## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-236-TP1.bam --OUTPUT POR-236-TP1.md.bam --METRICS_FILE POR-236-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 18:15:29 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	4568	18184285	10243644	0	4410	13744334	4360044	0.755862	4684974

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.033426	2097603	0	2698054
2.0	1.054737	999171	678111	961276
3.0	1.055177	485239	278546	319003
4.0	1.055186	252733	144248	122745
5.0	1.055186	144895	81317	62562
6.0	1.055186	89630	49701	39999
7.0	1.055186	60351	31396	29199
8.0	1.055186	42867	20854	22548
9.0	1.055186	31730	14601	17859
10.0	1.055186	24541	10535	15034
11.0	1.055186	19419	7844	12618
12.0	1.055186	16179	6075	10707
13.0	1.055186	13396	4808	9273
14.0	1.055186	11408	3926	8073
15.0	1.055186	9878	3247	7182
16.0	1.055186	8601	2864	6272
17.0	1.055186	7689	2526	5719
18.0	1.055186	6902	2088	5113
19.0	1.055186	6296	1869	4612
20.0	1.055186	5674	1655	4225
21.0	1.055186	5159	1471	3676
22.0	1.055186	4717	1345	3505
23.0	1.055186	4354	1150	3255
24.0	1.055186	4011	1092	2969
25.0	1.055186	3741	989	2810
26.0	1.055186	3472	862	2630
27.0	1.055186	3218	789	2292
28.0	1.055186	3074	744	2285
29.0	1.055186	2722	648	2091
30.0	1.055186	2596	604	1963
31.0	1.055186	2405	580	1820
32.0	1.055186	2322	514	1729
33.0	1.055186	2109	491	1643
34.0	1.055186	2023	475	1457
35.0	1.055186	1890	453	1429
36.0	1.055186	1792	403	1341
37.0	1.055186	1783	403	1307
38.0	1.055186	1634	331	1167
39.0	1.055186	1586	335	1144
40.0	1.055186	1539	326	1127
41.0	1.055186	1402	305	1037
42.0	1.055186	1346	291	988
43.0	1.055186	1315	241	901
44.0	1.055186	1173	248	883
45.0	1.055186	1165	204	838
46.0	1.055186	1052	236	781
47.0	1.055186	1029	206	778
48.0	1.055186	1047	218	766
49.0	1.055186	983	181	723
50.0	1.055186	951	195	681
51.0	1.055186	878	184	650
52.0	1.055186	850	180	648
53.0	1.055186	822	171	580
54.0	1.055186	840	150	574
55.0	1.055186	746	144	573
56.0	1.055186	741	151	533
57.0	1.055186	682	124	535
58.0	1.055186	632	123	546
59.0	1.055186	650	131	481
60.0	1.055186	662	106	495
61.0	1.055186	617	105	438
62.0	1.055186	582	119	439
63.0	1.055186	568	109	423
64.0	1.055186	582	99	382
65.0	1.055186	537	113	409
66.0	1.055186	496	90	402
67.0	1.055186	498	96	358
68.0	1.055186	472	80	370
69.0	1.055186	458	79	381
70.0	1.055186	435	80	376
71.0	1.055186	423	76	342
72.0	1.055186	459	62	295
73.0	1.055186	454	64	306
74.0	1.055186	433	81	276
75.0	1.055186	415	68	283
76.0	1.055186	434	59	305
77.0	1.055186	373	87	286
78.0	1.055186	380	63	254
79.0	1.055186	344	47	256
80.0	1.055186	347	51	270
81.0	1.055186	365	63	255
82.0	1.055186	317	53	228
83.0	1.055186	286	53	237
84.0	1.055186	306	43	247
85.0	1.055186	335	65	217
86.0	1.055186	303	64	217
87.0	1.055186	298	55	212
88.0	1.055186	270	46	214
89.0	1.055186	272	41	198
90.0	1.055186	267	41	209
91.0	1.055186	243	41	210
92.0	1.055186	245	46	162
93.0	1.055186	264	46	205
94.0	1.055186	247	38	175
95.0	1.055186	231	27	183
96.0	1.055186	241	36	184
97.0	1.055186	245	33	196
98.0	1.055186	215	24	161
99.0	1.055186	212	29	155
100.0	1.055186	211	25	169
101.0	0	219	36	159
102.0	0	229	27	145
103.0	0	219	31	150
104.0	0	211	29	156
105.0	0	199	25	132
106.0	0	191	28	141
107.0	0	217	29	143
108.0	0	213	26	139
109.0	0	196	17	124
110.0	0	174	28	124
111.0	0	172	33	133
112.0	0	190	24	137
113.0	0	163	18	110
114.0	0	168	20	107
115.0	0	153	18	105
116.0	0	119	23	101
117.0	0	183	28	105
118.0	0	138	25	108
119.0	0	149	26	125
120.0	0	141	21	85
121.0	0	142	11	76
122.0	0	155	15	93
123.0	0	106	20	91
124.0	0	118	22	99
125.0	0	118	28	101
126.0	0	128	15	104
127.0	0	121	14	80
128.0	0	113	23	104
129.0	0	121	19	97
130.0	0	114	20	75
131.0	0	121	9	92
132.0	0	107	11	80
133.0	0	105	15	78
134.0	0	114	13	97
135.0	0	105	14	80
136.0	0	101	16	97
137.0	0	106	13	72
138.0	0	106	14	67
139.0	0	79	18	72
140.0	0	94	11	92
141.0	0	115	12	68
142.0	0	116	15	63
143.0	0	97	13	88
144.0	0	103	9	71
145.0	0	103	13	55
146.0	0	99	10	58
147.0	0	93	15	72
148.0	0	85	5	65
149.0	0	115	11	54
150.0	0	83	11	67
151.0	0	87	10	61
152.0	0	76	14	54
153.0	0	93	10	67
154.0	0	77	9	55
155.0	0	82	13	58
156.0	0	89	8	68
157.0	0	78	8	63
158.0	0	70	7	67
159.0	0	97	7	52
160.0	0	92	9	65
161.0	0	74	12	50
162.0	0	66	7	47
163.0	0	79	7	52
164.0	0	82	7	49
165.0	0	71	9	65
166.0	0	80	7	62
167.0	0	72	5	53
168.0	0	60	8	63
169.0	0	68	5	54
170.0	0	71	9	39
171.0	0	57	3	39
172.0	0	83	6	45
173.0	0	67	7	40
174.0	0	64	11	45
175.0	0	65	9	60
176.0	0	55	4	51
177.0	0	56	9	47
178.0	0	64	8	44
179.0	0	67	8	44
180.0	0	68	6	48
181.0	0	54	9	52
182.0	0	57	1	49
183.0	0	44	6	32
184.0	0	61	6	36
185.0	0	63	6	40
186.0	0	53	5	28
187.0	0	46	9	42
188.0	0	40	6	42
189.0	0	59	2	33
190.0	0	55	5	42
191.0	0	58	9	37
192.0	0	47	7	36
193.0	0	42	6	26
194.0	0	31	5	29
195.0	0	49	5	27
196.0	0	35	8	37
197.0	0	38	5	27
198.0	0	46	6	30
199.0	0	38	7	28
200.0	0	58	2	26
201.0	0	39	6	33
202.0	0	33	6	29
203.0	0	43	7	30
204.0	0	44	4	27
205.0	0	32	9	24
206.0	0	41	4	33
207.0	0	51	5	30
208.0	0	39	5	23
209.0	0	36	2	23
210.0	0	38	4	25
211.0	0	48	7	24
212.0	0	47	6	25
213.0	0	40	4	35
214.0	0	42	4	23
215.0	0	40	4	20
216.0	0	42	8	24
217.0	0	43	2	22
218.0	0	41	2	25
219.0	0	33	4	17
220.0	0	39	4	28
221.0	0	38	2	31
222.0	0	45	7	27
223.0	0	27	6	24
224.0	0	36	3	27
225.0	0	36	2	27
226.0	0	38	3	29
227.0	0	41	3	19
228.0	0	31	4	22
229.0	0	29	4	19
230.0	0	37	5	21
231.0	0	30	2	18
232.0	0	31	2	17
233.0	0	34	3	20
234.0	0	30	5	16
235.0	0	27	5	14
236.0	0	30	2	18
237.0	0	17	2	22
238.0	0	34	1	28
239.0	0	40	6	24
240.0	0	25	0	18
241.0	0	28	2	25
242.0	0	19	6	16
243.0	0	20	4	19
244.0	0	31	0	15
245.0	0	22	3	19
246.0	0	24	3	19
247.0	0	26	1	21
248.0	0	23	2	24
249.0	0	22	5	17
250.0	0	24	1	26
251.0	0	33	4	21
252.0	0	26	4	21
253.0	0	20	2	15
254.0	0	29	1	13
255.0	0	28	4	17
256.0	0	28	5	14
257.0	0	26	2	15
258.0	0	22	3	20
259.0	0	25	5	23
260.0	0	17	1	15
261.0	0	28	2	18
262.0	0	15	3	16
263.0	0	23	2	8
264.0	0	26	1	13
265.0	0	20	1	22
266.0	0	18	2	24
267.0	0	15	6	14
268.0	0	15	0	23
269.0	0	18	1	18
270.0	0	21	2	15
271.0	0	16	3	11
272.0	0	17	1	15
273.0	0	21	3	13
274.0	0	26	2	20
275.0	0	18	2	11
276.0	0	23	1	9
277.0	0	33	4	16
278.0	0	28	0	16
279.0	0	20	1	13
280.0	0	17	1	11
281.0	0	24	2	13
282.0	0	21	3	16
283.0	0	28	1	21
284.0	0	18	1	19
285.0	0	20	2	10
286.0	0	18	2	14
287.0	0	24	1	11
288.0	0	19	0	17
289.0	0	12	0	18
290.0	0	17	1	15
291.0	0	14	2	23
292.0	0	14	0	19
293.0	0	18	2	8
294.0	0	18	3	12
295.0	0	19	4	14
296.0	0	18	1	13
297.0	0	20	5	16
298.0	0	22	0	18
299.0	0	15	0	18
300.0	0	16	1	9
301.0	0	12	2	11
302.0	0	13	1	14
303.0	0	17	2	12
304.0	0	18	0	6
305.0	0	19	2	15
306.0	0	20	2	9
307.0	0	20	2	8
308.0	0	18	0	15
309.0	0	19	1	12
310.0	0	13	0	18
311.0	0	13	4	10
312.0	0	15	1	10
313.0	0	16	1	13
314.0	0	19	2	6
315.0	0	13	1	12
316.0	0	14	1	12
317.0	0	17	1	6
318.0	0	18	0	11
319.0	0	15	1	17
320.0	0	12	1	6
321.0	0	9	2	13
322.0	0	17	2	8
323.0	0	15	1	12
324.0	0	19	1	8
325.0	0	15	2	8
326.0	0	15	3	13
327.0	0	11	0	9
328.0	0	13	1	6
329.0	0	11	1	9
330.0	0	20	4	11
331.0	0	6	1	7
332.0	0	11	0	7
333.0	0	18	0	8
334.0	0	12	1	13
335.0	0	9	0	9
336.0	0	8	0	15
337.0	0	22	0	10
338.0	0	12	0	8
339.0	0	13	1	5
340.0	0	7	1	13
341.0	0	10	3	5
342.0	0	14	0	10
343.0	0	14	2	14
344.0	0	12	1	8
345.0	0	12	0	7
346.0	0	16	2	6
347.0	0	12	0	11
348.0	0	13	2	7
349.0	0	12	1	11
350.0	0	10	0	12
351.0	0	13	1	9
352.0	0	11	0	4
353.0	0	9	3	5
354.0	0	9	0	10
355.0	0	11	1	7
356.0	0	9	1	7
357.0	0	9	0	4
358.0	0	8	1	8
359.0	0	15	2	12
360.0	0	5	0	8
361.0	0	10	2	6
362.0	0	7	0	3
363.0	0	6	2	5
364.0	0	16	1	11
365.0	0	9	1	6
366.0	0	10	0	9
367.0	0	11	2	5
368.0	0	8	2	11
369.0	0	14	0	4
370.0	0	6	3	9
371.0	0	15	2	5
372.0	0	7	1	4
373.0	0	9	0	9
374.0	0	11	0	12
375.0	0	8	2	5
376.0	0	9	0	11
377.0	0	14	3	6
378.0	0	11	0	13
379.0	0	9	0	9
380.0	0	15	0	7
381.0	0	12	0	6
382.0	0	6	0	5
383.0	0	4	0	4
384.0	0	15	0	5
385.0	0	13	1	8
386.0	0	8	0	5
387.0	0	11	0	6
388.0	0	8	1	7
389.0	0	6	0	9
390.0	0	13	3	5
391.0	0	8	0	3
392.0	0	11	0	5
393.0	0	5	1	5
394.0	0	11	0	4
395.0	0	10	4	10
396.0	0	4	0	3
397.0	0	6	0	10
398.0	0	9	0	7
399.0	0	8	0	8
400.0	0	3	0	6
401.0	0	3	0	6
402.0	0	5	1	9
403.0	0	7	0	7
404.0	0	7	1	5
405.0	0	11	0	5
406.0	0	10	0	10
407.0	0	10	1	4
408.0	0	10	2	7
409.0	0	3	0	5
410.0	0	6	0	7
411.0	0	3	0	7
412.0	0	5	1	6
413.0	0	5	0	9
414.0	0	7	0	7
415.0	0	7	0	1
416.0	0	7	0	6
417.0	0	9	0	5
418.0	0	4	1	9
419.0	0	6	1	5
420.0	0	9	1	6
421.0	0	11	0	7
422.0	0	7	0	3
423.0	0	11	1	4
424.0	0	4	2	4
425.0	0	10	0	6
426.0	0	6	0	4
427.0	0	11	0	2
428.0	0	5	0	7
429.0	0	5	0	4
430.0	0	13	0	1
431.0	0	6	1	4
432.0	0	6	1	9
433.0	0	10	2	3
434.0	0	10	0	4
435.0	0	6	0	6
436.0	0	6	0	6
437.0	0	9	0	0
438.0	0	9	1	7
439.0	0	7	2	5
440.0	0	9	0	4
441.0	0	10	0	4
442.0	0	5	2	4
443.0	0	6	1	8
444.0	0	5	1	9
445.0	0	6	4	5
446.0	0	5	1	9
447.0	0	3	0	2
448.0	0	11	1	2
449.0	0	7	0	3
450.0	0	8	0	3
451.0	0	6	1	4
452.0	0	8	0	3
453.0	0	6	0	3
454.0	0	6	0	4
455.0	0	4	1	1
456.0	0	7	0	4
457.0	0	7	0	4
458.0	0	9	1	2
459.0	0	2	1	8
460.0	0	5	0	7
461.0	0	6	2	4
462.0	0	6	1	5
463.0	0	5	0	4
464.0	0	10	0	2
465.0	0	2	0	1
466.0	0	1	1	4
467.0	0	9	0	4
468.0	0	4	0	2
469.0	0	7	0	2
470.0	0	6	2	1
471.0	0	1	0	6
472.0	0	5	0	5
473.0	0	3	1	2
474.0	0	7	1	4
475.0	0	9	0	4
476.0	0	4	0	0
477.0	0	2	3	5
478.0	0	6	1	3
479.0	0	4	0	1
480.0	0	2	0	3
481.0	0	6	0	2
482.0	0	2	0	4
483.0	0	4	1	5
484.0	0	3	0	8
485.0	0	8	2	3
486.0	0	5	0	5
487.0	0	9	0	4
488.0	0	2	0	3
489.0	0	7	0	5
490.0	0	3	0	6
491.0	0	1	0	4
492.0	0	3	0	4
493.0	0	5	0	2
494.0	0	7	0	3
495.0	0	5	0	6
496.0	0	5	0	7
497.0	0	6	0	3
498.0	0	3	0	2
499.0	0	1	0	2
500.0	0	3	1	7
501.0	0	6	0	4
502.0	0	5	0	2
503.0	0	2	0	1
504.0	0	5	0	2
505.0	0	3	0	4
506.0	0	4	0	6
507.0	0	7	0	5
508.0	0	3	0	3
509.0	0	2	0	3
510.0	0	3	0	5
511.0	0	2	0	5
512.0	0	4	0	4
513.0	0	6	0	3
514.0	0	3	0	4
515.0	0	3	1	1
516.0	0	7	0	5
517.0	0	7	0	2
518.0	0	1	0	4
519.0	0	6	0	3
520.0	0	2	0	3
521.0	0	3	0	3
522.0	0	6	0	6
523.0	0	2	0	3
524.0	0	5	1	3
525.0	0	6	0	3
526.0	0	5	1	4
527.0	0	3	0	6
528.0	0	4	0	2
529.0	0	4	0	6
530.0	0	5	0	0
531.0	0	4	0	2
532.0	0	7	0	4
533.0	0	2	0	2
534.0	0	4	0	3
535.0	0	6	0	6
536.0	0	4	0	0
537.0	0	8	0	4
538.0	0	3	0	2
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