## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-74-TP4.bam --OUTPUT POR-74-TP4.md.bam --METRICS_FILE POR-74-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 18:18:44 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	446	16830224	11521842	0	339	14053764	3416845	0.83503	2799709

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.005902	1522938	0	1862807
2.0	1.008368	467386	371274	368005
3.0	1.008374	202310	153720	124480
4.0	1.008374	112512	82099	69813
5.0	1.008374	73184	48600	48458
6.0	1.008374	51308	30852	36008
7.0	1.008374	38685	21184	28413
8.0	1.008374	30625	15223	22743
9.0	1.008374	24535	11406	18671
10.0	1.008374	20215	8666	15539
11.0	1.008374	17319	7185	13578
12.0	1.008374	14943	5745	11716
13.0	1.008374	13140	4825	10409
14.0	1.008374	11538	3949	9020
15.0	1.008374	10235	3443	8015
16.0	1.008374	9257	2909	7145
17.0	1.008374	8222	2595	6381
18.0	1.008374	7530	2308	5826
19.0	1.008374	6856	2021	5375
20.0	1.008374	6221	1691	4849
21.0	1.008374	5619	1584	4393
22.0	1.008374	5206	1460	4088
23.0	1.008374	4864	1306	3890
24.0	1.008374	4528	1193	3552
25.0	1.008374	4166	1044	3215
26.0	1.008374	3913	1029	3163
27.0	1.008374	3556	890	2788
28.0	1.008374	3390	905	2674
29.0	1.008374	3225	746	2495
30.0	1.008374	2962	721	2271
31.0	1.008374	2791	660	2091
32.0	1.008374	2539	616	2092
33.0	1.008374	2440	523	1921
34.0	1.008374	2362	505	1845
35.0	1.008374	2246	505	1818
36.0	1.008374	2169	450	1700
37.0	1.008374	2020	415	1506
38.0	1.008374	1945	427	1522
39.0	1.008374	1912	361	1449
40.0	1.008374	1745	365	1338
41.0	1.008374	1695	321	1336
42.0	1.008374	1541	330	1268
43.0	1.008374	1477	311	1236
44.0	1.008374	1475	297	1169
45.0	1.008374	1388	249	1113
46.0	1.008374	1304	243	1062
47.0	1.008374	1276	248	1004
48.0	1.008374	1239	232	964
49.0	1.008374	1208	234	949
50.0	1.008374	1205	197	916
51.0	1.008374	1115	227	843
52.0	1.008374	1097	218	833
53.0	1.008374	1053	160	742
54.0	1.008374	935	195	731
55.0	1.008374	941	163	737
56.0	1.008374	930	160	649
57.0	1.008374	905	129	667
58.0	1.008374	832	156	678
59.0	1.008374	839	141	606
60.0	1.008374	826	129	646
61.0	1.008374	782	116	587
62.0	1.008374	783	119	557
63.0	1.008374	728	84	548
64.0	1.008374	690	114	551
65.0	1.008374	691	107	525
66.0	1.008374	676	110	512
67.0	1.008374	637	104	538
68.0	1.008374	610	96	497
69.0	1.008374	619	79	473
70.0	1.008374	589	87	453
71.0	1.008374	569	79	454
72.0	1.008374	544	76	421
73.0	1.008374	525	79	410
74.0	1.008374	522	74	398
75.0	1.008374	534	70	431
76.0	1.008374	471	85	369
77.0	1.008374	475	58	362
78.0	1.008374	470	65	342
79.0	1.008374	446	60	374
80.0	1.008374	478	65	312
81.0	1.008374	460	62	378
82.0	1.008374	429	76	326
83.0	1.008374	443	42	314
84.0	1.008374	384	65	294
85.0	1.008374	397	55	324
86.0	1.008374	412	48	313
87.0	1.008374	377	41	290
88.0	1.008374	370	46	280
89.0	1.008374	330	41	292
90.0	1.008374	320	54	267
91.0	1.008374	337	52	279
92.0	1.008374	365	45	249
93.0	1.008374	282	44	240
94.0	1.008374	289	33	228
95.0	1.008374	314	35	252
96.0	1.008374	353	37	254
97.0	1.008374	316	33	220
98.0	1.008374	287	35	212
99.0	1.008374	292	39	211
100.0	1.008374	285	36	203
101.0	0	277	42	176
102.0	0	280	39	216
103.0	0	250	34	184
104.0	0	252	28	185
105.0	0	249	30	209
106.0	0	224	27	215
107.0	0	244	28	168
108.0	0	238	25	182
109.0	0	215	33	185
110.0	0	210	26	180
111.0	0	242	28	197
112.0	0	234	21	173
113.0	0	225	26	178
114.0	0	196	30	162
115.0	0	222	36	153
116.0	0	199	27	157
117.0	0	204	20	133
118.0	0	212	24	165
119.0	0	212	26	172
120.0	0	174	11	142
121.0	0	162	22	151
122.0	0	191	28	149
123.0	0	215	19	145
124.0	0	215	22	137
125.0	0	192	21	134
126.0	0	152	17	125
127.0	0	177	19	139
128.0	0	174	17	150
129.0	0	162	23	141
130.0	0	175	21	119
131.0	0	138	18	140
132.0	0	159	16	118
133.0	0	193	18	124
134.0	0	162	14	113
135.0	0	142	13	118
136.0	0	134	17	112
137.0	0	151	13	96
138.0	0	135	12	96
139.0	0	132	17	107
140.0	0	116	14	104
141.0	0	127	12	101
142.0	0	128	13	84
143.0	0	150	19	104
144.0	0	126	21	98
145.0	0	130	9	98
146.0	0	127	17	97
147.0	0	116	15	93
148.0	0	105	11	88
149.0	0	127	14	84
150.0	0	99	16	84
151.0	0	107	13	108
152.0	0	103	10	78
153.0	0	120	11	67
154.0	0	102	9	89
155.0	0	105	14	86
156.0	0	104	16	91
157.0	0	122	15	73
158.0	0	103	8	73
159.0	0	94	9	71
160.0	0	107	7	75
161.0	0	96	8	69
162.0	0	114	13	68
163.0	0	91	13	72
164.0	0	77	8	63
165.0	0	99	7	82
166.0	0	83	7	74
167.0	0	92	3	71
168.0	0	96	7	63
169.0	0	87	15	61
170.0	0	89	10	65
171.0	0	84	18	69
172.0	0	82	11	73
173.0	0	79	10	79
174.0	0	84	7	59
175.0	0	75	14	59
176.0	0	65	15	50
177.0	0	78	4	62
178.0	0	70	10	61
179.0	0	65	13	46
180.0	0	81	10	71
181.0	0	74	3	54
182.0	0	80	11	61
183.0	0	77	4	69
184.0	0	92	5	58
185.0	0	72	7	50
186.0	0	73	11	68
187.0	0	66	7	54
188.0	0	75	6	54
189.0	0	79	4	55
190.0	0	70	5	40
191.0	0	85	9	64
192.0	0	71	12	49
193.0	0	61	5	51
194.0	0	54	9	57
195.0	0	64	6	44
196.0	0	62	10	42
197.0	0	65	4	39
198.0	0	69	4	46
199.0	0	66	6	56
200.0	0	46	5	45
201.0	0	54	9	45
202.0	0	55	7	33
203.0	0	59	7	46
204.0	0	54	5	38
205.0	0	61	8	52
206.0	0	47	4	38
207.0	0	58	7	46
208.0	0	54	4	42
209.0	0	55	6	37
210.0	0	52	4	43
211.0	0	32	6	38
212.0	0	50	3	42
213.0	0	57	5	38
214.0	0	67	2	41
215.0	0	45	4	33
216.0	0	51	6	37
217.0	0	48	4	40
218.0	0	55	5	38
219.0	0	36	3	34
220.0	0	52	5	28
221.0	0	46	7	29
222.0	0	53	6	42
223.0	0	47	6	44
224.0	0	54	6	37
225.0	0	51	4	36
226.0	0	40	4	25
227.0	0	43	6	24
228.0	0	42	2	33
229.0	0	43	3	38
230.0	0	41	6	32
231.0	0	41	2	31
232.0	0	43	7	37
233.0	0	48	1	37
234.0	0	39	7	30
235.0	0	36	3	21
236.0	0	51	3	30
237.0	0	43	3	31
238.0	0	40	1	36
239.0	0	36	1	23
240.0	0	33	3	24
241.0	0	53	3	40
242.0	0	36	2	29
243.0	0	37	1	37
244.0	0	43	8	28
245.0	0	38	7	33
246.0	0	25	6	30
247.0	0	36	2	23
248.0	0	37	2	24
249.0	0	33	4	30
250.0	0	45	2	32
251.0	0	41	5	30
252.0	0	49	4	38
253.0	0	33	2	30
254.0	0	38	1	22
255.0	0	39	4	23
256.0	0	31	2	34
257.0	0	38	3	24
258.0	0	35	2	28
259.0	0	40	4	25
260.0	0	34	1	29
261.0	0	33	5	26
262.0	0	29	4	23
263.0	0	40	3	28
264.0	0	31	3	36
265.0	0	43	3	33
266.0	0	33	0	25
267.0	0	26	2	28
268.0	0	33	6	23
269.0	0	26	3	25
270.0	0	27	1	26
271.0	0	25	2	28
272.0	0	27	4	26
273.0	0	20	1	21
274.0	0	27	4	22
275.0	0	25	1	25
276.0	0	20	1	27
277.0	0	25	3	27
278.0	0	25	1	22
279.0	0	35	1	24
280.0	0	42	2	26
281.0	0	30	4	23
282.0	0	23	1	29
283.0	0	21	1	19
284.0	0	25	3	26
285.0	0	39	2	17
286.0	0	30	0	32
287.0	0	28	1	30
288.0	0	28	3	16
289.0	0	28	5	22
290.0	0	29	0	22
291.0	0	29	1	21
292.0	0	21	2	19
293.0	0	29	0	26
294.0	0	25	0	13
295.0	0	21	2	27
296.0	0	29	2	19
297.0	0	30	4	13
298.0	0	23	2	24
299.0	0	24	1	21
300.0	0	19	1	23
301.0	0	27	2	14
302.0	0	26	1	17
303.0	0	28	3	16
304.0	0	25	2	20
305.0	0	23	0	21
306.0	0	21	1	13
307.0	0	24	1	14
308.0	0	15	0	16
309.0	0	21	0	19
310.0	0	20	1	13
311.0	0	24	2	18
312.0	0	25	1	12
313.0	0	27	3	12
314.0	0	21	1	17
315.0	0	21	4	19
316.0	0	18	3	19
317.0	0	21	2	13
318.0	0	20	2	13
319.0	0	12	1	20
320.0	0	12	0	20
321.0	0	17	2	23
322.0	0	19	5	12
323.0	0	26	3	12
324.0	0	20	1	11
325.0	0	17	0	23
326.0	0	15	2	20
327.0	0	14	0	10
328.0	0	17	0	17
329.0	0	22	2	8
330.0	0	14	1	19
331.0	0	16	1	12
332.0	0	23	3	15
333.0	0	16	1	8
334.0	0	21	0	14
335.0	0	24	4	13
336.0	0	16	1	19
337.0	0	20	0	10
338.0	0	21	1	11
339.0	0	17	1	12
340.0	0	15	0	12
341.0	0	20	1	19
342.0	0	15	3	11
343.0	0	19	0	19
344.0	0	17	2	11
345.0	0	19	3	15
346.0	0	23	0	11
347.0	0	15	1	12
348.0	0	17	0	13
349.0	0	27	0	18
350.0	0	14	1	12
351.0	0	21	2	7
352.0	0	15	2	6
353.0	0	8	0	10
354.0	0	16	0	10
355.0	0	14	0	10
356.0	0	10	3	14
357.0	0	17	2	10
358.0	0	20	1	10
359.0	0	15	2	8
360.0	0	16	3	14
361.0	0	20	2	12
362.0	0	18	1	12
363.0	0	14	1	8
364.0	0	14	0	6
365.0	0	17	2	11
366.0	0	14	3	13
367.0	0	10	0	9
368.0	0	14	2	12
369.0	0	5	3	15
370.0	0	13	3	12
371.0	0	16	1	8
372.0	0	15	1	16
373.0	0	17	2	12
374.0	0	9	2	10
375.0	0	15	0	11
376.0	0	12	3	10
377.0	0	12	3	12
378.0	0	16	2	12
379.0	0	7	3	7
380.0	0	13	1	13
381.0	0	12	1	10
382.0	0	18	1	11
383.0	0	13	0	8
384.0	0	10	2	18
385.0	0	13	1	9
386.0	0	18	0	16
387.0	0	13	3	9
388.0	0	16	2	8
389.0	0	14	2	9
390.0	0	18	0	9
391.0	0	15	2	8
392.0	0	18	0	12
393.0	0	14	0	12
394.0	0	13	0	11
395.0	0	14	0	8
396.0	0	16	1	5
397.0	0	12	0	14
398.0	0	23	0	8
399.0	0	13	0	7
400.0	0	7	0	8
401.0	0	12	0	7
402.0	0	11	0	13
403.0	0	7	1	6
404.0	0	15	3	13
405.0	0	6	3	13
406.0	0	10	0	13
407.0	0	10	0	9
408.0	0	6	0	8
409.0	0	12	1	10
410.0	0	6	1	9
411.0	0	11	0	8
412.0	0	14	1	8
413.0	0	9	0	9
414.0	0	13	3	16
415.0	0	12	1	4
416.0	0	9	2	7
417.0	0	7	0	11
418.0	0	14	0	7
419.0	0	8	1	5
420.0	0	13	0	8
421.0	0	4	2	9
422.0	0	10	1	5
423.0	0	8	3	14
424.0	0	16	0	5
425.0	0	12	1	7
426.0	0	13	1	5
427.0	0	9	0	12
428.0	0	13	1	12
429.0	0	16	1	14
430.0	0	7	1	14
431.0	0	11	1	7
432.0	0	17	2	13
433.0	0	8	1	10
434.0	0	13	1	6
435.0	0	13	0	4
436.0	0	8	2	10
437.0	0	10	0	5
438.0	0	15	1	3
439.0	0	10	0	7
440.0	0	11	0	9
441.0	0	10	0	8
442.0	0	11	1	7
443.0	0	6	0	11
444.0	0	10	0	10
445.0	0	10	3	4
446.0	0	9	2	10
447.0	0	8	0	10
448.0	0	9	4	8
449.0	0	9	2	6
450.0	0	6	0	8
451.0	0	10	0	6
452.0	0	4	0	8
453.0	0	9	1	3
454.0	0	14	1	8
455.0	0	10	1	8
456.0	0	9	0	8
457.0	0	12	0	6
458.0	0	11	0	4
459.0	0	12	1	5
460.0	0	7	1	8
461.0	0	11	1	10
462.0	0	10	2	8
463.0	0	6	2	9
464.0	0	7	0	3
465.0	0	8	0	6
466.0	0	8	0	7
467.0	0	5	0	11
468.0	0	9	1	3
469.0	0	10	0	3
470.0	0	12	0	6
471.0	0	8	0	5
472.0	0	3	0	4
473.0	0	12	0	6
474.0	0	6	0	4
475.0	0	4	1	9
476.0	0	9	0	5
477.0	0	6	1	14
478.0	0	9	1	5
479.0	0	7	0	6
480.0	0	11	2	8
481.0	0	10	1	4
482.0	0	6	1	7
483.0	0	11	0	5
484.0	0	9	0	6
485.0	0	10	0	6
486.0	0	2	0	12
487.0	0	10	0	7
488.0	0	11	0	8
489.0	0	11	1	7
490.0	0	7	0	4
491.0	0	13	0	4
492.0	0	9	0	8
493.0	0	6	0	4
494.0	0	4	0	6
495.0	0	4	0	9
496.0	0	6	0	3
497.0	0	5	0	5
498.0	0	5	0	8
499.0	0	9	1	4
500.0	0	11	0	6
501.0	0	8	0	5
502.0	0	5	1	5
503.0	0	10	0	1
504.0	0	8	0	7
505.0	0	7	0	1
506.0	0	7	1	1
507.0	0	6	0	5
508.0	0	3	0	11
509.0	0	5	0	5
510.0	0	9	1	8
511.0	0	7	0	3
512.0	0	3	1	7
513.0	0	8	1	2
514.0	0	10	1	7
515.0	0	9	0	3
516.0	0	6	0	4
517.0	0	5	1	2
518.0	0	6	0	9
519.0	0	7	1	7
520.0	0	6	1	10
521.0	0	7	1	8
522.0	0	6	1	10
523.0	0	6	0	4
524.0	0	5	1	7
525.0	0	4	1	5
526.0	0	7	2	3
527.0	0	8	0	2
528.0	0	6	0	8
529.0	0	4	1	4
530.0	0	10	0	3
531.0	0	8	1	4
532.0	0	2	0	8
533.0	0	6	0	1
534.0	0	8	0	4
535.0	0	12	0	1
536.0	0	9	0	5
537.0	0	8	0	3
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