## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-73-TP1.bam --OUTPUT POR-73-TP1.md.bam --METRICS_FILE POR-73-TP1.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 18:18:34 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	3810	17810130	11340685	0	3659	14599857	4110354	0.819765	3258961

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.01087	1391136	0	1772741
2.0	1.015148	689101	490703	695902
3.0	1.015166	352864	211366	259716
4.0	1.015166	195334	113105	112302
5.0	1.015166	117281	67211	61961
6.0	1.015166	76864	42348	40787
7.0	1.015166	54291	28532	30783
8.0	1.015166	39919	19739	23918
9.0	1.015166	30785	14561	19699
10.0	1.015166	24635	10591	16465
11.0	1.015166	19846	8463	13878
12.0	1.015166	16588	6629	11992
13.0	1.015166	14310	5365	10380
14.0	1.015166	12439	4574	9050
15.0	1.015166	11025	3834	8125
16.0	1.015166	9529	3165	7181
17.0	1.015166	8574	2775	6434
18.0	1.015166	7787	2510	5766
19.0	1.015166	7019	2193	5343
20.0	1.015166	6336	1862	4805
21.0	1.015166	5763	1729	4284
22.0	1.015166	5507	1504	4050
23.0	1.015166	4935	1383	3758
24.0	1.015166	4486	1278	3499
25.0	1.015166	4268	1157	3181
26.0	1.015166	3930	1056	2975
27.0	1.015166	3580	926	2744
28.0	1.015166	3430	907	2537
29.0	1.015166	3269	799	2440
30.0	1.015166	2998	739	2299
31.0	1.015166	2768	726	2091
32.0	1.015166	2719	598	1922
33.0	1.015166	2470	622	1873
34.0	1.015166	2380	593	1734
35.0	1.015166	2216	526	1628
36.0	1.015166	2097	481	1578
37.0	1.015166	2018	452	1490
38.0	1.015166	1942	423	1472
39.0	1.015166	1792	439	1371
40.0	1.015166	1800	356	1327
41.0	1.015166	1650	346	1221
42.0	1.015166	1572	366	1189
43.0	1.015166	1468	321	1121
44.0	1.015166	1351	303	1078
45.0	1.015166	1364	287	1013
46.0	1.015166	1253	266	974
47.0	1.015166	1291	270	970
48.0	1.015166	1190	234	889
49.0	1.015166	1190	249	850
50.0	1.015166	1114	212	846
51.0	1.015166	1041	206	765
52.0	1.015166	1001	183	755
53.0	1.015166	980	184	747
54.0	1.015166	962	168	717
55.0	1.015166	952	199	709
56.0	1.015166	874	167	651
57.0	1.015166	873	163	639
58.0	1.015166	858	130	607
59.0	1.015166	785	115	589
60.0	1.015166	734	140	613
61.0	1.015166	747	116	531
62.0	1.015166	741	136	580
63.0	1.015166	668	136	496
64.0	1.015166	706	127	508
65.0	1.015166	631	113	491
66.0	1.015166	635	112	479
67.0	1.015166	583	109	465
68.0	1.015166	615	97	445
69.0	1.015166	550	103	389
70.0	1.015166	549	105	421
71.0	1.015166	565	94	434
72.0	1.015166	521	89	395
73.0	1.015166	532	93	361
74.0	1.015166	502	68	367
75.0	1.015166	501	89	350
76.0	1.015166	428	83	374
77.0	1.015166	437	88	367
78.0	1.015166	438	92	343
79.0	1.015166	447	87	338
80.0	1.015166	428	77	344
81.0	1.015166	420	61	306
82.0	1.015166	422	73	263
83.0	1.015166	374	44	293
84.0	1.015166	379	63	288
85.0	1.015166	390	56	266
86.0	1.015166	372	59	268
87.0	1.015166	372	66	284
88.0	1.015166	325	52	248
89.0	1.015166	345	50	264
90.0	1.015166	324	53	231
91.0	1.015166	320	48	251
92.0	1.015166	319	56	260
93.0	1.015166	321	57	235
94.0	1.015166	298	51	218
95.0	1.015166	298	54	229
96.0	1.015166	320	36	197
97.0	1.015166	259	43	201
98.0	1.015166	288	46	214
99.0	1.015166	231	29	195
100.0	1.015166	302	41	206
101.0	0	278	30	185
102.0	0	270	28	201
103.0	0	242	41	170
104.0	0	235	36	208
105.0	0	267	34	172
106.0	0	241	43	168
107.0	0	220	37	161
108.0	0	228	28	140
109.0	0	216	26	167
110.0	0	219	30	173
111.0	0	203	26	163
112.0	0	178	20	153
113.0	0	207	27	137
114.0	0	180	24	144
115.0	0	215	25	135
116.0	0	190	33	135
117.0	0	179	28	140
118.0	0	183	24	149
119.0	0	171	30	132
120.0	0	162	27	149
121.0	0	148	18	124
122.0	0	164	19	123
123.0	0	178	12	129
124.0	0	171	25	111
125.0	0	159	22	99
126.0	0	135	27	144
127.0	0	175	16	114
128.0	0	158	21	108
129.0	0	164	22	117
130.0	0	130	21	125
131.0	0	153	24	113
132.0	0	140	29	121
133.0	0	142	13	112
134.0	0	160	21	89
135.0	0	156	11	100
136.0	0	134	20	93
137.0	0	136	21	94
138.0	0	142	21	110
139.0	0	137	18	102
140.0	0	124	13	89
141.0	0	131	13	82
142.0	0	132	10	86
143.0	0	131	16	97
144.0	0	128	10	91
145.0	0	121	17	87
146.0	0	124	10	80
147.0	0	127	9	77
148.0	0	122	15	85
149.0	0	86	13	70
150.0	0	105	8	94
151.0	0	93	15	80
152.0	0	113	13	80
153.0	0	97	17	72
154.0	0	112	17	79
155.0	0	104	16	75
156.0	0	97	10	62
157.0	0	89	14	66
158.0	0	84	6	80
159.0	0	79	12	66
160.0	0	99	9	63
161.0	0	88	7	59
162.0	0	91	6	64
163.0	0	98	8	56
164.0	0	82	9	66
165.0	0	87	15	64
166.0	0	94	11	68
167.0	0	97	9	64
168.0	0	84	4	59
169.0	0	91	9	71
170.0	0	90	6	65
171.0	0	90	11	50
172.0	0	79	9	51
173.0	0	70	11	68
174.0	0	90	10	52
175.0	0	79	6	54
176.0	0	60	8	53
177.0	0	87	16	58
178.0	0	72	8	55
179.0	0	63	6	51
180.0	0	74	16	44
181.0	0	67	5	44
182.0	0	72	5	47
183.0	0	80	8	44
184.0	0	69	12	57
185.0	0	63	8	42
186.0	0	74	9	59
187.0	0	65	8	50
188.0	0	59	11	53
189.0	0	59	8	52
190.0	0	70	8	50
191.0	0	62	4	39
192.0	0	72	6	47
193.0	0	56	12	42
194.0	0	50	11	44
195.0	0	62	4	49
196.0	0	49	6	33
197.0	0	50	5	46
198.0	0	53	9	46
199.0	0	68	5	45
200.0	0	44	3	39
201.0	0	53	4	37
202.0	0	39	2	34
203.0	0	64	2	37
204.0	0	65	5	37
205.0	0	53	5	43
206.0	0	56	4	30
207.0	0	56	7	34
208.0	0	59	4	31
209.0	0	43	5	51
210.0	0	49	2	39
211.0	0	63	5	41
212.0	0	45	3	43
213.0	0	66	4	44
214.0	0	51	9	33
215.0	0	49	5	30
216.0	0	45	2	35
217.0	0	41	7	35
218.0	0	49	6	41
219.0	0	47	6	31
220.0	0	34	4	35
221.0	0	56	6	33
222.0	0	40	7	30
223.0	0	38	3	39
224.0	0	42	6	28
225.0	0	39	3	32
226.0	0	44	3	38
227.0	0	39	3	28
228.0	0	41	7	30
229.0	0	45	4	30
230.0	0	32	4	22
231.0	0	38	5	22
232.0	0	39	8	34
233.0	0	34	5	33
234.0	0	41	4	31
235.0	0	37	1	24
236.0	0	41	6	20
237.0	0	41	3	29
238.0	0	35	2	22
239.0	0	24	8	31
240.0	0	35	3	32
241.0	0	43	2	21
242.0	0	34	1	22
243.0	0	35	6	20
244.0	0	34	3	26
245.0	0	46	5	24
246.0	0	30	3	29
247.0	0	37	2	29
248.0	0	31	1	30
249.0	0	31	4	28
250.0	0	39	3	22
251.0	0	32	3	19
252.0	0	27	4	26
253.0	0	35	3	25
254.0	0	25	4	21
255.0	0	24	5	18
256.0	0	28	3	31
257.0	0	30	5	24
258.0	0	26	2	20
259.0	0	23	5	34
260.0	0	31	3	18
261.0	0	37	0	16
262.0	0	24	2	19
263.0	0	39	4	19
264.0	0	33	0	22
265.0	0	29	2	22
266.0	0	36	3	21
267.0	0	25	1	19
268.0	0	31	3	19
269.0	0	24	4	24
270.0	0	32	6	24
271.0	0	30	1	14
272.0	0	28	1	29
273.0	0	21	3	19
274.0	0	24	2	12
275.0	0	35	3	12
276.0	0	20	1	20
277.0	0	17	3	22
278.0	0	25	1	20
279.0	0	24	2	13
280.0	0	40	2	16
281.0	0	32	1	9
282.0	0	21	2	15
283.0	0	23	1	20
284.0	0	29	3	21
285.0	0	34	4	14
286.0	0	24	0	21
287.0	0	25	1	25
288.0	0	19	0	20
289.0	0	27	3	18
290.0	0	19	0	17
291.0	0	27	1	27
292.0	0	23	3	21
293.0	0	22	2	21
294.0	0	34	3	21
295.0	0	27	4	14
296.0	0	22	2	13
297.0	0	22	1	20
298.0	0	28	1	9
299.0	0	23	1	15
300.0	0	22	1	18
301.0	0	21	1	14
302.0	0	19	3	14
303.0	0	23	0	9
304.0	0	23	3	15
305.0	0	24	1	14
306.0	0	18	1	10
307.0	0	23	0	15
308.0	0	15	4	14
309.0	0	8	0	14
310.0	0	20	0	21
311.0	0	22	1	13
312.0	0	23	2	11
313.0	0	19	2	11
314.0	0	17	3	14
315.0	0	17	0	14
316.0	0	11	1	16
317.0	0	19	2	11
318.0	0	19	2	12
319.0	0	18	1	9
320.0	0	24	1	13
321.0	0	18	1	13
322.0	0	20	1	12
323.0	0	9	1	11
324.0	0	9	1	11
325.0	0	20	0	21
326.0	0	17	2	12
327.0	0	11	1	12
328.0	0	17	4	12
329.0	0	17	2	12
330.0	0	13	0	11
331.0	0	23	0	8
332.0	0	13	3	11
333.0	0	20	3	8
334.0	0	17	2	11
335.0	0	15	0	19
336.0	0	9	2	10
337.0	0	13	1	12
338.0	0	18	2	10
339.0	0	12	0	16
340.0	0	15	1	21
341.0	0	18	2	10
342.0	0	19	3	10
343.0	0	20	5	14
344.0	0	18	0	14
345.0	0	16	2	10
346.0	0	20	0	13
347.0	0	12	2	13
348.0	0	17	3	12
349.0	0	16	5	11
350.0	0	16	0	8
351.0	0	11	2	9
352.0	0	18	1	13
353.0	0	12	2	16
354.0	0	11	0	6
355.0	0	11	2	5
356.0	0	9	0	11
357.0	0	12	1	7
358.0	0	17	2	16
359.0	0	7	0	16
360.0	0	15	0	13
361.0	0	17	2	14
362.0	0	14	0	3
363.0	0	14	2	8
364.0	0	19	2	12
365.0	0	11	1	6
366.0	0	16	2	11
367.0	0	8	0	12
368.0	0	13	0	8
369.0	0	6	1	13
370.0	0	15	1	10
371.0	0	14	1	8
372.0	0	9	0	9
373.0	0	17	3	6
374.0	0	16	1	8
375.0	0	15	1	7
376.0	0	6	0	12
377.0	0	14	1	7
378.0	0	12	0	6
379.0	0	14	2	7
380.0	0	12	0	7
381.0	0	14	0	8
382.0	0	13	0	13
383.0	0	5	2	11
384.0	0	8	0	13
385.0	0	21	1	10
386.0	0	16	3	13
387.0	0	18	0	8
388.0	0	8	2	7
389.0	0	13	1	11
390.0	0	13	0	6
391.0	0	10	1	4
392.0	0	7	2	12
393.0	0	12	1	4
394.0	0	7	1	5
395.0	0	15	0	8
396.0	0	17	0	2
397.0	0	12	0	10
398.0	0	9	3	8
399.0	0	14	1	8
400.0	0	11	0	6
401.0	0	14	0	5
402.0	0	11	3	7
403.0	0	11	0	3
404.0	0	8	0	7
405.0	0	9	0	4
406.0	0	8	1	8
407.0	0	6	0	7
408.0	0	13	1	5
409.0	0	9	0	10
410.0	0	16	1	4
411.0	0	8	0	6
412.0	0	7	1	6
413.0	0	10	0	3
414.0	0	7	0	6
415.0	0	5	1	1
416.0	0	10	0	8
417.0	0	12	0	8
418.0	0	15	0	6
419.0	0	11	0	6
420.0	0	2	1	5
421.0	0	5	0	12
422.0	0	7	0	6
423.0	0	11	1	12
424.0	0	11	0	7
425.0	0	11	0	12
426.0	0	7	1	6
427.0	0	3	0	6
428.0	0	8	0	8
429.0	0	7	1	9
430.0	0	15	0	3
431.0	0	13	1	5
432.0	0	8	2	6
433.0	0	7	2	8
434.0	0	8	1	7
435.0	0	8	0	5
436.0	0	8	1	7
437.0	0	2	0	9
438.0	0	7	1	3
439.0	0	7	0	7
440.0	0	10	1	5
441.0	0	3	0	9
442.0	0	6	0	10
443.0	0	15	0	7
444.0	0	6	0	9
445.0	0	8	0	7
446.0	0	11	0	4
447.0	0	10	2	7
448.0	0	8	1	3
449.0	0	7	0	9
450.0	0	7	1	4
451.0	0	5	0	9
452.0	0	7	0	2
453.0	0	12	1	5
454.0	0	7	0	7
455.0	0	10	0	3
456.0	0	8	1	5
457.0	0	6	1	6
458.0	0	4	0	2
459.0	0	6	1	5
460.0	0	8	0	6
461.0	0	5	0	3
462.0	0	5	2	8
463.0	0	7	0	7
464.0	0	8	3	3
465.0	0	8	1	6
466.0	0	6	0	7
467.0	0	6	1	5
468.0	0	6	1	7
469.0	0	3	1	5
470.0	0	8	1	2
471.0	0	3	2	2
472.0	0	9	0	7
473.0	0	11	0	5
474.0	0	12	1	7
475.0	0	7	0	7
476.0	0	6	0	4
477.0	0	6	1	3
478.0	0	3	0	2
479.0	0	5	1	1
480.0	0	4	0	2
481.0	0	9	1	9
482.0	0	11	0	4
483.0	0	7	0	8
484.0	0	6	0	6
485.0	0	9	0	7
486.0	0	9	1	4
487.0	0	8	0	5
488.0	0	6	0	8
489.0	0	7	2	1
490.0	0	6	0	2
491.0	0	2	0	3
492.0	0	7	0	3
493.0	0	7	0	2
494.0	0	4	0	2
495.0	0	4	0	9
496.0	0	4	0	6
497.0	0	4	0	5
498.0	0	7	0	5
499.0	0	6	0	4
500.0	0	4	0	4
501.0	0	3	0	10
502.0	0	3	1	8
503.0	0	7	0	4
504.0	0	7	1	2
505.0	0	4	1	2
506.0	0	4	2	10
507.0	0	5	0	8
508.0	0	7	0	3
509.0	0	9	1	4
510.0	0	2	1	2
511.0	0	4	0	4
512.0	0	7	0	5
513.0	0	6	0	1
514.0	0	2	0	3
515.0	0	7	0	8
516.0	0	10	0	7
517.0	0	7	0	7
518.0	0	3	0	7
519.0	0	7	0	6
520.0	0	4	1	3
521.0	0	2	0	4
522.0	0	9	0	2
523.0	0	9	0	7
524.0	0	8	0	1
525.0	0	7	1	1
526.0	0	2	2	4
527.0	0	5	0	4
528.0	0	10	0	1
529.0	0	5	0	2
530.0	0	3	1	4
531.0	0	3	1	2
532.0	0	5	0	5
533.0	0	8	0	5
534.0	0	4	1	2
535.0	0	6	0	5
536.0	0	9	1	3
537.0	0	10	0	1
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