## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-83-TP1.bam --OUTPUT POR-83-TP1.md.bam --METRICS_FILE POR-83-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 18:18:00 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	520	15214476	8088616	0	355	10878568	3749879	0.715014	4765855

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.054013	2712706	0	3449697
2.0	1.097305	745709	605343	444351
3.0	1.099083	296468	237060	116862
4.0	1.099156	152598	118838	61510
5.0	1.099159	89709	64971	41010
6.0	1.09916	57452	38298	29876
7.0	1.09916	39648	23787	22536
8.0	1.09916	28773	15902	17984
9.0	1.09916	22464	11118	14775
10.0	1.09916	17694	8064	11971
11.0	1.09916	14523	6259	10316
12.0	1.09916	12224	4918	8656
13.0	1.09916	10468	4120	7563
14.0	1.09916	9088	3387	6589
15.0	1.09916	7872	2849	5770
16.0	1.09916	7053	2514	5246
17.0	1.09916	6375	2142	4670
18.0	1.09916	5875	1913	4166
19.0	1.09916	5109	1639	3793
20.0	1.09916	4741	1468	3576
21.0	1.09916	4191	1302	3085
22.0	1.09916	3853	1129	2940
23.0	1.09916	3603	1050	2726
24.0	1.09916	3400	974	2331
25.0	1.09916	3138	843	2285
26.0	1.09916	2857	814	2146
27.0	1.09916	2671	720	2003
28.0	1.09916	2437	693	1784
29.0	1.09916	2375	634	1710
30.0	1.09916	2241	593	1614
31.0	1.09916	2074	530	1506
32.0	1.09916	1892	482	1420
33.0	1.09916	1791	462	1292
34.0	1.09916	1670	430	1257
35.0	1.09916	1573	376	1227
36.0	1.09916	1591	348	1076
37.0	1.09916	1475	352	1116
38.0	1.09916	1392	305	1000
39.0	1.09916	1292	307	960
40.0	1.09916	1236	305	899
41.0	1.09916	1191	256	832
42.0	1.09916	1140	255	865
43.0	1.09916	1026	225	776
44.0	1.09916	1055	234	779
45.0	1.09916	1031	229	697
46.0	1.09916	956	205	658
47.0	1.09916	886	198	664
48.0	1.09916	863	172	659
49.0	1.09916	761	186	570
50.0	1.09916	803	168	554
51.0	1.09916	776	162	470
52.0	1.09916	742	137	577
53.0	1.09916	699	142	555
54.0	1.09916	677	151	481
55.0	1.09916	630	137	471
56.0	1.09916	648	141	468
57.0	1.09916	610	126	441
58.0	1.09916	614	101	454
59.0	1.09916	571	111	419
60.0	1.09916	549	138	408
61.0	1.09916	488	93	342
62.0	1.09916	515	109	362
63.0	1.09916	500	86	368
64.0	1.09916	524	93	341
65.0	1.09916	495	95	374
66.0	1.09916	439	80	316
67.0	1.09916	431	92	314
68.0	1.09916	456	98	324
69.0	1.09916	405	73	291
70.0	1.09916	395	77	286
71.0	1.09916	396	70	270
72.0	1.09916	390	67	254
73.0	1.09916	364	64	259
74.0	1.09916	349	59	245
75.0	1.09916	326	67	256
76.0	1.09916	338	58	252
77.0	1.09916	345	58	253
78.0	1.09916	290	61	209
79.0	1.09916	299	57	227
80.0	1.09916	292	51	193
81.0	1.09916	291	50	210
82.0	1.09916	283	52	222
83.0	1.09916	258	45	183
84.0	1.09916	266	41	175
85.0	1.09916	233	51	183
86.0	1.09916	254	39	174
87.0	1.09916	218	41	164
88.0	1.09916	258	28	165
89.0	1.09916	213	43	163
90.0	1.09916	237	37	168
91.0	1.09916	210	31	150
92.0	1.09916	227	30	167
93.0	1.09916	216	35	149
94.0	1.09916	208	38	149
95.0	1.09916	194	32	169
96.0	1.09916	209	26	146
97.0	1.09916	197	34	123
98.0	1.09916	199	31	122
99.0	1.09916	175	23	121
100.0	1.09916	185	27	122
101.0	0	198	37	111
102.0	0	177	28	131
103.0	0	151	23	121
104.0	0	160	24	109
105.0	0	155	14	129
106.0	0	178	23	111
107.0	0	139	24	120
108.0	0	147	16	129
109.0	0	188	29	116
110.0	0	162	26	101
111.0	0	127	25	103
112.0	0	127	28	106
113.0	0	148	27	85
114.0	0	136	27	79
115.0	0	121	23	105
116.0	0	136	24	89
117.0	0	131	27	85
118.0	0	125	12	78
119.0	0	128	16	84
120.0	0	123	15	84
121.0	0	109	11	105
122.0	0	119	15	69
123.0	0	119	14	77
124.0	0	136	17	72
125.0	0	100	14	77
126.0	0	108	19	85
127.0	0	116	20	67
128.0	0	110	15	74
129.0	0	91	22	78
130.0	0	97	13	78
131.0	0	110	19	82
132.0	0	106	12	79
133.0	0	93	12	63
134.0	0	98	17	64
135.0	0	89	14	91
136.0	0	85	17	67
137.0	0	87	9	69
138.0	0	91	8	60
139.0	0	81	14	71
140.0	0	96	8	58
141.0	0	91	10	48
142.0	0	89	14	68
143.0	0	83	15	71
144.0	0	77	12	57
145.0	0	89	8	45
146.0	0	79	11	69
147.0	0	79	13	52
148.0	0	74	8	64
149.0	0	68	9	58
150.0	0	70	8	46
151.0	0	76	9	42
152.0	0	84	10	50
153.0	0	65	15	54
154.0	0	74	6	44
155.0	0	69	6	61
156.0	0	55	11	55
157.0	0	65	8	48
158.0	0	64	15	53
159.0	0	66	9	44
160.0	0	65	8	52
161.0	0	74	16	46
162.0	0	69	11	41
163.0	0	59	7	44
164.0	0	58	5	34
165.0	0	65	5	42
166.0	0	62	8	35
167.0	0	65	4	37
168.0	0	56	6	47
169.0	0	59	12	41
170.0	0	63	11	56
171.0	0	50	11	51
172.0	0	59	4	34
173.0	0	58	9	37
174.0	0	53	4	47
175.0	0	48	7	48
176.0	0	48	7	35
177.0	0	53	8	44
178.0	0	54	13	25
179.0	0	49	6	44
180.0	0	40	5	30
181.0	0	54	7	42
182.0	0	44	11	34
183.0	0	52	3	39
184.0	0	48	7	40
185.0	0	49	5	35
186.0	0	49	9	22
187.0	0	49	4	32
188.0	0	42	7	35
189.0	0	40	7	22
190.0	0	36	3	42
191.0	0	41	6	29
192.0	0	49	3	24
193.0	0	43	5	28
194.0	0	46	6	19
195.0	0	33	1	42
196.0	0	53	9	34
197.0	0	36	5	29
198.0	0	40	5	27
199.0	0	37	8	29
200.0	0	42	6	34
201.0	0	52	8	26
202.0	0	47	3	30
203.0	0	34	2	24
204.0	0	42	6	20
205.0	0	25	6	24
206.0	0	28	5	31
207.0	0	27	8	22
208.0	0	32	7	25
209.0	0	34	6	35
210.0	0	41	4	29
211.0	0	29	2	29
212.0	0	35	5	27
213.0	0	39	3	25
214.0	0	37	6	21
215.0	0	35	1	21
216.0	0	27	4	21
217.0	0	33	4	22
218.0	0	42	8	36
219.0	0	31	1	19
220.0	0	36	4	30
221.0	0	40	8	17
222.0	0	30	5	9
223.0	0	24	5	22
224.0	0	31	4	20
225.0	0	29	4	22
226.0	0	21	7	23
227.0	0	27	7	23
228.0	0	27	5	17
229.0	0	26	5	28
230.0	0	31	2	13
231.0	0	24	4	20
232.0	0	28	5	27
233.0	0	29	5	20
234.0	0	27	7	23
235.0	0	29	1	20
236.0	0	20	3	14
237.0	0	27	2	11
238.0	0	27	2	14
239.0	0	36	1	20
240.0	0	24	4	16
241.0	0	23	0	16
242.0	0	31	6	19
243.0	0	19	4	12
244.0	0	30	2	20
245.0	0	27	2	16
246.0	0	33	2	23
247.0	0	21	0	29
248.0	0	14	4	12
249.0	0	17	2	25
250.0	0	26	1	14
251.0	0	19	1	12
252.0	0	27	3	15
253.0	0	29	2	20
254.0	0	18	2	18
255.0	0	24	3	20
256.0	0	19	1	12
257.0	0	24	7	15
258.0	0	18	2	19
259.0	0	32	2	21
260.0	0	21	7	11
261.0	0	21	3	17
262.0	0	19	1	13
263.0	0	32	2	15
264.0	0	15	1	19
265.0	0	16	0	16
266.0	0	21	4	13
267.0	0	15	5	12
268.0	0	25	1	11
269.0	0	23	4	19
270.0	0	19	2	13
271.0	0	27	2	20
272.0	0	19	4	20
273.0	0	18	1	13
274.0	0	16	2	8
275.0	0	22	3	14
276.0	0	20	2	15
277.0	0	20	1	16
278.0	0	18	1	13
279.0	0	14	1	13
280.0	0	16	2	12
281.0	0	18	3	17
282.0	0	15	1	13
283.0	0	15	1	9
284.0	0	16	1	14
285.0	0	14	2	9
286.0	0	14	1	6
287.0	0	21	3	11
288.0	0	16	1	9
289.0	0	26	3	11
290.0	0	11	0	22
291.0	0	17	2	11
292.0	0	19	0	15
293.0	0	14	2	11
294.0	0	17	1	11
295.0	0	22	2	11
296.0	0	15	3	17
297.0	0	22	5	11
298.0	0	15	2	11
299.0	0	11	1	10
300.0	0	15	4	10
301.0	0	16	2	10
302.0	0	17	0	14
303.0	0	9	1	14
304.0	0	18	0	9
305.0	0	17	3	11
306.0	0	15	1	8
307.0	0	15	2	9
308.0	0	16	0	11
309.0	0	14	0	11
310.0	0	21	0	10
311.0	0	13	1	16
312.0	0	12	2	15
313.0	0	17	1	11
314.0	0	15	0	8
315.0	0	15	1	11
316.0	0	8	3	12
317.0	0	14	2	10
318.0	0	8	2	11
319.0	0	13	2	12
320.0	0	13	3	6
321.0	0	14	2	9
322.0	0	21	2	5
323.0	0	15	4	11
324.0	0	3	1	7
325.0	0	10	0	12
326.0	0	14	2	7
327.0	0	12	2	15
328.0	0	8	1	12
329.0	0	16	0	13
330.0	0	12	0	9
331.0	0	8	1	6
332.0	0	9	1	12
333.0	0	10	1	6
334.0	0	12	2	10
335.0	0	14	4	8
336.0	0	12	0	8
337.0	0	11	2	8
338.0	0	14	3	7
339.0	0	10	0	8
340.0	0	15	3	13
341.0	0	14	1	5
342.0	0	8	0	4
343.0	0	9	0	6
344.0	0	11	1	5
345.0	0	6	2	6
346.0	0	9	1	6
347.0	0	7	2	7
348.0	0	8	1	4
349.0	0	15	0	4
350.0	0	8	0	6
351.0	0	14	2	3
352.0	0	7	1	7
353.0	0	20	0	6
354.0	0	8	4	6
355.0	0	9	0	8
356.0	0	4	3	6
357.0	0	6	0	3
358.0	0	6	0	8
359.0	0	8	1	6
360.0	0	5	3	3
361.0	0	6	1	11
362.0	0	15	1	4
363.0	0	13	2	8
364.0	0	8	1	9
365.0	0	9	1	7
366.0	0	13	1	5
367.0	0	8	0	7
368.0	0	9	1	5
369.0	0	13	4	4
370.0	0	10	1	5
371.0	0	6	2	7
372.0	0	7	0	4
373.0	0	9	0	7
374.0	0	8	0	5
375.0	0	7	0	6
376.0	0	8	1	6
377.0	0	15	0	4
378.0	0	4	0	8
379.0	0	8	1	7
380.0	0	8	0	2
381.0	0	9	0	2
382.0	0	11	1	5
383.0	0	5	1	5
384.0	0	8	1	5
385.0	0	11	2	4
386.0	0	5	1	7
387.0	0	3	1	5
388.0	0	5	0	9
389.0	0	5	2	4
390.0	0	5	1	4
391.0	0	8	0	2
392.0	0	6	3	7
393.0	0	10	2	7
394.0	0	4	1	8
395.0	0	7	0	5
396.0	0	7	1	7
397.0	0	3	0	4
398.0	0	8	0	6
399.0	0	7	0	4
400.0	0	9	2	6
401.0	0	12	1	6
402.0	0	4	0	4
403.0	0	9	1	5
404.0	0	10	1	3
405.0	0	6	1	2
406.0	0	9	1	4
407.0	0	4	0	7
408.0	0	4	1	8
409.0	0	5	1	7
410.0	0	7	0	4
411.0	0	5	1	2
412.0	0	11	1	5
413.0	0	6	0	6
414.0	0	5	1	4
415.0	0	4	0	5
416.0	0	9	1	6
417.0	0	9	0	5
418.0	0	5	1	4
419.0	0	8	1	6
420.0	0	8	0	3
421.0	0	4	0	5
422.0	0	6	3	4
423.0	0	10	1	6
424.0	0	12	0	4
425.0	0	3	0	4
426.0	0	8	0	7
427.0	0	6	0	3
428.0	0	5	0	4
429.0	0	5	2	6
430.0	0	7	0	4
431.0	0	5	0	6
432.0	0	7	0	5
433.0	0	8	0	5
434.0	0	6	0	5
435.0	0	5	0	3
436.0	0	4	0	2
437.0	0	6	2	1
438.0	0	5	0	3
439.0	0	8	3	6
440.0	0	9	0	6
441.0	0	6	0	2
442.0	0	7	2	5
443.0	0	5	0	2
444.0	0	7	0	3
445.0	0	7	2	3
446.0	0	4	0	3
447.0	0	5	0	1
448.0	0	9	1	7
449.0	0	7	1	5
450.0	0	7	0	4
451.0	0	3	2	3
452.0	0	8	0	3
453.0	0	6	0	5
454.0	0	5	0	5
455.0	0	4	1	4
456.0	0	3	0	7
457.0	0	5	0	6
458.0	0	6	0	2
459.0	0	7	0	2
460.0	0	3	1	6
461.0	0	7	0	8
462.0	0	1	0	6
463.0	0	3	0	6
464.0	0	5	0	5
465.0	0	5	0	2
466.0	0	0	0	4
467.0	0	4	1	4
468.0	0	7	1	5
469.0	0	5	0	4
470.0	0	3	0	5
471.0	0	4	0	1
472.0	0	5	0	6
473.0	0	6	0	5
474.0	0	5	1	3
475.0	0	6	0	4
476.0	0	3	0	2
477.0	0	6	0	4
478.0	0	6	0	1
479.0	0	11	1	4
480.0	0	2	0	3
481.0	0	7	0	6
482.0	0	5	0	1
483.0	0	3	1	3
484.0	0	9	1	1
485.0	0	4	2	3
486.0	0	4	0	4
487.0	0	4	1	5
488.0	0	4	1	6
489.0	0	2	1	2
490.0	0	2	0	6
491.0	0	5	1	3
492.0	0	1	0	5
493.0	0	4	1	2
494.0	0	3	2	3
495.0	0	13	0	6
496.0	0	6	2	5
497.0	0	4	2	0
498.0	0	2	0	2
499.0	0	5	0	4
500.0	0	5	1	3
501.0	0	7	1	6
502.0	0	3	1	2
503.0	0	3	0	1
504.0	0	3	0	2
505.0	0	5	0	2
506.0	0	3	1	6
507.0	0	4	0	3
508.0	0	3	0	3
509.0	0	4	0	4
510.0	0	2	0	3
511.0	0	5	0	3
512.0	0	6	0	3
513.0	0	3	0	3
514.0	0	3	0	4
515.0	0	3	1	2
516.0	0	2	1	3
517.0	0	3	1	2
518.0	0	7	1	8
519.0	0	6	0	1
520.0	0	3	0	2
521.0	0	2	0	3
522.0	0	2	0	3
523.0	0	2	0	5
524.0	0	6	0	2
525.0	0	3	1	2
526.0	0	3	0	2
527.0	0	5	1	4
528.0	0	9	0	5
529.0	0	6	0	5
530.0	0	4	0	5
531.0	0	4	3	3
532.0	0	6	1	3
533.0	0	7	0	2
534.0	0	8	0	2
535.0	0	3	0	4
536.0	0	3	0	3
537.0	0	4	0	2
538.0	0	4	1	2
539.0	0	6	0	4
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