## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-69-TP4.bam --OUTPUT POR-69-TP4.md.bam --METRICS_FILE POR-69-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 18:17:39 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	397	14917472	9244071	0	306	11857958	3156733	0.794904	3132902

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.015229	1763283	0	2175000
2.0	1.023912	522586	411919	383734
3.0	1.023986	219778	165401	123136
4.0	1.023987	119993	85876	67839
5.0	1.023987	74716	49316	45936
6.0	1.023987	51319	30494	33470
7.0	1.023987	37592	20003	25871
8.0	1.023987	28862	14084	20830
9.0	1.023987	23075	10311	16837
10.0	1.023987	18785	7736	14136
11.0	1.023987	15790	6073	12054
12.0	1.023987	13539	5121	10263
13.0	1.023987	11638	4139	8850
14.0	1.023987	10151	3517	7878
15.0	1.023987	9049	2944	6851
16.0	1.023987	8004	2542	6352
17.0	1.023987	7316	2226	5525
18.0	1.023987	6616	1955	5107
19.0	1.023987	5863	1715	4593
20.0	1.023987	5312	1473	4211
21.0	1.023987	4915	1369	3701
22.0	1.023987	4536	1199	3482
23.0	1.023987	4100	1129	3186
24.0	1.023987	3940	1027	2982
25.0	1.023987	3625	838	2730
26.0	1.023987	3370	860	2564
27.0	1.023987	3107	777	2361
28.0	1.023987	2839	691	2243
29.0	1.023987	2697	644	2136
30.0	1.023987	2634	571	2034
31.0	1.023987	2418	608	1856
32.0	1.023987	2302	480	1778
33.0	1.023987	2202	474	1659
34.0	1.023987	2014	408	1476
35.0	1.023987	1886	383	1454
36.0	1.023987	1778	359	1333
37.0	1.023987	1707	353	1285
38.0	1.023987	1564	334	1242
39.0	1.023987	1531	327	1184
40.0	1.023987	1438	292	1150
41.0	1.023987	1438	265	1056
42.0	1.023987	1300	274	1040
43.0	1.023987	1285	249	1021
44.0	1.023987	1207	242	912
45.0	1.023987	1148	251	877
46.0	1.023987	1131	193	884
47.0	1.023987	1086	218	786
48.0	1.023987	1046	170	835
49.0	1.023987	951	192	802
50.0	1.023987	950	150	705
51.0	1.023987	933	183	654
52.0	1.023987	940	137	670
53.0	1.023987	828	128	680
54.0	1.023987	801	140	634
55.0	1.023987	814	121	576
56.0	1.023987	736	117	564
57.0	1.023987	703	127	568
58.0	1.023987	693	114	546
59.0	1.023987	707	113	545
60.0	1.023987	675	98	521
61.0	1.023987	670	98	485
62.0	1.023987	588	99	438
63.0	1.023987	605	86	427
64.0	1.023987	612	77	453
65.0	1.023987	536	74	400
66.0	1.023987	526	71	432
67.0	1.023987	493	85	378
68.0	1.023987	497	97	429
69.0	1.023987	508	69	398
70.0	1.023987	490	81	336
71.0	1.023987	462	65	331
72.0	1.023987	459	54	328
73.0	1.023987	434	67	328
74.0	1.023987	424	57	311
75.0	1.023987	426	87	317
76.0	1.023987	411	61	292
77.0	1.023987	385	45	310
78.0	1.023987	417	50	269
79.0	1.023987	382	45	315
80.0	1.023987	322	58	281
81.0	1.023987	369	57	259
82.0	1.023987	346	47	276
83.0	1.023987	362	40	253
84.0	1.023987	324	47	230
85.0	1.023987	300	58	269
86.0	1.023987	338	48	228
87.0	1.023987	339	53	216
88.0	1.023987	326	44	240
89.0	1.023987	278	37	217
90.0	1.023987	263	28	196
91.0	1.023987	281	38	226
92.0	1.023987	271	33	181
93.0	1.023987	260	30	210
94.0	1.023987	257	23	217
95.0	1.023987	264	18	208
96.0	1.023987	240	45	203
97.0	1.023987	283	34	182
98.0	1.023987	250	25	173
99.0	1.023987	251	30	161
100.0	1.023987	236	30	174
101.0	0	214	27	155
102.0	0	229	27	152
103.0	0	215	22	148
104.0	0	218	29	158
105.0	0	183	27	139
106.0	0	184	21	154
107.0	0	176	28	128
108.0	0	174	26	141
109.0	0	182	26	124
110.0	0	170	25	135
111.0	0	170	18	152
112.0	0	158	21	143
113.0	0	157	20	133
114.0	0	156	32	120
115.0	0	168	17	114
116.0	0	153	17	119
117.0	0	173	18	130
118.0	0	134	18	138
119.0	0	160	10	124
120.0	0	159	7	121
121.0	0	155	23	109
122.0	0	162	23	102
123.0	0	147	21	115
124.0	0	131	19	90
125.0	0	133	10	109
126.0	0	152	18	117
127.0	0	131	15	105
128.0	0	113	11	103
129.0	0	134	18	86
130.0	0	115	11	82
131.0	0	136	15	93
132.0	0	98	15	96
133.0	0	121	16	90
134.0	0	97	10	98
135.0	0	121	17	89
136.0	0	109	16	80
137.0	0	105	11	67
138.0	0	100	8	75
139.0	0	108	13	74
140.0	0	109	15	83
141.0	0	99	8	75
142.0	0	101	12	77
143.0	0	95	17	69
144.0	0	102	11	83
145.0	0	89	14	76
146.0	0	87	13	50
147.0	0	88	5	81
148.0	0	97	11	70
149.0	0	101	8	65
150.0	0	92	18	79
151.0	0	93	11	52
152.0	0	84	11	59
153.0	0	81	8	74
154.0	0	85	14	59
155.0	0	85	10	67
156.0	0	85	9	56
157.0	0	96	10	51
158.0	0	97	8	61
159.0	0	84	6	68
160.0	0	77	7	62
161.0	0	87	14	50
162.0	0	75	5	49
163.0	0	56	4	66
164.0	0	74	10	58
165.0	0	74	11	58
166.0	0	68	7	59
167.0	0	59	4	46
168.0	0	75	7	51
169.0	0	77	6	51
170.0	0	57	8	51
171.0	0	64	9	68
172.0	0	50	4	51
173.0	0	54	7	51
174.0	0	60	4	55
175.0	0	73	5	45
176.0	0	70	11	57
177.0	0	66	6	52
178.0	0	77	10	43
179.0	0	59	7	34
180.0	0	53	3	42
181.0	0	50	7	44
182.0	0	59	3	42
183.0	0	55	4	33
184.0	0	71	11	52
185.0	0	54	9	46
186.0	0	41	8	55
187.0	0	73	5	41
188.0	0	59	12	43
189.0	0	65	7	47
190.0	0	58	2	47
191.0	0	61	8	37
192.0	0	57	3	40
193.0	0	45	4	27
194.0	0	47	3	43
195.0	0	41	5	31
196.0	0	49	6	47
197.0	0	60	7	48
198.0	0	50	4	43
199.0	0	51	4	36
200.0	0	45	5	37
201.0	0	56	2	41
202.0	0	41	5	40
203.0	0	61	9	36
204.0	0	36	2	38
205.0	0	43	7	33
206.0	0	48	8	40
207.0	0	45	7	29
208.0	0	47	2	33
209.0	0	46	5	31
210.0	0	29	6	36
211.0	0	40	5	33
212.0	0	28	5	32
213.0	0	54	3	23
214.0	0	38	1	34
215.0	0	38	6	26
216.0	0	37	2	38
217.0	0	57	5	32
218.0	0	37	4	26
219.0	0	28	5	23
220.0	0	37	0	30
221.0	0	37	3	21
222.0	0	38	2	30
223.0	0	35	1	25
224.0	0	48	7	29
225.0	0	29	1	26
226.0	0	40	2	21
227.0	0	36	3	24
228.0	0	26	2	36
229.0	0	29	4	32
230.0	0	39	0	25
231.0	0	35	0	23
232.0	0	35	3	26
233.0	0	29	5	30
234.0	0	39	4	28
235.0	0	31	4	27
236.0	0	31	6	17
237.0	0	28	2	31
238.0	0	38	4	11
239.0	0	27	1	26
240.0	0	38	6	21
241.0	0	29	6	29
242.0	0	32	2	29
243.0	0	31	2	24
244.0	0	35	3	28
245.0	0	34	3	25
246.0	0	25	5	29
247.0	0	29	2	24
248.0	0	28	3	21
249.0	0	22	2	23
250.0	0	26	1	22
251.0	0	38	1	25
252.0	0	26	2	18
253.0	0	27	6	14
254.0	0	20	1	17
255.0	0	31	4	12
256.0	0	20	3	16
257.0	0	29	1	28
258.0	0	22	2	19
259.0	0	20	5	19
260.0	0	25	1	18
261.0	0	24	0	16
262.0	0	23	3	19
263.0	0	25	3	16
264.0	0	24	3	21
265.0	0	24	5	20
266.0	0	21	1	25
267.0	0	31	2	16
268.0	0	15	1	26
269.0	0	25	1	13
270.0	0	25	1	15
271.0	0	21	4	23
272.0	0	20	2	11
273.0	0	24	0	14
274.0	0	23	0	21
275.0	0	19	3	13
276.0	0	24	2	20
277.0	0	32	2	25
278.0	0	22	3	17
279.0	0	21	2	19
280.0	0	28	2	23
281.0	0	22	1	12
282.0	0	22	1	18
283.0	0	26	3	17
284.0	0	15	0	16
285.0	0	21	0	12
286.0	0	7	1	13
287.0	0	16	1	11
288.0	0	18	1	16
289.0	0	25	1	9
290.0	0	29	4	16
291.0	0	24	2	18
292.0	0	21	1	18
293.0	0	23	3	17
294.0	0	18	2	14
295.0	0	16	3	20
296.0	0	18	1	12
297.0	0	19	2	13
298.0	0	17	0	18
299.0	0	17	1	12
300.0	0	25	1	14
301.0	0	17	1	14
302.0	0	20	2	11
303.0	0	14	0	12
304.0	0	16	1	11
305.0	0	22	1	18
306.0	0	21	0	20
307.0	0	13	3	16
308.0	0	19	1	24
309.0	0	11	0	10
310.0	0	21	4	9
311.0	0	16	2	19
312.0	0	25	1	13
313.0	0	11	0	11
314.0	0	22	1	17
315.0	0	17	0	11
316.0	0	14	0	16
317.0	0	12	3	8
318.0	0	16	3	12
319.0	0	26	1	13
320.0	0	23	1	10
321.0	0	16	1	5
322.0	0	17	0	12
323.0	0	13	3	12
324.0	0	13	0	14
325.0	0	11	1	12
326.0	0	16	2	12
327.0	0	8	3	14
328.0	0	18	2	11
329.0	0	26	1	12
330.0	0	14	2	11
331.0	0	12	0	15
332.0	0	15	2	7
333.0	0	16	2	11
334.0	0	13	1	12
335.0	0	14	0	9
336.0	0	14	2	18
337.0	0	14	4	11
338.0	0	17	0	11
339.0	0	9	1	8
340.0	0	12	1	10
341.0	0	15	1	9
342.0	0	11	0	8
343.0	0	18	2	9
344.0	0	16	0	5
345.0	0	16	1	11
346.0	0	12	2	10
347.0	0	16	0	7
348.0	0	13	0	15
349.0	0	16	2	6
350.0	0	11	0	8
351.0	0	7	1	9
352.0	0	11	0	15
353.0	0	11	0	9
354.0	0	17	3	9
355.0	0	16	2	6
356.0	0	14	3	6
357.0	0	12	0	8
358.0	0	20	1	8
359.0	0	10	0	15
360.0	0	16	1	10
361.0	0	9	2	6
362.0	0	13	1	5
363.0	0	4	0	6
364.0	0	11	3	6
365.0	0	9	1	10
366.0	0	13	2	13
367.0	0	17	0	10
368.0	0	7	2	8
369.0	0	11	0	17
370.0	0	8	0	5
371.0	0	9	0	12
372.0	0	11	1	10
373.0	0	8	1	8
374.0	0	14	0	11
375.0	0	10	0	8
376.0	0	11	3	5
377.0	0	13	0	12
378.0	0	9	2	9
379.0	0	7	3	8
380.0	0	9	0	8
381.0	0	10	0	12
382.0	0	10	1	9
383.0	0	9	0	10
384.0	0	12	0	7
385.0	0	11	0	8
386.0	0	12	2	8
387.0	0	11	1	11
388.0	0	10	3	5
389.0	0	12	0	11
390.0	0	7	2	8
391.0	0	13	0	9
392.0	0	8	1	8
393.0	0	10	2	8
394.0	0	9	0	8
395.0	0	14	0	8
396.0	0	10	1	6
397.0	0	16	0	10
398.0	0	10	3	4
399.0	0	6	1	9
400.0	0	10	0	5
401.0	0	17	1	8
402.0	0	6	0	13
403.0	0	7	0	8
404.0	0	12	0	6
405.0	0	9	3	11
406.0	0	7	1	6
407.0	0	9	1	8
408.0	0	7	0	11
409.0	0	8	0	7
410.0	0	10	1	8
411.0	0	21	1	10
412.0	0	5	2	2
413.0	0	8	1	3
414.0	0	5	1	9
415.0	0	8	0	10
416.0	0	10	2	4
417.0	0	5	1	10
418.0	0	11	0	2
419.0	0	10	0	4
420.0	0	12	0	7
421.0	0	7	0	9
422.0	0	10	0	3
423.0	0	4	0	8
424.0	0	7	0	5
425.0	0	5	3	5
426.0	0	6	1	3
427.0	0	12	0	4
428.0	0	11	1	9
429.0	0	15	1	4
430.0	0	9	0	5
431.0	0	7	0	4
432.0	0	7	0	7
433.0	0	3	0	2
434.0	0	10	1	11
435.0	0	10	0	5
436.0	0	4	1	7
437.0	0	4	0	5
438.0	0	10	0	8
439.0	0	3	0	5
440.0	0	4	2	5
441.0	0	7	0	3
442.0	0	8	0	7
443.0	0	10	0	5
444.0	0	6	1	6
445.0	0	6	2	8
446.0	0	12	0	8
447.0	0	5	1	4
448.0	0	5	2	7
449.0	0	8	1	7
450.0	0	7	1	6
451.0	0	12	1	7
452.0	0	4	0	3
453.0	0	6	0	4
454.0	0	6	0	3
455.0	0	9	0	7
456.0	0	8	2	2
457.0	0	5	0	5
458.0	0	7	0	7
459.0	0	5	0	2
460.0	0	4	0	4
461.0	0	8	0	3
462.0	0	5	0	2
463.0	0	6	0	1
464.0	0	6	0	4
465.0	0	8	1	6
466.0	0	5	1	3
467.0	0	5	0	7
468.0	0	6	1	6
469.0	0	6	1	5
470.0	0	7	0	3
471.0	0	6	0	9
472.0	0	7	1	5
473.0	0	2	0	7
474.0	0	14	0	2
475.0	0	6	0	8
476.0	0	2	1	5
477.0	0	10	0	4
478.0	0	5	0	7
479.0	0	2	0	3
480.0	0	9	0	3
481.0	0	9	1	2
482.0	0	4	0	5
483.0	0	6	0	3
484.0	0	2	0	8
485.0	0	6	0	5
486.0	0	7	1	2
487.0	0	8	0	5
488.0	0	6	0	5
489.0	0	2	0	4
490.0	0	8	0	8
491.0	0	6	0	2
492.0	0	6	0	6
493.0	0	5	0	3
494.0	0	6	0	5
495.0	0	4	2	3
496.0	0	11	0	4
497.0	0	5	0	8
498.0	0	7	2	3
499.0	0	5	1	2
500.0	0	6	1	8
501.0	0	1	0	8
502.0	0	8	1	2
503.0	0	3	0	5
504.0	0	5	0	2
505.0	0	6	1	6
506.0	0	3	0	2
507.0	0	5	0	5
508.0	0	2	0	5
509.0	0	9	0	6
510.0	0	9	0	5
511.0	0	7	0	1
512.0	0	2	0	1
513.0	0	6	1	0
514.0	0	4	1	4
515.0	0	6	0	4
516.0	0	2	0	3
517.0	0	3	1	7
518.0	0	3	0	1
519.0	0	5	0	3
520.0	0	4	1	2
521.0	0	2	1	2
522.0	0	10	0	4
523.0	0	5	1	4
524.0	0	8	0	3
525.0	0	9	0	4
526.0	0	5	0	2
527.0	0	3	1	4
528.0	0	5	0	4
529.0	0	4	0	6
530.0	0	3	0	5
531.0	0	4	1	1
532.0	0	7	1	1
533.0	0	5	0	3
534.0	0	2	0	4
535.0	0	3	0	2
536.0	0	8	0	3
537.0	0	7	0	3
538.0	0	5	1	5
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