## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-245-TP3.bam --OUTPUT POR-245-TP3.md.bam --METRICS_FILE POR-245-TP3.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 18:15:35 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	3315	16233699	11499759	0	3208	13703686	3759694	0.844163	2549119

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.005824	1024120	0	1303725
2.0	1.007549	530512	390653	542294
3.0	1.007552	283357	170397	220591
4.0	1.007552	159756	92898	102696
5.0	1.007552	98771	56950	59314
6.0	1.007552	66350	36358	40157
7.0	1.007552	47429	24860	29656
8.0	1.007552	35657	17820	23706
9.0	1.007552	28109	13087	19265
10.0	1.007552	22917	10138	16420
11.0	1.007552	19090	8082	13797
12.0	1.007552	16093	6432	11698
13.0	1.007552	13814	5435	10238
14.0	1.007552	12161	4408	8829
15.0	1.007552	10652	3858	7848
16.0	1.007552	9434	3361	6923
17.0	1.007552	8346	2849	6329
18.0	1.007552	7557	2464	5696
19.0	1.007552	6840	2153	5164
20.0	1.007552	6253	2048	4739
21.0	1.007552	5639	1693	4148
22.0	1.007552	5253	1593	3954
23.0	1.007552	4829	1421	3645
24.0	1.007552	4461	1243	3427
25.0	1.007552	4184	1185	3157
26.0	1.007552	3959	1067	2869
27.0	1.007552	3593	997	2704
28.0	1.007552	3427	924	2539
29.0	1.007552	3121	857	2331
30.0	1.007552	3019	755	2233
31.0	1.007552	2802	719	2162
32.0	1.007552	2611	652	1971
33.0	1.007552	2456	672	1813
34.0	1.007552	2365	538	1696
35.0	1.007552	2211	529	1606
36.0	1.007552	2091	469	1562
37.0	1.007552	1917	465	1491
38.0	1.007552	1865	446	1353
39.0	1.007552	1803	372	1335
40.0	1.007552	1683	387	1298
41.0	1.007552	1581	362	1244
42.0	1.007552	1582	370	1103
43.0	1.007552	1499	287	1093
44.0	1.007552	1426	310	1068
45.0	1.007552	1332	286	995
46.0	1.007552	1304	268	929
47.0	1.007552	1229	255	954
48.0	1.007552	1151	251	946
49.0	1.007552	1194	246	874
50.0	1.007552	1135	225	863
51.0	1.007552	1031	214	778
52.0	1.007552	1012	204	750
53.0	1.007552	987	173	683
54.0	1.007552	926	199	704
55.0	1.007552	894	170	733
56.0	1.007552	929	177	658
57.0	1.007552	813	150	656
58.0	1.007552	774	150	614
59.0	1.007552	763	144	570
60.0	1.007552	741	153	550
61.0	1.007552	767	136	589
62.0	1.007552	774	129	534
63.0	1.007552	726	114	477
64.0	1.007552	716	135	512
65.0	1.007552	669	106	442
66.0	1.007552	617	113	475
67.0	1.007552	629	110	479
68.0	1.007552	605	80	451
69.0	1.007552	580	88	401
70.0	1.007552	539	107	375
71.0	1.007552	541	99	375
72.0	1.007552	584	104	400
73.0	1.007552	492	90	339
74.0	1.007552	508	95	370
75.0	1.007552	471	82	348
76.0	1.007552	470	84	335
77.0	1.007552	443	73	342
78.0	1.007552	387	77	330
79.0	1.007552	430	73	336
80.0	1.007552	434	61	298
81.0	1.007552	377	75	296
82.0	1.007552	394	81	288
83.0	1.007552	407	53	291
84.0	1.007552	398	65	304
85.0	1.007552	371	60	261
86.0	1.007552	364	70	268
87.0	1.007552	374	56	257
88.0	1.007552	348	52	244
89.0	1.007552	327	45	243
90.0	1.007552	336	50	224
91.0	1.007552	328	50	249
92.0	1.007552	293	51	193
93.0	1.007552	280	49	204
94.0	1.007552	293	46	239
95.0	1.007552	313	49	201
96.0	1.007552	284	48	211
97.0	1.007552	248	39	223
98.0	1.007552	285	44	196
99.0	1.007552	263	43	195
100.0	1.007552	259	55	206
101.0	0	258	30	196
102.0	0	270	34	183
103.0	0	247	35	174
104.0	0	219	32	178
105.0	0	226	32	188
106.0	0	229	36	171
107.0	0	225	38	159
108.0	0	216	27	161
109.0	0	233	43	160
110.0	0	216	23	149
111.0	0	214	14	151
112.0	0	205	31	147
113.0	0	206	32	145
114.0	0	183	27	132
115.0	0	202	32	142
116.0	0	194	30	140
117.0	0	174	30	123
118.0	0	176	19	139
119.0	0	184	27	118
120.0	0	175	26	137
121.0	0	169	24	140
122.0	0	172	25	140
123.0	0	196	25	107
124.0	0	156	15	125
125.0	0	134	18	123
126.0	0	158	30	122
127.0	0	155	25	103
128.0	0	132	21	124
129.0	0	156	18	112
130.0	0	145	20	103
131.0	0	141	19	92
132.0	0	150	21	92
133.0	0	125	19	91
134.0	0	147	15	100
135.0	0	117	18	91
136.0	0	114	15	95
137.0	0	129	13	89
138.0	0	119	11	84
139.0	0	126	15	71
140.0	0	105	20	90
141.0	0	120	14	85
142.0	0	133	22	84
143.0	0	111	15	100
144.0	0	125	27	88
145.0	0	98	15	82
146.0	0	100	9	81
147.0	0	108	13	84
148.0	0	100	18	75
149.0	0	101	22	85
150.0	0	90	10	75
151.0	0	104	10	79
152.0	0	114	9	65
153.0	0	118	9	64
154.0	0	102	13	71
155.0	0	101	8	62
156.0	0	103	17	74
157.0	0	117	19	76
158.0	0	97	11	59
159.0	0	98	17	60
160.0	0	79	11	55
161.0	0	87	12	69
162.0	0	91	13	52
163.0	0	82	14	47
164.0	0	106	8	71
165.0	0	86	13	80
166.0	0	86	14	55
167.0	0	98	5	63
168.0	0	77	12	59
169.0	0	79	10	50
170.0	0	67	8	56
171.0	0	79	13	52
172.0	0	61	12	57
173.0	0	71	9	51
174.0	0	79	5	42
175.0	0	69	5	56
176.0	0	75	5	54
177.0	0	72	6	46
178.0	0	74	8	42
179.0	0	74	11	49
180.0	0	66	4	52
181.0	0	62	7	42
182.0	0	78	7	34
183.0	0	73	8	62
184.0	0	66	5	56
185.0	0	81	5	61
186.0	0	73	3	67
187.0	0	61	9	54
188.0	0	63	9	43
189.0	0	51	5	38
190.0	0	80	5	41
191.0	0	45	6	50
192.0	0	76	5	39
193.0	0	58	6	43
194.0	0	61	5	41
195.0	0	58	9	49
196.0	0	62	6	44
197.0	0	51	7	48
198.0	0	55	9	51
199.0	0	40	5	49
200.0	0	56	7	51
201.0	0	66	7	43
202.0	0	47	9	33
203.0	0	54	5	25
204.0	0	43	0	34
205.0	0	57	6	36
206.0	0	52	6	40
207.0	0	52	8	47
208.0	0	46	5	38
209.0	0	40	6	38
210.0	0	38	3	46
211.0	0	51	2	28
212.0	0	62	6	31
213.0	0	61	3	33
214.0	0	51	5	33
215.0	0	49	5	31
216.0	0	44	4	43
217.0	0	46	3	29
218.0	0	41	2	26
219.0	0	43	2	38
220.0	0	39	10	27
221.0	0	35	8	27
222.0	0	41	2	35
223.0	0	36	5	38
224.0	0	35	6	29
225.0	0	48	6	29
226.0	0	32	10	16
227.0	0	38	5	38
228.0	0	43	5	31
229.0	0	56	3	32
230.0	0	32	3	27
231.0	0	46	4	28
232.0	0	40	4	28
233.0	0	29	4	21
234.0	0	33	5	26
235.0	0	34	3	20
236.0	0	43	4	29
237.0	0	38	3	24
238.0	0	38	2	29
239.0	0	38	1	27
240.0	0	35	4	24
241.0	0	31	2	29
242.0	0	38	3	26
243.0	0	42	5	23
244.0	0	36	0	27
245.0	0	31	5	20
246.0	0	31	4	31
247.0	0	36	4	30
248.0	0	29	1	25
249.0	0	33	0	29
250.0	0	35	1	23
251.0	0	45	1	19
252.0	0	38	2	20
253.0	0	36	6	21
254.0	0	27	2	23
255.0	0	30	6	18
256.0	0	28	2	18
257.0	0	27	2	25
258.0	0	37	0	21
259.0	0	35	3	22
260.0	0	38	4	26
261.0	0	32	4	19
262.0	0	32	1	20
263.0	0	32	2	21
264.0	0	32	2	24
265.0	0	37	3	15
266.0	0	33	3	12
267.0	0	31	2	21
268.0	0	25	2	25
269.0	0	27	1	21
270.0	0	24	0	18
271.0	0	24	5	20
272.0	0	23	3	19
273.0	0	27	2	22
274.0	0	20	6	10
275.0	0	18	2	18
276.0	0	36	4	28
277.0	0	20	0	24
278.0	0	18	3	14
279.0	0	30	3	20
280.0	0	23	1	17
281.0	0	26	2	12
282.0	0	24	2	17
283.0	0	20	2	19
284.0	0	19	1	16
285.0	0	28	2	18
286.0	0	27	5	15
287.0	0	19	2	21
288.0	0	23	3	14
289.0	0	26	1	17
290.0	0	18	2	23
291.0	0	25	2	15
292.0	0	25	1	11
293.0	0	23	5	23
294.0	0	20	6	12
295.0	0	13	2	15
296.0	0	28	3	23
297.0	0	24	3	18
298.0	0	22	2	14
299.0	0	20	3	8
300.0	0	19	2	17
301.0	0	22	1	16
302.0	0	27	1	11
303.0	0	22	6	13
304.0	0	22	4	15
305.0	0	20	4	19
306.0	0	22	3	12
307.0	0	24	1	13
308.0	0	25	3	9
309.0	0	26	2	8
310.0	0	22	2	13
311.0	0	19	3	18
312.0	0	18	1	13
313.0	0	17	2	18
314.0	0	23	4	14
315.0	0	25	2	10
316.0	0	23	1	17
317.0	0	12	2	14
318.0	0	17	0	10
319.0	0	14	2	11
320.0	0	12	2	7
321.0	0	12	1	12
322.0	0	16	2	7
323.0	0	17	5	13
324.0	0	12	1	9
325.0	0	16	1	14
326.0	0	13	1	15
327.0	0	18	0	14
328.0	0	12	1	15
329.0	0	16	1	17
330.0	0	15	2	8
331.0	0	7	0	17
332.0	0	21	6	9
333.0	0	14	3	15
334.0	0	23	1	9
335.0	0	25	0	11
336.0	0	19	1	5
337.0	0	13	3	8
338.0	0	23	0	13
339.0	0	15	0	7
340.0	0	17	0	12
341.0	0	9	0	9
342.0	0	14	2	13
343.0	0	17	0	12
344.0	0	16	0	17
345.0	0	16	0	12
346.0	0	17	0	16
347.0	0	10	0	13
348.0	0	13	3	7
349.0	0	16	4	13
350.0	0	14	3	10
351.0	0	14	0	11
352.0	0	18	1	12
353.0	0	10	0	4
354.0	0	10	1	8
355.0	0	9	0	6
356.0	0	13	0	12
357.0	0	12	1	11
358.0	0	12	0	11
359.0	0	19	0	8
360.0	0	14	0	11
361.0	0	11	2	6
362.0	0	13	1	10
363.0	0	14	0	10
364.0	0	9	0	7
365.0	0	15	2	12
366.0	0	10	0	10
367.0	0	8	3	7
368.0	0	11	1	11
369.0	0	8	1	8
370.0	0	7	0	8
371.0	0	11	1	14
372.0	0	8	1	3
373.0	0	11	1	11
374.0	0	16	2	11
375.0	0	9	2	8
376.0	0	22	1	10
377.0	0	10	1	9
378.0	0	13	0	12
379.0	0	13	1	7
380.0	0	14	3	8
381.0	0	12	1	9
382.0	0	6	1	8
383.0	0	10	0	9
384.0	0	13	1	14
385.0	0	9	0	7
386.0	0	17	0	8
387.0	0	14	3	6
388.0	0	11	0	6
389.0	0	11	1	8
390.0	0	13	0	12
391.0	0	8	4	7
392.0	0	13	2	8
393.0	0	6	1	6
394.0	0	13	1	8
395.0	0	7	0	6
396.0	0	9	0	7
397.0	0	16	0	6
398.0	0	10	0	11
399.0	0	9	1	6
400.0	0	11	0	8
401.0	0	8	0	8
402.0	0	12	1	5
403.0	0	12	0	8
404.0	0	8	1	5
405.0	0	12	0	8
406.0	0	10	1	4
407.0	0	12	1	5
408.0	0	7	0	9
409.0	0	11	1	6
410.0	0	12	3	7
411.0	0	8	2	4
412.0	0	13	1	3
413.0	0	12	0	5
414.0	0	10	0	11
415.0	0	6	1	7
416.0	0	12	0	9
417.0	0	9	1	7
418.0	0	8	0	11
419.0	0	9	1	6
420.0	0	9	0	3
421.0	0	9	1	8
422.0	0	12	0	7
423.0	0	11	1	6
424.0	0	12	0	5
425.0	0	7	1	8
426.0	0	7	0	7
427.0	0	11	1	6
428.0	0	6	1	5
429.0	0	8	0	15
430.0	0	6	0	10
431.0	0	11	0	8
432.0	0	8	1	7
433.0	0	9	2	4
434.0	0	4	0	4
435.0	0	5	0	12
436.0	0	7	1	9
437.0	0	4	1	7
438.0	0	10	1	4
439.0	0	5	0	4
440.0	0	7	1	8
441.0	0	9	0	5
442.0	0	12	0	7
443.0	0	8	0	4
444.0	0	6	0	7
445.0	0	5	0	5
446.0	0	4	0	5
447.0	0	10	0	4
448.0	0	5	0	2
449.0	0	9	0	12
450.0	0	8	1	3
451.0	0	6	1	5
452.0	0	5	0	2
453.0	0	7	0	6
454.0	0	8	1	9
455.0	0	11	2	9
456.0	0	12	2	5
457.0	0	11	1	7
458.0	0	6	2	11
459.0	0	3	0	1
460.0	0	8	0	2
461.0	0	7	1	5
462.0	0	8	0	7
463.0	0	7	0	4
464.0	0	11	0	2
465.0	0	7	3	3
466.0	0	10	0	7
467.0	0	11	0	7
468.0	0	12	0	3
469.0	0	3	1	5
470.0	0	4	0	7
471.0	0	8	2	4
472.0	0	6	3	3
473.0	0	10	1	5
474.0	0	8	1	2
475.0	0	6	0	2
476.0	0	3	0	3
477.0	0	2	0	4
478.0	0	7	1	7
479.0	0	6	0	0
480.0	0	9	0	5
481.0	0	6	2	6
482.0	0	7	0	2
483.0	0	6	0	1
484.0	0	7	0	6
485.0	0	9	1	4
486.0	0	7	0	6
487.0	0	4	1	7
488.0	0	8	0	4
489.0	0	3	0	2
490.0	0	11	0	6
491.0	0	10	0	3
492.0	0	5	1	10
493.0	0	6	0	7
494.0	0	6	0	4
495.0	0	6	0	5
496.0	0	7	0	3
497.0	0	4	0	0
498.0	0	1	0	2
499.0	0	4	1	3
500.0	0	8	0	3
501.0	0	5	0	1
502.0	0	7	0	1
503.0	0	6	0	3
504.0	0	3	0	4
505.0	0	5	0	1
506.0	0	8	1	5
507.0	0	3	1	4
508.0	0	2	0	2
509.0	0	3	0	5
510.0	0	0	0	2
511.0	0	7	0	3
512.0	0	1	0	5
513.0	0	8	2	1
514.0	0	6	1	7
515.0	0	4	0	3
516.0	0	6	0	6
517.0	0	3	0	12
518.0	0	7	0	3
519.0	0	6	0	3
520.0	0	6	0	1
521.0	0	2	1	3
522.0	0	4	0	2
523.0	0	5	2	5
524.0	0	4	0	1
525.0	0	6	1	2
526.0	0	4	0	2
527.0	0	4	0	3
528.0	0	6	0	4
529.0	0	4	0	1
530.0	0	4	0	10
531.0	0	5	1	4
532.0	0	6	0	3
533.0	0	3	2	3
534.0	0	4	1	2
535.0	0	3	0	3
536.0	0	7	0	3
537.0	0	4	1	5
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