## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-83-TP2.bam --OUTPUT POR-83-TP2.md.bam --METRICS_FILE POR-83-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 18:20:00 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	3249	16342694	9881948	0	3117	12450886	3594711	0.761882	4069208

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.02674	2067997	0	2601605
2.0	1.045243	800140	552812	688245
3.0	1.045577	350560	220781	202921
4.0	1.045583	178175	112370	85724
5.0	1.045583	103432	64090	49785
6.0	1.045583	66295	38234	34851
7.0	1.045583	45861	24426	26421
8.0	1.045583	33630	16514	20811
9.0	1.045583	25734	11574	16981
10.0	1.045583	20738	8656	14081
11.0	1.045583	16659	6708	12086
12.0	1.045583	13979	5184	10347
13.0	1.045583	12005	4101	8947
14.0	1.045583	10473	3533	7949
15.0	1.045583	9304	2940	7052
16.0	1.045583	8172	2572	6172
17.0	1.045583	7142	2217	5465
18.0	1.045583	6523	1922	5116
19.0	1.045583	5867	1670	4476
20.0	1.045583	5473	1533	4144
21.0	1.045583	4943	1321	3609
22.0	1.045583	4463	1217	3434
23.0	1.045583	4237	1053	3165
24.0	1.045583	3825	949	2956
25.0	1.045583	3506	911	2748
26.0	1.045583	3336	757	2494
27.0	1.045583	3033	732	2423
28.0	1.045583	2857	695	2161
29.0	1.045583	2722	629	2052
30.0	1.045583	2482	548	1912
31.0	1.045583	2422	561	1832
32.0	1.045583	2255	464	1724
33.0	1.045583	2048	484	1540
34.0	1.045583	2021	403	1451
35.0	1.045583	1845	397	1450
36.0	1.045583	1776	332	1298
37.0	1.045583	1653	299	1348
38.0	1.045583	1610	311	1236
39.0	1.045583	1476	302	1196
40.0	1.045583	1492	259	1134
41.0	1.045583	1409	270	1077
42.0	1.045583	1288	252	913
43.0	1.045583	1293	233	980
44.0	1.045583	1165	225	835
45.0	1.045583	1099	206	854
46.0	1.045583	1087	188	850
47.0	1.045583	1052	186	754
48.0	1.045583	1023	195	756
49.0	1.045583	992	139	721
50.0	1.045583	907	166	723
51.0	1.045583	890	146	698
52.0	1.045583	851	145	669
53.0	1.045583	783	151	642
54.0	1.045583	760	120	596
55.0	1.045583	772	153	588
56.0	1.045583	744	116	578
57.0	1.045583	724	129	545
58.0	1.045583	677	119	491
59.0	1.045583	662	108	493
60.0	1.045583	671	100	493
61.0	1.045583	634	100	483
62.0	1.045583	579	106	480
63.0	1.045583	556	71	447
64.0	1.045583	546	78	461
65.0	1.045583	534	85	386
66.0	1.045583	540	88	421
67.0	1.045583	519	71	429
68.0	1.045583	508	87	370
69.0	1.045583	476	70	339
70.0	1.045583	503	67	323
71.0	1.045583	461	78	334
72.0	1.045583	421	66	334
73.0	1.045583	415	69	339
74.0	1.045583	404	61	327
75.0	1.045583	380	55	316
76.0	1.045583	385	66	291
77.0	1.045583	406	53	283
78.0	1.045583	369	62	301
79.0	1.045583	386	53	242
80.0	1.045583	346	47	268
81.0	1.045583	352	58	256
82.0	1.045583	337	50	252
83.0	1.045583	308	48	211
84.0	1.045583	318	47	247
85.0	1.045583	313	46	234
86.0	1.045583	316	27	229
87.0	1.045583	276	38	231
88.0	1.045583	289	35	204
89.0	1.045583	295	23	206
90.0	1.045583	268	36	203
91.0	1.045583	258	43	187
92.0	1.045583	235	38	199
93.0	1.045583	225	34	184
94.0	1.045583	269	35	174
95.0	1.045583	228	33	180
96.0	1.045583	219	35	186
97.0	1.045583	211	35	183
98.0	1.045583	218	20	187
99.0	1.045583	236	22	144
100.0	1.045583	215	28	165
101.0	0	207	28	185
102.0	0	241	28	177
103.0	0	192	26	159
104.0	0	222	20	145
105.0	0	209	19	135
106.0	0	204	28	121
107.0	0	182	22	139
108.0	0	195	24	130
109.0	0	172	24	115
110.0	0	194	13	126
111.0	0	161	17	160
112.0	0	174	16	142
113.0	0	143	28	122
114.0	0	150	20	123
115.0	0	161	16	112
116.0	0	177	15	95
117.0	0	149	23	110
118.0	0	145	21	114
119.0	0	138	14	119
120.0	0	164	20	116
121.0	0	123	9	96
122.0	0	140	20	96
123.0	0	137	26	103
124.0	0	137	22	97
125.0	0	124	20	106
126.0	0	133	14	94
127.0	0	117	10	89
128.0	0	123	15	91
129.0	0	130	18	94
130.0	0	135	16	85
131.0	0	111	11	97
132.0	0	101	9	94
133.0	0	97	9	87
134.0	0	102	16	69
135.0	0	121	12	90
136.0	0	118	12	92
137.0	0	100	12	86
138.0	0	95	10	80
139.0	0	108	14	76
140.0	0	127	16	82
141.0	0	95	5	76
142.0	0	112	13	65
143.0	0	102	9	87
144.0	0	88	16	67
145.0	0	91	13	67
146.0	0	96	11	70
147.0	0	91	7	75
148.0	0	84	6	54
149.0	0	93	11	58
150.0	0	100	11	63
151.0	0	96	5	72
152.0	0	79	11	60
153.0	0	70	12	58
154.0	0	72	5	52
155.0	0	83	9	67
156.0	0	93	7	65
157.0	0	73	11	55
158.0	0	84	11	63
159.0	0	68	7	57
160.0	0	95	8	60
161.0	0	73	8	67
162.0	0	66	6	48
163.0	0	82	4	47
164.0	0	85	11	55
165.0	0	67	7	61
166.0	0	54	7	49
167.0	0	65	10	63
168.0	0	57	6	59
169.0	0	65	5	36
170.0	0	65	12	43
171.0	0	65	6	44
172.0	0	65	6	36
173.0	0	55	9	49
174.0	0	61	6	43
175.0	0	68	10	48
176.0	0	61	7	41
177.0	0	55	4	58
178.0	0	65	7	40
179.0	0	55	7	50
180.0	0	40	7	42
181.0	0	62	5	50
182.0	0	62	5	55
183.0	0	50	4	36
184.0	0	58	4	36
185.0	0	59	7	46
186.0	0	51	5	37
187.0	0	51	5	45
188.0	0	61	5	39
189.0	0	62	5	49
190.0	0	50	1	35
191.0	0	56	2	48
192.0	0	52	8	33
193.0	0	55	4	35
194.0	0	45	2	33
195.0	0	42	6	39
196.0	0	52	6	46
197.0	0	37	3	29
198.0	0	49	4	32
199.0	0	49	3	39
200.0	0	50	4	31
201.0	0	52	5	35
202.0	0	61	3	36
203.0	0	41	1	31
204.0	0	42	1	24
205.0	0	38	1	32
206.0	0	34	2	26
207.0	0	37	8	34
208.0	0	44	6	30
209.0	0	41	6	39
210.0	0	47	4	36
211.0	0	36	4	31
212.0	0	41	1	22
213.0	0	30	4	38
214.0	0	34	2	34
215.0	0	40	5	27
216.0	0	40	3	28
217.0	0	36	3	23
218.0	0	32	3	27
219.0	0	33	2	23
220.0	0	39	3	27
221.0	0	40	3	22
222.0	0	33	2	27
223.0	0	44	4	26
224.0	0	41	4	27
225.0	0	29	2	20
226.0	0	44	4	22
227.0	0	28	2	24
228.0	0	41	5	23
229.0	0	30	3	23
230.0	0	40	3	24
231.0	0	38	3	30
232.0	0	27	2	25
233.0	0	26	6	28
234.0	0	32	1	17
235.0	0	31	1	25
236.0	0	35	2	19
237.0	0	25	1	18
238.0	0	30	4	22
239.0	0	31	2	17
240.0	0	16	4	23
241.0	0	30	3	15
242.0	0	25	6	21
243.0	0	23	2	16
244.0	0	39	1	18
245.0	0	27	3	33
246.0	0	29	5	28
247.0	0	22	2	23
248.0	0	25	1	15
249.0	0	17	0	16
250.0	0	21	1	25
251.0	0	40	1	24
252.0	0	21	2	17
253.0	0	25	4	12
254.0	0	21	2	20
255.0	0	20	2	16
256.0	0	22	2	17
257.0	0	19	2	22
258.0	0	23	4	20
259.0	0	30	6	18
260.0	0	23	4	17
261.0	0	24	5	25
262.0	0	26	0	24
263.0	0	17	2	19
264.0	0	25	3	17
265.0	0	19	2	12
266.0	0	22	1	13
267.0	0	24	4	16
268.0	0	22	1	13
269.0	0	21	1	16
270.0	0	29	1	15
271.0	0	16	4	20
272.0	0	23	4	18
273.0	0	24	1	15
274.0	0	22	3	15
275.0	0	26	1	21
276.0	0	14	0	16
277.0	0	20	1	16
278.0	0	23	1	19
279.0	0	22	0	15
280.0	0	17	2	12
281.0	0	19	2	19
282.0	0	13	3	16
283.0	0	21	3	12
284.0	0	16	1	11
285.0	0	22	2	29
286.0	0	18	2	15
287.0	0	18	1	15
288.0	0	21	2	9
289.0	0	14	1	14
290.0	0	15	3	22
291.0	0	27	1	11
292.0	0	20	1	14
293.0	0	15	1	12
294.0	0	18	3	9
295.0	0	27	0	12
296.0	0	25	3	26
297.0	0	21	1	16
298.0	0	18	0	12
299.0	0	16	0	14
300.0	0	15	1	11
301.0	0	17	2	10
302.0	0	16	1	6
303.0	0	15	1	12
304.0	0	18	0	12
305.0	0	14	0	13
306.0	0	27	1	17
307.0	0	22	3	11
308.0	0	13	2	11
309.0	0	16	1	11
310.0	0	20	1	14
311.0	0	19	1	16
312.0	0	15	1	8
313.0	0	24	0	7
314.0	0	15	2	12
315.0	0	15	0	9
316.0	0	17	1	10
317.0	0	16	4	18
318.0	0	11	1	16
319.0	0	13	1	9
320.0	0	12	1	11
321.0	0	16	2	12
322.0	0	8	1	11
323.0	0	15	1	17
324.0	0	21	0	13
325.0	0	11	0	15
326.0	0	9	0	10
327.0	0	14	0	6
328.0	0	23	1	12
329.0	0	12	1	8
330.0	0	10	0	16
331.0	0	12	0	10
332.0	0	12	0	10
333.0	0	15	1	14
334.0	0	11	2	10
335.0	0	16	4	6
336.0	0	15	1	14
337.0	0	13	2	10
338.0	0	9	4	16
339.0	0	10	0	6
340.0	0	11	0	9
341.0	0	11	2	8
342.0	0	9	1	9
343.0	0	9	0	10
344.0	0	8	2	10
345.0	0	10	2	9
346.0	0	16	0	10
347.0	0	13	1	10
348.0	0	8	0	7
349.0	0	8	1	9
350.0	0	13	0	5
351.0	0	12	0	6
352.0	0	10	0	5
353.0	0	9	1	9
354.0	0	7	0	8
355.0	0	16	0	10
356.0	0	12	0	10
357.0	0	14	2	6
358.0	0	15	1	5
359.0	0	18	1	8
360.0	0	10	1	7
361.0	0	10	1	6
362.0	0	16	1	8
363.0	0	14	0	9
364.0	0	13	1	8
365.0	0	14	1	7
366.0	0	10	1	7
367.0	0	13	2	5
368.0	0	13	1	13
369.0	0	5	1	12
370.0	0	9	1	10
371.0	0	14	1	8
372.0	0	10	1	9
373.0	0	9	3	3
374.0	0	9	1	11
375.0	0	12	1	4
376.0	0	11	2	7
377.0	0	13	0	6
378.0	0	7	1	7
379.0	0	11	0	6
380.0	0	7	2	7
381.0	0	14	0	12
382.0	0	13	0	5
383.0	0	9	0	5
384.0	0	11	1	8
385.0	0	14	1	11
386.0	0	10	0	7
387.0	0	14	1	5
388.0	0	7	0	8
389.0	0	11	1	3
390.0	0	9	2	5
391.0	0	8	2	9
392.0	0	8	0	4
393.0	0	9	0	6
394.0	0	9	0	5
395.0	0	5	0	8
396.0	0	8	0	4
397.0	0	6	0	5
398.0	0	9	3	10
399.0	0	8	1	5
400.0	0	7	0	1
401.0	0	3	0	7
402.0	0	11	0	3
403.0	0	10	1	8
404.0	0	11	0	9
405.0	0	7	1	12
406.0	0	9	0	4
407.0	0	7	0	8
408.0	0	8	0	9
409.0	0	7	1	5
410.0	0	7	0	6
411.0	0	8	1	3
412.0	0	10	1	6
413.0	0	5	1	5
414.0	0	8	0	10
415.0	0	9	2	9
416.0	0	9	1	9
417.0	0	7	0	7
418.0	0	11	0	6
419.0	0	5	1	9
420.0	0	7	1	7
421.0	0	10	0	8
422.0	0	5	0	7
423.0	0	11	0	7
424.0	0	9	0	5
425.0	0	6	1	6
426.0	0	5	0	8
427.0	0	5	2	8
428.0	0	8	0	3
429.0	0	7	0	5
430.0	0	9	0	6
431.0	0	6	0	2
432.0	0	4	0	4
433.0	0	9	0	6
434.0	0	10	1	5
435.0	0	12	1	2
436.0	0	2	0	2
437.0	0	9	0	11
438.0	0	5	1	2
439.0	0	4	0	8
440.0	0	7	0	8
441.0	0	6	0	2
442.0	0	6	0	2
443.0	0	12	0	2
444.0	0	4	0	6
445.0	0	6	0	3
446.0	0	4	0	3
447.0	0	3	1	4
448.0	0	4	0	8
449.0	0	12	1	5
450.0	0	5	0	7
451.0	0	8	0	9
452.0	0	6	0	5
453.0	0	3	1	8
454.0	0	7	0	6
455.0	0	4	0	4
456.0	0	9	0	2
457.0	0	7	0	5
458.0	0	7	1	5
459.0	0	2	0	7
460.0	0	7	0	3
461.0	0	7	0	6
462.0	0	4	0	4
463.0	0	9	0	4
464.0	0	6	0	5
465.0	0	6	0	2
466.0	0	4	0	6
467.0	0	5	1	5
468.0	0	8	0	8
469.0	0	5	1	3
470.0	0	5	0	8
471.0	0	8	0	2
472.0	0	10	0	6
473.0	0	4	0	4
474.0	0	3	0	1
475.0	0	5	1	4
476.0	0	6	0	6
477.0	0	10	0	5
478.0	0	3	0	2
479.0	0	1	0	5
480.0	0	10	0	5
481.0	0	7	0	4
482.0	0	7	0	4
483.0	0	7	0	3
484.0	0	5	0	2
485.0	0	6	0	2
486.0	0	2	1	3
487.0	0	5	0	4
488.0	0	5	0	3
489.0	0	3	1	5
490.0	0	3	0	6
491.0	0	2	1	2
492.0	0	5	0	4
493.0	0	3	0	3
494.0	0	7	1	0
495.0	0	8	1	1
496.0	0	5	0	3
497.0	0	5	0	1
498.0	0	9	0	7
499.0	0	5	1	7
500.0	0	5	0	3
501.0	0	4	1	6
502.0	0	4	0	4
503.0	0	6	0	6
504.0	0	7	0	4
505.0	0	7	1	0
506.0	0	3	0	2
507.0	0	4	0	3
508.0	0	3	0	5
509.0	0	4	0	4
510.0	0	3	0	2
511.0	0	6	0	3
512.0	0	3	0	6
513.0	0	3	0	4
514.0	0	4	1	0
515.0	0	6	0	1
516.0	0	1	2	4
517.0	0	2	0	3
518.0	0	5	0	4
519.0	0	5	0	6
520.0	0	1	0	4
521.0	0	4	0	5
522.0	0	3	0	5
523.0	0	5	1	1
524.0	0	4	0	3
525.0	0	3	1	5
526.0	0	6	1	2
527.0	0	4	0	2
528.0	0	5	0	7
529.0	0	2	0	3
530.0	0	3	0	3
531.0	0	2	0	5
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