## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-74-TP3.bam --OUTPUT POR-74-TP3.md.bam --METRICS_FILE POR-74-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 18:17:56 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	4134	18475535	11829018	0	3937	14358571	3417142	0.777186	4238358

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.01632	2172389	0	2628336
2.0	1.029318	861912	562300	773295
3.0	1.029484	373075	206482	243225
4.0	1.029486	182546	100140	101769
5.0	1.029486	103799	55591	58669
6.0	1.029486	66438	33453	40530
7.0	1.029486	46708	22028	30494
8.0	1.029486	34518	14980	24211
9.0	1.029486	26955	10910	19520
10.0	1.029486	21561	8094	16330
11.0	1.029486	18117	6241	14100
12.0	1.029486	15321	4998	12028
13.0	1.029486	13346	4104	10429
14.0	1.029486	11638	3545	9290
15.0	1.029486	10081	2987	8187
16.0	1.029486	9031	2484	7340
17.0	1.029486	8175	2189	6537
18.0	1.029486	7303	1901	5982
19.0	1.029486	6728	1670	5232
20.0	1.029486	6221	1457	4946
21.0	1.029486	5532	1374	4404
22.0	1.029486	5163	1212	4118
23.0	1.029486	4597	1084	3732
24.0	1.029486	4330	1010	3597
25.0	1.029486	4027	854	3263
26.0	1.029486	3747	821	3054
27.0	1.029486	3477	683	2761
28.0	1.029486	3271	688	2688
29.0	1.029486	3060	591	2419
30.0	1.029486	2849	561	2336
31.0	1.029486	2871	512	2144
32.0	1.029486	2551	476	2052
33.0	1.029486	2437	467	2002
34.0	1.029486	2288	418	1829
35.0	1.029486	2215	410	1689
36.0	1.029486	2118	354	1610
37.0	1.029486	2001	377	1538
38.0	1.029486	1885	278	1490
39.0	1.029486	1717	284	1383
40.0	1.029486	1665	283	1344
41.0	1.029486	1598	281	1244
42.0	1.029486	1497	241	1153
43.0	1.029486	1488	227	1174
44.0	1.029486	1350	235	1104
45.0	1.029486	1304	207	1090
46.0	1.029486	1291	180	999
47.0	1.029486	1165	177	973
48.0	1.029486	1161	151	931
49.0	1.029486	1134	183	948
50.0	1.029486	1094	154	889
51.0	1.029486	1066	156	837
52.0	1.029486	1017	156	822
53.0	1.029486	1003	137	778
54.0	1.029486	921	147	768
55.0	1.029486	910	124	746
56.0	1.029486	816	127	692
57.0	1.029486	817	115	643
58.0	1.029486	821	111	644
59.0	1.029486	781	94	638
60.0	1.029486	757	106	595
61.0	1.029486	752	97	602
62.0	1.029486	741	88	536
63.0	1.029486	672	86	543
64.0	1.029486	668	92	563
65.0	1.029486	618	89	516
66.0	1.029486	636	79	496
67.0	1.029486	548	75	457
68.0	1.029486	589	84	492
69.0	1.029486	552	66	489
70.0	1.029486	584	56	408
71.0	1.029486	546	76	439
72.0	1.029486	550	72	405
73.0	1.029486	476	55	361
74.0	1.029486	507	60	380
75.0	1.029486	470	58	421
76.0	1.029486	467	51	381
77.0	1.029486	477	64	325
78.0	1.029486	429	53	323
79.0	1.029486	362	48	365
80.0	1.029486	439	50	349
81.0	1.029486	401	55	320
82.0	1.029486	386	35	290
83.0	1.029486	411	51	316
84.0	1.029486	366	35	270
85.0	1.029486	374	46	287
86.0	1.029486	374	29	280
87.0	1.029486	367	35	250
88.0	1.029486	345	35	278
89.0	1.029486	350	38	248
90.0	1.029486	302	41	263
91.0	1.029486	303	30	276
92.0	1.029486	302	38	241
93.0	1.029486	315	35	270
94.0	1.029486	333	42	260
95.0	1.029486	328	22	265
96.0	1.029486	304	30	219
97.0	1.029486	299	27	209
98.0	1.029486	278	25	194
99.0	1.029486	260	19	220
100.0	1.029486	236	24	213
101.0	0	263	33	199
102.0	0	262	23	186
103.0	0	258	25	202
104.0	0	263	28	189
105.0	0	220	30	188
106.0	0	236	24	171
107.0	0	229	17	191
108.0	0	202	30	176
109.0	0	235	16	154
110.0	0	189	18	171
111.0	0	200	23	169
112.0	0	204	19	163
113.0	0	203	21	162
114.0	0	174	25	142
115.0	0	179	17	133
116.0	0	170	17	158
117.0	0	221	18	151
118.0	0	198	19	162
119.0	0	168	22	134
120.0	0	178	12	137
121.0	0	163	12	144
122.0	0	175	24	123
123.0	0	169	20	131
124.0	0	156	14	141
125.0	0	132	18	109
126.0	0	144	7	110
127.0	0	139	14	115
128.0	0	157	21	116
129.0	0	154	14	113
130.0	0	159	8	108
131.0	0	141	16	109
132.0	0	144	18	112
133.0	0	158	7	108
134.0	0	115	11	87
135.0	0	132	12	99
136.0	0	127	11	104
137.0	0	137	9	115
138.0	0	120	6	109
139.0	0	117	11	94
140.0	0	136	14	97
141.0	0	116	11	97
142.0	0	101	11	93
143.0	0	130	13	96
144.0	0	102	10	95
145.0	0	119	9	79
146.0	0	118	8	99
147.0	0	110	11	91
148.0	0	110	9	90
149.0	0	101	9	89
150.0	0	109	14	81
151.0	0	97	9	80
152.0	0	113	4	88
153.0	0	87	11	79
154.0	0	91	9	81
155.0	0	103	19	81
156.0	0	96	9	70
157.0	0	87	6	79
158.0	0	98	11	87
159.0	0	96	8	81
160.0	0	86	5	64
161.0	0	95	9	68
162.0	0	89	9	57
163.0	0	102	7	68
164.0	0	100	6	68
165.0	0	77	7	78
166.0	0	98	7	69
167.0	0	78	8	66
168.0	0	82	6	56
169.0	0	94	9	74
170.0	0	82	8	51
171.0	0	80	4	73
172.0	0	93	6	66
173.0	0	84	4	61
174.0	0	66	8	65
175.0	0	75	7	63
176.0	0	81	5	55
177.0	0	73	7	46
178.0	0	86	6	49
179.0	0	78	8	60
180.0	0	66	4	50
181.0	0	66	1	48
182.0	0	70	1	54
183.0	0	64	10	41
184.0	0	61	4	61
185.0	0	56	6	40
186.0	0	66	4	52
187.0	0	50	4	49
188.0	0	71	6	48
189.0	0	64	4	42
190.0	0	63	6	54
191.0	0	63	8	40
192.0	0	62	3	41
193.0	0	50	3	36
194.0	0	61	6	57
195.0	0	49	6	54
196.0	0	51	6	44
197.0	0	65	2	38
198.0	0	63	1	36
199.0	0	45	5	45
200.0	0	57	4	43
201.0	0	57	5	48
202.0	0	48	4	44
203.0	0	50	4	42
204.0	0	53	3	49
205.0	0	52	1	38
206.0	0	60	4	30
207.0	0	51	6	38
208.0	0	50	1	39
209.0	0	51	5	63
210.0	0	63	1	50
211.0	0	39	1	36
212.0	0	49	4	42
213.0	0	46	2	48
214.0	0	48	3	30
215.0	0	52	2	49
216.0	0	38	5	34
217.0	0	39	3	41
218.0	0	37	3	39
219.0	0	42	3	39
220.0	0	51	2	40
221.0	0	51	4	35
222.0	0	52	5	27
223.0	0	48	4	41
224.0	0	47	1	30
225.0	0	30	3	27
226.0	0	50	3	22
227.0	0	48	3	35
228.0	0	37	2	35
229.0	0	35	4	32
230.0	0	41	5	30
231.0	0	40	2	32
232.0	0	53	0	26
233.0	0	37	4	36
234.0	0	38	2	34
235.0	0	41	2	40
236.0	0	38	3	31
237.0	0	30	3	26
238.0	0	38	2	29
239.0	0	41	0	30
240.0	0	33	1	30
241.0	0	39	2	30
242.0	0	39	4	29
243.0	0	42	2	32
244.0	0	40	1	30
245.0	0	47	3	27
246.0	0	35	2	26
247.0	0	27	2	23
248.0	0	28	0	15
249.0	0	30	4	26
250.0	0	44	0	15
251.0	0	30	1	24
252.0	0	29	4	27
253.0	0	25	3	26
254.0	0	28	3	18
255.0	0	25	1	27
256.0	0	24	1	31
257.0	0	28	1	26
258.0	0	29	1	22
259.0	0	26	3	26
260.0	0	35	2	22
261.0	0	35	2	22
262.0	0	32	0	19
263.0	0	30	4	21
264.0	0	31	4	16
265.0	0	23	4	26
266.0	0	28	3	24
267.0	0	16	6	13
268.0	0	26	3	27
269.0	0	26	2	30
270.0	0	35	0	31
271.0	0	30	1	21
272.0	0	22	0	27
273.0	0	29	3	30
274.0	0	22	0	15
275.0	0	18	0	22
276.0	0	28	1	19
277.0	0	26	2	17
278.0	0	31	2	18
279.0	0	27	3	13
280.0	0	19	2	18
281.0	0	22	3	14
282.0	0	27	2	18
283.0	0	25	0	18
284.0	0	17	1	17
285.0	0	25	2	20
286.0	0	15	0	21
287.0	0	23	3	27
288.0	0	28	2	22
289.0	0	26	1	13
290.0	0	29	1	24
291.0	0	16	1	17
292.0	0	17	4	19
293.0	0	16	3	12
294.0	0	20	0	16
295.0	0	33	1	22
296.0	0	20	0	20
297.0	0	19	1	13
298.0	0	17	2	26
299.0	0	22	0	21
300.0	0	16	1	20
301.0	0	24	1	15
302.0	0	27	4	13
303.0	0	27	0	24
304.0	0	19	1	14
305.0	0	25	4	15
306.0	0	27	1	7
307.0	0	25	4	10
308.0	0	18	2	13
309.0	0	22	0	16
310.0	0	22	2	19
311.0	0	14	1	14
312.0	0	19	1	15
313.0	0	22	0	9
314.0	0	20	2	10
315.0	0	13	2	14
316.0	0	18	1	17
317.0	0	21	0	13
318.0	0	27	1	12
319.0	0	20	3	17
320.0	0	20	2	12
321.0	0	11	3	15
322.0	0	18	2	13
323.0	0	23	1	23
324.0	0	15	0	20
325.0	0	15	1	15
326.0	0	17	1	17
327.0	0	19	1	23
328.0	0	13	1	15
329.0	0	11	1	19
330.0	0	20	0	15
331.0	0	20	0	20
332.0	0	19	0	11
333.0	0	17	1	19
334.0	0	14	1	9
335.0	0	18	0	13
336.0	0	17	0	12
337.0	0	13	0	12
338.0	0	17	0	11
339.0	0	26	1	13
340.0	0	21	3	14
341.0	0	19	5	8
342.0	0	24	0	9
343.0	0	16	1	13
344.0	0	10	0	11
345.0	0	17	1	13
346.0	0	15	0	9
347.0	0	15	2	12
348.0	0	15	0	14
349.0	0	16	0	12
350.0	0	19	2	14
351.0	0	13	0	14
352.0	0	21	0	9
353.0	0	10	0	10
354.0	0	10	2	13
355.0	0	20	1	7
356.0	0	13	2	7
357.0	0	12	0	11
358.0	0	14	0	12
359.0	0	17	1	8
360.0	0	8	3	12
361.0	0	15	1	10
362.0	0	11	2	12
363.0	0	16	1	17
364.0	0	14	0	6
365.0	0	13	0	15
366.0	0	14	0	10
367.0	0	12	0	13
368.0	0	10	2	9
369.0	0	13	0	8
370.0	0	15	0	7
371.0	0	13	1	6
372.0	0	12	2	4
373.0	0	8	2	10
374.0	0	9	1	13
375.0	0	13	0	13
376.0	0	12	0	13
377.0	0	17	0	7
378.0	0	8	0	10
379.0	0	7	0	7
380.0	0	10	2	5
381.0	0	13	0	14
382.0	0	12	0	9
383.0	0	9	0	5
384.0	0	9	0	7
385.0	0	8	0	11
386.0	0	13	1	8
387.0	0	13	0	10
388.0	0	10	0	12
389.0	0	14	1	10
390.0	0	16	1	10
391.0	0	14	1	9
392.0	0	11	0	10
393.0	0	11	1	12
394.0	0	13	0	14
395.0	0	6	0	9
396.0	0	11	0	9
397.0	0	12	1	12
398.0	0	11	0	9
399.0	0	13	1	8
400.0	0	11	0	8
401.0	0	10	0	9
402.0	0	7	1	7
403.0	0	16	0	9
404.0	0	18	1	7
405.0	0	11	0	2
406.0	0	12	1	6
407.0	0	12	0	9
408.0	0	11	1	8
409.0	0	8	0	12
410.0	0	8	0	9
411.0	0	14	1	10
412.0	0	13	1	8
413.0	0	5	0	12
414.0	0	11	0	6
415.0	0	10	0	12
416.0	0	5	1	13
417.0	0	12	1	6
418.0	0	11	0	11
419.0	0	15	1	11
420.0	0	10	0	2
421.0	0	11	1	5
422.0	0	15	2	10
423.0	0	9	0	10
424.0	0	8	0	11
425.0	0	9	0	5
426.0	0	11	0	9
427.0	0	7	0	7
428.0	0	8	0	8
429.0	0	22	0	4
430.0	0	15	0	7
431.0	0	6	0	6
432.0	0	2	0	7
433.0	0	7	0	5
434.0	0	13	1	9
435.0	0	9	0	7
436.0	0	5	0	6
437.0	0	12	0	6
438.0	0	11	1	5
439.0	0	13	0	9
440.0	0	14	0	12
441.0	0	10	0	11
442.0	0	5	0	10
443.0	0	7	0	6
444.0	0	8	0	4
445.0	0	9	1	8
446.0	0	9	0	9
447.0	0	3	0	5
448.0	0	8	1	2
449.0	0	6	0	10
450.0	0	6	1	7
451.0	0	11	0	4
452.0	0	7	1	5
453.0	0	4	1	5
454.0	0	7	0	5
455.0	0	9	0	3
456.0	0	11	0	5
457.0	0	8	0	4
458.0	0	8	0	5
459.0	0	5	0	8
460.0	0	5	0	2
461.0	0	10	0	4
462.0	0	4	0	3
463.0	0	7	0	7
464.0	0	16	0	4
465.0	0	2	1	8
466.0	0	4	0	6
467.0	0	9	0	4
468.0	0	4	1	4
469.0	0	9	0	14
470.0	0	5	2	8
471.0	0	12	1	3
472.0	0	5	0	3
473.0	0	5	0	5
474.0	0	10	0	9
475.0	0	5	0	7
476.0	0	7	1	9
477.0	0	6	0	5
478.0	0	3	1	1
479.0	0	14	0	2
480.0	0	7	0	5
481.0	0	6	0	3
482.0	0	11	0	3
483.0	0	3	0	5
484.0	0	9	0	6
485.0	0	9	0	3
486.0	0	9	0	2
487.0	0	3	0	4
488.0	0	9	0	3
489.0	0	7	0	2
490.0	0	8	0	4
491.0	0	6	0	9
492.0	0	8	0	3
493.0	0	4	0	4
494.0	0	6	1	4
495.0	0	7	0	3
496.0	0	5	0	2
497.0	0	8	0	5
498.0	0	3	0	5
499.0	0	5	0	4
500.0	0	10	0	5
501.0	0	4	0	6
502.0	0	3	0	6
503.0	0	3	0	6
504.0	0	5	0	7
505.0	0	8	0	3
506.0	0	6	0	9
507.0	0	2	0	4
508.0	0	5	0	9
509.0	0	1	0	3
510.0	0	8	0	6
511.0	0	6	0	6
512.0	0	4	0	6
513.0	0	7	0	5
514.0	0	6	0	5
515.0	0	8	0	2
516.0	0	5	1	3
517.0	0	5	0	6
518.0	0	5	1	3
519.0	0	6	0	6
520.0	0	4	0	6
521.0	0	1	0	2
522.0	0	2	0	5
523.0	0	6	0	4
524.0	0	2	2	8
525.0	0	6	1	1
526.0	0	7	0	6
527.0	0	3	0	3
528.0	0	7	0	3
529.0	0	4	0	2
530.0	0	2	1	4
531.0	0	5	0	5
532.0	0	7	0	6
533.0	0	3	0	3
534.0	0	6	0	4
535.0	0	4	0	5
536.0	0	4	0	6
537.0	0	4	1	4
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