## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-74-TP2.bam --OUTPUT POR-74-TP2.md.bam --METRICS_FILE POR-74-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 18:17:51 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	2918	15470728	9004713	0	2817	12603049	3359540	0.814653	2913273

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.010881	1629589	0	2002996
2.0	1.015874	475034	381944	356691
3.0	1.015899	202911	157720	118527
4.0	1.015899	112661	83695	66682
5.0	1.015899	72272	49251	45893
6.0	1.015899	50507	31616	34070
7.0	1.015899	37781	21285	26502
8.0	1.015899	29269	15199	21362
9.0	1.015899	23739	11375	17553
10.0	1.015899	19510	8774	14638
11.0	1.015899	16392	7057	12443
12.0	1.015899	14150	5637	10859
13.0	1.015899	12305	4839	9524
14.0	1.015899	10657	4033	8251
15.0	1.015899	9650	3390	7313
16.0	1.015899	8627	2860	6421
17.0	1.015899	7718	2502	5884
18.0	1.015899	7108	2185	5403
19.0	1.015899	6269	1900	4750
20.0	1.015899	5766	1731	4457
21.0	1.015899	5368	1633	4089
22.0	1.015899	4908	1419	3754
23.0	1.015899	4476	1326	3422
24.0	1.015899	4086	1141	3187
25.0	1.015899	3884	1051	2891
26.0	1.015899	3617	948	2686
27.0	1.015899	3362	959	2615
28.0	1.015899	3098	767	2484
29.0	1.015899	3007	729	2216
30.0	1.015899	2722	679	2115
31.0	1.015899	2670	656	2013
32.0	1.015899	2395	614	1847
33.0	1.015899	2372	509	1800
34.0	1.015899	2157	515	1623
35.0	1.015899	2108	516	1485
36.0	1.015899	1966	431	1605
37.0	1.015899	1816	394	1360
38.0	1.015899	1774	386	1359
39.0	1.015899	1648	364	1273
40.0	1.015899	1640	351	1189
41.0	1.015899	1486	302	1109
42.0	1.015899	1442	288	1129
43.0	1.015899	1347	291	1061
44.0	1.015899	1375	257	961
45.0	1.015899	1308	246	1026
46.0	1.015899	1209	250	948
47.0	1.015899	1159	230	865
48.0	1.015899	1101	223	849
49.0	1.015899	1079	201	789
50.0	1.015899	1055	190	816
51.0	1.015899	987	198	770
52.0	1.015899	983	183	706
53.0	1.015899	953	194	685
54.0	1.015899	828	176	622
55.0	1.015899	895	137	670
56.0	1.015899	822	149	592
57.0	1.015899	783	128	597
58.0	1.015899	787	139	590
59.0	1.015899	714	149	564
60.0	1.015899	746	128	515
61.0	1.015899	699	131	517
62.0	1.015899	688	127	554
63.0	1.015899	649	123	477
64.0	1.015899	629	111	470
65.0	1.015899	600	95	484
66.0	1.015899	581	91	468
67.0	1.015899	589	97	424
68.0	1.015899	576	92	407
69.0	1.015899	561	90	409
70.0	1.015899	535	89	398
71.0	1.015899	481	81	357
72.0	1.015899	509	95	373
73.0	1.015899	442	78	385
74.0	1.015899	481	86	338
75.0	1.015899	487	91	355
76.0	1.015899	412	54	350
77.0	1.015899	468	51	368
78.0	1.015899	426	64	290
79.0	1.015899	417	66	286
80.0	1.015899	406	58	317
81.0	1.015899	413	70	263
82.0	1.015899	390	57	287
83.0	1.015899	345	53	262
84.0	1.015899	387	50	270
85.0	1.015899	377	49	275
86.0	1.015899	354	43	234
87.0	1.015899	326	39	244
88.0	1.015899	334	48	251
89.0	1.015899	339	52	240
90.0	1.015899	332	55	222
91.0	1.015899	261	41	220
92.0	1.015899	281	38	224
93.0	1.015899	291	45	226
94.0	1.015899	288	42	236
95.0	1.015899	263	37	225
96.0	1.015899	287	37	180
97.0	1.015899	249	40	194
98.0	1.015899	240	30	221
99.0	1.015899	250	39	171
100.0	1.015899	250	50	181
101.0	0	250	26	150
102.0	0	256	32	173
103.0	0	248	26	160
104.0	0	235	23	200
105.0	0	230	26	149
106.0	0	223	37	163
107.0	0	196	29	161
108.0	0	193	31	188
109.0	0	208	26	152
110.0	0	196	24	140
111.0	0	174	23	133
112.0	0	186	19	149
113.0	0	186	29	132
114.0	0	180	20	141
115.0	0	191	27	123
116.0	0	188	24	164
117.0	0	178	14	131
118.0	0	155	21	118
119.0	0	165	22	126
120.0	0	177	19	109
121.0	0	168	20	107
122.0	0	165	18	119
123.0	0	163	15	124
124.0	0	130	20	110
125.0	0	162	25	110
126.0	0	144	25	117
127.0	0	153	18	94
128.0	0	148	17	114
129.0	0	150	15	111
130.0	0	131	12	119
131.0	0	149	28	101
132.0	0	138	16	83
133.0	0	112	14	86
134.0	0	126	20	98
135.0	0	119	25	112
136.0	0	129	10	125
137.0	0	150	16	93
138.0	0	119	15	75
139.0	0	126	14	86
140.0	0	122	11	91
141.0	0	106	10	90
142.0	0	102	8	81
143.0	0	119	17	91
144.0	0	112	8	87
145.0	0	89	8	85
146.0	0	107	6	86
147.0	0	109	17	88
148.0	0	94	9	65
149.0	0	115	19	67
150.0	0	100	10	72
151.0	0	105	15	74
152.0	0	90	10	78
153.0	0	108	15	54
154.0	0	92	9	79
155.0	0	94	17	64
156.0	0	101	10	75
157.0	0	97	9	60
158.0	0	90	8	65
159.0	0	90	8	60
160.0	0	109	13	78
161.0	0	97	10	46
162.0	0	83	10	66
163.0	0	93	7	57
164.0	0	86	9	59
165.0	0	69	11	56
166.0	0	77	10	53
167.0	0	88	12	57
168.0	0	88	9	62
169.0	0	72	9	73
170.0	0	74	6	59
171.0	0	86	1	37
172.0	0	66	6	64
173.0	0	78	10	52
174.0	0	64	2	69
175.0	0	55	6	56
176.0	0	61	9	55
177.0	0	91	2	41
178.0	0	74	4	34
179.0	0	60	3	48
180.0	0	57	6	46
181.0	0	57	7	55
182.0	0	68	3	44
183.0	0	65	9	52
184.0	0	63	5	40
185.0	0	61	5	43
186.0	0	66	9	38
187.0	0	56	6	65
188.0	0	53	6	46
189.0	0	55	5	44
190.0	0	50	5	45
191.0	0	56	5	44
192.0	0	58	8	45
193.0	0	66	4	36
194.0	0	54	12	38
195.0	0	57	5	37
196.0	0	56	6	39
197.0	0	48	6	50
198.0	0	67	1	42
199.0	0	36	4	43
200.0	0	63	6	34
201.0	0	48	4	32
202.0	0	55	5	32
203.0	0	53	3	29
204.0	0	55	8	37
205.0	0	47	8	26
206.0	0	46	3	34
207.0	0	38	6	39
208.0	0	46	6	34
209.0	0	43	5	37
210.0	0	43	4	34
211.0	0	47	2	47
212.0	0	50	6	40
213.0	0	43	2	30
214.0	0	45	6	24
215.0	0	46	7	30
216.0	0	42	4	44
217.0	0	41	5	29
218.0	0	37	9	33
219.0	0	38	4	23
220.0	0	46	7	27
221.0	0	51	8	24
222.0	0	39	1	27
223.0	0	43	4	30
224.0	0	35	3	40
225.0	0	35	6	39
226.0	0	45	4	24
227.0	0	44	0	36
228.0	0	36	2	31
229.0	0	50	7	20
230.0	0	22	4	32
231.0	0	43	1	30
232.0	0	24	4	28
233.0	0	43	4	28
234.0	0	32	6	41
235.0	0	48	7	25
236.0	0	28	1	30
237.0	0	37	6	31
238.0	0	29	1	25
239.0	0	40	0	27
240.0	0	21	4	34
241.0	0	37	3	29
242.0	0	25	4	19
243.0	0	31	4	26
244.0	0	42	4	22
245.0	0	40	7	33
246.0	0	31	4	27
247.0	0	31	3	26
248.0	0	29	3	30
249.0	0	34	2	29
250.0	0	35	6	21
251.0	0	26	3	16
252.0	0	30	3	19
253.0	0	28	2	23
254.0	0	38	0	27
255.0	0	27	4	19
256.0	0	30	3	30
257.0	0	36	2	19
258.0	0	32	2	21
259.0	0	22	1	25
260.0	0	26	1	23
261.0	0	30	4	28
262.0	0	22	2	24
263.0	0	29	0	24
264.0	0	42	2	20
265.0	0	37	4	20
266.0	0	28	2	19
267.0	0	24	0	22
268.0	0	26	2	24
269.0	0	22	2	26
270.0	0	21	1	14
271.0	0	24	0	26
272.0	0	30	3	15
273.0	0	23	1	17
274.0	0	26	0	19
275.0	0	26	4	19
276.0	0	25	1	25
277.0	0	15	1	17
278.0	0	22	2	23
279.0	0	22	4	12
280.0	0	25	2	20
281.0	0	23	2	21
282.0	0	24	2	8
283.0	0	31	1	22
284.0	0	33	2	14
285.0	0	24	2	23
286.0	0	35	5	20
287.0	0	15	3	12
288.0	0	14	1	11
289.0	0	29	1	19
290.0	0	21	2	12
291.0	0	26	4	18
292.0	0	16	4	19
293.0	0	20	0	14
294.0	0	20	2	21
295.0	0	24	2	16
296.0	0	19	5	15
297.0	0	27	5	11
298.0	0	13	3	20
299.0	0	23	0	24
300.0	0	19	0	13
301.0	0	20	1	11
302.0	0	26	0	19
303.0	0	22	1	16
304.0	0	21	2	17
305.0	0	15	3	14
306.0	0	24	2	9
307.0	0	22	2	13
308.0	0	16	0	10
309.0	0	12	1	10
310.0	0	20	0	14
311.0	0	14	1	13
312.0	0	20	3	12
313.0	0	29	2	20
314.0	0	19	2	21
315.0	0	14	0	11
316.0	0	14	1	15
317.0	0	14	1	14
318.0	0	17	0	14
319.0	0	15	3	15
320.0	0	21	1	10
321.0	0	18	1	16
322.0	0	23	1	15
323.0	0	21	1	12
324.0	0	16	5	14
325.0	0	20	1	15
326.0	0	16	1	12
327.0	0	16	2	14
328.0	0	11	3	13
329.0	0	16	1	14
330.0	0	21	5	14
331.0	0	16	2	9
332.0	0	17	2	22
333.0	0	19	1	18
334.0	0	11	0	14
335.0	0	15	0	15
336.0	0	18	5	13
337.0	0	23	1	13
338.0	0	13	1	17
339.0	0	12	1	10
340.0	0	13	0	14
341.0	0	11	0	9
342.0	0	19	1	8
343.0	0	15	1	12
344.0	0	11	1	9
345.0	0	13	2	10
346.0	0	15	2	13
347.0	0	15	1	6
348.0	0	16	2	14
349.0	0	17	1	10
350.0	0	12	1	8
351.0	0	15	2	17
352.0	0	11	2	12
353.0	0	12	2	7
354.0	0	18	0	11
355.0	0	13	0	15
356.0	0	12	1	9
357.0	0	17	1	12
358.0	0	11	0	12
359.0	0	15	3	9
360.0	0	15	0	11
361.0	0	13	0	11
362.0	0	20	1	6
363.0	0	19	2	9
364.0	0	11	2	13
365.0	0	11	0	12
366.0	0	7	0	14
367.0	0	12	3	6
368.0	0	8	1	5
369.0	0	11	1	7
370.0	0	11	0	5
371.0	0	12	2	14
372.0	0	17	1	10
373.0	0	12	2	17
374.0	0	16	0	10
375.0	0	12	0	15
376.0	0	15	0	6
377.0	0	17	2	6
378.0	0	12	2	10
379.0	0	17	0	12
380.0	0	13	0	8
381.0	0	15	0	6
382.0	0	13	1	21
383.0	0	11	0	11
384.0	0	17	1	4
385.0	0	16	3	6
386.0	0	10	2	7
387.0	0	13	1	4
388.0	0	11	1	2
389.0	0	13	1	11
390.0	0	7	1	6
391.0	0	12	1	6
392.0	0	12	0	6
393.0	0	11	0	10
394.0	0	10	0	5
395.0	0	12	1	5
396.0	0	10	0	11
397.0	0	8	0	6
398.0	0	13	0	8
399.0	0	10	0	9
400.0	0	7	0	9
401.0	0	10	2	7
402.0	0	6	1	8
403.0	0	10	3	6
404.0	0	9	0	8
405.0	0	15	0	7
406.0	0	19	1	7
407.0	0	10	0	5
408.0	0	5	0	5
409.0	0	6	0	9
410.0	0	15	1	9
411.0	0	11	0	7
412.0	0	9	0	12
413.0	0	7	1	4
414.0	0	11	1	8
415.0	0	9	0	7
416.0	0	5	3	8
417.0	0	10	1	5
418.0	0	13	0	9
419.0	0	13	0	5
420.0	0	5	0	8
421.0	0	12	0	13
422.0	0	9	1	6
423.0	0	9	0	9
424.0	0	9	0	10
425.0	0	8	1	7
426.0	0	10	0	6
427.0	0	9	0	3
428.0	0	6	0	2
429.0	0	8	0	3
430.0	0	6	1	13
431.0	0	9	1	4
432.0	0	10	0	5
433.0	0	12	0	5
434.0	0	9	0	4
435.0	0	10	0	4
436.0	0	7	2	3
437.0	0	3	1	4
438.0	0	9	0	3
439.0	0	10	0	6
440.0	0	8	0	4
441.0	0	10	0	6
442.0	0	9	0	6
443.0	0	12	0	10
444.0	0	5	0	4
445.0	0	8	1	8
446.0	0	6	1	7
447.0	0	7	3	6
448.0	0	9	1	9
449.0	0	8	0	11
450.0	0	3	0	4
451.0	0	11	0	5
452.0	0	3	0	4
453.0	0	7	0	4
454.0	0	4	0	3
455.0	0	8	0	9
456.0	0	5	0	9
457.0	0	5	0	10
458.0	0	7	0	4
459.0	0	2	0	6
460.0	0	7	0	3
461.0	0	4	1	3
462.0	0	6	2	4
463.0	0	12	0	4
464.0	0	6	0	9
465.0	0	7	3	4
466.0	0	7	1	7
467.0	0	5	0	9
468.0	0	7	1	5
469.0	0	7	0	5
470.0	0	17	0	7
471.0	0	7	0	3
472.0	0	9	0	4
473.0	0	5	1	4
474.0	0	9	0	3
475.0	0	9	0	4
476.0	0	7	0	2
477.0	0	7	0	4
478.0	0	7	1	6
479.0	0	2	1	4
480.0	0	3	1	4
481.0	0	11	1	3
482.0	0	6	1	6
483.0	0	7	1	6
484.0	0	4	0	8
485.0	0	7	0	3
486.0	0	6	1	3
487.0	0	7	2	6
488.0	0	6	0	6
489.0	0	9	0	6
490.0	0	7	0	6
491.0	0	5	0	2
492.0	0	8	0	3
493.0	0	8	0	6
494.0	0	10	2	5
495.0	0	9	0	7
496.0	0	2	0	2
497.0	0	1	0	7
498.0	0	3	2	1
499.0	0	5	0	4
500.0	0	5	0	6
501.0	0	5	0	3
502.0	0	8	0	4
503.0	0	5	0	10
504.0	0	8	0	6
505.0	0	12	0	4
506.0	0	3	0	6
507.0	0	10	0	5
508.0	0	7	0	4
509.0	0	5	0	4
510.0	0	3	1	7
511.0	0	3	0	4
512.0	0	2	1	5
513.0	0	7	0	8
514.0	0	5	0	0
515.0	0	2	0	4
516.0	0	8	0	4
517.0	0	7	0	6
518.0	0	3	0	5
519.0	0	7	1	6
520.0	0	4	0	3
521.0	0	8	1	2
522.0	0	4	0	4
524.0	0	6	1	5
525.0	0	5	0	3
526.0	0	6	0	5
527.0	0	6	0	2
528.0	0	5	0	5
529.0	0	2	1	5
530.0	0	6	0	5
531.0	0	7	1	2
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