## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-83-TP3.bam --OUTPUT POR-83-TP3.md.bam --METRICS_FILE POR-83-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 18:19:52 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	2863	16302884	11076497	0	2762	13584830	3639407	0.833289	2745298

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.007361	1356929	0	1708212
2.0	1.010016	516425	395596	444739
3.0	1.010023	235573	166676	149969
4.0	1.010023	128383	88847	75501
5.0	1.010023	80417	53165	48735
6.0	1.010023	55400	33640	36013
7.0	1.010023	41078	23035	27529
8.0	1.010023	31485	16382	22507
9.0	1.010023	25291	12008	18305
10.0	1.010023	20801	9282	15343
11.0	1.010023	17368	7461	12969
12.0	1.010023	14924	6089	11333
13.0	1.010023	13068	5044	9891
14.0	1.010023	11476	4316	8694
15.0	1.010023	10067	3636	7660
16.0	1.010023	8946	3157	6882
17.0	1.010023	8130	2664	6252
18.0	1.010023	7238	2442	5651
19.0	1.010023	6735	2042	5107
20.0	1.010023	6130	1932	4580
21.0	1.010023	5539	1677	4368
22.0	1.010023	5156	1490	3920
23.0	1.010023	4748	1363	3571
24.0	1.010023	4467	1229	3293
25.0	1.010023	3997	1095	3197
26.0	1.010023	3747	1006	2795
27.0	1.010023	3601	926	2617
28.0	1.010023	3218	923	2385
29.0	1.010023	3018	830	2394
30.0	1.010023	2885	700	2129
31.0	1.010023	2731	733	2041
32.0	1.010023	2431	604	1973
33.0	1.010023	2473	572	1843
34.0	1.010023	2206	588	1740
35.0	1.010023	2153	476	1677
36.0	1.010023	2118	523	1596
37.0	1.010023	2029	443	1470
38.0	1.010023	1813	421	1397
39.0	1.010023	1803	390	1356
40.0	1.010023	1669	416	1217
41.0	1.010023	1545	358	1257
42.0	1.010023	1521	338	1166
43.0	1.010023	1470	315	1115
44.0	1.010023	1402	278	1095
45.0	1.010023	1423	274	1047
46.0	1.010023	1325	263	981
47.0	1.010023	1257	255	887
48.0	1.010023	1205	218	921
49.0	1.010023	1157	229	893
50.0	1.010023	1080	208	779
51.0	1.010023	1058	197	768
52.0	1.010023	926	185	717
53.0	1.010023	940	175	775
54.0	1.010023	906	205	741
55.0	1.010023	928	181	713
56.0	1.010023	894	188	688
57.0	1.010023	914	148	638
58.0	1.010023	847	151	607
59.0	1.010023	768	123	555
60.0	1.010023	759	136	573
61.0	1.010023	743	129	553
62.0	1.010023	688	148	515
63.0	1.010023	712	127	552
64.0	1.010023	693	116	526
65.0	1.010023	603	106	501
66.0	1.010023	637	110	457
67.0	1.010023	591	111	449
68.0	1.010023	626	103	498
69.0	1.010023	616	91	418
70.0	1.010023	531	78	437
71.0	1.010023	567	86	371
72.0	1.010023	531	96	421
73.0	1.010023	495	94	401
74.0	1.010023	491	83	382
75.0	1.010023	458	102	380
76.0	1.010023	473	74	323
77.0	1.010023	467	80	372
78.0	1.010023	477	78	330
79.0	1.010023	438	69	353
80.0	1.010023	438	71	301
81.0	1.010023	458	67	290
82.0	1.010023	431	71	284
83.0	1.010023	401	55	273
84.0	1.010023	373	48	290
85.0	1.010023	363	60	279
86.0	1.010023	368	61	284
87.0	1.010023	360	67	255
88.0	1.010023	331	53	259
89.0	1.010023	334	48	262
90.0	1.010023	346	45	246
91.0	1.010023	310	42	232
92.0	1.010023	304	39	233
93.0	1.010023	287	50	232
94.0	1.010023	272	45	230
95.0	1.010023	321	42	203
96.0	1.010023	277	41	211
97.0	1.010023	307	34	223
98.0	1.010023	257	47	200
99.0	1.010023	259	39	189
100.0	1.010023	283	28	198
101.0	0	260	39	183
102.0	0	257	33	187
103.0	0	253	35	187
104.0	0	249	36	178
105.0	0	209	27	176
106.0	0	268	28	167
107.0	0	214	33	169
108.0	0	203	31	151
109.0	0	242	23	185
110.0	0	198	32	165
111.0	0	233	29	164
112.0	0	188	30	152
113.0	0	198	40	155
114.0	0	200	32	135
115.0	0	210	31	135
116.0	0	174	15	124
117.0	0	173	22	150
118.0	0	202	19	115
119.0	0	178	23	145
120.0	0	177	19	130
121.0	0	167	30	138
122.0	0	176	25	134
123.0	0	144	29	137
124.0	0	164	26	114
125.0	0	158	22	129
126.0	0	168	26	123
127.0	0	155	23	106
128.0	0	153	22	102
129.0	0	148	24	136
130.0	0	164	15	108
131.0	0	147	19	120
132.0	0	165	10	87
133.0	0	146	21	94
134.0	0	144	22	99
135.0	0	145	21	98
136.0	0	124	19	111
137.0	0	118	17	102
138.0	0	140	19	90
139.0	0	134	19	97
140.0	0	136	12	104
141.0	0	131	17	101
142.0	0	116	18	92
143.0	0	117	21	95
144.0	0	119	14	82
145.0	0	121	13	90
146.0	0	91	13	97
147.0	0	122	16	96
148.0	0	121	10	84
149.0	0	120	21	78
150.0	0	124	17	99
151.0	0	97	18	87
152.0	0	83	11	83
153.0	0	96	14	82
154.0	0	128	12	66
155.0	0	92	14	59
156.0	0	94	13	71
157.0	0	98	15	89
158.0	0	84	7	76
159.0	0	104	19	70
160.0	0	95	16	69
161.0	0	113	6	65
162.0	0	93	14	61
163.0	0	86	14	77
164.0	0	101	6	71
165.0	0	96	10	72
166.0	0	92	9	51
167.0	0	83	9	72
168.0	0	100	14	53
169.0	0	80	4	56
170.0	0	67	10	72
171.0	0	86	5	61
172.0	0	74	9	52
173.0	0	79	11	52
174.0	0	72	10	46
175.0	0	69	8	56
176.0	0	83	7	57
177.0	0	73	7	45
178.0	0	78	4	46
179.0	0	73	7	56
180.0	0	76	7	42
181.0	0	68	9	51
182.0	0	82	8	49
183.0	0	59	9	53
184.0	0	76	11	61
185.0	0	79	6	59
186.0	0	67	5	59
187.0	0	59	6	51
188.0	0	52	6	37
189.0	0	37	4	43
190.0	0	74	13	41
191.0	0	66	5	38
192.0	0	72	2	48
193.0	0	53	3	40
194.0	0	52	10	41
195.0	0	56	8	40
196.0	0	70	9	48
197.0	0	62	5	43
198.0	0	52	5	40
199.0	0	67	4	43
200.0	0	60	6	48
201.0	0	54	4	43
202.0	0	54	6	38
203.0	0	66	6	36
204.0	0	66	6	35
205.0	0	60	7	41
206.0	0	48	3	41
207.0	0	55	4	42
208.0	0	36	12	35
209.0	0	49	8	30
210.0	0	46	1	38
211.0	0	51	8	52
212.0	0	59	9	37
213.0	0	56	6	36
214.0	0	48	9	35
215.0	0	43	7	44
216.0	0	49	3	31
217.0	0	61	5	49
218.0	0	43	3	36
219.0	0	51	6	38
220.0	0	48	6	38
221.0	0	52	4	34
222.0	0	40	2	33
223.0	0	48	2	29
224.0	0	40	5	28
225.0	0	32	6	18
226.0	0	40	5	19
227.0	0	47	2	22
228.0	0	54	6	37
229.0	0	38	4	26
230.0	0	46	2	24
231.0	0	38	4	39
232.0	0	32	3	23
233.0	0	32	7	21
234.0	0	32	2	23
235.0	0	32	5	31
236.0	0	37	2	32
237.0	0	27	2	26
238.0	0	41	4	24
239.0	0	45	4	33
240.0	0	37	6	31
241.0	0	41	2	26
242.0	0	31	8	30
243.0	0	35	2	26
244.0	0	40	5	25
245.0	0	25	4	34
246.0	0	41	4	26
247.0	0	42	4	19
248.0	0	33	1	26
249.0	0	27	4	23
250.0	0	28	3	31
251.0	0	25	2	18
252.0	0	27	5	18
253.0	0	38	2	16
254.0	0	32	3	22
255.0	0	33	5	25
256.0	0	34	2	32
257.0	0	30	1	27
258.0	0	36	2	29
259.0	0	25	2	15
260.0	0	27	2	33
261.0	0	25	4	19
262.0	0	30	2	20
263.0	0	28	3	26
264.0	0	29	8	28
265.0	0	41	2	19
266.0	0	35	3	13
267.0	0	28	2	29
268.0	0	20	1	15
269.0	0	30	2	17
270.0	0	26	2	13
271.0	0	27	4	23
272.0	0	24	4	23
273.0	0	25	5	14
274.0	0	25	3	24
275.0	0	24	3	20
276.0	0	27	3	18
277.0	0	28	3	18
278.0	0	31	3	25
279.0	0	34	4	20
280.0	0	23	1	22
281.0	0	30	3	27
282.0	0	25	3	19
283.0	0	17	1	18
284.0	0	23	4	15
285.0	0	24	1	23
286.0	0	22	1	22
287.0	0	25	1	22
288.0	0	28	2	19
289.0	0	28	3	16
290.0	0	21	2	15
291.0	0	23	0	15
292.0	0	22	2	16
293.0	0	27	2	11
294.0	0	23	1	16
295.0	0	22	1	12
296.0	0	25	1	19
297.0	0	24	2	28
298.0	0	21	3	21
299.0	0	23	2	19
300.0	0	22	1	18
301.0	0	22	0	19
302.0	0	23	3	9
303.0	0	20	1	13
304.0	0	18	3	17
305.0	0	33	1	12
306.0	0	30	1	18
307.0	0	30	1	15
308.0	0	23	3	8
309.0	0	27	2	9
310.0	0	20	1	16
311.0	0	13	0	14
312.0	0	23	3	13
313.0	0	16	3	21
314.0	0	17	2	14
315.0	0	15	1	13
316.0	0	21	2	12
317.0	0	12	2	16
318.0	0	15	1	13
319.0	0	20	3	23
320.0	0	15	2	19
321.0	0	17	3	13
322.0	0	20	1	11
323.0	0	12	2	16
324.0	0	16	1	12
325.0	0	13	3	11
326.0	0	16	2	16
327.0	0	17	2	9
328.0	0	21	2	9
329.0	0	13	0	14
330.0	0	10	2	15
331.0	0	15	1	17
332.0	0	12	2	12
333.0	0	15	4	6
334.0	0	15	2	21
335.0	0	15	2	13
336.0	0	30	0	16
337.0	0	16	1	9
338.0	0	20	0	10
339.0	0	11	0	12
340.0	0	25	0	18
341.0	0	13	1	13
342.0	0	19	0	17
343.0	0	19	1	7
344.0	0	15	1	14
345.0	0	16	3	6
346.0	0	23	1	14
347.0	0	10	1	12
348.0	0	16	0	9
349.0	0	14	0	6
350.0	0	15	1	6
351.0	0	26	3	9
352.0	0	10	2	12
353.0	0	19	1	15
354.0	0	14	1	7
355.0	0	10	0	11
356.0	0	18	2	14
357.0	0	5	0	7
358.0	0	14	2	15
359.0	0	8	0	12
360.0	0	18	4	11
361.0	0	11	1	6
362.0	0	13	0	14
363.0	0	10	0	9
364.0	0	15	0	13
365.0	0	11	1	15
366.0	0	10	0	15
367.0	0	11	3	9
368.0	0	12	2	6
369.0	0	14	0	12
370.0	0	15	2	12
371.0	0	16	0	9
372.0	0	6	1	14
373.0	0	10	1	8
374.0	0	15	3	8
375.0	0	7	1	14
376.0	0	14	2	6
377.0	0	19	0	14
378.0	0	12	1	11
379.0	0	15	1	13
380.0	0	21	0	10
381.0	0	7	0	9
382.0	0	13	1	5
383.0	0	9	1	17
384.0	0	13	3	9
385.0	0	12	1	9
386.0	0	20	1	7
387.0	0	10	3	6
388.0	0	12	2	7
389.0	0	13	1	15
390.0	0	18	2	9
391.0	0	10	0	5
392.0	0	11	2	8
393.0	0	7	1	6
394.0	0	14	0	10
395.0	0	9	2	10
396.0	0	12	0	6
397.0	0	8	0	7
398.0	0	16	3	11
399.0	0	15	0	6
400.0	0	10	2	10
401.0	0	10	2	7
402.0	0	5	0	8
403.0	0	9	0	7
404.0	0	16	1	6
405.0	0	12	0	11
406.0	0	13	1	7
407.0	0	16	0	7
408.0	0	9	0	5
409.0	0	13	1	8
410.0	0	7	2	8
411.0	0	9	1	7
412.0	0	14	1	8
413.0	0	13	1	9
414.0	0	11	2	3
415.0	0	9	1	11
416.0	0	7	1	5
417.0	0	12	0	9
418.0	0	10	1	8
419.0	0	8	0	8
420.0	0	10	2	12
421.0	0	11	1	11
422.0	0	11	3	9
423.0	0	10	3	12
424.0	0	3	0	7
425.0	0	7	1	5
426.0	0	10	1	8
427.0	0	7	0	9
428.0	0	10	1	5
429.0	0	14	1	9
430.0	0	10	0	8
431.0	0	6	0	5
432.0	0	10	0	5
433.0	0	9	0	6
434.0	0	12	0	5
435.0	0	12	2	7
436.0	0	9	1	9
437.0	0	10	0	8
438.0	0	7	2	5
439.0	0	8	0	12
440.0	0	10	1	4
441.0	0	10	0	9
442.0	0	11	1	7
443.0	0	8	0	10
444.0	0	9	0	2
445.0	0	8	1	9
446.0	0	4	1	5
447.0	0	14	0	5
448.0	0	10	1	5
449.0	0	15	0	10
450.0	0	9	0	7
451.0	0	9	0	7
452.0	0	18	0	3
453.0	0	10	0	5
454.0	0	7	1	13
455.0	0	8	1	9
456.0	0	9	1	3
457.0	0	9	0	8
458.0	0	12	1	8
459.0	0	9	0	4
460.0	0	6	0	9
461.0	0	16	1	6
462.0	0	5	0	4
463.0	0	4	1	7
464.0	0	8	0	9
465.0	0	12	1	6
466.0	0	6	1	9
467.0	0	7	0	2
468.0	0	5	0	10
469.0	0	7	2	4
470.0	0	7	1	9
471.0	0	14	0	5
472.0	0	3	1	7
473.0	0	6	0	5
474.0	0	4	2	4
475.0	0	10	1	7
476.0	0	9	1	4
477.0	0	8	0	5
478.0	0	10	0	7
479.0	0	7	1	3
480.0	0	4	1	5
481.0	0	7	1	6
482.0	0	8	0	7
483.0	0	9	2	4
484.0	0	5	4	5
485.0	0	5	1	6
486.0	0	9	1	4
487.0	0	8	0	5
488.0	0	5	0	9
489.0	0	4	0	6
490.0	0	5	1	10
491.0	0	2	0	6
492.0	0	5	0	9
493.0	0	6	1	8
494.0	0	8	0	7
495.0	0	8	0	4
496.0	0	7	1	10
497.0	0	6	2	0
498.0	0	2	0	1
499.0	0	3	0	0
500.0	0	11	1	4
501.0	0	9	0	2
502.0	0	7	3	3
503.0	0	5	0	3
504.0	0	8	0	9
505.0	0	4	1	4
506.0	0	6	0	2
507.0	0	8	2	5
508.0	0	14	0	5
509.0	0	8	1	3
510.0	0	12	0	4
511.0	0	3	0	3
512.0	0	4	0	1
513.0	0	5	1	2
514.0	0	7	0	2
515.0	0	7	0	4
516.0	0	4	2	4
517.0	0	4	1	7
518.0	0	8	0	5
519.0	0	6	0	4
520.0	0	11	0	4
521.0	0	4	0	6
522.0	0	4	0	3
523.0	0	6	0	3
524.0	0	2	0	4
525.0	0	5	2	10
526.0	0	5	0	3
527.0	0	9	0	4
528.0	0	5	0	8
529.0	0	11	0	4
530.0	0	5	0	6
531.0	0	5	0	6
532.0	0	2	0	6
533.0	0	4	0	0
534.0	0	3	0	4
535.0	0	6	0	5
536.0	0	1	0	4
537.0	0	4	0	2
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