## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-260-TP1.bam --OUTPUT POR-260-TP1.md.bam --METRICS_FILE POR-260-TP1.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 18:17:40 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	435	14636160	6488189	0	258	8888777	3665911	0.607316	7463925

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.115905	3160167	0	4116123
2.0	1.272945	1270372	873700	1058183
3.0	1.295045	559417	345400	273729
4.0	1.298156	274673	168213	92540
5.0	1.298593	148323	89134	45046
6.0	1.298655	86858	48950	27705
7.0	1.298664	53942	28415	19690
8.0	1.298665	35580	16702	14677
9.0	1.298665	24733	10402	11688
10.0	1.298665	17860	6922	9310
11.0	1.298665	13609	4653	7777
12.0	1.298665	10644	3294	6357
13.0	1.298665	8478	2562	5404
14.0	1.298665	7058	1963	4814
15.0	1.298665	5871	1577	4034
16.0	1.298665	5174	1276	3587
17.0	1.298665	4478	1057	3118
18.0	1.298665	3961	873	2779
19.0	1.298665	3526	742	2571
20.0	1.298665	3087	676	2286
21.0	1.298665	2935	586	2038
22.0	1.298665	2609	558	1945
23.0	1.298665	2249	473	1647
24.0	1.298665	2225	437	1563
25.0	1.298665	1984	348	1428
26.0	1.298665	1772	365	1270
27.0	1.298665	1686	284	1206
28.0	1.298665	1487	277	1133
29.0	1.298665	1426	251	1047
30.0	1.298665	1306	230	950
31.0	1.298665	1236	245	882
32.0	1.298665	1184	182	825
33.0	1.298665	1040	160	796
34.0	1.298665	1055	176	684
35.0	1.298665	938	159	699
36.0	1.298665	884	140	652
37.0	1.298665	847	150	640
38.0	1.298665	793	127	589
39.0	1.298665	737	116	549
40.0	1.298665	752	122	500
41.0	1.298665	654	107	508
42.0	1.298665	590	92	463
43.0	1.298665	570	98	454
44.0	1.298665	564	70	442
45.0	1.298665	533	91	391
46.0	1.298665	515	57	393
47.0	1.298665	494	56	299
48.0	1.298665	464	64	343
49.0	1.298665	426	57	314
50.0	1.298665	447	69	303
51.0	1.298665	378	55	308
52.0	1.298665	390	60	272
53.0	1.298665	388	54	283
54.0	1.298665	371	41	223
55.0	1.298665	356	49	261
56.0	1.298665	316	43	233
57.0	1.298665	295	51	219
58.0	1.298665	305	26	216
59.0	1.298665	265	37	197
60.0	1.298665	291	33	213
61.0	1.298665	266	42	207
62.0	1.298665	254	39	205
63.0	1.298665	253	23	185
64.0	1.298665	249	34	151
65.0	1.298665	235	24	167
66.0	1.298665	215	33	162
67.0	1.298665	236	26	167
68.0	1.298665	223	26	151
69.0	1.298665	211	19	169
70.0	1.298665	187	25	146
71.0	1.298665	183	14	170
72.0	1.298665	180	26	142
73.0	1.298665	164	19	143
74.0	1.298665	210	15	132
75.0	1.298665	162	22	99
76.0	1.298665	170	22	117
77.0	1.298665	163	20	97
78.0	1.298665	162	11	111
79.0	1.298665	157	18	98
80.0	1.298665	145	15	123
81.0	1.298665	144	25	97
82.0	1.298665	161	10	96
83.0	1.298665	133	11	119
84.0	1.298665	139	17	104
85.0	1.298665	128	10	100
86.0	1.298665	149	11	89
87.0	1.298665	110	20	97
88.0	1.298665	130	9	98
89.0	1.298665	113	12	77
90.0	1.298665	116	16	87
91.0	1.298665	113	10	84
92.0	1.298665	113	15	71
93.0	1.298665	107	6	68
94.0	1.298665	84	12	77
95.0	1.298665	112	10	70
96.0	1.298665	91	9	78
97.0	1.298665	89	9	60
98.0	1.298665	108	9	70
99.0	1.298665	82	13	71
100.0	1.298665	92	9	60
101.0	0	65	9	58
102.0	0	91	11	56
103.0	0	90	11	54
104.0	0	82	6	59
105.0	0	69	4	51
106.0	0	72	14	56
107.0	0	91	13	37
108.0	0	82	9	56
109.0	0	57	2	47
110.0	0	59	7	39
111.0	0	47	6	39
112.0	0	68	2	50
113.0	0	47	6	39
114.0	0	63	4	47
115.0	0	60	2	60
116.0	0	52	5	48
117.0	0	81	7	50
118.0	0	58	1	39
119.0	0	59	9	40
120.0	0	70	3	49
121.0	0	53	3	37
122.0	0	44	6	31
123.0	0	38	2	34
124.0	0	50	4	39
125.0	0	50	2	36
126.0	0	43	3	34
127.0	0	31	1	31
128.0	0	39	5	26
129.0	0	39	4	39
130.0	0	46	9	31
131.0	0	50	4	34
132.0	0	40	2	21
133.0	0	48	4	33
134.0	0	50	5	38
135.0	0	47	1	34
136.0	0	43	6	33
137.0	0	37	3	30
138.0	0	37	1	30
139.0	0	38	4	21
140.0	0	40	4	22
141.0	0	35	4	25
142.0	0	40	3	26
143.0	0	41	2	26
144.0	0	33	2	27
145.0	0	32	2	20
146.0	0	37	4	26
147.0	0	31	3	31
148.0	0	39	3	23
149.0	0	21	1	15
150.0	0	36	2	35
151.0	0	33	2	17
152.0	0	38	3	25
153.0	0	27	3	13
154.0	0	24	1	20
155.0	0	26	4	30
156.0	0	27	3	20
157.0	0	16	4	17
158.0	0	26	2	22
159.0	0	24	0	20
160.0	0	26	2	14
161.0	0	32	3	26
162.0	0	28	4	30
163.0	0	38	3	26
164.0	0	26	2	17
165.0	0	21	3	20
166.0	0	29	4	12
167.0	0	14	3	15
168.0	0	31	2	16
169.0	0	18	2	18
170.0	0	25	1	17
171.0	0	22	1	20
172.0	0	18	1	12
173.0	0	26	1	15
174.0	0	15	2	15
175.0	0	34	0	16
176.0	0	22	1	8
177.0	0	14	0	23
178.0	0	19	1	18
179.0	0	22	1	16
180.0	0	27	2	23
181.0	0	13	2	14
182.0	0	20	1	15
183.0	0	14	4	15
184.0	0	19	2	14
185.0	0	17	0	12
186.0	0	21	0	14
187.0	0	21	2	10
188.0	0	23	1	16
189.0	0	7	1	19
190.0	0	19	0	15
191.0	0	19	2	15
192.0	0	15	2	9
193.0	0	18	0	14
194.0	0	14	0	19
195.0	0	18	2	6
196.0	0	12	0	13
197.0	0	19	0	9
198.0	0	20	1	10
199.0	0	15	1	14
200.0	0	17	3	9
201.0	0	19	2	13
202.0	0	19	2	9
203.0	0	11	0	10
204.0	0	20	1	3
205.0	0	16	2	15
206.0	0	13	3	14
207.0	0	16	0	15
208.0	0	15	0	11
209.0	0	10	0	12
210.0	0	10	2	13
211.0	0	15	1	8
212.0	0	9	0	11
213.0	0	20	1	10
214.0	0	13	1	10
215.0	0	11	0	7
216.0	0	17	1	15
217.0	0	17	1	6
218.0	0	14	0	11
219.0	0	16	1	11
220.0	0	15	2	12
221.0	0	11	0	14
222.0	0	17	0	14
223.0	0	8	1	10
224.0	0	9	0	12
225.0	0	14	1	14
226.0	0	19	1	10
227.0	0	13	1	10
228.0	0	10	1	8
229.0	0	9	1	10
230.0	0	13	0	4
231.0	0	17	1	14
232.0	0	11	1	9
233.0	0	15	2	7
234.0	0	16	0	9
235.0	0	12	0	5
236.0	0	9	1	8
237.0	0	6	0	8
238.0	0	8	2	12
239.0	0	9	0	10
240.0	0	7	0	6
241.0	0	14	0	6
242.0	0	9	1	7
243.0	0	11	0	7
244.0	0	7	0	4
245.0	0	10	1	7
246.0	0	11	0	2
247.0	0	8	0	8
248.0	0	4	0	6
249.0	0	8	0	8
250.0	0	11	0	8
251.0	0	6	0	11
252.0	0	5	0	6
253.0	0	15	1	6
254.0	0	8	0	10
255.0	0	11	3	1
256.0	0	5	0	2
257.0	0	7	0	3
258.0	0	7	0	13
259.0	0	9	1	5
260.0	0	8	0	5
261.0	0	11	0	7
262.0	0	9	3	10
263.0	0	9	0	5
264.0	0	6	0	7
265.0	0	14	0	7
266.0	0	6	1	5
267.0	0	6	1	6
268.0	0	11	0	5
269.0	0	5	1	9
270.0	0	12	0	3
271.0	0	3	0	6
272.0	0	2	1	3
273.0	0	8	0	5
274.0	0	9	0	5
275.0	0	11	0	4
276.0	0	10	1	6
277.0	0	8	1	3
278.0	0	7	0	4
279.0	0	3	0	7
280.0	0	6	0	7
281.0	0	10	0	7
282.0	0	6	0	5
283.0	0	11	1	7
284.0	0	6	1	1
285.0	0	10	0	4
286.0	0	6	0	5
287.0	0	8	0	3
288.0	0	2	2	3
289.0	0	7	0	6
290.0	0	6	1	8
291.0	0	3	0	3
292.0	0	7	0	4
293.0	0	4	0	2
294.0	0	7	1	3
295.0	0	5	1	5
296.0	0	2	0	5
297.0	0	14	0	4
298.0	0	7	0	4
299.0	0	2	1	2
300.0	0	9	0	4
301.0	0	8	0	7
302.0	0	6	0	1
303.0	0	8	0	2
304.0	0	6	0	2
305.0	0	4	1	4
306.0	0	8	0	5
307.0	0	4	0	1
308.0	0	5	1	0
309.0	0	7	0	6
310.0	0	5	1	0
311.0	0	8	0	3
312.0	0	5	2	2
313.0	0	6	0	3
314.0	0	1	0	5
315.0	0	4	0	2
316.0	0	2	2	0
317.0	0	5	0	2
318.0	0	3	0	2
319.0	0	2	1	2
320.0	0	2	1	3
321.0	0	3	0	5
322.0	0	1	0	3
323.0	0	2	0	0
324.0	0	6	0	5
325.0	0	3	0	2
326.0	0	3	0	1
327.0	0	0	0	4
328.0	0	3	2	3
329.0	0	4	0	3
330.0	0	5	0	3
331.0	0	6	0	3
332.0	0	4	0	7
333.0	0	5	0	2
334.0	0	5	0	2
335.0	0	6	0	0
336.0	0	3	0	3
337.0	0	4	0	1
338.0	0	5	0	6
339.0	0	5	0	2
340.0	0	1	0	4
341.0	0	1	0	2
342.0	0	6	0	7
343.0	0	7	0	5
344.0	0	5	0	1
345.0	0	3	2	3
346.0	0	6	0	4
347.0	0	3	0	3
348.0	0	2	0	2
349.0	0	4	1	2
350.0	0	3	0	6
351.0	0	5	0	2
352.0	0	6	0	2
353.0	0	2	0	4
354.0	0	2	0	2
355.0	0	2	0	5
356.0	0	4	0	3
357.0	0	2	1	3
358.0	0	3	0	3
359.0	0	5	0	3
360.0	0	2	0	3
361.0	0	3	0	1
362.0	0	1	0	2
363.0	0	6	0	1
364.0	0	3	1	3
365.0	0	4	0	1
366.0	0	2	0	1
367.0	0	5	0	3
368.0	0	3	0	1
369.0	0	1	0	3
370.0	0	7	0	2
371.0	0	6	0	2
372.0	0	2	0	6
373.0	0	2	1	0
374.0	0	1	0	3
375.0	0	2	0	1
376.0	0	1	0	3
377.0	0	4	0	1
378.0	0	3	0	1
379.0	0	4	0	2
380.0	0	3	0	2
381.0	0	3	0	1
382.0	0	3	0	0
383.0	0	1	0	0
384.0	0	5	0	1
385.0	0	1	0	1
386.0	0	5	1	2
387.0	0	5	0	2
388.0	0	5	0	3
389.0	0	3	1	3
390.0	0	3	0	2
391.0	0	2	0	3
392.0	0	5	0	2
393.0	0	2	1	2
394.0	0	4	0	1
395.0	0	3	0	0
396.0	0	2	0	1
397.0	0	2	0	3
398.0	0	1	1	2
399.0	0	2	0	2
400.0	0	3	0	1
401.0	0	6	0	1
402.0	0	4	1	2
403.0	0	2	1	1
404.0	0	2	0	2
405.0	0	2	0	1
406.0	0	6	1	1
407.0	0	3	0	2
408.0	0	1	0	2
409.0	0	4	0	0
410.0	0	1	0	0
411.0	0	2	1	0
412.0	0	4	2	1
413.0	0	4	0	4
414.0	0	3	0	2
415.0	0	3	0	1
416.0	0	0	0	1
417.0	0	1	0	2
418.0	0	2	0	1
419.0	0	0	0	2
420.0	0	2	0	0
421.0	0	0	0	4
422.0	0	3	0	1
423.0	0	1	2	0
424.0	0	4	1	2
425.0	0	1	0	0
426.0	0	1	0	1
427.0	0	2	0	2
428.0	0	1	0	3
429.0	0	2	0	2
430.0	0	3	0	3
431.0	0	2	0	0
433.0	0	1	0	2
434.0	0	2	0	0
435.0	0	2	0	3
436.0	0	1	0	1
437.0	0	1	0	3
438.0	0	1	0	1
439.0	0	4	0	2
440.0	0	2	0	2
441.0	0	1	0	2
442.0	0	1	0	2
443.0	0	4	0	1
445.0	0	0	0	1
446.0	0	1	0	1
447.0	0	3	0	0
448.0	0	4	1	3
449.0	0	1	0	1
451.0	0	3	0	3
452.0	0	3	0	3
453.0	0	2	0	1
454.0	0	3	0	2
455.0	0	3	0	1
456.0	0	3	0	0
457.0	0	2	0	0
458.0	0	0	0	1
459.0	0	0	0	1
460.0	0	4	0	0
461.0	0	1	0	1
462.0	0	2	0	3
463.0	0	0	0	1
464.0	0	2	0	0
465.0	0	2	0	1
466.0	0	2	0	1
467.0	0	2	0	1
468.0	0	1	0	0
469.0	0	2	0	1
470.0	0	0	0	3
471.0	0	2	0	2
472.0	0	0	0	1
473.0	0	2	0	1
474.0	0	0	0	2
475.0	0	1	1	1
477.0	0	0	0	1
478.0	0	2	0	1
479.0	0	1	0	2
480.0	0	2	0	0
481.0	0	1	0	1
482.0	0	2	0	0
483.0	0	1	0	3
484.0	0	2	0	1
485.0	0	3	0	0
486.0	0	0	0	2
487.0	0	2	0	1
488.0	0	1	0	0
489.0	0	2	0	2
491.0	0	0	0	1
492.0	0	4	0	1
493.0	0	1	0	1
494.0	0	0	0	1
495.0	0	1	0	0
496.0	0	1	0	1
497.0	0	1	0	0
498.0	0	0	0	3
499.0	0	3	0	2
500.0	0	3	0	0
501.0	0	2	0	0
502.0	0	1	0	1
503.0	0	1	0	2
504.0	0	0	0	1
505.0	0	1	0	0
506.0	0	1	0	1
507.0	0	0	0	1
508.0	0	0	0	3
510.0	0	3	0	0
511.0	0	2	0	4
512.0	0	3	0	2
514.0	0	1	0	1
515.0	0	2	0	1
516.0	0	1	0	1
518.0	0	1	0	1
519.0	0	4	0	0
520.0	0	1	0	0
521.0	0	4	0	1
522.0	0	1	0	1
523.0	0	1	0	0
524.0	0	2	0	0
526.0	0	2	0	3
528.0	0	1	1	2
529.0	0	1	0	3
530.0	0	1	0	0
531.0	0	2	0	0
532.0	0	1	0	0
533.0	0	1	0	1
534.0	0	0	0	1
535.0	0	1	0	1
536.0	0	2	0	1
537.0	0	0	0	2
539.0	0	2	0	0
541.0	0	0	0	1
542.0	0	0	0	2
545.0	0	2	0	0
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