## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-73-TP3.bam --OUTPUT POR-73-TP3.md.bam --METRICS_FILE POR-73-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 18:17:44 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	3297	16639186	12345432	0	3222	14537776	3376861	0.873717	2105277

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.00147	916514	0	1132456
2.0	1.00184	389367	302567	372505
3.0	1.00184	191228	134214	145186
4.0	1.00184	110942	75116	77306
5.0	1.00184	72833	46487	51082
6.0	1.00184	52061	30612	37717
7.0	1.00184	39921	21574	29914
8.0	1.00184	31872	15767	24016
9.0	1.00184	25862	11906	20073
10.0	1.00184	21520	9479	16886
11.0	1.00184	18684	7540	14439
12.0	1.00184	16089	6331	12264
13.0	1.00184	13919	5188	10925
14.0	1.00184	12217	4275	9642
15.0	1.00184	10774	3726	8613
16.0	1.00184	9795	3145	7729
17.0	1.00184	8816	2758	7005
18.0	1.00184	7957	2479	6201
19.0	1.00184	7299	2175	5912
20.0	1.00184	6554	1908	5234
21.0	1.00184	6163	1724	4722
22.0	1.00184	5628	1511	4517
23.0	1.00184	5113	1417	4018
24.0	1.00184	4833	1223	3777
25.0	1.00184	4494	1150	3572
26.0	1.00184	4368	1039	3417
27.0	1.00184	3889	936	3035
28.0	1.00184	3680	907	2775
29.0	1.00184	3444	847	2659
30.0	1.00184	3238	732	2407
31.0	1.00184	2964	728	2308
32.0	1.00184	2873	615	2188
33.0	1.00184	2688	632	2147
34.0	1.00184	2563	529	1977
35.0	1.00184	2407	522	1858
36.0	1.00184	2371	477	1773
37.0	1.00184	2115	466	1693
38.0	1.00184	2056	442	1600
39.0	1.00184	1977	399	1599
40.0	1.00184	1847	375	1528
41.0	1.00184	1887	323	1405
42.0	1.00184	1782	340	1413
43.0	1.00184	1671	317	1271
44.0	1.00184	1585	313	1201
45.0	1.00184	1458	279	1163
46.0	1.00184	1448	262	1143
47.0	1.00184	1419	252	1117
48.0	1.00184	1311	254	1047
49.0	1.00184	1269	217	997
50.0	1.00184	1266	217	995
51.0	1.00184	1182	217	948
52.0	1.00184	1104	213	865
53.0	1.00184	1147	182	863
54.0	1.00184	1021	181	775
55.0	1.00184	966	186	765
56.0	1.00184	1023	169	778
57.0	1.00184	997	143	803
58.0	1.00184	927	164	685
59.0	1.00184	880	147	726
60.0	1.00184	867	140	657
61.0	1.00184	851	165	668
62.0	1.00184	846	140	652
63.0	1.00184	754	131	606
64.0	1.00184	755	117	589
65.0	1.00184	749	129	546
66.0	1.00184	732	94	598
67.0	1.00184	749	95	536
68.0	1.00184	687	97	527
69.0	1.00184	670	90	483
70.0	1.00184	637	89	458
71.0	1.00184	566	99	488
72.0	1.00184	591	91	459
73.0	1.00184	580	79	438
74.0	1.00184	563	101	448
75.0	1.00184	552	79	465
76.0	1.00184	518	68	407
77.0	1.00184	547	80	415
78.0	1.00184	486	68	396
79.0	1.00184	466	76	390
80.0	1.00184	462	76	334
81.0	1.00184	470	52	384
82.0	1.00184	447	59	359
83.0	1.00184	464	59	310
84.0	1.00184	434	75	364
85.0	1.00184	426	74	333
86.0	1.00184	408	76	316
87.0	1.00184	409	50	294
88.0	1.00184	431	58	317
89.0	1.00184	423	39	289
90.0	1.00184	362	53	285
91.0	1.00184	365	52	289
92.0	1.00184	391	51	270
93.0	1.00184	345	39	236
94.0	1.00184	345	50	252
95.0	1.00184	325	37	250
96.0	1.00184	322	41	264
97.0	1.00184	328	42	249
98.0	1.00184	258	31	240
99.0	1.00184	297	33	218
100.0	1.00184	288	35	230
101.0	0	277	35	222
102.0	0	282	46	225
103.0	0	319	39	215
104.0	0	270	39	228
105.0	0	271	36	199
106.0	0	254	33	202
107.0	0	258	31	198
108.0	0	249	22	192
109.0	0	254	30	199
110.0	0	234	33	193
111.0	0	256	22	193
112.0	0	226	31	165
113.0	0	206	30	155
114.0	0	213	22	187
115.0	0	268	33	169
116.0	0	223	25	159
117.0	0	218	30	151
118.0	0	238	20	140
119.0	0	209	25	151
120.0	0	195	29	173
121.0	0	222	28	162
122.0	0	186	22	155
123.0	0	190	24	154
124.0	0	172	16	134
125.0	0	208	15	141
126.0	0	189	18	143
127.0	0	172	25	109
128.0	0	186	15	154
129.0	0	177	20	140
130.0	0	162	17	118
131.0	0	177	21	125
132.0	0	177	17	126
133.0	0	143	19	117
134.0	0	147	16	137
135.0	0	161	14	127
136.0	0	170	17	129
137.0	0	149	17	119
138.0	0	170	13	125
139.0	0	172	19	105
140.0	0	126	28	103
141.0	0	132	16	121
142.0	0	162	16	107
143.0	0	137	8	103
144.0	0	123	8	86
145.0	0	125	16	102
146.0	0	124	12	108
147.0	0	144	14	96
148.0	0	121	15	104
149.0	0	118	13	87
150.0	0	150	10	108
151.0	0	128	14	98
152.0	0	122	17	99
153.0	0	113	13	106
154.0	0	101	12	87
155.0	0	119	10	96
156.0	0	117	10	99
157.0	0	96	7	68
158.0	0	135	7	83
159.0	0	122	16	67
160.0	0	103	15	86
161.0	0	99	12	76
162.0	0	96	8	69
163.0	0	102	7	107
164.0	0	95	7	106
165.0	0	111	11	68
166.0	0	92	5	73
167.0	0	90	9	79
168.0	0	104	6	68
169.0	0	83	6	60
170.0	0	95	12	62
171.0	0	118	15	64
172.0	0	113	12	70
173.0	0	87	13	63
174.0	0	80	7	68
175.0	0	72	8	53
176.0	0	98	10	78
177.0	0	89	5	69
178.0	0	88	5	82
179.0	0	76	7	73
180.0	0	78	11	75
181.0	0	79	9	48
182.0	0	87	9	55
183.0	0	77	10	58
184.0	0	81	7	68
185.0	0	69	6	67
186.0	0	68	3	51
187.0	0	80	7	42
188.0	0	79	13	59
189.0	0	68	9	63
190.0	0	56	4	39
191.0	0	73	8	64
192.0	0	89	6	58
193.0	0	72	2	50
194.0	0	66	3	43
195.0	0	79	7	56
196.0	0	58	6	52
197.0	0	59	7	62
198.0	0	67	7	49
199.0	0	62	8	47
200.0	0	79	2	62
201.0	0	70	8	38
202.0	0	60	4	48
203.0	0	61	7	47
204.0	0	73	4	47
205.0	0	58	9	41
206.0	0	50	9	52
207.0	0	62	2	46
208.0	0	65	6	49
209.0	0	46	6	39
210.0	0	63	3	50
211.0	0	59	4	41
212.0	0	65	3	43
213.0	0	47	5	41
214.0	0	43	5	28
215.0	0	50	5	39
216.0	0	49	5	38
217.0	0	47	8	50
218.0	0	51	7	35
219.0	0	35	6	46
220.0	0	49	5	36
221.0	0	58	4	40
222.0	0	45	8	33
223.0	0	49	4	34
224.0	0	57	9	37
225.0	0	42	3	43
226.0	0	36	2	43
227.0	0	39	4	33
228.0	0	48	5	38
229.0	0	48	6	38
230.0	0	46	5	32
231.0	0	47	3	26
232.0	0	41	4	32
233.0	0	46	4	21
234.0	0	48	4	22
235.0	0	46	2	43
236.0	0	38	4	26
237.0	0	38	5	32
238.0	0	30	4	41
239.0	0	40	2	28
240.0	0	33	5	34
241.0	0	43	5	29
242.0	0	35	3	30
243.0	0	38	5	35
244.0	0	38	3	32
245.0	0	40	7	24
246.0	0	53	6	33
247.0	0	39	1	29
248.0	0	42	5	25
249.0	0	43	1	35
250.0	0	42	1	34
251.0	0	42	1	27
252.0	0	38	4	42
253.0	0	42	3	27
254.0	0	47	3	29
255.0	0	43	4	30
256.0	0	35	6	29
257.0	0	30	3	25
258.0	0	35	4	25
259.0	0	33	2	23
260.0	0	36	0	24
261.0	0	42	1	22
262.0	0	34	0	25
263.0	0	42	0	32
264.0	0	36	3	31
265.0	0	36	4	30
266.0	0	34	4	38
267.0	0	29	2	14
268.0	0	34	3	25
269.0	0	31	5	29
270.0	0	31	2	23
271.0	0	21	0	29
272.0	0	40	3	22
273.0	0	33	3	22
274.0	0	38	3	18
275.0	0	36	4	23
276.0	0	29	1	22
277.0	0	32	2	25
278.0	0	27	2	30
279.0	0	31	2	22
280.0	0	34	3	23
281.0	0	25	1	39
282.0	0	24	2	19
283.0	0	32	3	26
284.0	0	37	1	19
285.0	0	29	3	21
286.0	0	34	2	26
287.0	0	23	1	40
288.0	0	20	1	11
289.0	0	22	5	28
290.0	0	31	0	18
291.0	0	42	3	22
292.0	0	27	1	19
293.0	0	30	1	20
294.0	0	38	2	25
295.0	0	24	7	14
296.0	0	24	6	21
297.0	0	22	4	23
298.0	0	21	3	22
299.0	0	32	1	17
300.0	0	30	1	26
301.0	0	26	1	20
302.0	0	26	0	23
303.0	0	29	2	21
304.0	0	30	5	24
305.0	0	32	2	12
306.0	0	25	2	15
307.0	0	15	1	17
308.0	0	23	2	17
309.0	0	16	1	21
310.0	0	27	1	14
311.0	0	23	2	16
312.0	0	26	0	10
313.0	0	26	2	17
314.0	0	25	0	18
315.0	0	21	1	16
316.0	0	26	1	18
317.0	0	22	3	16
318.0	0	17	0	18
319.0	0	25	3	18
320.0	0	19	1	14
321.0	0	25	1	16
322.0	0	30	0	18
323.0	0	18	2	12
324.0	0	16	0	11
325.0	0	28	2	16
326.0	0	13	1	16
327.0	0	27	3	13
328.0	0	18	1	20
329.0	0	23	0	21
330.0	0	21	0	21
331.0	0	23	0	17
332.0	0	17	0	15
333.0	0	12	1	18
334.0	0	14	1	22
335.0	0	28	0	14
336.0	0	23	2	9
337.0	0	14	0	6
338.0	0	19	1	12
339.0	0	21	2	13
340.0	0	18	1	20
341.0	0	27	0	17
342.0	0	23	0	18
343.0	0	15	3	10
344.0	0	11	0	10
345.0	0	20	0	9
346.0	0	13	2	14
347.0	0	15	2	15
348.0	0	17	1	12
349.0	0	15	1	10
350.0	0	17	1	15
351.0	0	13	0	10
352.0	0	22	2	17
353.0	0	19	2	15
354.0	0	13	0	13
355.0	0	16	0	8
356.0	0	20	1	22
357.0	0	21	0	12
358.0	0	17	4	9
359.0	0	25	1	8
360.0	0	16	3	9
361.0	0	10	2	10
362.0	0	19	1	17
363.0	0	23	2	13
364.0	0	10	2	8
365.0	0	22	0	10
366.0	0	16	1	13
367.0	0	18	0	11
368.0	0	15	2	12
369.0	0	20	2	16
370.0	0	23	1	11
371.0	0	10	1	11
372.0	0	12	0	12
373.0	0	9	0	10
374.0	0	17	1	15
375.0	0	12	0	12
376.0	0	15	4	9
377.0	0	14	0	12
378.0	0	15	1	12
379.0	0	14	1	14
380.0	0	15	1	10
381.0	0	10	1	11
382.0	0	16	1	11
383.0	0	17	0	16
384.0	0	9	2	11
385.0	0	11	2	11
386.0	0	5	1	12
387.0	0	11	0	15
388.0	0	5	0	7
389.0	0	11	3	9
390.0	0	14	0	8
391.0	0	13	2	12
392.0	0	12	0	13
393.0	0	9	2	10
394.0	0	10	1	7
395.0	0	16	1	12
396.0	0	18	0	12
397.0	0	19	1	5
398.0	0	18	3	4
399.0	0	8	1	12
400.0	0	14	0	8
401.0	0	10	2	7
402.0	0	14	1	7
403.0	0	10	1	10
404.0	0	10	3	12
405.0	0	11	0	9
406.0	0	6	2	14
407.0	0	11	0	7
408.0	0	15	1	15
409.0	0	14	0	10
410.0	0	15	0	10
411.0	0	13	0	4
412.0	0	12	0	10
413.0	0	10	0	14
414.0	0	10	1	8
415.0	0	11	2	8
416.0	0	13	0	6
417.0	0	11	1	8
418.0	0	12	0	11
419.0	0	10	2	9
420.0	0	10	0	11
421.0	0	17	2	5
422.0	0	7	2	5
423.0	0	10	0	3
424.0	0	11	1	9
425.0	0	6	1	8
426.0	0	10	0	5
427.0	0	13	0	9
428.0	0	12	1	10
429.0	0	11	2	6
430.0	0	15	1	14
431.0	0	9	0	10
432.0	0	14	0	10
433.0	0	8	0	3
434.0	0	8	0	7
435.0	0	9	1	6
436.0	0	9	0	10
437.0	0	9	0	8
438.0	0	6	1	8
439.0	0	12	0	9
440.0	0	9	2	7
441.0	0	9	0	9
442.0	0	11	0	7
443.0	0	9	1	10
444.0	0	16	0	8
445.0	0	9	1	9
446.0	0	8	1	5
447.0	0	7	2	14
448.0	0	11	1	10
449.0	0	9	1	8
450.0	0	8	0	6
451.0	0	11	0	10
452.0	0	8	0	3
453.0	0	7	0	7
454.0	0	13	0	12
455.0	0	9	1	4
456.0	0	8	0	8
457.0	0	11	0	11
458.0	0	7	0	5
459.0	0	7	1	7
460.0	0	7	1	6
461.0	0	10	0	5
462.0	0	8	2	5
463.0	0	11	0	5
464.0	0	9	1	7
465.0	0	12	2	4
466.0	0	10	0	4
467.0	0	5	0	4
468.0	0	7	1	3
469.0	0	5	0	9
470.0	0	11	0	7
471.0	0	12	1	5
472.0	0	7	0	6
473.0	0	5	0	8
474.0	0	11	0	8
475.0	0	9	0	7
476.0	0	9	0	8
477.0	0	8	0	7
478.0	0	10	1	4
479.0	0	9	0	5
480.0	0	10	0	8
481.0	0	9	2	6
482.0	0	10	0	7
483.0	0	7	1	11
484.0	0	4	0	11
485.0	0	7	2	6
486.0	0	6	0	8
487.0	0	12	0	6
488.0	0	11	0	3
489.0	0	6	1	8
490.0	0	7	0	6
491.0	0	9	1	4
492.0	0	8	0	9
493.0	0	10	0	5
494.0	0	5	0	4
495.0	0	12	0	4
496.0	0	5	0	4
497.0	0	7	0	6
498.0	0	8	0	6
499.0	0	6	0	3
500.0	0	3	0	3
501.0	0	9	1	4
502.0	0	11	0	4
503.0	0	11	0	7
504.0	0	7	1	3
505.0	0	9	0	1
506.0	0	10	1	5
507.0	0	6	0	6
508.0	0	7	0	1
509.0	0	7	0	3
510.0	0	8	0	4
511.0	0	8	2	6
512.0	0	7	0	8
513.0	0	12	0	2
514.0	0	5	2	7
515.0	0	1	0	7
516.0	0	8	1	11
517.0	0	4	0	6
518.0	0	6	0	5
519.0	0	7	0	5
520.0	0	8	0	3
521.0	0	6	1	7
522.0	0	8	1	6
523.0	0	6	0	6
524.0	0	2	0	3
525.0	0	5	0	5
526.0	0	3	0	9
527.0	0	10	0	7
528.0	0	5	0	2
529.0	0	3	0	3
530.0	0	3	0	4
531.0	0	9	1	9
532.0	0	7	0	2
533.0	0	5	1	4
534.0	0	8	0	3
535.0	0	6	0	5
536.0	0	12	0	7
537.0	0	6	0	8
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