## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-245-TP2.bam --OUTPUT POR-245-TP2.md.bam --METRICS_FILE POR-245-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 17:57:42 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	2494	14672542	9710193	0	2423	12066036	3689518	0.822368	2648378

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.012076	1382787	0	1788802
2.0	1.016049	452814	387451	332381
3.0	1.016064	206935	167733	114990
4.0	1.016064	117368	90863	65471
5.0	1.016064	75522	53999	44805
6.0	1.016064	52446	34383	33207
7.0	1.016064	38906	23325	25722
8.0	1.016064	29786	16491	20670
9.0	1.016064	23852	12139	16571
10.0	1.016064	19937	9423	13905
11.0	1.016064	16315	7495	11811
12.0	1.016064	13938	6088	10184
13.0	1.016064	12128	4977	8851
14.0	1.016064	10659	4259	7849
15.0	1.016064	9364	3548	6958
16.0	1.016064	8318	3074	6064
17.0	1.016064	7599	2691	5470
18.0	1.016064	6740	2394	4942
19.0	1.016064	6028	2117	4459
20.0	1.016064	5518	1853	4146
21.0	1.016064	5151	1607	3887
22.0	1.016064	4688	1471	3370
23.0	1.016064	4354	1412	3289
24.0	1.016064	4088	1187	2942
25.0	1.016064	3698	1117	2653
26.0	1.016064	3302	1055	2536
27.0	1.016064	3173	940	2375
28.0	1.016064	2990	853	2177
29.0	1.016064	2873	785	2045
30.0	1.016064	2581	724	1869
31.0	1.016064	2518	720	1789
32.0	1.016064	2402	694	1690
33.0	1.016064	2211	602	1608
34.0	1.016064	2081	586	1533
35.0	1.016064	1976	526	1378
36.0	1.016064	1888	473	1336
37.0	1.016064	1781	446	1321
38.0	1.016064	1719	451	1140
39.0	1.016064	1563	377	1105
40.0	1.016064	1489	381	1170
41.0	1.016064	1412	390	1060
42.0	1.016064	1367	320	1007
43.0	1.016064	1357	327	982
44.0	1.016064	1213	278	936
45.0	1.016064	1214	317	866
46.0	1.016064	1086	264	829
47.0	1.016064	1044	286	790
48.0	1.016064	1041	260	782
49.0	1.016064	997	235	772
50.0	1.016064	969	239	714
51.0	1.016064	931	225	677
52.0	1.016064	893	223	687
53.0	1.016064	879	175	656
54.0	1.016064	844	194	595
55.0	1.016064	795	155	579
56.0	1.016064	805	159	555
57.0	1.016064	723	157	530
58.0	1.016064	739	153	518
59.0	1.016064	713	128	489
60.0	1.016064	728	138	518
61.0	1.016064	672	117	472
62.0	1.016064	664	114	465
63.0	1.016064	623	134	454
64.0	1.016064	589	127	418
65.0	1.016064	588	103	455
66.0	1.016064	531	111	393
67.0	1.016064	511	114	387
68.0	1.016064	527	99	416
69.0	1.016064	531	99	386
70.0	1.016064	474	95	340
71.0	1.016064	540	79	330
72.0	1.016064	473	101	313
73.0	1.016064	440	90	313
74.0	1.016064	415	84	301
75.0	1.016064	431	99	323
76.0	1.016064	433	100	310
77.0	1.016064	445	66	289
78.0	1.016064	367	73	270
79.0	1.016064	368	66	270
80.0	1.016064	398	63	260
81.0	1.016064	346	65	264
82.0	1.016064	339	73	240
83.0	1.016064	326	59	261
84.0	1.016064	330	49	238
85.0	1.016064	309	53	253
86.0	1.016064	321	66	236
87.0	1.016064	332	52	191
88.0	1.016064	337	63	231
89.0	1.016064	316	59	215
90.0	1.016064	290	53	209
91.0	1.016064	282	44	200
92.0	1.016064	279	36	189
93.0	1.016064	284	50	196
94.0	1.016064	285	34	205
95.0	1.016064	299	49	195
96.0	1.016064	230	50	164
97.0	1.016064	245	37	177
98.0	1.016064	265	38	164
99.0	1.016064	251	45	171
100.0	1.016064	210	35	191
101.0	0	267	42	143
102.0	0	193	45	157
103.0	0	225	26	156
104.0	0	218	34	156
105.0	0	217	22	145
106.0	0	217	29	154
107.0	0	203	23	121
108.0	0	181	36	126
109.0	0	186	40	127
110.0	0	183	33	111
111.0	0	190	33	122
112.0	0	192	32	123
113.0	0	187	27	122
114.0	0	176	27	113
115.0	0	184	29	109
116.0	0	164	18	108
117.0	0	152	16	132
118.0	0	145	28	124
119.0	0	180	24	141
120.0	0	155	29	108
121.0	0	154	24	96
122.0	0	152	16	100
123.0	0	147	19	110
124.0	0	129	30	100
125.0	0	122	21	93
126.0	0	142	23	106
127.0	0	133	23	100
128.0	0	125	22	91
129.0	0	138	14	96
130.0	0	140	33	95
131.0	0	127	23	79
132.0	0	122	17	85
133.0	0	121	20	78
134.0	0	127	13	86
135.0	0	102	13	74
136.0	0	112	18	72
137.0	0	124	14	78
138.0	0	94	17	71
139.0	0	131	11	72
140.0	0	97	10	78
141.0	0	107	17	70
142.0	0	122	14	81
143.0	0	93	19	68
144.0	0	107	10	72
145.0	0	125	20	76
146.0	0	102	12	63
147.0	0	103	11	61
148.0	0	106	19	60
149.0	0	86	13	61
150.0	0	86	13	73
151.0	0	93	13	69
152.0	0	85	16	56
153.0	0	91	16	69
154.0	0	90	10	67
155.0	0	78	14	81
156.0	0	98	11	51
157.0	0	83	10	64
158.0	0	99	13	59
159.0	0	68	13	53
160.0	0	75	14	64
161.0	0	62	15	56
162.0	0	80	13	52
163.0	0	67	6	49
164.0	0	77	11	47
165.0	0	71	7	61
166.0	0	77	6	50
167.0	0	72	2	53
168.0	0	85	8	57
169.0	0	69	8	42
170.0	0	56	10	50
171.0	0	69	8	47
172.0	0	69	9	43
173.0	0	68	5	54
174.0	0	69	11	63
175.0	0	65	5	40
176.0	0	77	15	38
177.0	0	65	8	37
178.0	0	61	13	52
179.0	0	59	7	42
180.0	0	51	7	44
181.0	0	49	8	40
182.0	0	61	14	41
183.0	0	59	6	35
184.0	0	71	9	37
185.0	0	45	7	35
186.0	0	54	1	39
187.0	0	45	12	43
188.0	0	60	7	47
189.0	0	46	7	41
190.0	0	60	9	47
191.0	0	57	10	41
192.0	0	50	11	35
193.0	0	41	11	40
194.0	0	45	9	37
195.0	0	53	12	30
196.0	0	50	8	35
197.0	0	65	10	30
198.0	0	57	7	38
199.0	0	40	7	33
200.0	0	44	3	46
201.0	0	62	3	38
202.0	0	55	4	39
203.0	0	50	4	40
204.0	0	44	5	39
205.0	0	38	5	38
206.0	0	57	9	25
207.0	0	56	5	36
208.0	0	53	6	36
209.0	0	53	8	32
210.0	0	47	5	24
211.0	0	32	10	37
212.0	0	47	2	35
213.0	0	42	9	25
214.0	0	46	5	21
215.0	0	51	8	35
216.0	0	43	6	30
217.0	0	45	6	27
218.0	0	44	6	27
219.0	0	38	4	31
220.0	0	29	6	38
221.0	0	46	5	31
222.0	0	32	8	28
223.0	0	45	7	29
224.0	0	28	5	24
225.0	0	47	2	25
226.0	0	38	5	27
227.0	0	36	3	35
228.0	0	37	4	27
229.0	0	42	1	29
230.0	0	27	5	23
231.0	0	34	6	23
232.0	0	31	3	23
233.0	0	37	3	16
234.0	0	35	4	13
235.0	0	28	2	30
236.0	0	28	5	18
237.0	0	34	6	17
238.0	0	29	6	25
239.0	0	29	4	23
240.0	0	34	7	30
241.0	0	32	0	30
242.0	0	17	4	17
243.0	0	23	3	20
244.0	0	37	7	19
245.0	0	25	3	22
246.0	0	24	5	20
247.0	0	31	3	26
248.0	0	28	5	22
249.0	0	38	9	18
250.0	0	24	1	16
251.0	0	31	5	22
252.0	0	31	1	23
253.0	0	24	2	17
254.0	0	29	6	30
255.0	0	32	3	12
256.0	0	35	2	19
257.0	0	28	6	20
258.0	0	20	1	25
259.0	0	26	6	24
260.0	0	18	4	13
261.0	0	22	8	11
262.0	0	24	7	16
263.0	0	29	5	31
264.0	0	29	5	17
265.0	0	24	3	15
266.0	0	24	2	14
267.0	0	21	4	18
268.0	0	27	2	21
269.0	0	24	8	24
270.0	0	16	5	15
271.0	0	26	3	19
272.0	0	28	4	11
273.0	0	25	3	18
274.0	0	33	4	15
275.0	0	19	5	16
276.0	0	23	6	17
277.0	0	22	4	10
278.0	0	20	0	20
279.0	0	17	4	18
280.0	0	26	1	15
281.0	0	16	0	12
282.0	0	15	3	15
283.0	0	21	1	21
284.0	0	28	2	19
285.0	0	23	2	19
286.0	0	20	0	22
287.0	0	24	1	24
288.0	0	18	1	12
289.0	0	16	3	12
290.0	0	19	4	7
291.0	0	17	1	17
292.0	0	22	2	9
293.0	0	16	4	18
294.0	0	21	2	9
295.0	0	23	3	20
296.0	0	15	3	17
297.0	0	14	1	15
298.0	0	20	1	20
299.0	0	24	3	14
300.0	0	25	2	10
301.0	0	15	4	9
302.0	0	14	2	16
303.0	0	15	5	13
304.0	0	15	4	18
305.0	0	20	2	13
306.0	0	18	3	5
307.0	0	22	7	8
308.0	0	21	1	14
309.0	0	11	2	15
310.0	0	12	0	14
311.0	0	22	0	10
312.0	0	14	2	9
313.0	0	19	3	11
314.0	0	14	1	15
315.0	0	16	3	14
316.0	0	16	1	12
317.0	0	15	1	14
318.0	0	17	3	16
319.0	0	18	1	17
320.0	0	18	0	13
321.0	0	10	1	9
322.0	0	13	2	20
323.0	0	14	2	13
324.0	0	12	2	10
325.0	0	12	1	13
326.0	0	17	0	15
327.0	0	24	0	9
328.0	0	8	1	14
329.0	0	15	1	7
330.0	0	22	1	8
331.0	0	27	1	6
332.0	0	21	0	8
333.0	0	8	0	14
334.0	0	17	1	11
335.0	0	17	0	10
336.0	0	18	3	5
337.0	0	12	2	17
338.0	0	15	1	10
339.0	0	13	0	10
340.0	0	13	1	9
341.0	0	14	2	11
342.0	0	13	0	6
343.0	0	14	2	11
344.0	0	10	4	11
345.0	0	15	3	16
346.0	0	13	5	6
347.0	0	16	0	11
348.0	0	9	2	10
349.0	0	19	0	9
350.0	0	13	3	14
351.0	0	13	2	8
352.0	0	14	2	12
353.0	0	13	2	17
354.0	0	15	1	9
355.0	0	8	0	7
356.0	0	14	0	8
357.0	0	20	0	14
358.0	0	8	3	6
359.0	0	17	3	8
360.0	0	16	1	13
361.0	0	14	3	7
362.0	0	21	2	10
363.0	0	14	0	9
364.0	0	17	1	8
365.0	0	15	3	5
366.0	0	11	0	7
367.0	0	14	2	13
368.0	0	7	0	7
369.0	0	12	2	7
370.0	0	18	1	5
371.0	0	10	0	6
372.0	0	14	1	4
373.0	0	16	1	8
374.0	0	9	0	2
375.0	0	8	3	12
376.0	0	14	1	10
377.0	0	7	1	8
378.0	0	19	1	7
379.0	0	11	0	8
380.0	0	6	1	6
381.0	0	18	0	4
382.0	0	12	1	12
383.0	0	14	1	4
384.0	0	12	0	4
385.0	0	11	0	12
386.0	0	9	2	4
387.0	0	16	1	8
388.0	0	10	1	10
389.0	0	4	0	10
390.0	0	8	0	11
391.0	0	4	0	10
392.0	0	11	0	8
393.0	0	14	3	8
394.0	0	8	2	9
395.0	0	5	1	11
396.0	0	14	1	9
397.0	0	7	1	10
398.0	0	4	0	3
399.0	0	11	1	4
400.0	0	13	2	9
401.0	0	6	0	8
402.0	0	7	0	4
403.0	0	8	2	9
404.0	0	10	1	7
405.0	0	5	3	2
406.0	0	11	2	1
407.0	0	15	1	6
408.0	0	10	0	4
409.0	0	12	1	9
410.0	0	10	2	5
411.0	0	15	0	5
412.0	0	11	0	10
413.0	0	8	0	3
414.0	0	9	1	5
415.0	0	9	3	6
416.0	0	3	1	10
417.0	0	5	0	5
418.0	0	13	0	2
419.0	0	8	2	6
420.0	0	10	0	4
421.0	0	9	1	6
422.0	0	6	0	6
423.0	0	6	0	5
424.0	0	6	2	6
425.0	0	9	0	7
426.0	0	6	0	6
427.0	0	10	1	8
428.0	0	11	4	6
429.0	0	11	1	4
430.0	0	9	1	8
431.0	0	4	0	6
432.0	0	7	0	5
433.0	0	9	1	5
434.0	0	12	0	10
435.0	0	17	0	2
436.0	0	7	0	6
437.0	0	8	0	6
438.0	0	8	2	7
439.0	0	6	0	8
440.0	0	6	0	3
441.0	0	5	1	7
442.0	0	10	1	5
443.0	0	8	1	7
444.0	0	7	0	3
445.0	0	5	0	2
446.0	0	9	0	5
447.0	0	4	0	3
448.0	0	6	1	5
449.0	0	7	0	7
450.0	0	7	0	2
451.0	0	3	0	5
452.0	0	6	2	5
453.0	0	8	0	1
454.0	0	11	1	4
455.0	0	7	0	2
456.0	0	5	2	5
457.0	0	7	0	3
458.0	0	8	0	4
459.0	0	4	3	4
460.0	0	5	1	6
461.0	0	9	2	6
462.0	0	7	1	6
463.0	0	6	2	7
464.0	0	8	2	1
465.0	0	6	0	5
466.0	0	7	0	6
467.0	0	6	2	3
468.0	0	4	0	8
469.0	0	10	2	3
470.0	0	6	2	6
471.0	0	2	1	7
472.0	0	7	0	1
473.0	0	7	1	4
474.0	0	5	0	4
475.0	0	5	0	2
476.0	0	6	1	3
477.0	0	10	3	5
478.0	0	3	2	4
479.0	0	10	1	4
480.0	0	4	0	4
481.0	0	7	1	6
482.0	0	9	1	2
483.0	0	5	1	7
484.0	0	6	0	1
485.0	0	6	0	1
486.0	0	6	0	4
487.0	0	7	0	3
488.0	0	6	1	5
489.0	0	5	1	4
490.0	0	2	0	3
491.0	0	4	2	6
492.0	0	6	2	3
493.0	0	2	0	3
494.0	0	6	1	7
495.0	0	4	0	5
496.0	0	13	0	3
497.0	0	5	0	7
498.0	0	4	0	4
499.0	0	10	0	6
500.0	0	5	1	3
501.0	0	1	0	3
502.0	0	4	2	5
503.0	0	9	0	3
504.0	0	5	0	4
505.0	0	5	2	4
506.0	0	3	2	2
507.0	0	2	2	3
508.0	0	8	1	4
509.0	0	8	0	5
510.0	0	6	1	3
511.0	0	5	0	1
512.0	0	4	0	3
513.0	0	7	0	3
514.0	0	2	0	5
515.0	0	5	0	5
516.0	0	5	0	0
517.0	0	4	2	1
518.0	0	4	0	4
519.0	0	2	1	1
520.0	0	6	2	5
521.0	0	5	1	3
522.0	0	5	0	1
523.0	0	4	0	4
524.0	0	4	1	0
525.0	0	5	2	2
526.0	0	4	1	1
527.0	0	3	0	2
528.0	0	4	0	3
529.0	0	8	1	4
530.0	0	6	1	4
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