1	0	1
1866.0	0	0	0	1
1871.0	0	0	0	1
1874.0	0	1	0	0
1881.0	0	0	0	1
1896.0	0	0	0	1
1914.0	0	2	0	0
1929.0	0	1	0	0
1939.0	0	1	0	0
1942.0	0	1	0	0
1959.0	0	1	0	0
1968.0	0	1	0	0
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2025.0	0	0	0	1
2038.0	0	1	0	0
2051.0	0	1	0	0
2064.0	0	1	0	0
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2100.0	0	0	0	1
2154.0	0	0	0	1
2200.0	0	0	0	1
2234.0	0	0	0	1
2294.0	0	0	0	1
2296.0	0	1	0	0
2309.0	0	1	0	0
2356.0	0	1	0	0
2368.0	0	0	0	1
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2465.0	0	1	0	0
2472.0	0	1	0	0
2474.0	0	1	0	0
2480.0	0	0	0	1
2482.0	0	0	0	1
2546.0	0	1	0	0
2567.0	0	0	0	1
2569.0	0	1	0	0
2575.0	0	1	0	0
2580.0	0	0	0	1
2582.0	0	0	0	1
2620.0	0	1	0	0
2623.0	0	1	0	0
2674.0	0	0	0	1
2690.0	0	1	0	0
2716.0	0	1	0	0
2750.0	0	0	0	1
2847.0	0	0	0	1
2862.0	0	1	0	0
2883.0	0	1	0	0
2907.0	0	1	0	0
2919.0	0	1	0	0
2976.0	0	1	0	0
2979.0	0	0	0	1
3044.0	0	1	0	0
3130.0	0	1	0	0
3169.0	0	1	0	0
3223.0	0	0	0	1
3235.0	0	0	0	1
3357.0	0	1	0	0
3404.0	0	1	0	0
3440.0	0	0	0	1
3489.0	0	0	0	1
3616.0	0	1	0	0
3708.0	0	1	0	0
3910.0	0	1	0	0
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4541.0	0	1	0	0
6793.0	0	0	0	1
7100.0	0	1	0	0