## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-262-TP3.bam --OUTPUT POR-262-TP3.md.bam --METRICS_FILE POR-262-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 18:17:54 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	2493	18450480	11101332	0	2362	13850067	4146219	0.750675	4855587

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.031852	2610583	0	3292428
2.0	1.054939	894744	653187	693919
3.0	1.055456	375250	258359	189667
4.0	1.055467	189320	128164	84642
5.0	1.055468	109784	71010	52817
6.0	1.055468	70581	41800	37781
7.0	1.055468	48818	26530	28884
8.0	1.055468	35493	17508	22916
9.0	1.055468	27409	12311	18435
10.0	1.055468	22030	9135	15357
11.0	1.055468	17805	7062	12917
12.0	1.055468	15093	5422	11159
13.0	1.055468	12877	4646	9551
14.0	1.055468	11065	3911	8551
15.0	1.055468	9868	3226	7457
16.0	1.055468	8786	2640	6755
17.0	1.055468	7734	2403	6008
18.0	1.055468	7049	2168	5505
19.0	1.055468	6525	1919	4875
20.0	1.055468	5881	1672	4370
21.0	1.055468	5215	1551	4114
22.0	1.055468	4898	1300	3742
23.0	1.055468	4499	1190	3407
24.0	1.055468	4174	1084	3188
25.0	1.055468	3932	1012	2969
26.0	1.055468	3562	974	2735
27.0	1.055468	3354	857	2585
28.0	1.055468	3095	729	2464
29.0	1.055468	2913	744	2238
30.0	1.055468	2828	673	2114
31.0	1.055468	2555	590	2003
32.0	1.055468	2336	568	1878
33.0	1.055468	2195	507	1747
34.0	1.055468	2186	500	1596
35.0	1.055468	2003	487	1588
36.0	1.055468	1909	442	1479
37.0	1.055468	1735	402	1425
38.0	1.055468	1779	363	1343
39.0	1.055468	1612	331	1233
40.0	1.055468	1597	303	1198
41.0	1.055468	1479	325	1090
42.0	1.055468	1470	266	1169
43.0	1.055468	1453	274	1038
44.0	1.055468	1269	259	972
45.0	1.055468	1264	288	928
46.0	1.055468	1242	233	882
47.0	1.055468	1158	231	910
48.0	1.055468	1104	222	848
49.0	1.055468	1119	193	774
50.0	1.055468	1007	204	772
51.0	1.055468	961	193	714
52.0	1.055468	868	192	693
53.0	1.055468	895	163	659
54.0	1.055468	870	175	631
55.0	1.055468	861	139	628
56.0	1.055468	784	149	608
57.0	1.055468	816	127	609
58.0	1.055468	742	133	612
59.0	1.055468	710	116	585
60.0	1.055468	730	127	513
61.0	1.055468	686	141	512
62.0	1.055468	643	101	469
63.0	1.055468	648	106	511
64.0	1.055468	616	108	485
65.0	1.055468	537	95	435
66.0	1.055468	552	91	459
67.0	1.055468	572	93	404
68.0	1.055468	527	94	399
69.0	1.055468	519	99	376
70.0	1.055468	528	82	376
71.0	1.055468	491	73	403
72.0	1.055468	520	69	339
73.0	1.055468	505	74	361
74.0	1.055468	480	73	343
75.0	1.055468	447	72	327
76.0	1.055468	416	76	317
77.0	1.055468	390	58	355
78.0	1.055468	430	62	314
79.0	1.055468	395	47	285
80.0	1.055468	359	68	283
81.0	1.055468	388	61	305
82.0	1.055468	394	58	283
83.0	1.055468	344	49	260
84.0	1.055468	372	58	267
85.0	1.055468	340	55	255
86.0	1.055468	337	42	221
87.0	1.055468	311	50	262
88.0	1.055468	308	51	214
89.0	1.055468	292	41	223
90.0	1.055468	315	43	233
91.0	1.055468	299	39	214
92.0	1.055468	289	51	203
93.0	1.055468	279	48	222
94.0	1.055468	257	33	208
95.0	1.055468	276	36	198
96.0	1.055468	272	38	197
97.0	1.055468	256	38	190
98.0	1.055468	239	32	186
99.0	1.055468	238	52	179
100.0	1.055468	226	45	176
101.0	0	252	24	171
102.0	0	260	25	166
103.0	0	223	30	186
104.0	0	213	36	153
105.0	0	246	28	169
106.0	0	241	26	151
107.0	0	195	10	169
108.0	0	202	31	158
109.0	0	216	24	154
110.0	0	191	26	142
111.0	0	182	28	138
112.0	0	200	17	135
113.0	0	181	26	140
114.0	0	179	26	146
115.0	0	156	24	148
116.0	0	173	24	135
117.0	0	195	21	133
118.0	0	163	23	121
119.0	0	169	28	134
120.0	0	149	11	118
121.0	0	157	22	109
122.0	0	190	22	110
123.0	0	154	15	127
124.0	0	184	24	100
125.0	0	125	18	102
126.0	0	158	17	108
127.0	0	140	15	101
128.0	0	125	11	103
129.0	0	139	15	97
130.0	0	143	17	99
131.0	0	132	22	92
132.0	0	131	28	81
133.0	0	123	10	93
134.0	0	137	10	81
135.0	0	136	19	90
136.0	0	107	13	86
137.0	0	105	16	92
138.0	0	136	13	96
139.0	0	99	15	83
140.0	0	104	17	78
141.0	0	89	15	82
142.0	0	98	15	83
143.0	0	113	10	91
144.0	0	105	14	84
145.0	0	116	14	90
146.0	0	118	8	76
147.0	0	89	20	81
148.0	0	94	8	70
149.0	0	109	9	78
150.0	0	102	7	76
151.0	0	93	15	60
152.0	0	102	9	65
153.0	0	91	11	88
154.0	0	99	11	67
155.0	0	76	8	65
156.0	0	91	10	65
157.0	0	106	13	55
158.0	0	69	10	75
159.0	0	86	7	70
160.0	0	86	7	66
161.0	0	91	9	67
162.0	0	93	7	58
163.0	0	91	9	70
164.0	0	81	8	50
165.0	0	75	10	62
166.0	0	80	7	60
167.0	0	64	12	58
168.0	0	72	9	63
169.0	0	73	13	55
170.0	0	71	10	56
171.0	0	66	6	46
172.0	0	84	5	54
173.0	0	60	4	65
174.0	0	71	10	58
175.0	0	62	10	53
176.0	0	64	5	55
177.0	0	63	7	52
178.0	0	66	7	51
179.0	0	72	7	41
180.0	0	83	10	41
181.0	0	78	7	53
182.0	0	57	12	49
183.0	0	73	12	32
184.0	0	60	7	46
185.0	0	53	14	46
186.0	0	67	7	46
187.0	0	69	10	46
188.0	0	57	10	47
189.0	0	65	6	36
190.0	0	53	8	41
191.0	0	47	3	46
192.0	0	65	7	36
193.0	0	56	9	42
194.0	0	51	4	36
195.0	0	53	5	51
196.0	0	62	8	38
197.0	0	58	5	30
198.0	0	46	4	42
199.0	0	57	11	40
200.0	0	54	4	30
201.0	0	57	4	31
202.0	0	41	4	40
203.0	0	55	5	28
204.0	0	43	6	29
205.0	0	46	12	40
206.0	0	51	6	36
207.0	0	39	5	38
208.0	0	47	5	37
209.0	0	45	6	35
210.0	0	40	4	32
211.0	0	48	7	41
212.0	0	41	6	34
213.0	0	32	4	31
214.0	0	41	3	36
215.0	0	55	3	27
216.0	0	50	2	31
217.0	0	50	2	25
218.0	0	41	4	33
219.0	0	48	3	42
220.0	0	45	4	34
221.0	0	48	10	28
222.0	0	35	7	35
223.0	0	46	5	31
224.0	0	35	2	29
225.0	0	37	6	27
226.0	0	39	3	23
227.0	0	34	9	27
228.0	0	35	2	24
229.0	0	35	2	32
230.0	0	32	3	27
231.0	0	28	3	25
232.0	0	29	2	22
233.0	0	31	3	19
234.0	0	40	3	31
235.0	0	29	5	28
236.0	0	16	4	26
237.0	0	34	5	26
238.0	0	29	3	30
239.0	0	28	0	30
240.0	0	36	3	25
241.0	0	33	2	25
242.0	0	42	3	21
243.0	0	27	2	21
244.0	0	35	0	22
245.0	0	27	5	18
246.0	0	23	6	26
247.0	0	34	2	25
248.0	0	37	5	23
249.0	0	42	4	28
250.0	0	38	7	23
251.0	0	27	3	28
252.0	0	25	6	17
253.0	0	28	4	24
254.0	0	31	5	17
255.0	0	36	2	23
256.0	0	27	7	19
257.0	0	36	2	20
258.0	0	28	2	19
259.0	0	20	0	21
260.0	0	33	2	24
261.0	0	21	2	19
262.0	0	20	2	19
263.0	0	25	3	18
264.0	0	24	7	22
265.0	0	29	3	19
266.0	0	26	0	26
267.0	0	24	4	18
268.0	0	24	2	21
269.0	0	15	2	19
270.0	0	29	3	19
271.0	0	27	4	17
272.0	0	28	0	19
273.0	0	25	1	17
274.0	0	25	4	19
275.0	0	18	1	7
276.0	0	25	1	13
277.0	0	20	4	24
278.0	0	29	4	19
279.0	0	19	1	22
280.0	0	17	3	24
281.0	0	16	0	18
282.0	0	21	3	17
283.0	0	19	1	18
284.0	0	34	5	21
285.0	0	21	1	15
286.0	0	23	1	21
287.0	0	27	1	16
288.0	0	22	2	19
289.0	0	24	4	11
290.0	0	21	4	13
291.0	0	25	3	13
292.0	0	25	2	14
293.0	0	20	5	15
294.0	0	19	3	18
295.0	0	19	1	8
296.0	0	21	2	13
297.0	0	15	1	13
298.0	0	16	2	18
299.0	0	23	2	14
300.0	0	17	0	13
301.0	0	20	1	16
302.0	0	26	2	14
303.0	0	34	0	9
304.0	0	12	0	15
305.0	0	23	0	10
306.0	0	15	0	15
307.0	0	15	0	10
308.0	0	11	3	16
309.0	0	12	2	18
310.0	0	16	3	17
311.0	0	21	0	19
312.0	0	22	1	12
313.0	0	15	3	9
314.0	0	15	1	17
315.0	0	14	1	10
316.0	0	16	1	15
317.0	0	18	2	15
318.0	0	19	1	9
319.0	0	27	2	19
320.0	0	12	2	15
321.0	0	9	3	11
322.0	0	15	1	7
323.0	0	15	1	11
324.0	0	17	2	10
325.0	0	14	3	11
326.0	0	14	0	21
327.0	0	12	1	9
328.0	0	15	0	13
329.0	0	12	2	12
330.0	0	14	2	12
331.0	0	19	2	4
332.0	0	26	0	11
333.0	0	16	2	8
334.0	0	24	2	16
335.0	0	14	1	16
336.0	0	15	0	12
337.0	0	21	0	16
338.0	0	15	1	13
339.0	0	14	0	10
340.0	0	12	0	13
341.0	0	11	0	9
342.0	0	16	1	9
343.0	0	13	0	14
344.0	0	17	1	13
345.0	0	17	1	6
346.0	0	14	1	13
347.0	0	15	1	14
348.0	0	11	0	14
349.0	0	13	1	7
350.0	0	11	0	10
351.0	0	9	0	15
352.0	0	13	1	7
353.0	0	13	1	11
354.0	0	10	0	11
355.0	0	19	1	6
356.0	0	8	0	12
357.0	0	9	3	12
358.0	0	14	3	9
359.0	0	9	1	12
360.0	0	17	2	9
361.0	0	12	4	12
362.0	0	12	1	7
363.0	0	14	1	17
364.0	0	11	2	7
365.0	0	10	1	13
366.0	0	19	0	15
367.0	0	10	0	5
368.0	0	10	1	13
369.0	0	14	1	9
370.0	0	17	0	7
371.0	0	11	0	10
372.0	0	11	2	13
373.0	0	17	0	9
374.0	0	11	1	15
375.0	0	10	4	7
376.0	0	12	2	10
377.0	0	15	2	15
378.0	0	10	2	11
379.0	0	12	1	14
380.0	0	11	1	7
381.0	0	15	1	7
382.0	0	14	1	7
383.0	0	18	1	7
384.0	0	6	2	4
385.0	0	14	1	5
386.0	0	12	0	6
387.0	0	7	2	12
388.0	0	15	2	6
389.0	0	12	0	7
390.0	0	12	1	7
391.0	0	9	2	10
392.0	0	17	0	12
393.0	0	6	0	13
394.0	0	10	3	8
395.0	0	8	0	7
396.0	0	9	1	9
397.0	0	17	2	4
398.0	0	7	0	7
399.0	0	6	0	4
400.0	0	14	2	6
401.0	0	11	3	10
402.0	0	5	1	9
403.0	0	11	0	7
404.0	0	9	3	9
405.0	0	16	0	12
406.0	0	12	2	5
407.0	0	12	1	5
408.0	0	9	0	7
409.0	0	7	1	11
410.0	0	12	2	9
411.0	0	8	1	8
412.0	0	8	3	8
413.0	0	7	1	6
414.0	0	4	0	7
415.0	0	9	1	5
416.0	0	11	1	6
417.0	0	10	2	5
418.0	0	10	0	6
419.0	0	7	0	7
420.0	0	7	0	5
421.0	0	8	0	9
422.0	0	7	0	6
423.0	0	11	1	6
424.0	0	8	2	4
425.0	0	14	2	8
426.0	0	4	1	7
427.0	0	7	2	8
428.0	0	8	0	9
429.0	0	14	1	4
430.0	0	12	1	8
431.0	0	7	2	8
432.0	0	12	1	5
433.0	0	8	0	7
434.0	0	11	3	2
435.0	0	10	2	10
436.0	0	9	3	6
437.0	0	6	0	6
438.0	0	6	0	6
439.0	0	8	1	1
440.0	0	7	0	9
441.0	0	7	0	4
442.0	0	10	1	8
443.0	0	8	0	5
444.0	0	6	0	3
445.0	0	11	1	6
446.0	0	6	0	7
447.0	0	9	2	4
448.0	0	9	0	5
449.0	0	6	0	9
450.0	0	5	0	3
451.0	0	11	0	8
452.0	0	6	0	4
453.0	0	6	0	2
454.0	0	8	0	3
455.0	0	6	0	3
456.0	0	11	0	5
457.0	0	4	1	4
458.0	0	7	1	2
459.0	0	6	1	6
460.0	0	8	1	6
461.0	0	8	0	7
462.0	0	8	0	9
463.0	0	7	3	5
464.0	0	7	0	3
465.0	0	12	2	8
466.0	0	6	0	6
467.0	0	4	1	9
468.0	0	6	0	8
469.0	0	12	0	3
470.0	0	6	1	6
471.0	0	6	1	4
472.0	0	12	1	3
473.0	0	6	1	7
474.0	0	5	2	4
475.0	0	7	0	5
476.0	0	6	0	5
477.0	0	8	0	3
478.0	0	10	2	7
479.0	0	6	0	4
480.0	0	5	0	10
481.0	0	12	0	4
482.0	0	8	0	1
483.0	0	9	0	2
484.0	0	7	1	10
485.0	0	7	0	6
486.0	0	4	1	6
487.0	0	5	0	4
488.0	0	5	0	4
489.0	0	2	1	8
490.0	0	3	1	2
491.0	0	9	2	4
492.0	0	4	1	2
493.0	0	5	0	7
494.0	0	5	1	7
495.0	0	6	0	5
496.0	0	2	0	5
497.0	0	8	2	2
498.0	0	6	0	8
499.0	0	7	1	4
500.0	0	9	0	2
501.0	0	4	0	6
502.0	0	7	0	1
503.0	0	6	0	4
504.0	0	9	1	3
505.0	0	9	1	4
506.0	0	4	0	2
507.0	0	8	1	5
508.0	0	4	1	5
509.0	0	8	3	1
510.0	0	5	0	6
511.0	0	4	0	3
512.0	0	7	1	2
513.0	0	2	1	7
514.0	0	5	0	5
515.0	0	8	0	6
516.0	0	3	0	1
517.0	0	5	0	2
518.0	0	6	0	4
519.0	0	8	0	5
520.0	0	4	0	3
521.0	0	8	0	2
522.0	0	5	1	5
523.0	0	3	0	4
524.0	0	1	0	3
525.0	0	2	0	0
526.0	0	1	1	5
527.0	0	5	1	1
528.0	0	3	0	1
529.0	0	8	1	3
530.0	0	2	0	3
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