## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-216-TP4.bam --OUTPUT POR-216-TP4.md.bam --METRICS_FILE POR-216-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 18:10:39 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	3298	18102348	12138703	0	3121	15321874	3499070	0.846412	2795533

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.003867	1133120	0	1380375
2.0	1.005414	602855	409026	622124
3.0	1.005416	315846	165371	260142
4.0	1.005416	172307	86790	118826
5.0	1.005416	103082	52196	65614
6.0	1.005416	67882	33690	43438
7.0	1.005416	48165	23019	32168
8.0	1.005416	36315	16690	25370
9.0	1.005416	28410	12526	20378
10.0	1.005416	23125	9685	17441
11.0	1.005416	19439	7437	14684
12.0	1.005416	16390	6129	12686
13.0	1.005416	14421	5145	11263
14.0	1.005416	12385	4364	9521
15.0	1.005416	11008	3602	8799
16.0	1.005416	9930	3109	7769
17.0	1.005416	8992	2692	7064
18.0	1.005416	8012	2275	6100
19.0	1.005416	7257	2080	5702
20.0	1.005416	6634	1840	5337
21.0	1.005416	5959	1670	4786
22.0	1.005416	5648	1512	4523
23.0	1.005416	5226	1299	4028
24.0	1.005416	4764	1171	3852
25.0	1.005416	4451	1090	3530
26.0	1.005416	4160	962	3217
27.0	1.005416	3856	904	3081
28.0	1.005416	3670	794	2819
29.0	1.005416	3431	731	2680
30.0	1.005416	3041	700	2498
31.0	1.005416	2993	663	2259
32.0	1.005416	2869	595	2271
33.0	1.005416	2689	583	2132
34.0	1.005416	2567	522	2007
35.0	1.005416	2384	485	1816
36.0	1.005416	2227	495	1742
37.0	1.005416	2115	462	1662
38.0	1.005416	2105	432	1623
39.0	1.005416	1981	371	1555
40.0	1.005416	1910	332	1474
41.0	1.005416	1704	343	1368
42.0	1.005416	1661	280	1326
43.0	1.005416	1605	270	1265
44.0	1.005416	1561	293	1268
45.0	1.005416	1541	233	1173
46.0	1.005416	1461	272	1117
47.0	1.005416	1390	243	1047
48.0	1.005416	1292	220	1061
49.0	1.005416	1225	196	950
50.0	1.005416	1186	207	954
51.0	1.005416	1199	206	906
52.0	1.005416	1077	196	869
53.0	1.005416	1060	186	797
54.0	1.005416	984	165	804
55.0	1.005416	991	167	817
56.0	1.005416	1002	164	728
57.0	1.005416	967	145	774
58.0	1.005416	920	137	677
59.0	1.005416	902	135	679
60.0	1.005416	841	126	708
61.0	1.005416	817	123	681
62.0	1.005416	791	120	628
63.0	1.005416	778	110	575
64.0	1.005416	728	130	574
65.0	1.005416	707	103	546
66.0	1.005416	656	101	526
67.0	1.005416	672	93	550
68.0	1.005416	597	103	473
69.0	1.005416	631	100	447
70.0	1.005416	602	90	492
71.0	1.005416	590	96	468
72.0	1.005416	618	95	452
73.0	1.005416	563	101	469
74.0	1.005416	560	77	426
75.0	1.005416	550	69	463
76.0	1.005416	485	70	394
77.0	1.005416	525	78	384
78.0	1.005416	496	72	388
79.0	1.005416	492	73	376
80.0	1.005416	454	52	378
81.0	1.005416	446	53	337
82.0	1.005416	435	52	359
83.0	1.005416	452	65	348
84.0	1.005416	417	53	319
85.0	1.005416	414	58	313
86.0	1.005416	396	49	312
87.0	1.005416	346	45	282
88.0	1.005416	417	48	306
89.0	1.005416	385	49	295
90.0	1.005416	320	52	267
91.0	1.005416	370	47	290
92.0	1.005416	371	42	271
93.0	1.005416	331	49	286
94.0	1.005416	330	40	279
95.0	1.005416	347	41	262
96.0	1.005416	346	41	236
97.0	1.005416	310	41	271
98.0	1.005416	340	42	244
99.0	1.005416	299	38	249
100.0	1.005416	337	35	238
101.0	0	308	35	236
102.0	0	274	25	201
103.0	0	283	34	217
104.0	0	293	36	193
105.0	0	254	31	211
106.0	0	258	25	223
107.0	0	224	31	214
108.0	0	231	31	206
109.0	0	216	25	190
110.0	0	230	23	166
111.0	0	226	30	188
112.0	0	220	37	194
113.0	0	242	21	170
114.0	0	253	24	170
115.0	0	199	19	171
116.0	0	209	25	173
117.0	0	219	20	171
118.0	0	212	15	150
119.0	0	190	25	154
120.0	0	196	23	152
121.0	0	220	24	164
122.0	0	181	15	139
123.0	0	178	15	151
124.0	0	204	14	152
125.0	0	196	17	133
126.0	0	197	16	138
127.0	0	184	23	124
128.0	0	163	22	109
129.0	0	166	15	127
130.0	0	198	17	141
131.0	0	162	12	126
132.0	0	162	19	144
133.0	0	133	17	146
134.0	0	154	25	122
135.0	0	159	13	110
136.0	0	147	17	115
137.0	0	154	15	117
138.0	0	154	18	106
139.0	0	161	14	98
140.0	0	144	10	108
141.0	0	161	9	108
142.0	0	133	17	102
143.0	0	140	13	97
144.0	0	160	10	121
145.0	0	131	11	94
146.0	0	121	9	93
147.0	0	156	14	108
148.0	0	131	13	101
149.0	0	125	9	98
150.0	0	104	9	81
151.0	0	110	13	94
152.0	0	118	11	89
153.0	0	107	3	90
154.0	0	125	17	87
155.0	0	99	10	78
156.0	0	107	10	96
157.0	0	129	11	89
158.0	0	102	9	87
159.0	0	90	9	86
160.0	0	92	7	101
161.0	0	87	13	77
162.0	0	108	5	82
163.0	0	95	8	85
164.0	0	108	9	89
165.0	0	104	7	77
166.0	0	95	6	74
167.0	0	99	3	59
168.0	0	104	12	71
169.0	0	78	7	73
170.0	0	88	5	58
171.0	0	86	6	62
172.0	0	101	6	73
173.0	0	96	6	58
174.0	0	99	6	66
175.0	0	78	4	60
176.0	0	74	7	71
177.0	0	83	4	57
178.0	0	72	10	62
179.0	0	79	4	76
180.0	0	91	1	51
181.0	0	81	13	62
182.0	0	84	7	58
183.0	0	77	10	66
184.0	0	79	8	54
185.0	0	71	11	72
186.0	0	80	3	54
187.0	0	61	7	56
188.0	0	73	3	63
189.0	0	70	10	58
190.0	0	84	7	48
191.0	0	65	6	60
192.0	0	65	8	57
193.0	0	83	8	52
194.0	0	73	5	50
195.0	0	59	5	43
196.0	0	78	7	42
197.0	0	59	3	47
198.0	0	66	2	38
199.0	0	64	7	47
200.0	0	74	6	52
201.0	0	59	3	53
202.0	0	55	5	43
203.0	0	74	4	51
204.0	0	70	3	61
205.0	0	64	4	39
206.0	0	56	3	50
207.0	0	48	3	54
208.0	0	47	5	38
209.0	0	55	6	39
210.0	0	61	7	46
211.0	0	58	7	48
212.0	0	74	3	52
213.0	0	64	2	45
214.0	0	51	3	35
215.0	0	53	6	40
216.0	0	55	3	42
217.0	0	60	4	34
218.0	0	44	7	45
219.0	0	49	3	39
220.0	0	41	3	37
221.0	0	62	5	40
222.0	0	46	2	54
223.0	0	55	3	35
224.0	0	40	4	33
225.0	0	48	5	27
226.0	0	45	1	45
227.0	0	50	3	45
228.0	0	45	4	39
229.0	0	59	3	52
230.0	0	36	3	33
231.0	0	54	5	32
232.0	0	38	3	47
233.0	0	45	6	35
234.0	0	40	1	27
235.0	0	50	2	33
236.0	0	49	2	39
237.0	0	45	4	34
238.0	0	61	3	41
239.0	0	43	4	27
240.0	0	46	4	32
241.0	0	51	1	37
242.0	0	47	3	31
243.0	0	46	6	27
244.0	0	43	1	35
245.0	0	36	4	38
246.0	0	40	6	26
247.0	0	45	1	30
248.0	0	34	3	23
249.0	0	52	5	28
250.0	0	30	2	39
251.0	0	46	3	25
252.0	0	33	3	20
253.0	0	38	4	34
254.0	0	31	4	30
255.0	0	39	0	34
256.0	0	42	2	37
257.0	0	32	4	25
258.0	0	37	3	14
259.0	0	41	1	26
260.0	0	37	0	36
261.0	0	28	3	25
262.0	0	29	5	23
263.0	0	28	0	27
264.0	0	29	1	25
265.0	0	40	2	23
266.0	0	30	0	22
267.0	0	40	2	27
268.0	0	44	1	15
269.0	0	36	3	28
270.0	0	34	0	30
271.0	0	27	2	17
272.0	0	22	1	19
273.0	0	32	3	28
274.0	0	35	1	24
275.0	0	31	2	20
276.0	0	32	3	27
277.0	0	24	0	30
278.0	0	27	3	14
279.0	0	32	3	19
280.0	0	29	4	21
281.0	0	26	0	17
282.0	0	22	4	32
283.0	0	30	1	32
284.0	0	27	2	28
285.0	0	29	4	16
286.0	0	25	1	26
287.0	0	41	1	19
288.0	0	33	2	22
289.0	0	26	4	19
290.0	0	28	4	22
291.0	0	20	0	22
292.0	0	26	2	17
293.0	0	20	2	20
294.0	0	31	1	15
295.0	0	22	2	14
296.0	0	26	1	18
297.0	0	32	2	14
298.0	0	18	0	17
299.0	0	19	0	22
300.0	0	21	2	22
301.0	0	22	1	21
302.0	0	24	1	18
303.0	0	24	1	22
304.0	0	24	2	16
305.0	0	25	2	14
306.0	0	23	3	25
307.0	0	18	1	20
308.0	0	12	3	10
309.0	0	24	2	18
310.0	0	24	1	18
311.0	0	23	0	15
312.0	0	26	0	20
313.0	0	16	2	24
314.0	0	20	2	13
315.0	0	27	3	12
316.0	0	20	0	17
317.0	0	19	1	16
318.0	0	18	2	18
319.0	0	18	0	18
320.0	0	24	0	17
321.0	0	25	0	17
322.0	0	15	0	13
323.0	0	16	3	23
324.0	0	18	3	16
325.0	0	26	1	17
326.0	0	17	3	15
327.0	0	20	2	13
328.0	0	25	2	15
329.0	0	16	1	18
330.0	0	21	1	12
331.0	0	15	2	17
332.0	0	16	4	14
333.0	0	15	2	13
334.0	0	20	2	22
335.0	0	14	1	11
336.0	0	16	2	11
337.0	0	13	1	19
338.0	0	27	2	16
339.0	0	15	1	8
340.0	0	16	0	14
341.0	0	21	1	7
342.0	0	18	1	17
343.0	0	21	4	18
344.0	0	18	2	14
345.0	0	17	1	16
346.0	0	15	0	12
347.0	0	19	1	16
348.0	0	17	0	12
349.0	0	20	1	13
350.0	0	17	0	13
351.0	0	15	0	11
352.0	0	13	0	14
353.0	0	15	1	14
354.0	0	15	1	8
355.0	0	20	0	15
356.0	0	16	1	12
357.0	0	20	0	8
358.0	0	10	3	9
359.0	0	15	0	15
360.0	0	12	0	15
361.0	0	16	1	10
362.0	0	11	0	15
363.0	0	28	0	10
364.0	0	13	1	16
365.0	0	15	0	12
366.0	0	16	0	18
367.0	0	13	0	11
368.0	0	21	0	13
369.0	0	12	4	9
370.0	0	17	1	6
371.0	0	18	0	12
372.0	0	12	1	11
373.0	0	10	0	15
374.0	0	18	0	12
375.0	0	11	1	14
376.0	0	26	0	15
377.0	0	16	2	16
378.0	0	18	0	16
379.0	0	19	0	10
380.0	0	15	0	16
381.0	0	11	0	15
382.0	0	9	0	12
383.0	0	17	0	10
384.0	0	10	0	6
385.0	0	11	1	11
386.0	0	11	1	8
387.0	0	10	2	14
388.0	0	20	1	6
389.0	0	13	0	11
390.0	0	12	1	11
391.0	0	16	0	11
392.0	0	14	0	10
393.0	0	13	0	5
394.0	0	16	0	9
395.0	0	12	1	4
396.0	0	11	2	12
397.0	0	13	1	5
398.0	0	13	1	8
399.0	0	14	0	10
400.0	0	19	0	6
401.0	0	9	0	8
402.0	0	13	0	13
403.0	0	7	0	8
404.0	0	13	0	5
405.0	0	14	1	14
406.0	0	15	1	13
407.0	0	13	0	14
408.0	0	7	0	6
409.0	0	6	1	15
410.0	0	13	1	13
411.0	0	6	0	8
412.0	0	12	0	8
413.0	0	17	0	7
414.0	0	14	0	9
415.0	0	9	0	9
416.0	0	11	0	8
417.0	0	9	1	7
418.0	0	8	1	14
419.0	0	8	0	8
420.0	0	8	0	4
421.0	0	10	0	13
422.0	0	11	0	4
423.0	0	16	1	15
424.0	0	12	1	10
425.0	0	9	0	5
426.0	0	8	1	11
427.0	0	14	0	8
428.0	0	11	2	6
429.0	0	5	0	7
430.0	0	13	0	12
431.0	0	9	0	8
432.0	0	6	0	5
433.0	0	13	1	5
434.0	0	7	0	9
435.0	0	5	1	7
436.0	0	6	1	8
437.0	0	9	1	9
438.0	0	7	0	13
439.0	0	9	0	7
440.0	0	14	0	8
441.0	0	8	1	6
442.0	0	10	1	6
443.0	0	14	0	6
444.0	0	8	1	8
445.0	0	9	1	12
446.0	0	10	2	8
447.0	0	8	0	13
448.0	0	8	0	9
449.0	0	12	0	8
450.0	0	14	1	8
451.0	0	14	0	7
452.0	0	12	1	5
453.0	0	7	0	6
454.0	0	12	0	5
455.0	0	9	0	7
456.0	0	13	0	7
457.0	0	9	0	6
458.0	0	12	0	10
459.0	0	15	0	5
460.0	0	12	1	6
461.0	0	12	0	4
462.0	0	4	1	10
463.0	0	10	0	6
464.0	0	10	1	6
465.0	0	7	0	2
466.0	0	9	1	2
467.0	0	11	0	9
468.0	0	12	0	4
469.0	0	9	0	10
470.0	0	10	0	7
471.0	0	14	1	5
472.0	0	9	0	6
473.0	0	6	0	11
474.0	0	11	0	5
475.0	0	9	0	5
476.0	0	5	2	9
477.0	0	12	0	11
478.0	0	11	0	3
479.0	0	8	0	5
480.0	0	9	0	0
481.0	0	8	0	2
482.0	0	16	0	4
483.0	0	9	0	9
484.0	0	7	0	6
485.0	0	4	1	8
486.0	0	5	0	5
487.0	0	8	0	4
488.0	0	6	0	4
489.0	0	10	0	8
490.0	0	5	0	7
491.0	0	8	0	6
492.0	0	10	0	9
493.0	0	10	1	9
494.0	0	3	0	9
495.0	0	9	0	6
496.0	0	8	0	5
497.0	0	6	1	4
498.0	0	4	0	6
499.0	0	8	1	3
500.0	0	5	1	1
501.0	0	9	1	4
502.0	0	7	0	2
503.0	0	12	0	6
504.0	0	7	1	5
505.0	0	6	0	5
506.0	0	4	1	3
507.0	0	6	0	3
508.0	0	8	1	8
509.0	0	5	0	6
510.0	0	4	0	4
511.0	0	4	0	6
512.0	0	9	0	8
513.0	0	5	0	9
514.0	0	12	0	10
515.0	0	7	0	0
516.0	0	8	0	5
517.0	0	10	1	2
518.0	0	11	0	6
519.0	0	5	0	7
520.0	0	7	0	3
521.0	0	5	0	7
522.0	0	4	0	6
523.0	0	2	0	3
524.0	0	4	0	6
525.0	0	6	0	3
526.0	0	7	0	6
527.0	0	5	0	7
528.0	0	8	0	4
529.0	0	3	1	2
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