## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-262-TP2.bam --OUTPUT POR-262-TP2.md.bam --METRICS_FILE POR-262-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 18:17:40 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	625	17828766	9235998	0	410	12420807	4635227	0.696672	6114823

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.06946	3111352	0	4041714
2.0	1.12739	1067772	804108	794819
3.0	1.130528	450780	321212	196972
4.0	1.130698	228369	162775	81816
5.0	1.130708	131036	90266	49643
6.0	1.130708	81849	54064	34173
7.0	1.130708	55266	33401	25783
8.0	1.130708	38854	21679	20181
9.0	1.130708	28927	14616	16336
10.0	1.130708	22304	10645	13437
11.0	1.130708	18079	7893	11308
12.0	1.130708	14523	5998	9747
13.0	1.130708	12179	4900	8207
14.0	1.130708	10354	3886	7238
15.0	1.130708	9154	3309	6312
16.0	1.130708	7987	2881	5674
17.0	1.130708	6923	2417	5032
18.0	1.130708	6381	2070	4739
19.0	1.130708	5818	1845	4089
20.0	1.130708	5202	1704	3802
21.0	1.130708	4873	1444	3354
22.0	1.130708	4276	1352	3086
23.0	1.130708	3965	1174	2842
24.0	1.130708	3627	1069	2636
25.0	1.130708	3345	975	2306
26.0	1.130708	3127	876	2124
27.0	1.130708	2994	789	2081
28.0	1.130708	2644	742	1813
29.0	1.130708	2492	643	1822
30.0	1.130708	2415	609	1699
31.0	1.130708	2181	596	1541
32.0	1.130708	2023	531	1435
33.0	1.130708	1987	529	1429
34.0	1.130708	1864	422	1284
35.0	1.130708	1716	436	1210
36.0	1.130708	1675	388	1238
37.0	1.130708	1575	371	1163
38.0	1.130708	1468	337	1009
39.0	1.130708	1423	325	1007
40.0	1.130708	1330	300	931
41.0	1.130708	1273	263	910
42.0	1.130708	1249	289	836
43.0	1.130708	1081	246	795
44.0	1.130708	1073	219	816
45.0	1.130708	1051	215	711
46.0	1.130708	1002	214	674
47.0	1.130708	918	234	645
48.0	1.130708	939	196	624
49.0	1.130708	886	180	591
50.0	1.130708	823	171	585
51.0	1.130708	756	179	589
52.0	1.130708	721	165	579
53.0	1.130708	760	142	546
54.0	1.130708	704	137	543
55.0	1.130708	720	145	517
56.0	1.130708	642	157	432
57.0	1.130708	657	124	512
58.0	1.130708	614	124	435
59.0	1.130708	571	127	421
60.0	1.130708	601	112	419
61.0	1.130708	571	92	387
62.0	1.130708	512	97	377
63.0	1.130708	515	72	362
64.0	1.130708	525	112	353
65.0	1.130708	498	98	333
66.0	1.130708	424	77	316
67.0	1.130708	498	77	322
68.0	1.130708	456	77	314
69.0	1.130708	429	78	284
70.0	1.130708	407	78	305
71.0	1.130708	396	70	284
72.0	1.130708	380	77	260
73.0	1.130708	388	72	271
74.0	1.130708	360	49	277
75.0	1.130708	346	82	239
76.0	1.130708	309	57	236
77.0	1.130708	376	66	213
78.0	1.130708	321	55	242
79.0	1.130708	321	60	207
80.0	1.130708	294	62	200
81.0	1.130708	295	53	228
82.0	1.130708	292	47	208
83.0	1.130708	296	55	207
84.0	1.130708	276	43	213
85.0	1.130708	263	35	186
86.0	1.130708	291	43	192
87.0	1.130708	264	37	187
88.0	1.130708	255	50	192
89.0	1.130708	238	39	170
90.0	1.130708	246	38	157
91.0	1.130708	234	29	162
92.0	1.130708	240	45	145
93.0	1.130708	229	29	164
94.0	1.130708	192	31	160
95.0	1.130708	218	31	159
96.0	1.130708	207	36	154
97.0	1.130708	203	29	132
98.0	1.130708	197	24	150
99.0	1.130708	198	27	130
100.0	1.130708	173	32	139
101.0	0	207	23	133
102.0	0	179	25	112
103.0	0	189	37	137
104.0	0	160	32	110
105.0	0	161	31	117
106.0	0	172	21	110
107.0	0	172	35	127
108.0	0	152	24	112
109.0	0	163	18	112
110.0	0	157	26	102
111.0	0	164	23	90
112.0	0	192	25	94
113.0	0	150	21	106
114.0	0	130	16	89
115.0	0	140	21	98
116.0	0	127	24	105
117.0	0	122	24	110
118.0	0	112	20	76
119.0	0	124	14	102
120.0	0	137	24	93
121.0	0	112	22	96
122.0	0	140	14	88
123.0	0	138	26	96
124.0	0	130	8	64
125.0	0	97	30	77
126.0	0	104	20	81
127.0	0	108	13	92
128.0	0	103	12	64
129.0	0	104	14	75
130.0	0	111	15	63
131.0	0	114	16	71
132.0	0	106	17	62
133.0	0	85	12	64
134.0	0	87	13	70
135.0	0	103	12	68
136.0	0	106	14	55
137.0	0	96	14	76
138.0	0	99	9	67
139.0	0	75	10	52
140.0	0	84	11	62
141.0	0	76	11	64
142.0	0	83	11	64
143.0	0	86	19	58
144.0	0	84	7	56
145.0	0	83	10	51
146.0	0	81	18	54
147.0	0	78	8	49
148.0	0	77	11	47
149.0	0	65	14	51
150.0	0	74	17	59
151.0	0	77	11	37
152.0	0	59	3	54
153.0	0	69	8	51
154.0	0	59	15	35
155.0	0	74	9	57
156.0	0	69	10	50
157.0	0	71	3	54
158.0	0	63	7	52
159.0	0	59	8	36
160.0	0	63	4	57
161.0	0	55	8	37
162.0	0	50	6	42
163.0	0	57	9	45
164.0	0	58	8	50
165.0	0	63	5	41
166.0	0	70	9	38
167.0	0	59	4	49
168.0	0	59	8	38
169.0	0	55	11	35
170.0	0	57	4	36
171.0	0	62	5	29
172.0	0	47	2	35
173.0	0	50	4	35
174.0	0	52	7	51
175.0	0	47	4	46
176.0	0	46	9	42
177.0	0	49	6	25
178.0	0	53	5	37
179.0	0	54	5	41
180.0	0	45	7	30
181.0	0	49	7	50
182.0	0	46	7	41
183.0	0	49	7	28
184.0	0	45	6	27
185.0	0	58	9	44
186.0	0	44	3	37
187.0	0	50	7	37
188.0	0	55	4	32
189.0	0	46	4	30
190.0	0	49	6	33
191.0	0	32	5	28
192.0	0	39	5	25
193.0	0	39	5	29
194.0	0	40	4	27
195.0	0	30	4	35
196.0	0	32	5	23
197.0	0	48	1	31
198.0	0	35	1	28
199.0	0	44	5	21
200.0	0	33	7	33
201.0	0	38	5	21
202.0	0	53	8	18
203.0	0	43	5	20
204.0	0	38	3	33
205.0	0	42	3	22
206.0	0	36	4	22
207.0	0	40	3	25
208.0	0	32	7	30
209.0	0	22	4	23
210.0	0	33	1	23
211.0	0	32	2	22
212.0	0	28	5	25
213.0	0	34	2	21
214.0	0	34	3	20
215.0	0	29	4	19
216.0	0	40	4	30
217.0	0	26	3	18
218.0	0	27	5	22
219.0	0	35	0	28
220.0	0	39	5	23
221.0	0	29	2	14
222.0	0	33	4	33
223.0	0	28	2	26
224.0	0	34	2	17
225.0	0	19	6	25
226.0	0	32	3	24
227.0	0	26	3	15
228.0	0	36	3	25
229.0	0	17	3	23
230.0	0	30	6	20
231.0	0	33	2	26
232.0	0	26	0	16
233.0	0	29	4	17
234.0	0	37	1	28
235.0	0	33	3	10
236.0	0	35	0	23
237.0	0	27	3	8
238.0	0	27	1	10
239.0	0	30	2	17
240.0	0	24	4	18
241.0	0	27	1	11
242.0	0	28	1	14
243.0	0	25	0	22
244.0	0	18	0	18
245.0	0	13	2	18
246.0	0	26	3	15
247.0	0	21	2	19
248.0	0	27	2	22
249.0	0	22	4	19
250.0	0	15	2	13
251.0	0	27	2	17
252.0	0	24	2	19
253.0	0	25	5	18
254.0	0	22	2	22
255.0	0	24	1	12
256.0	0	16	1	25
257.0	0	27	2	15
258.0	0	23	1	11
259.0	0	20	3	21
260.0	0	21	2	19
261.0	0	15	0	13
262.0	0	27	3	8
263.0	0	20	4	12
264.0	0	21	2	13
265.0	0	20	4	15
266.0	0	15	2	25
267.0	0	16	0	12
268.0	0	17	3	13
269.0	0	17	1	19
270.0	0	20	1	14
271.0	0	15	3	9
272.0	0	22	3	11
273.0	0	13	4	12
274.0	0	15	0	14
275.0	0	17	3	14
276.0	0	23	4	17
277.0	0	24	4	9
278.0	0	13	4	11
279.0	0	21	1	14
280.0	0	24	3	10
281.0	0	20	1	15
282.0	0	14	1	18
283.0	0	18	2	11
284.0	0	19	1	18
285.0	0	20	4	11
286.0	0	26	1	10
287.0	0	12	4	23
288.0	0	17	1	10
289.0	0	16	1	17
290.0	0	15	2	8
291.0	0	17	0	12
292.0	0	12	0	8
293.0	0	15	3	10
294.0	0	23	3	6
295.0	0	13	2	9
296.0	0	13	0	4
297.0	0	15	1	15
298.0	0	14	1	11
299.0	0	16	0	13
300.0	0	10	1	10
301.0	0	16	1	15
302.0	0	19	1	8
303.0	0	17	0	10
304.0	0	13	5	5
305.0	0	13	1	9
306.0	0	15	2	8
307.0	0	10	2	6
308.0	0	15	1	10
309.0	0	11	2	10
310.0	0	11	2	13
311.0	0	11	3	13
312.0	0	20	0	8
313.0	0	18	5	8
314.0	0	15	2	6
315.0	0	15	0	7
316.0	0	5	1	9
317.0	0	10	1	5
318.0	0	16	0	10
319.0	0	18	0	7
320.0	0	19	0	6
321.0	0	11	1	8
322.0	0	7	0	10
323.0	0	15	1	11
324.0	0	14	2	14
325.0	0	13	1	10
326.0	0	9	1	13
327.0	0	11	0	5
328.0	0	8	0	14
329.0	0	9	4	7
330.0	0	7	2	9
331.0	0	12	1	12
332.0	0	9	1	6
333.0	0	13	1	3
334.0	0	10	2	11
335.0	0	11	2	5
336.0	0	12	0	11
337.0	0	16	1	5
338.0	0	13	0	5
339.0	0	10	1	5
340.0	0	9	1	11
341.0	0	8	0	3
342.0	0	18	1	5
343.0	0	6	1	12
344.0	0	12	0	8
345.0	0	18	3	11
346.0	0	8	1	10
347.0	0	10	1	4
348.0	0	11	1	8
349.0	0	11	0	5
350.0	0	12	0	9
351.0	0	11	0	5
352.0	0	11	2	6
353.0	0	14	0	4
354.0	0	12	1	6
355.0	0	8	1	10
356.0	0	11	2	4
357.0	0	9	1	5
358.0	0	8	3	6
359.0	0	12	0	9
360.0	0	7	1	6
361.0	0	12	0	5
362.0	0	6	1	9
363.0	0	6	0	11
364.0	0	9	0	4
365.0	0	6	0	4
366.0	0	6	1	8
367.0	0	13	1	5
368.0	0	10	1	9
369.0	0	8	0	13
370.0	0	15	0	4
371.0	0	6	0	3
372.0	0	8	2	3
373.0	0	11	2	9
374.0	0	8	1	4
375.0	0	4	0	6
376.0	0	10	1	7
377.0	0	11	0	6
378.0	0	11	1	5
379.0	0	9	0	5
380.0	0	7	1	5
381.0	0	8	0	8
382.0	0	7	0	4
383.0	0	12	2	3
384.0	0	9	0	3
385.0	0	8	0	1
386.0	0	4	0	5
387.0	0	9	0	12
388.0	0	7	2	5
389.0	0	12	1	6
390.0	0	7	0	6
391.0	0	9	0	8
392.0	0	7	0	8
393.0	0	8	0	3
394.0	0	11	1	2
395.0	0	6	0	4
396.0	0	10	0	1
397.0	0	7	1	5
398.0	0	9	0	3
399.0	0	8	0	10
400.0	0	9	0	7
401.0	0	8	0	4
402.0	0	9	0	4
403.0	0	6	0	5
404.0	0	3	1	6
405.0	0	5	0	6
406.0	0	7	0	4
407.0	0	4	0	5
408.0	0	2	0	1
409.0	0	10	0	2
410.0	0	4	0	8
411.0	0	6	1	2
412.0	0	5	2	4
413.0	0	8	0	7
414.0	0	4	1	3
415.0	0	6	1	3
416.0	0	6	2	9
417.0	0	6	1	4
418.0	0	7	0	5
419.0	0	10	0	4
420.0	0	4	1	3
421.0	0	10	1	5
422.0	0	6	0	5
423.0	0	5	0	8
424.0	0	9	0	4
425.0	0	7	0	4
426.0	0	8	0	3
427.0	0	6	1	4
428.0	0	9	0	5
429.0	0	3	1	2
430.0	0	2	1	4
431.0	0	8	1	4
432.0	0	2	1	3
433.0	0	4	0	2
434.0	0	8	1	4
435.0	0	7	0	4
436.0	0	5	0	3
437.0	0	4	0	3
438.0	0	5	0	3
439.0	0	5	0	1
440.0	0	6	0	2
441.0	0	6	1	6
442.0	0	4	2	4
443.0	0	4	1	3
444.0	0	2	0	6
445.0	0	3	0	3
446.0	0	6	0	5
447.0	0	5	1	5
448.0	0	3	0	4
449.0	0	4	0	2
450.0	0	6	0	4
451.0	0	8	0	2
452.0	0	3	0	2
453.0	0	5	0	2
454.0	0	4	0	2
455.0	0	6	1	3
456.0	0	3	0	3
457.0	0	5	0	4
458.0	0	7	0	3
459.0	0	7	2	6
460.0	0	1	1	0
461.0	0	4	0	0
462.0	0	4	0	3
463.0	0	3	0	3
464.0	0	6	0	6
465.0	0	8	0	5
466.0	0	1	0	1
467.0	0	5	0	2
468.0	0	3	0	4
469.0	0	7	1	5
470.0	0	3	0	3
471.0	0	5	0	6
472.0	0	2	0	2
473.0	0	4	0	3
474.0	0	2	0	6
475.0	0	5	0	3
476.0	0	2	0	2
477.0	0	5	1	2
478.0	0	2	0	6
479.0	0	2	1	2
480.0	0	4	0	3
481.0	0	1	0	0
482.0	0	5	0	6
483.0	0	3	0	2
484.0	0	6	1	2
485.0	0	3	0	3
486.0	0	3	0	3
487.0	0	7	0	2
488.0	0	4	1	2
489.0	0	5	0	3
490.0	0	4	0	3
491.0	0	1	0	4
492.0	0	5	1	2
493.0	0	2	0	3
494.0	0	3	0	1
495.0	0	6	0	1
496.0	0	4	0	1
497.0	0	2	0	4
498.0	0	7	0	0
499.0	0	5	1	2
500.0	0	3	0	2
501.0	0	2	0	3
502.0	0	1	0	4
503.0	0	9	0	4
504.0	0	4	0	3
505.0	0	2	1	1
506.0	0	4	0	1
507.0	0	6	2	1
508.0	0	3	0	1
509.0	0	5	1	2
510.0	0	4	0	3
511.0	0	2	1	1
512.0	0	3	0	4
513.0	0	1	0	0
514.0	0	5	1	0
515.0	0	5	0	4
516.0	0	1	1	2
517.0	0	3	1	1
518.0	0	4	0	0
519.0	0	5	0	7
520.0	0	4	0	4
521.0	0	3	0	4
522.0	0	6	1	2
523.0	0	3	0	2
524.0	0	2	0	5
525.0	0	4	0	4
526.0	0	4	0	1
527.0	0	3	1	0
528.0	0	3	0	0
529.0	0	6	0	3
530.0	0	2	0	2
531.0	0	6	0	3
532.0	0	2	1	0
533.0	0	2	1	2
534.0	0	3	0	1
535.0	0	2	0	3
536.0	0	3	0	2
537.0	0	1	0	2
538.0	0	4	0	4
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