## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-73-TP2.bam --OUTPUT POR-73-TP2.md.bam --METRICS_FILE POR-73-TP2.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 18:18:35 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	3255	18516078	12317955	0	3148	15315445	3694639	0.827155	3233679

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.007031	1597509	0	1983007
2.0	1.010314	631402	468147	549583
3.0	1.010325	285641	186578	186741
4.0	1.010325	152145	94412	91550
5.0	1.010325	92853	54690	58129
6.0	1.010325	62609	34052	41645
7.0	1.010325	45457	22937	31824
8.0	1.010325	35070	16233	25556
9.0	1.010325	28053	11893	21054
10.0	1.010325	22778	9117	17486
11.0	1.010325	19158	7230	14794
12.0	1.010325	16222	5852	12757
13.0	1.010325	14342	4977	11057
14.0	1.010325	12422	4120	9772
15.0	1.010325	11042	3462	8773
16.0	1.010325	9796	3032	7834
17.0	1.010325	8767	2580	6934
18.0	1.010325	7819	2393	6355
19.0	1.010325	7101	2075	5682
20.0	1.010325	6705	1826	5141
21.0	1.010325	5996	1624	4701
22.0	1.010325	5379	1448	4396
23.0	1.010325	5106	1284	4185
24.0	1.010325	4819	1152	3889
25.0	1.010325	4452	1112	3428
26.0	1.010325	4107	991	3136
27.0	1.010325	3871	919	3005
28.0	1.010325	3613	810	2791
29.0	1.010325	3357	780	2630
30.0	1.010325	3145	703	2492
31.0	1.010325	2940	680	2355
32.0	1.010325	2773	560	2159
33.0	1.010325	2619	578	2045
34.0	1.010325	2498	519	1967
35.0	1.010325	2264	539	1859
36.0	1.010325	2310	460	1759
37.0	1.010325	2076	398	1744
38.0	1.010325	1978	409	1651
39.0	1.010325	1954	375	1543
40.0	1.010325	1871	369	1416
41.0	1.010325	1761	319	1347
42.0	1.010325	1718	283	1421
43.0	1.010325	1688	282	1276
44.0	1.010325	1511	278	1204
45.0	1.010325	1454	255	1153
46.0	1.010325	1391	244	1105
47.0	1.010325	1319	217	1025
48.0	1.010325	1318	245	1004
49.0	1.010325	1264	209	900
50.0	1.010325	1150	180	925
51.0	1.010325	1109	201	873
52.0	1.010325	1121	187	892
53.0	1.010325	1091	170	852
54.0	1.010325	979	165	805
55.0	1.010325	974	187	765
56.0	1.010325	940	162	815
57.0	1.010325	910	141	711
58.0	1.010325	906	156	712
59.0	1.010325	846	139	647
60.0	1.010325	860	112	650
61.0	1.010325	820	140	643
62.0	1.010325	785	139	648
63.0	1.010325	780	143	574
64.0	1.010325	758	105	552
65.0	1.010325	718	98	520
66.0	1.010325	725	112	523
67.0	1.010325	635	94	524
68.0	1.010325	656	96	469
69.0	1.010325	569	93	542
70.0	1.010325	656	94	450
71.0	1.010325	591	86	439
72.0	1.010325	540	96	441
73.0	1.010325	556	80	462
74.0	1.010325	538	78	436
75.0	1.010325	492	74	448
76.0	1.010325	484	75	418
77.0	1.010325	501	79	413
78.0	1.010325	506	77	396
79.0	1.010325	451	83	365
80.0	1.010325	472	66	346
81.0	1.010325	454	57	343
82.0	1.010325	414	64	348
83.0	1.010325	431	38	320
84.0	1.010325	449	53	338
85.0	1.010325	398	67	327
86.0	1.010325	391	53	307
87.0	1.010325	401	61	287
88.0	1.010325	392	48	284
89.0	1.010325	397	43	301
90.0	1.010325	352	44	292
91.0	1.010325	386	51	283
92.0	1.010325	343	48	284
93.0	1.010325	343	37	276
94.0	1.010325	348	38	279
95.0	1.010325	346	41	244
96.0	1.010325	312	53	223
97.0	1.010325	322	48	219
98.0	1.010325	306	34	263
99.0	1.010325	283	39	252
100.0	1.010325	288	33	221
101.0	0	260	32	230
102.0	0	265	36	237
103.0	0	269	38	238
104.0	0	267	39	231
105.0	0	278	32	189
106.0	0	262	29	200
107.0	0	253	33	203
108.0	0	250	34	179
109.0	0	258	27	190
110.0	0	244	30	204
111.0	0	210	28	201
112.0	0	237	33	175
113.0	0	223	30	156
114.0	0	236	24	159
115.0	0	259	29	194
116.0	0	204	32	179
117.0	0	226	32	153
118.0	0	238	21	151
119.0	0	186	26	167
120.0	0	203	22	154
121.0	0	201	21	130
122.0	0	186	23	152
123.0	0	196	17	130
124.0	0	204	15	131
125.0	0	177	18	148
126.0	0	178	25	131
127.0	0	203	19	140
128.0	0	180	17	124
129.0	0	167	15	133
130.0	0	165	14	132
131.0	0	173	17	127
132.0	0	136	20	130
133.0	0	168	24	116
134.0	0	154	12	114
135.0	0	161	12	111
136.0	0	146	14	88
137.0	0	156	21	125
138.0	0	134	11	110
139.0	0	160	17	110
140.0	0	133	18	94
141.0	0	140	15	101
142.0	0	116	20	109
143.0	0	139	16	104
144.0	0	108	11	89
145.0	0	147	13	102
146.0	0	142	23	82
147.0	0	137	16	107
148.0	0	99	14	95
149.0	0	96	13	91
150.0	0	106	10	93
151.0	0	132	9	89
152.0	0	116	17	75
153.0	0	122	8	87
154.0	0	126	11	98
155.0	0	94	19	94
156.0	0	115	19	90
157.0	0	111	10	78
158.0	0	117	13	96
159.0	0	116	8	70
160.0	0	94	4	85
161.0	0	104	15	79
162.0	0	97	15	71
163.0	0	91	10	93
164.0	0	104	7	84
165.0	0	89	9	74
166.0	0	108	12	84
167.0	0	89	16	77
168.0	0	96	10	74
169.0	0	103	9	62
170.0	0	102	9	66
171.0	0	90	7	72
172.0	0	83	5	65
173.0	0	69	7	56
174.0	0	92	4	63
175.0	0	73	10	64
176.0	0	63	10	72
177.0	0	101	7	64
178.0	0	68	11	66
179.0	0	80	8	64
180.0	0	79	7	57
181.0	0	80	6	54
182.0	0	66	10	60
183.0	0	74	10	65
184.0	0	75	6	64
185.0	0	78	7	62
186.0	0	74	7	59
187.0	0	76	8	75
188.0	0	78	6	50
189.0	0	71	5	71
190.0	0	70	4	49
191.0	0	68	6	52
192.0	0	77	4	63
193.0	0	72	6	47
194.0	0	73	8	44
195.0	0	76	12	55
196.0	0	72	6	44
197.0	0	66	5	50
198.0	0	72	5	45
199.0	0	63	7	49
200.0	0	66	4	60
201.0	0	70	7	49
202.0	0	66	9	43
203.0	0	46	5	45
204.0	0	56	6	45
205.0	0	60	3	54
206.0	0	61	3	38
207.0	0	75	2	51
208.0	0	62	10	48
209.0	0	53	4	39
210.0	0	49	5	43
211.0	0	48	8	51
212.0	0	57	5	49
213.0	0	49	4	32
214.0	0	71	5	36
215.0	0	48	2	44
216.0	0	49	3	41
217.0	0	66	3	45
218.0	0	39	3	44
219.0	0	49	4	42
220.0	0	49	6	37
221.0	0	46	4	36
222.0	0	52	5	37
223.0	0	53	6	48
224.0	0	51	4	32
225.0	0	46	2	26
226.0	0	58	2	39
227.0	0	44	5	43
228.0	0	47	3	29
229.0	0	58	3	37
230.0	0	45	3	33
231.0	0	45	4	32
232.0	0	35	4	46
233.0	0	56	2	32
234.0	0	38	7	32
235.0	0	42	3	39
236.0	0	39	2	39
237.0	0	39	2	32
238.0	0	35	4	36
239.0	0	45	4	35
240.0	0	53	4	34
241.0	0	37	4	38
242.0	0	40	2	40
243.0	0	41	4	24
244.0	0	55	5	32
245.0	0	40	4	30
246.0	0	30	3	27
247.0	0	37	4	29
248.0	0	44	3	26
249.0	0	42	2	32
250.0	0	42	3	28
251.0	0	37	9	27
252.0	0	39	1	28
253.0	0	25	2	34
254.0	0	48	2	37
255.0	0	39	5	17
256.0	0	43	5	29
257.0	0	42	3	22
258.0	0	43	3	27
259.0	0	35	3	24
260.0	0	36	3	20
261.0	0	45	3	30
262.0	0	32	2	24
263.0	0	37	1	26
264.0	0	37	5	29
265.0	0	28	1	23
266.0	0	34	1	26
267.0	0	32	4	17
268.0	0	28	0	24
269.0	0	36	2	23
270.0	0	32	3	29
271.0	0	31	1	25
272.0	0	35	4	23
273.0	0	38	2	21
274.0	0	31	2	23
275.0	0	28	5	24
276.0	0	26	1	19
277.0	0	35	4	24
278.0	0	21	1	19
279.0	0	39	4	20
280.0	0	34	0	20
281.0	0	37	2	17
282.0	0	35	2	27
283.0	0	24	2	24
284.0	0	20	0	15
285.0	0	21	2	28
286.0	0	24	1	20
287.0	0	29	2	20
288.0	0	14	1	24
289.0	0	23	2	28
290.0	0	28	1	23
291.0	0	23	1	24
292.0	0	19	2	18
293.0	0	22	1	17
294.0	0	22	6	20
295.0	0	29	1	21
296.0	0	32	1	14
297.0	0	26	1	28
298.0	0	21	1	22
299.0	0	15	4	18
300.0	0	21	0	17
301.0	0	28	5	19
302.0	0	25	0	19
303.0	0	21	1	16
304.0	0	23	0	21
305.0	0	21	1	21
306.0	0	22	0	17
307.0	0	28	3	12
308.0	0	32	2	22
309.0	0	23	1	16
310.0	0	22	3	18
311.0	0	25	2	21
312.0	0	20	0	14
313.0	0	23	1	22
314.0	0	25	2	27
315.0	0	20	1	10
316.0	0	28	1	21
317.0	0	28	3	22
318.0	0	27	1	11
319.0	0	22	2	19
320.0	0	20	2	18
321.0	0	26	2	13
322.0	0	36	4	9
323.0	0	20	2	13
324.0	0	17	4	14
325.0	0	21	4	20
326.0	0	17	0	19
327.0	0	29	2	16
328.0	0	15	3	18
329.0	0	22	3	16
330.0	0	17	2	16
331.0	0	16	2	14
332.0	0	11	3	21
333.0	0	16	2	16
334.0	0	20	1	20
335.0	0	19	1	14
336.0	0	21	0	12
337.0	0	21	3	10
338.0	0	24	3	11
339.0	0	14	3	24
340.0	0	14	3	9
341.0	0	16	1	12
342.0	0	22	2	16
343.0	0	15	4	18
344.0	0	18	1	10
345.0	0	26	3	13
346.0	0	14	1	10
347.0	0	13	0	8
348.0	0	18	1	20
349.0	0	17	1	11
350.0	0	15	1	7
351.0	0	19	3	11
352.0	0	18	2	13
353.0	0	17	0	9
354.0	0	23	1	20
355.0	0	17	1	12
356.0	0	22	0	15
357.0	0	19	3	13
358.0	0	9	2	13
359.0	0	13	2	15
360.0	0	10	0	14
361.0	0	12	2	10
362.0	0	16	1	10
363.0	0	13	0	13
364.0	0	25	1	17
365.0	0	14	0	9
366.0	0	18	4	21
367.0	0	18	1	10
368.0	0	12	0	17
369.0	0	16	0	13
370.0	0	12	1	15
371.0	0	14	3	12
372.0	0	13	0	12
373.0	0	11	3	8
374.0	0	15	1	14
375.0	0	14	2	15
376.0	0	11	3	13
377.0	0	13	0	13
378.0	0	13	0	12
379.0	0	21	0	4
380.0	0	17	1	10
381.0	0	17	1	8
382.0	0	19	2	9
383.0	0	9	1	11
384.0	0	19	2	10
385.0	0	13	2	8
386.0	0	11	1	6
387.0	0	17	1	14
388.0	0	14	1	12
389.0	0	12	0	12
390.0	0	13	1	9
391.0	0	18	1	6
392.0	0	14	0	9
393.0	0	10	1	7
394.0	0	16	3	8
395.0	0	18	1	10
396.0	0	10	1	10
397.0	0	18	2	13
398.0	0	15	2	7
399.0	0	12	1	9
400.0	0	10	0	8
401.0	0	11	3	15
402.0	0	12	1	7
403.0	0	12	0	11
404.0	0	12	1	11
405.0	0	11	0	5
406.0	0	10	0	9
407.0	0	7	1	11
408.0	0	16	1	7
409.0	0	11	2	10
410.0	0	9	0	10
411.0	0	7	1	19
412.0	0	14	0	9
413.0	0	12	0	10
414.0	0	13	1	16
415.0	0	9	0	11
416.0	0	7	1	11
417.0	0	13	2	9
418.0	0	7	1	9
419.0	0	10	1	9
420.0	0	14	1	3
421.0	0	7	0	7
422.0	0	10	0	12
423.0	0	8	0	12
424.0	0	11	2	13
425.0	0	9	0	6
426.0	0	9	1	6
427.0	0	13	1	8
428.0	0	14	0	12
429.0	0	14	2	3
430.0	0	9	0	6
431.0	0	7	1	6
432.0	0	14	1	12
433.0	0	15	0	6
434.0	0	12	1	7
435.0	0	13	1	5
436.0	0	10	1	7
437.0	0	13	0	11
438.0	0	14	1	6
439.0	0	8	1	7
440.0	0	13	0	2
441.0	0	8	0	10
442.0	0	7	0	9
443.0	0	11	0	15
444.0	0	8	0	10
445.0	0	9	1	6
446.0	0	8	0	11
447.0	0	14	0	8
448.0	0	6	0	10
449.0	0	12	0	4
450.0	0	15	0	5
451.0	0	8	0	6
452.0	0	11	2	5
453.0	0	14	1	8
454.0	0	12	0	14
455.0	0	11	0	3
456.0	0	7	1	7
457.0	0	9	0	9
458.0	0	6	0	3
459.0	0	10	0	7
460.0	0	5	1	7
461.0	0	10	0	6
462.0	0	6	1	4
463.0	0	10	1	1
464.0	0	9	1	6
465.0	0	13	0	2
466.0	0	4	0	8
467.0	0	10	2	9
468.0	0	5	2	5
469.0	0	14	0	2
470.0	0	11	1	5
471.0	0	8	1	1
472.0	0	7	1	8
473.0	0	11	0	1
474.0	0	10	0	9
475.0	0	5	0	10
476.0	0	6	0	13
477.0	0	9	0	3
478.0	0	7	1	2
479.0	0	10	0	6
480.0	0	9	0	7
481.0	0	8	0	10
482.0	0	8	2	1
483.0	0	7	1	7
484.0	0	6	1	6
485.0	0	19	0	5
486.0	0	10	2	7
487.0	0	9	0	3
488.0	0	5	0	6
489.0	0	5	0	3
490.0	0	8	1	9
491.0	0	9	0	3
492.0	0	10	1	5
493.0	0	9	0	6
494.0	0	12	0	7
495.0	0	6	0	3
496.0	0	9	0	4
497.0	0	6	0	5
498.0	0	8	0	4
499.0	0	5	0	7
500.0	0	6	1	5
501.0	0	4	0	12
502.0	0	5	0	1
503.0	0	6	0	5
504.0	0	7	2	6
505.0	0	9	0	6
506.0	0	10	0	9
507.0	0	4	1	10
508.0	0	4	0	7
509.0	0	5	2	4
510.0	0	3	1	4
511.0	0	6	0	8
512.0	0	5	0	8
513.0	0	9	0	2
514.0	0	2	1	2
515.0	0	8	0	4
516.0	0	6	0	4
517.0	0	8	0	2
518.0	0	4	1	10
519.0	0	5	0	9
520.0	0	11	0	5
521.0	0	8	0	8
522.0	0	2	0	4
523.0	0	10	0	8
524.0	0	9	0	8
525.0	0	6	0	4
526.0	0	6	1	4
527.0	0	9	0	2
528.0	0	4	0	6
529.0	0	8	1	8
530.0	0	3	0	5
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