## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-260-TP4.bam --OUTPUT POR-260-TP4.md.bam --METRICS_FILE POR-260-TP4.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 18:17:47 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	551	16660708	9455426	0	344	12557276	3729872	0.753704	4319961

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.030514	2027263	0	2554405
2.0	1.052297	899729	600181	840882
3.0	1.052758	418687	239048	273690
4.0	1.052768	215426	122840	108357
5.0	1.052768	122661	69466	58138
6.0	1.052768	77467	42075	38400
7.0	1.052768	52257	26775	27941
8.0	1.052768	38079	17803	22064
9.0	1.052768	28679	12515	17533
10.0	1.052768	22467	9129	14649
11.0	1.052768	17938	6911	12407
12.0	1.052768	14926	5474	10576
13.0	1.052768	12683	4264	8917
14.0	1.052768	10897	3650	7978
15.0	1.052768	9433	3025	6998
16.0	1.052768	8530	2591	6234
17.0	1.052768	7330	2216	5435
18.0	1.052768	6575	1925	4979
19.0	1.052768	5946	1655	4561
20.0	1.052768	5603	1513	4164
21.0	1.052768	4938	1329	3731
22.0	1.052768	4520	1170	3350
23.0	1.052768	4199	1063	3240
24.0	1.052768	3905	920	2924
25.0	1.052768	3619	887	2644
26.0	1.052768	3370	778	2509
27.0	1.052768	3148	648	2249
28.0	1.052768	2891	657	2146
29.0	1.052768	2677	611	1994
30.0	1.052768	2502	523	1882
31.0	1.052768	2366	501	1712
32.0	1.052768	2168	486	1600
33.0	1.052768	1992	454	1636
34.0	1.052768	1936	415	1420
35.0	1.052768	1870	365	1386
36.0	1.052768	1812	345	1234
37.0	1.052768	1647	311	1262
38.0	1.052768	1569	308	1189
39.0	1.052768	1540	288	1114
40.0	1.052768	1400	269	1042
41.0	1.052768	1381	271	1008
42.0	1.052768	1241	267	892
43.0	1.052768	1251	241	920
44.0	1.052768	1121	213	896
45.0	1.052768	1064	199	839
46.0	1.052768	1047	213	806
47.0	1.052768	985	184	760
48.0	1.052768	932	172	751
49.0	1.052768	885	177	672
50.0	1.052768	856	149	661
51.0	1.052768	871	153	626
52.0	1.052768	871	146	658
53.0	1.052768	816	138	569
54.0	1.052768	770	149	558
55.0	1.052768	730	102	544
56.0	1.052768	726	114	521
57.0	1.052768	652	102	489
58.0	1.052768	589	103	490
59.0	1.052768	666	117	479
60.0	1.052768	632	99	472
61.0	1.052768	585	98	442
62.0	1.052768	618	95	409
63.0	1.052768	554	85	423
64.0	1.052768	524	83	383
65.0	1.052768	529	71	412
66.0	1.052768	544	76	408
67.0	1.052768	483	81	373
68.0	1.052768	487	74	378
69.0	1.052768	474	61	344
70.0	1.052768	425	74	348
71.0	1.052768	422	58	300
72.0	1.052768	405	67	324
73.0	1.052768	388	54	287
74.0	1.052768	341	64	255
75.0	1.052768	379	64	288
76.0	1.052768	346	53	274
77.0	1.052768	337	54	280
78.0	1.052768	386	48	258
79.0	1.052768	319	47	270
80.0	1.052768	335	36	250
81.0	1.052768	317	38	235
82.0	1.052768	333	44	225
83.0	1.052768	333	37	225
84.0	1.052768	312	49	238
85.0	1.052768	262	38	216
86.0	1.052768	268	39	217
87.0	1.052768	270	46	209
88.0	1.052768	291	26	184
89.0	1.052768	260	31	188
90.0	1.052768	262	39	187
91.0	1.052768	258	37	171
92.0	1.052768	257	25	194
93.0	1.052768	242	34	177
94.0	1.052768	215	33	157
95.0	1.052768	237	29	166
96.0	1.052768	260	28	176
97.0	1.052768	226	29	160
98.0	1.052768	214	17	144
99.0	1.052768	197	29	169
100.0	1.052768	188	28	138
101.0	0	222	27	143
102.0	0	203	18	149
103.0	0	208	21	137
104.0	0	194	29	102
105.0	0	160	22	133
106.0	0	167	20	122
107.0	0	184	17	133
108.0	0	172	16	132
109.0	0	150	21	124
110.0	0	162	21	96
111.0	0	156	13	122
112.0	0	126	22	106
113.0	0	149	20	114
114.0	0	148	14	107
115.0	0	139	13	102
116.0	0	135	14	110
117.0	0	130	13	112
118.0	0	152	15	101
119.0	0	153	17	93
120.0	0	153	12	83
121.0	0	123	20	97
122.0	0	132	17	98
123.0	0	127	13	90
124.0	0	110	11	95
125.0	0	115	17	87
126.0	0	118	16	90
127.0	0	132	11	99
128.0	0	103	13	82
129.0	0	128	13	84
130.0	0	110	11	85
131.0	0	126	18	88
132.0	0	115	15	98
133.0	0	99	11	78
134.0	0	107	10	93
135.0	0	107	11	75
136.0	0	106	13	80
137.0	0	92	14	82
138.0	0	96	13	58
139.0	0	86	13	73
140.0	0	100	4	76
141.0	0	106	9	61
142.0	0	95	9	73
143.0	0	100	11	79
144.0	0	86	11	75
145.0	0	78	6	63
146.0	0	83	5	67
147.0	0	96	6	54
148.0	0	74	11	61
149.0	0	84	13	58
150.0	0	72	9	69
151.0	0	66	9	46
152.0	0	80	5	62
153.0	0	79	7	58
154.0	0	69	10	65
155.0	0	83	5	66
156.0	0	74	15	54
157.0	0	71	6	45
158.0	0	88	8	53
159.0	0	67	14	45
160.0	0	73	9	58
161.0	0	72	6	56
162.0	0	71	9	65
163.0	0	57	8	55
164.0	0	59	6	50
165.0	0	68	4	46
166.0	0	72	6	37
167.0	0	72	5	48
168.0	0	66	5	54
169.0	0	61	11	47
170.0	0	65	3	35
171.0	0	57	9	49
172.0	0	44	6	49
173.0	0	68	4	53
174.0	0	59	7	61
175.0	0	60	3	44
176.0	0	59	4	49
177.0	0	48	5	34
178.0	0	59	7	47
179.0	0	48	7	46
180.0	0	57	7	32
181.0	0	47	6	34
182.0	0	61	5	27
183.0	0	63	10	53
184.0	0	55	3	39
185.0	0	56	5	31
186.0	0	40	1	30
187.0	0	52	8	30
188.0	0	56	6	28
189.0	0	34	7	29
190.0	0	36	2	29
191.0	0	50	1	36
192.0	0	45	3	37
193.0	0	49	2	31
194.0	0	48	4	34
195.0	0	52	5	34
196.0	0	31	6	38
197.0	0	40	3	27
198.0	0	35	1	20
199.0	0	46	3	34
200.0	0	39	4	31
201.0	0	59	1	27
202.0	0	42	3	30
203.0	0	37	3	28
204.0	0	40	8	37
205.0	0	29	1	35
206.0	0	39	4	28
207.0	0	40	4	31
208.0	0	38	5	27
209.0	0	31	7	29
210.0	0	27	5	22
211.0	0	36	5	33
212.0	0	38	4	24
213.0	0	34	1	27
214.0	0	36	4	28
215.0	0	41	2	23
216.0	0	37	6	22
217.0	0	28	5	17
218.0	0	36	3	33
219.0	0	29	6	22
220.0	0	35	2	27
221.0	0	38	3	23
222.0	0	34	1	28
223.0	0	28	0	19
224.0	0	26	7	26
225.0	0	33	2	24
226.0	0	30	2	18
227.0	0	35	0	22
228.0	0	30	2	16
229.0	0	34	2	23
230.0	0	30	1	24
231.0	0	23	1	18
232.0	0	45	3	17
233.0	0	31	0	27
234.0	0	26	1	19
235.0	0	34	3	14
236.0	0	29	2	21
237.0	0	21	3	17
238.0	0	32	2	24
239.0	0	28	5	24
240.0	0	20	3	18
241.0	0	26	2	22
242.0	0	17	1	21
243.0	0	25	3	17
244.0	0	17	1	21
245.0	0	26	1	19
246.0	0	29	1	15
247.0	0	30	5	19
248.0	0	25	0	15
249.0	0	24	0	13
250.0	0	16	1	16
251.0	0	27	2	17
252.0	0	21	4	16
253.0	0	26	1	25
254.0	0	23	2	17
255.0	0	29	2	17
256.0	0	39	2	15
257.0	0	23	1	14
258.0	0	20	0	14
259.0	0	19	4	15
260.0	0	24	2	18
261.0	0	23	0	16
262.0	0	16	2	13
263.0	0	23	2	8
264.0	0	18	0	13
265.0	0	27	3	19
266.0	0	19	1	14
267.0	0	13	6	14
268.0	0	25	0	17
269.0	0	24	1	15
270.0	0	18	1	13
271.0	0	18	0	16
272.0	0	20	0	15
273.0	0	12	3	12
274.0	0	15	5	12
275.0	0	20	2	16
276.0	0	13	1	7
277.0	0	22	1	16
278.0	0	17	0	13
279.0	0	19	2	10
280.0	0	18	1	11
281.0	0	21	2	13
282.0	0	29	3	15
283.0	0	17	2	19
284.0	0	17	0	12
285.0	0	11	1	15
286.0	0	14	0	13
287.0	0	22	3	19
288.0	0	15	0	15
289.0	0	16	1	15
290.0	0	17	1	12
291.0	0	15	0	8
292.0	0	18	1	10
293.0	0	16	2	16
294.0	0	21	1	17
295.0	0	25	0	8
296.0	0	24	0	12
297.0	0	12	0	20
298.0	0	18	1	11
299.0	0	14	0	13
300.0	0	12	2	14
301.0	0	15	0	6
302.0	0	14	0	11
303.0	0	13	2	10
304.0	0	17	1	17
305.0	0	15	0	12
306.0	0	10	0	7
307.0	0	11	2	5
308.0	0	15	2	12
309.0	0	11	1	19
310.0	0	14	0	7
311.0	0	18	4	10
312.0	0	11	0	15
313.0	0	11	1	13
314.0	0	12	2	12
315.0	0	13	2	14
316.0	0	11	2	9
317.0	0	24	1	13
318.0	0	23	0	19
319.0	0	4	1	13
320.0	0	14	0	10
321.0	0	9	0	12
322.0	0	19	1	11
323.0	0	10	0	10
324.0	0	18	0	7
325.0	0	17	0	12
326.0	0	11	1	11
327.0	0	17	1	8
328.0	0	13	1	12
329.0	0	10	0	10
330.0	0	13	0	7
331.0	0	13	2	6
332.0	0	12	0	21
333.0	0	14	0	7
334.0	0	13	1	10
335.0	0	19	1	6
336.0	0	15	1	15
337.0	0	4	0	6
338.0	0	10	1	8
339.0	0	9	2	7
340.0	0	20	2	6
341.0	0	9	1	9
342.0	0	10	1	8
343.0	0	6	0	9
344.0	0	7	1	6
345.0	0	10	0	8
346.0	0	13	0	10
347.0	0	18	1	7
348.0	0	6	1	8
349.0	0	13	1	10
350.0	0	15	1	3
351.0	0	12	0	9
352.0	0	10	2	9
353.0	0	16	0	7
354.0	0	5	0	4
355.0	0	9	1	8
356.0	0	4	2	8
357.0	0	8	0	4
358.0	0	3	1	9
359.0	0	9	1	2
360.0	0	9	0	10
361.0	0	12	0	6
362.0	0	14	1	3
363.0	0	15	1	10
364.0	0	4	0	6
365.0	0	17	0	10
366.0	0	14	0	5
367.0	0	8	2	13
368.0	0	10	0	11
369.0	0	6	0	13
370.0	0	7	1	5
371.0	0	9	1	7
372.0	0	6	2	5
373.0	0	8	0	5
374.0	0	7	0	14
375.0	0	10	2	7
376.0	0	6	0	6
377.0	0	10	0	3
378.0	0	5	0	10
379.0	0	6	1	7
380.0	0	7	1	5
381.0	0	15	1	8
382.0	0	7	1	7
383.0	0	7	1	8
384.0	0	2	0	4
385.0	0	10	0	7
386.0	0	13	1	2
387.0	0	6	0	4
388.0	0	9	0	6
389.0	0	7	0	7
390.0	0	9	0	6
391.0	0	9	1	5
392.0	0	9	0	2
393.0	0	4	1	4
394.0	0	7	0	5
395.0	0	5	1	6
396.0	0	5	0	5
397.0	0	7	0	5
398.0	0	10	0	3
399.0	0	12	0	3
400.0	0	6	0	3
401.0	0	8	0	3
402.0	0	12	0	11
403.0	0	11	1	7
404.0	0	6	0	5
405.0	0	8	0	6
406.0	0	8	2	8
407.0	0	7	2	3
408.0	0	5	0	4
409.0	0	5	0	5
410.0	0	2	0	5
411.0	0	5	0	4
412.0	0	14	1	6
413.0	0	7	0	3
414.0	0	10	1	6
415.0	0	3	1	11
416.0	0	5	0	7
417.0	0	4	0	6
418.0	0	6	0	6
419.0	0	9	1	7
420.0	0	9	0	5
421.0	0	5	1	3
422.0	0	9	0	7
423.0	0	6	0	2
424.0	0	3	0	7
425.0	0	8	0	6
426.0	0	3	0	4
427.0	0	9	0	4
428.0	0	4	0	6
429.0	0	4	0	1
430.0	0	7	1	6
431.0	0	8	0	11
432.0	0	7	0	2
433.0	0	3	0	2
434.0	0	7	0	2
435.0	0	6	0	8
436.0	0	5	0	5
437.0	0	6	1	4
438.0	0	4	0	7
439.0	0	9	1	3
440.0	0	3	0	7
441.0	0	4	0	3
442.0	0	6	2	6
443.0	0	6	0	4
444.0	0	6	2	9
445.0	0	10	0	4
446.0	0	4	0	6
447.0	0	6	0	3
448.0	0	4	1	6
449.0	0	3	1	6
450.0	0	9	0	6
451.0	0	10	0	5
452.0	0	8	1	3
453.0	0	1	0	2
454.0	0	6	0	6
455.0	0	6	0	2
456.0	0	9	0	3
457.0	0	7	0	1
458.0	0	5	1	3
459.0	0	5	1	5
460.0	0	5	1	4
461.0	0	6	0	2
462.0	0	3	0	3
463.0	0	9	0	2
464.0	0	9	2	4
465.0	0	4	0	2
466.0	0	10	0	1
467.0	0	6	0	6
468.0	0	4	0	7
469.0	0	5	0	4
470.0	0	2	2	5
471.0	0	3	0	3
472.0	0	3	1	1
473.0	0	3	0	2
474.0	0	4	0	5
475.0	0	4	0	2
476.0	0	7	0	4
477.0	0	4	0	5
478.0	0	3	0	4
479.0	0	4	0	2
480.0	0	4	0	5
481.0	0	7	0	2
482.0	0	6	1	3
483.0	0	1	0	2
484.0	0	9	0	4
485.0	0	4	0	6
486.0	0	6	0	2
487.0	0	4	0	3
488.0	0	1	0	4
489.0	0	2	0	5
490.0	0	5	0	4
491.0	0	6	0	1
492.0	0	1	0	8
493.0	0	5	0	2
494.0	0	4	0	2
495.0	0	5	0	4
496.0	0	6	1	1
497.0	0	4	1	1
498.0	0	7	0	2
499.0	0	6	0	0
500.0	0	4	0	2
501.0	0	5	0	5
502.0	0	5	0	4
503.0	0	2	0	2
504.0	0	0	1	2
505.0	0	5	0	3
506.0	0	5	0	0
507.0	0	0	0	1
508.0	0	1	0	3
509.0	0	5	0	1
510.0	0	2	0	3
511.0	0	7	0	2
512.0	0	5	1	0
513.0	0	6	0	7
514.0	0	7	0	4
515.0	0	4	1	3
516.0	0	5	0	4
517.0	0	6	1	2
518.0	0	5	0	2
519.0	0	4	1	4
520.0	0	1	0	1
521.0	0	4	0	2
522.0	0	6	0	4
523.0	0	6	0	2
524.0	0	3	0	2
525.0	0	5	1	3
526.0	0	3	0	3
527.0	0	5	0	4
528.0	0	2	0	0
529.0	0	3	0	4
530.0	0	2	0	4
531.0	0	0	0	1
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