## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-83-TP4.bam --OUTPUT POR-83-TP4.md.bam --METRICS_FILE POR-83-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 18:20:58 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	4229	20148156	13799542	0	4072	16823279	3401703	0.834992	3347366

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.004316	1475383	0	1758734
2.0	1.006758	731955	466760	729820
3.0	1.006764	361565	176341	286205
4.0	1.006764	186840	87627	125582
5.0	1.006764	107151	50031	68268
6.0	1.006764	68101	31348	45241
7.0	1.006764	47792	21003	33996
8.0	1.006764	36099	14836	26698
9.0	1.006764	28662	11156	21922
10.0	1.006764	23023	8566	18108
11.0	1.006764	19470	6717	15520
12.0	1.006764	16605	5551	13516
13.0	1.006764	14430	4494	11829
14.0	1.006764	12779	3874	10366
15.0	1.006764	11320	3303	9095
16.0	1.006764	9882	2807	8245
17.0	1.006764	9092	2392	7303
18.0	1.006764	8255	2206	6668
19.0	1.006764	7302	1882	6023
20.0	1.006764	6699	1650	5545
21.0	1.006764	6256	1505	5293
22.0	1.006764	5850	1306	4781
23.0	1.006764	5356	1176	4304
24.0	1.006764	4904	1090	4030
25.0	1.006764	4629	1016	3757
26.0	1.006764	4325	827	3495
27.0	1.006764	3993	838	3257
28.0	1.006764	3712	756	2967
29.0	1.006764	3290	710	2836
30.0	1.006764	3310	666	2675
31.0	1.006764	3076	583	2595
32.0	1.006764	2871	590	2443
33.0	1.006764	2807	551	2263
34.0	1.006764	2642	512	2176
35.0	1.006764	2527	429	2063
36.0	1.006764	2365	425	2018
37.0	1.006764	2193	393	1821
38.0	1.006764	2225	369	1758
39.0	1.006764	2020	318	1635
40.0	1.006764	1916	316	1604
41.0	1.006764	1851	286	1544
42.0	1.006764	1780	306	1434
43.0	1.006764	1676	274	1438
44.0	1.006764	1607	227	1307
45.0	1.006764	1567	256	1275
46.0	1.006764	1507	248	1235
47.0	1.006764	1413	226	1159
48.0	1.006764	1407	192	1085
49.0	1.006764	1389	215	1061
50.0	1.006764	1279	181	1042
51.0	1.006764	1245	171	1037
52.0	1.006764	1187	159	971
53.0	1.006764	1173	152	966
54.0	1.006764	1094	144	865
55.0	1.006764	1081	139	843
56.0	1.006764	1027	146	857
57.0	1.006764	1029	137	799
58.0	1.006764	952	140	712
59.0	1.006764	963	123	744
60.0	1.006764	879	107	765
61.0	1.006764	847	91	689
62.0	1.006764	834	90	699
63.0	1.006764	769	112	677
64.0	1.006764	801	104	636
65.0	1.006764	775	90	623
66.0	1.006764	701	107	588
67.0	1.006764	671	92	602
68.0	1.006764	677	62	582
69.0	1.006764	701	90	573
70.0	1.006764	666	85	524
71.0	1.006764	648	88	494
72.0	1.006764	633	77	506
73.0	1.006764	646	78	485
74.0	1.006764	524	78	474
75.0	1.006764	579	67	472
76.0	1.006764	530	68	458
77.0	1.006764	518	61	434
78.0	1.006764	535	64	444
79.0	1.006764	553	49	410
80.0	1.006764	501	60	392
81.0	1.006764	516	67	375
82.0	1.006764	487	73	415
83.0	1.006764	457	45	390
84.0	1.006764	473	46	381
85.0	1.006764	450	47	360
86.0	1.006764	421	35	347
87.0	1.006764	417	46	302
88.0	1.006764	388	38	286
89.0	1.006764	414	37	317
90.0	1.006764	387	48	356
91.0	1.006764	389	40	343
92.0	1.006764	386	35	323
93.0	1.006764	334	40	283
94.0	1.006764	357	37	238
95.0	1.006764	360	42	251
96.0	1.006764	346	29	321
97.0	1.006764	335	48	282
98.0	1.006764	319	38	278
99.0	1.006764	312	37	261
100.0	1.006764	335	38	286
101.0	0	329	33	253
102.0	0	296	22	237
103.0	0	270	28	225
104.0	0	289	39	228
105.0	0	275	23	233
106.0	0	296	31	203
107.0	0	255	28	226
108.0	0	293	28	211
109.0	0	256	28	212
110.0	0	269	20	216
111.0	0	253	27	218
112.0	0	270	27	220
113.0	0	234	20	194
114.0	0	262	23	215
115.0	0	257	25	187
116.0	0	266	23	203
117.0	0	241	25	180
118.0	0	246	25	191
119.0	0	215	16	169
120.0	0	234	19	191
121.0	0	201	18	174
122.0	0	194	17	177
123.0	0	206	14	168
124.0	0	189	17	143
125.0	0	207	24	175
126.0	0	185	19	145
127.0	0	192	13	154
128.0	0	197	10	148
129.0	0	178	20	166
130.0	0	188	18	149
131.0	0	181	19	162
132.0	0	190	12	146
133.0	0	179	12	125
134.0	0	177	13	127
135.0	0	174	14	154
136.0	0	178	20	128
137.0	0	158	13	124
138.0	0	161	21	126
139.0	0	165	14	117
140.0	0	140	18	149
141.0	0	130	15	123
142.0	0	140	10	125
143.0	0	149	9	128
144.0	0	162	10	129
145.0	0	177	8	108
146.0	0	146	10	132
147.0	0	126	10	114
148.0	0	136	13	87
149.0	0	143	15	120
150.0	0	125	13	96
151.0	0	131	8	104
152.0	0	138	8	102
153.0	0	134	14	108
154.0	0	128	10	109
155.0	0	132	11	111
156.0	0	139	16	108
157.0	0	116	9	87
158.0	0	107	10	93
159.0	0	112	4	82
160.0	0	106	11	97
161.0	0	111	8	82
162.0	0	105	7	87
163.0	0	100	10	104
164.0	0	117	10	94
165.0	0	94	14	98
166.0	0	97	2	90
167.0	0	92	6	82
168.0	0	117	7	84
169.0	0	110	6	76
170.0	0	101	6	76
171.0	0	101	5	65
172.0	0	85	7	70
173.0	0	88	6	91
174.0	0	104	7	78
175.0	0	93	4	71
176.0	0	93	5	65
177.0	0	80	8	64
178.0	0	83	9	55
179.0	0	110	10	78
180.0	0	84	7	70
181.0	0	91	8	70
182.0	0	88	2	54
183.0	0	81	1	77
184.0	0	104	6	79
185.0	0	83	6	58
186.0	0	81	6	72
187.0	0	88	7	73
188.0	0	78	5	68
189.0	0	90	9	48
190.0	0	80	6	57
191.0	0	73	2	69
192.0	0	79	8	72
193.0	0	61	6	61
194.0	0	80	5	74
195.0	0	54	9	44
196.0	0	69	6	61
197.0	0	79	5	60
198.0	0	87	4	68
199.0	0	65	4	53
200.0	0	64	4	58
201.0	0	67	2	55
202.0	0	67	3	49
203.0	0	72	2	53
204.0	0	72	5	59
205.0	0	63	7	36
206.0	0	59	1	61
207.0	0	73	4	51
208.0	0	64	5	49
209.0	0	74	4	52
210.0	0	65	5	45
211.0	0	60	5	54
212.0	0	63	7	46
213.0	0	60	5	44
214.0	0	64	7	53
215.0	0	60	4	60
216.0	0	46	8	48
217.0	0	60	4	40
218.0	0	59	0	39
219.0	0	56	4	32
220.0	0	54	3	38
221.0	0	55	6	55
222.0	0	56	6	43
223.0	0	66	2	56
224.0	0	47	3	47
225.0	0	62	6	52
226.0	0	50	3	46
227.0	0	58	4	36
228.0	0	61	3	38
229.0	0	40	2	50
230.0	0	65	1	41
231.0	0	53	3	45
232.0	0	39	2	45
233.0	0	50	2	37
234.0	0	46	5	51
235.0	0	51	3	40
236.0	0	45	3	47
237.0	0	50	9	38
238.0	0	48	0	30
239.0	0	49	6	40
240.0	0	55	5	38
241.0	0	53	2	40
242.0	0	48	1	41
243.0	0	42	3	31
244.0	0	45	5	35
245.0	0	55	2	25
246.0	0	49	2	37
247.0	0	51	5	30
248.0	0	45	3	22
249.0	0	41	8	32
250.0	0	45	2	29
251.0	0	38	4	36
252.0	0	38	3	32
253.0	0	42	4	38
254.0	0	52	9	26
255.0	0	46	0	37
256.0	0	39	3	25
257.0	0	28	1	38
258.0	0	35	4	32
259.0	0	39	3	23
260.0	0	47	0	32
261.0	0	37	2	30
262.0	0	37	1	30
263.0	0	39	2	33
264.0	0	37	1	34
265.0	0	37	2	35
266.0	0	31	0	30
267.0	0	24	2	35
268.0	0	35	0	34
269.0	0	40	1	31
270.0	0	28	5	22
271.0	0	30	1	33
272.0	0	49	4	25
273.0	0	33	1	25
274.0	0	30	0	30
275.0	0	24	1	23
276.0	0	32	2	20
277.0	0	31	4	19
278.0	0	25	3	25
279.0	0	28	2	29
280.0	0	37	0	27
281.0	0	33	4	20
282.0	0	32	2	32
283.0	0	31	5	24
284.0	0	25	3	22
285.0	0	28	0	25
286.0	0	30	2	22
287.0	0	46	1	22
288.0	0	35	4	27
289.0	0	26	4	24
290.0	0	29	1	16
291.0	0	29	2	26
292.0	0	30	2	22
293.0	0	31	2	33
294.0	0	36	2	22
295.0	0	15	1	19
296.0	0	23	2	15
297.0	0	29	0	20
298.0	0	28	2	18
299.0	0	25	1	28
300.0	0	33	0	29
301.0	0	25	1	11
302.0	0	21	1	17
303.0	0	18	1	21
304.0	0	31	1	29
305.0	0	29	1	22
306.0	0	20	3	19
307.0	0	26	2	15
308.0	0	21	3	20
309.0	0	26	2	21
310.0	0	20	0	28
311.0	0	25	3	27
312.0	0	35	3	22
313.0	0	20	0	28
314.0	0	22	0	18
315.0	0	29	0	21
316.0	0	31	1	18
317.0	0	20	0	17
318.0	0	22	2	19
319.0	0	26	1	24
320.0	0	26	2	21
321.0	0	21	1	21
322.0	0	22	1	16
323.0	0	34	3	18
324.0	0	19	0	18
325.0	0	19	0	23
326.0	0	24	0	13
327.0	0	18	0	23
328.0	0	21	3	25
329.0	0	22	1	18
330.0	0	26	1	15
331.0	0	18	2	17
332.0	0	30	1	17
333.0	0	20	2	9
334.0	0	27	0	20
335.0	0	17	1	12
336.0	0	21	0	18
337.0	0	19	0	13
338.0	0	25	0	29
339.0	0	20	1	10
340.0	0	31	3	25
341.0	0	18	0	12
342.0	0	17	0	14
343.0	0	20	0	16
344.0	0	19	1	11
345.0	0	24	0	24
346.0	0	19	2	16
347.0	0	15	1	12
348.0	0	18	2	17
349.0	0	18	3	12
350.0	0	19	0	12
351.0	0	20	1	17
352.0	0	11	2	20
353.0	0	18	0	8
354.0	0	19	1	22
355.0	0	17	3	18
356.0	0	17	0	14
357.0	0	20	1	11
358.0	0	10	2	15
359.0	0	14	3	15
360.0	0	14	4	12
361.0	0	19	1	15
362.0	0	21	1	20
363.0	0	23	1	22
364.0	0	25	0	12
365.0	0	12	2	10
366.0	0	16	1	14
367.0	0	26	0	15
368.0	0	18	0	13
369.0	0	21	1	17
370.0	0	17	1	12
371.0	0	19	2	18
372.0	0	21	2	14
373.0	0	18	2	16
374.0	0	15	2	14
375.0	0	13	1	13
376.0	0	13	1	11
377.0	0	17	0	13
378.0	0	9	1	12
379.0	0	15	2	14
380.0	0	11	0	16
381.0	0	18	2	10
382.0	0	14	1	13
383.0	0	15	1	7
384.0	0	20	0	7
385.0	0	13	1	12
386.0	0	10	1	10
387.0	0	16	1	14
388.0	0	16	0	15
389.0	0	22	0	14
390.0	0	13	0	12
391.0	0	9	0	8
392.0	0	13	0	13
393.0	0	11	1	14
394.0	0	11	3	13
395.0	0	16	1	11
396.0	0	17	2	13
397.0	0	20	0	14
398.0	0	13	0	11
399.0	0	11	2	10
400.0	0	12	1	18
401.0	0	8	1	9
402.0	0	18	1	12
403.0	0	14	0	18
404.0	0	9	0	7
405.0	0	20	0	10
406.0	0	8	0	16
407.0	0	14	1	9
408.0	0	16	0	14
409.0	0	12	0	10
410.0	0	15	1	11
411.0	0	8	0	9
412.0	0	15	0	17
413.0	0	16	0	12
414.0	0	13	1	4
415.0	0	19	0	7
416.0	0	9	0	13
417.0	0	17	1	7
418.0	0	7	0	9
419.0	0	7	2	5
420.0	0	13	1	12
421.0	0	18	1	7
422.0	0	15	1	7
423.0	0	14	1	8
424.0	0	8	0	12
425.0	0	8	1	14
426.0	0	17	0	9
427.0	0	12	0	14
428.0	0	17	1	11
429.0	0	10	0	8
430.0	0	15	0	10
431.0	0	13	0	13
432.0	0	7	0	14
433.0	0	22	1	6
434.0	0	13	2	7
435.0	0	13	0	10
436.0	0	11	2	13
437.0	0	13	2	12
438.0	0	10	0	9
439.0	0	11	1	12
440.0	0	15	0	7
441.0	0	13	0	8
442.0	0	11	1	7
443.0	0	11	0	13
444.0	0	11	1	9
445.0	0	9	1	3
446.0	0	13	1	16
447.0	0	12	0	5
448.0	0	10	0	8
449.0	0	7	0	3
450.0	0	8	1	11
451.0	0	13	1	11
452.0	0	12	0	9
453.0	0	16	1	5
454.0	0	9	1	11
455.0	0	11	0	8
456.0	0	10	0	11
457.0	0	9	0	8
458.0	0	8	0	10
459.0	0	8	1	9
460.0	0	13	0	11
461.0	0	9	0	9
462.0	0	5	1	8
463.0	0	9	1	9
464.0	0	8	0	14
465.0	0	9	0	7
466.0	0	14	0	13
467.0	0	10	0	5
468.0	0	9	1	5
469.0	0	9	0	5
470.0	0	13	1	7
471.0	0	5	0	12
472.0	0	15	0	8
473.0	0	7	0	6
474.0	0	15	1	5
475.0	0	11	0	9
476.0	0	14	0	3
477.0	0	10	0	7
478.0	0	11	0	5
479.0	0	8	0	5
480.0	0	12	0	6
481.0	0	10	0	6
482.0	0	10	0	4
483.0	0	11	0	4
484.0	0	7	0	3
485.0	0	10	0	4
486.0	0	8	1	7
487.0	0	14	0	7
488.0	0	13	0	10
489.0	0	8	0	7
490.0	0	10	0	5
491.0	0	5	0	5
492.0	0	6	0	10
493.0	0	6	0	7
494.0	0	5	0	7
495.0	0	5	0	8
496.0	0	6	0	11
497.0	0	12	0	5
498.0	0	10	0	7
499.0	0	7	1	9
500.0	0	6	0	9
501.0	0	12	0	3
502.0	0	11	0	13
503.0	0	11	1	4
504.0	0	6	1	4
505.0	0	10	0	7
506.0	0	4	0	8
507.0	0	6	0	11
508.0	0	11	0	7
509.0	0	4	0	5
510.0	0	7	0	11
511.0	0	9	0	4
512.0	0	7	1	5
513.0	0	10	0	10
514.0	0	11	0	6
515.0	0	5	0	3
516.0	0	10	0	7
517.0	0	9	0	2
518.0	0	6	1	6
519.0	0	14	1	5
520.0	0	13	1	8
521.0	0	8	0	4
522.0	0	8	0	4
523.0	0	8	0	10
524.0	0	13	0	6
525.0	0	6	0	5
526.0	0	6	0	6
527.0	0	6	0	4
528.0	0	7	1	4
529.0	0	10	0	5
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585.0	0	6	0	4
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