## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-236-TP2.bam --OUTPUT POR-236-TP2.md.bam --METRICS_FILE POR-236-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 18:17:39 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	3033	17049778	11839131	0	2945	14068440	3876717	0.825152	3019843

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.009338	1594585	0	2013724
2.0	1.012903	533736	429486	414409
3.0	1.012915	236752	178627	136051
4.0	1.012915	129397	94680	73019
5.0	1.012915	81425	55665	49246
6.0	1.012915	56254	35107	36079
7.0	1.012915	41428	23468	27804
8.0	1.012915	31337	16601	22632
9.0	1.012915	25215	12320	18638
10.0	1.012915	21096	9845	15570
11.0	1.012915	17686	7572	13017
12.0	1.012915	15028	6096	11490
13.0	1.012915	13225	4978	10064
14.0	1.012915	11577	4265	8979
15.0	1.012915	10107	3614	7791
16.0	1.012915	9218	3279	7047
17.0	1.012915	8176	2859	6224
18.0	1.012915	7550	2378	5605
19.0	1.012915	6764	2176	5172
20.0	1.012915	6148	1967	4737
21.0	1.012915	5449	1798	4328
22.0	1.012915	5055	1585	3874
23.0	1.012915	4804	1394	3671
24.0	1.012915	4442	1253	3480
25.0	1.012915	4115	1188	3116
26.0	1.012915	3781	1121	2875
27.0	1.012915	3648	1010	2793
28.0	1.012915	3304	932	2478
29.0	1.012915	3166	831	2396
30.0	1.012915	2906	795	2256
31.0	1.012915	2640	713	2132
32.0	1.012915	2681	652	1997
33.0	1.012915	2415	623	1790
34.0	1.012915	2317	545	1802
35.0	1.012915	2122	537	1642
36.0	1.012915	2136	506	1565
37.0	1.012915	2007	462	1512
38.0	1.012915	1923	435	1460
39.0	1.012915	1783	416	1343
40.0	1.012915	1729	424	1330
41.0	1.012915	1658	386	1169
42.0	1.012915	1581	377	1159
43.0	1.012915	1533	341	1136
44.0	1.012915	1452	309	1057
45.0	1.012915	1412	308	1044
46.0	1.012915	1316	307	961
47.0	1.012915	1236	280	1044
48.0	1.012915	1164	257	823
49.0	1.012915	1179	219	867
50.0	1.012915	1106	220	903
51.0	1.012915	1093	224	773
52.0	1.012915	979	227	792
53.0	1.012915	1035	188	761
54.0	1.012915	958	188	730
55.0	1.012915	950	207	733
56.0	1.012915	856	177	692
57.0	1.012915	871	168	626
58.0	1.012915	818	158	640
59.0	1.012915	839	166	589
60.0	1.012915	772	160	559
61.0	1.012915	776	128	562
62.0	1.012915	739	150	547
63.0	1.012915	689	124	514
64.0	1.012915	672	126	520
65.0	1.012915	699	143	496
66.0	1.012915	665	125	494
67.0	1.012915	588	111	468
68.0	1.012915	546	119	484
69.0	1.012915	603	102	465
70.0	1.012915	619	110	416
71.0	1.012915	540	90	382
72.0	1.012915	489	94	404
73.0	1.012915	533	102	406
74.0	1.012915	534	87	416
75.0	1.012915	488	85	388
76.0	1.012915	453	74	371
77.0	1.012915	458	83	366
78.0	1.012915	485	75	318
79.0	1.012915	445	92	305
80.0	1.012915	416	78	323
81.0	1.012915	452	72	317
82.0	1.012915	412	44	295
83.0	1.012915	416	77	264
84.0	1.012915	377	60	305
85.0	1.012915	386	67	262
86.0	1.012915	376	56	259
87.0	1.012915	345	49	257
88.0	1.012915	334	53	289
89.0	1.012915	366	74	260
90.0	1.012915	340	58	246
91.0	1.012915	326	48	237
92.0	1.012915	323	47	243
93.0	1.012915	336	52	262
94.0	1.012915	318	43	226
95.0	1.012915	299	53	229
96.0	1.012915	298	38	203
97.0	1.012915	280	41	201
98.0	1.012915	267	37	255
99.0	1.012915	276	52	202
100.0	1.012915	267	38	193
101.0	0	260	31	204
102.0	0	297	41	199
103.0	0	259	49	182
104.0	0	281	48	179
105.0	0	232	38	188
106.0	0	239	41	181
107.0	0	244	38	176
108.0	0	245	26	185
109.0	0	253	31	155
110.0	0	222	25	158
111.0	0	211	27	166
112.0	0	232	29	157
113.0	0	218	34	150
114.0	0	219	38	145
115.0	0	209	25	141
116.0	0	195	26	144
117.0	0	187	32	138
118.0	0	216	33	144
119.0	0	175	22	153
120.0	0	200	25	135
121.0	0	174	19	132
122.0	0	193	25	124
123.0	0	163	27	126
124.0	0	166	26	143
125.0	0	160	33	116
126.0	0	170	21	113
127.0	0	154	26	108
128.0	0	152	29	129
129.0	0	173	24	105
130.0	0	156	22	135
131.0	0	141	20	137
132.0	0	147	20	108
133.0	0	147	19	93
134.0	0	163	23	99
135.0	0	159	22	101
136.0	0	123	28	105
137.0	0	159	18	92
138.0	0	144	19	107
139.0	0	133	20	117
140.0	0	125	25	86
141.0	0	128	14	94
142.0	0	105	13	89
143.0	0	119	10	84
144.0	0	111	21	103
145.0	0	119	19	82
146.0	0	116	11	94
147.0	0	101	12	102
148.0	0	126	13	93
149.0	0	109	9	74
150.0	0	142	18	77
151.0	0	120	21	74
152.0	0	115	17	77
153.0	0	125	13	77
154.0	0	90	11	79
155.0	0	103	11	80
156.0	0	89	9	74
157.0	0	106	16	79
158.0	0	109	12	94
159.0	0	104	12	79
160.0	0	85	18	73
161.0	0	111	9	74
162.0	0	102	13	62
163.0	0	93	14	75
164.0	0	74	6	56
165.0	0	95	8	52
166.0	0	90	11	54
167.0	0	97	11	74
168.0	0	96	5	51
169.0	0	92	11	70
170.0	0	75	5	68
171.0	0	75	13	69
172.0	0	79	8	49
173.0	0	77	9	54
174.0	0	76	18	63
175.0	0	69	8	65
176.0	0	75	13	49
177.0	0	76	6	60
178.0	0	77	9	48
179.0	0	78	9	61
180.0	0	58	6	49
181.0	0	64	7	46
182.0	0	83	3	63
183.0	0	76	9	63
184.0	0	58	7	53
185.0	0	79	12	47
186.0	0	68	6	47
187.0	0	74	11	45
188.0	0	64	10	57
189.0	0	63	17	47
190.0	0	66	10	40
191.0	0	74	10	54
192.0	0	70	13	43
193.0	0	52	6	42
194.0	0	71	10	37
195.0	0	80	10	33
196.0	0	51	6	42
197.0	0	75	7	48
198.0	0	59	8	52
199.0	0	54	4	50
200.0	0	65	13	44
201.0	0	51	9	50
202.0	0	48	8	53
203.0	0	52	6	49
204.0	0	63	5	50
205.0	0	64	4	44
206.0	0	53	4	39
207.0	0	70	9	32
208.0	0	46	11	38
209.0	0	45	11	43
210.0	0	43	8	35
211.0	0	49	4	35
212.0	0	54	8	31
213.0	0	39	2	49
214.0	0	48	3	45
215.0	0	49	2	40
216.0	0	59	6	39
217.0	0	41	4	44
218.0	0	45	8	31
219.0	0	49	4	39
220.0	0	44	5	32
221.0	0	50	2	33
222.0	0	42	4	35
223.0	0	41	5	26
224.0	0	44	6	43
225.0	0	43	6	26
226.0	0	31	4	39
227.0	0	60	6	33
228.0	0	46	4	26
229.0	0	31	8	35
230.0	0	52	5	36
231.0	0	36	3	34
232.0	0	54	5	27
233.0	0	38	3	33
234.0	0	50	5	30
235.0	0	44	5	28
236.0	0	45	5	27
237.0	0	38	5	25
238.0	0	38	6	22
239.0	0	33	2	24
240.0	0	39	4	28
241.0	0	36	2	26
242.0	0	35	4	33
243.0	0	35	4	23
244.0	0	53	1	27
245.0	0	48	6	24
246.0	0	43	3	28
247.0	0	32	2	29
248.0	0	49	3	34
249.0	0	30	5	33
250.0	0	32	2	32
251.0	0	23	8	36
252.0	0	42	3	32
253.0	0	36	4	24
254.0	0	31	7	21
255.0	0	43	4	31
256.0	0	27	3	22
257.0	0	28	2	30
258.0	0	38	1	31
259.0	0	31	1	21
260.0	0	33	7	26
261.0	0	27	5	21
262.0	0	31	6	20
263.0	0	23	4	15
264.0	0	41	5	20
265.0	0	37	2	16
266.0	0	31	2	18
267.0	0	27	3	22
268.0	0	34	4	27
269.0	0	34	4	14
270.0	0	38	5	30
271.0	0	31	3	24
272.0	0	21	6	27
273.0	0	22	4	22
274.0	0	30	2	19
275.0	0	32	5	24
276.0	0	24	2	15
277.0	0	20	6	13
278.0	0	22	3	22
279.0	0	20	5	20
280.0	0	28	2	17
281.0	0	29	2	25
282.0	0	22	4	17
283.0	0	23	2	25
284.0	0	32	3	19
285.0	0	24	2	25
286.0	0	26	4	26
287.0	0	20	5	22
288.0	0	26	2	28
289.0	0	29	1	15
290.0	0	22	4	22
291.0	0	21	4	10
292.0	0	18	3	14
293.0	0	20	2	17
294.0	0	26	3	19
295.0	0	27	0	16
296.0	0	27	2	16
297.0	0	25	3	15
298.0	0	22	3	24
299.0	0	29	6	19
300.0	0	18	1	19
301.0	0	28	1	10
302.0	0	25	2	16
303.0	0	25	1	14
304.0	0	22	5	23
305.0	0	22	2	16
306.0	0	19	1	25
307.0	0	26	5	21
308.0	0	16	3	14
309.0	0	20	0	15
310.0	0	18	5	19
311.0	0	20	2	15
312.0	0	25	3	18
313.0	0	19	0	10
314.0	0	24	0	16
315.0	0	26	1	16
316.0	0	20	0	13
317.0	0	26	1	14
318.0	0	16	3	9
319.0	0	35	4	17
320.0	0	18	0	9
321.0	0	25	1	15
322.0	0	20	1	16
323.0	0	17	2	18
324.0	0	26	3	11
325.0	0	18	0	18
326.0	0	15	2	10
327.0	0	16	0	14
328.0	0	16	2	20
329.0	0	11	2	14
330.0	0	25	0	13
331.0	0	23	1	8
332.0	0	14	2	11
333.0	0	23	1	11
334.0	0	15	3	14
335.0	0	20	3	11
336.0	0	14	0	15
337.0	0	17	2	12
338.0	0	15	1	13
339.0	0	22	1	20
340.0	0	17	1	11
341.0	0	13	2	14
342.0	0	18	0	10
343.0	0	17	3	11
344.0	0	13	2	11
345.0	0	16	1	14
346.0	0	17	0	13
347.0	0	18	2	12
348.0	0	18	2	10
349.0	0	18	0	12
350.0	0	22	1	11
351.0	0	10	2	13
352.0	0	13	2	9
353.0	0	14	3	14
354.0	0	17	2	15
355.0	0	6	1	21
356.0	0	17	0	6
357.0	0	17	1	8
358.0	0	18	2	7
359.0	0	14	4	13
360.0	0	13	0	15
361.0	0	12	1	13
362.0	0	18	0	13
363.0	0	13	1	9
364.0	0	19	3	11
365.0	0	11	0	12
366.0	0	21	1	11
367.0	0	12	1	15
368.0	0	9	3	15
369.0	0	14	1	7
370.0	0	10	1	9
371.0	0	11	1	9
372.0	0	12	1	10
373.0	0	14	1	5
374.0	0	13	0	12
375.0	0	16	1	7
376.0	0	14	2	13
377.0	0	7	1	5
378.0	0	18	1	16
379.0	0	12	2	9
380.0	0	10	0	5
381.0	0	10	1	16
382.0	0	16	1	10
383.0	0	14	0	14
384.0	0	17	3	12
385.0	0	11	0	14
386.0	0	19	2	19
387.0	0	18	1	7
388.0	0	15	2	5
389.0	0	9	0	14
390.0	0	18	1	9
391.0	0	11	1	12
392.0	0	18	2	9
393.0	0	15	1	9
394.0	0	5	0	9
395.0	0	10	1	9
396.0	0	15	0	10
397.0	0	15	0	6
398.0	0	15	2	8
399.0	0	15	1	11
400.0	0	10	1	11
401.0	0	9	1	11
402.0	0	7	2	6
403.0	0	11	3	10
404.0	0	16	1	9
405.0	0	8	1	9
406.0	0	15	0	7
407.0	0	11	0	6
408.0	0	14	4	12
409.0	0	7	3	12
410.0	0	7	1	11
411.0	0	9	0	7
412.0	0	11	1	11
413.0	0	12	1	6
414.0	0	16	1	4
415.0	0	8	0	11
416.0	0	11	2	8
417.0	0	12	2	12
418.0	0	11	2	7
419.0	0	19	0	10
420.0	0	12	2	9
421.0	0	9	2	3
422.0	0	9	1	5
423.0	0	11	1	7
424.0	0	6	0	6
425.0	0	10	0	6
426.0	0	10	1	7
427.0	0	6	0	7
428.0	0	18	2	9
429.0	0	11	0	8
430.0	0	16	1	12
431.0	0	5	1	4
432.0	0	12	1	6
433.0	0	14	1	5
434.0	0	12	2	12
435.0	0	13	2	5
436.0	0	18	0	6
437.0	0	8	1	14
438.0	0	10	0	6
439.0	0	5	2	8
440.0	0	10	0	11
441.0	0	13	2	1
442.0	0	10	1	3
443.0	0	16	2	10
444.0	0	18	1	6
445.0	0	7	1	7
446.0	0	12	1	6
447.0	0	9	0	5
448.0	0	7	1	10
449.0	0	11	1	5
450.0	0	4	1	10
451.0	0	10	0	7
452.0	0	8	0	6
453.0	0	9	0	7
454.0	0	11	2	7
455.0	0	13	0	8
456.0	0	8	1	2
457.0	0	10	0	8
458.0	0	9	1	4
459.0	0	11	0	4
460.0	0	8	0	8
461.0	0	10	2	10
462.0	0	12	0	2
463.0	0	9	0	5
464.0	0	5	1	7
465.0	0	6	2	11
466.0	0	6	1	11
467.0	0	5	1	4
468.0	0	7	0	3
469.0	0	12	0	7
470.0	0	12	0	5
471.0	0	6	2	7
472.0	0	11	2	4
473.0	0	7	0	5
474.0	0	8	0	6
475.0	0	1	2	6
476.0	0	6	2	4
477.0	0	9	0	4
478.0	0	5	1	2
479.0	0	13	1	4
480.0	0	6	1	6
481.0	0	3	0	2
482.0	0	11	1	7
483.0	0	5	0	4
484.0	0	10	1	5
485.0	0	11	0	5
486.0	0	11	1	1
487.0	0	12	0	4
488.0	0	2	0	4
489.0	0	7	0	10
490.0	0	10	1	2
491.0	0	4	0	4
492.0	0	6	1	2
493.0	0	8	0	3
494.0	0	4	0	7
495.0	0	3	0	2
496.0	0	3	1	5
497.0	0	5	0	6
498.0	0	8	0	3
499.0	0	4	1	3
500.0	0	5	1	9
501.0	0	8	1	3
502.0	0	3	3	8
503.0	0	7	2	5
504.0	0	4	0	4
505.0	0	2	0	7
506.0	0	7	0	6
507.0	0	5	1	14
508.0	0	9	0	5
509.0	0	4	0	4
510.0	0	6	0	5
511.0	0	4	1	7
512.0	0	10	1	4
513.0	0	5	0	8
514.0	0	7	1	5
515.0	0	6	2	3
516.0	0	9	1	4
517.0	0	10	3	5
518.0	0	6	0	4
519.0	0	10	0	2
520.0	0	11	1	5
521.0	0	4	0	2
522.0	0	5	2	2
523.0	0	4	1	5
524.0	0	2	0	6
525.0	0	5	0	6
526.0	0	12	1	5
527.0	0	7	0	5
528.0	0	5	1	3
529.0	0	5	1	7
530.0	0	5	1	4
531.0	0	6	0	8
532.0	0	3	1	5
533.0	0	7	0	3
534.0	0	15	1	6
535.0	0	4	0	5
536.0	0	2	0	3
537.0	0	6	1	3
538.0	0	8	0	4
539.0	0	4	1	4
540.0	0	10	1	6
541.0	0	3	1	3
542.0	0	3	0	5
543.0	0	5	2	5
544.0	0	4	0	2
545.0	0	6	0	7
546.0	0	5	2	1
547.0	0	9	0	5
548.0	0	6	1	6
549.0	0	5	0	4
550.0	0	8	0	6
551.0	0	8	1	3
552.0	0	8	0	6
553.0	0	5	0	4
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561.0	0	3	0	6
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564.0	0	5	0	5
565.0	0	5	1	5
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569.0	0	6	0	3
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572.0	0	0	0	6
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574.0	0	4	1	4
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577.0	0	5	0	6
578.0	0	5	1	6
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580.0	0	9	0	1
581.0	0	3	1	2
582.0	0	1	0	0
583.0	0	5	1	6
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585.0	0	4	0	4
586.0	0	5	0	3
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592.0	0	4	0	2
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594.0	0	4	1	4
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597.0	0	3	1	1
598.0	0	2	1	5
599.0	0	7	0	5
600.0	0	6	1	6
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605.0	0	6	1	4
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616.0	0	3	1	2
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619.0	0	5	0	5
620.0	0	4	1	4
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631.0	0	2	1	3
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649.0	0	5	0	7
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