## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-72-TP1.bam --OUTPUT POR-72-TP1.md.bam --METRICS_FILE POR-72-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 18:17:31 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	552	12788535	6636063	0	327	9297515	3186567	0.727017	3792603

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.049101	1254560	0	1636191
2.0	1.085108	830630	570704	943707
3.0	1.086344	505159	244432	442588
4.0	1.086387	297209	130410	190049
5.0	1.086388	177117	77002	84802
6.0	1.086388	108955	47932	42963
7.0	1.086388	71231	30748	25723
8.0	1.086388	47936	20313	18048
9.0	1.086388	34230	13512	13331
10.0	1.086388	25133	9369	10528
11.0	1.086388	18797	6637	8517
12.0	1.086388	14610	4773	6986
13.0	1.086388	11452	3552	5880
14.0	1.086388	9193	2733	5014
15.0	1.086388	7779	2196	4387
16.0	1.086388	6446	1634	3951
17.0	1.086388	5547	1329	3402
18.0	1.086388	4578	1130	2989
19.0	1.086388	4091	927	2631
20.0	1.086388	3559	832	2402
21.0	1.086388	3291	675	2184
22.0	1.086388	2950	581	2001
23.0	1.086388	2514	545	1722
24.0	1.086388	2399	477	1614
25.0	1.086388	2148	431	1463
26.0	1.086388	2032	386	1369
27.0	1.086388	1811	366	1286
28.0	1.086388	1648	320	1130
29.0	1.086388	1549	273	1088
30.0	1.086388	1365	268	972
31.0	1.086388	1265	206	903
32.0	1.086388	1208	206	926
33.0	1.086388	1224	176	797
34.0	1.086388	1101	202	790
35.0	1.086388	1024	154	720
36.0	1.086388	975	162	699
37.0	1.086388	873	161	598
38.0	1.086388	867	173	544
39.0	1.086388	784	107	552
40.0	1.086388	730	101	539
41.0	1.086388	726	104	514
42.0	1.086388	669	97	471
43.0	1.086388	638	92	417
44.0	1.086388	597	105	412
45.0	1.086388	599	84	403
46.0	1.086388	504	84	427
47.0	1.086388	522	85	364
48.0	1.086388	474	67	398
49.0	1.086388	498	76	348
50.0	1.086388	473	60	328
51.0	1.086388	418	55	294
52.0	1.086388	395	48	300
53.0	1.086388	375	56	294
54.0	1.086388	392	52	265
55.0	1.086388	334	55	242
56.0	1.086388	342	40	247
57.0	1.086388	338	38	245
58.0	1.086388	324	39	230
59.0	1.086388	286	33	203
60.0	1.086388	262	39	180
61.0	1.086388	281	35	216
62.0	1.086388	269	30	183
63.0	1.086388	289	34	207
64.0	1.086388	258	25	165
65.0	1.086388	238	33	163
66.0	1.086388	218	31	177
67.0	1.086388	234	30	152
68.0	1.086388	241	24	149
69.0	1.086388	197	30	169
70.0	1.086388	185	34	138
71.0	1.086388	206	28	136
72.0	1.086388	185	22	141
73.0	1.086388	190	18	126
74.0	1.086388	195	18	128
75.0	1.086388	146	21	118
76.0	1.086388	155	21	129
77.0	1.086388	170	16	118
78.0	1.086388	174	14	129
79.0	1.086388	152	23	105
80.0	1.086388	137	12	113
81.0	1.086388	143	20	128
82.0	1.086388	166	24	102
83.0	1.086388	142	12	90
84.0	1.086388	129	16	93
85.0	1.086388	144	10	79
86.0	1.086388	130	13	95
87.0	1.086388	133	11	90
88.0	1.086388	125	13	92
89.0	1.086388	98	8	74
90.0	1.086388	110	15	93
91.0	1.086388	116	13	84
92.0	1.086388	105	12	83
93.0	1.086388	110	11	66
94.0	1.086388	114	9	76
95.0	1.086388	93	14	69
96.0	1.086388	98	11	93
97.0	1.086388	108	8	65
98.0	1.086388	83	10	54
99.0	1.086388	83	11	61
100.0	1.086388	86	13	55
101.0	0	74	7	68
102.0	0	76	8	49
103.0	0	94	11	68
104.0	0	72	3	54
105.0	0	68	8	43
106.0	0	77	7	59
107.0	0	74	6	49
108.0	0	75	9	54
109.0	0	69	10	63
110.0	0	64	3	48
111.0	0	73	11	46
112.0	0	63	6	48
113.0	0	77	6	51
114.0	0	61	9	44
115.0	0	72	3	54
116.0	0	63	9	43
117.0	0	52	9	53
118.0	0	54	5	36
119.0	0	72	7	35
120.0	0	65	6	43
121.0	0	58	10	46
122.0	0	55	3	39
123.0	0	65	6	39
124.0	0	45	5	32
125.0	0	53	3	26
126.0	0	43	7	26
127.0	0	58	4	42
128.0	0	50	4	39
129.0	0	47	3	28
130.0	0	50	1	35
131.0	0	48	2	30
132.0	0	35	5	19
133.0	0	44	7	26
134.0	0	46	2	48
135.0	0	42	3	33
136.0	0	37	4	36
137.0	0	45	1	21
138.0	0	44	2	35
139.0	0	38	4	25
140.0	0	57	2	18
141.0	0	39	3	33
142.0	0	32	2	30
143.0	0	29	2	23
144.0	0	30	2	22
145.0	0	38	3	31
146.0	0	39	0	18
147.0	0	38	4	27
148.0	0	32	1	27
149.0	0	30	0	20
150.0	0	47	1	20
151.0	0	39	3	14
152.0	0	28	7	27
153.0	0	14	1	17
154.0	0	21	6	20
155.0	0	28	2	24
156.0	0	29	1	26
157.0	0	35	2	20
158.0	0	38	1	14
159.0	0	23	2	22
160.0	0	30	4	12
161.0	0	31	0	34
162.0	0	31	2	20
163.0	0	17	1	15
164.0	0	21	2	14
165.0	0	25	1	9
166.0	0	18	0	20
167.0	0	15	0	11
168.0	0	22	1	21
169.0	0	26	1	11
170.0	0	20	2	24
171.0	0	18	1	14
172.0	0	17	0	17
173.0	0	20	1	17
174.0	0	22	2	15
175.0	0	24	1	15
176.0	0	25	3	14
177.0	0	26	4	15
178.0	0	21	2	6
179.0	0	21	0	15
180.0	0	18	2	13
181.0	0	20	2	15
182.0	0	14	0	14
183.0	0	21	1	20
184.0	0	19	1	11
185.0	0	22	1	9
186.0	0	24	2	11
187.0	0	14	0	9
188.0	0	16	1	15
189.0	0	21	0	6
190.0	0	17	0	18
191.0	0	10	1	13
192.0	0	16	0	12
193.0	0	14	1	14
194.0	0	18	0	9
195.0	0	18	1	13
196.0	0	21	0	10
197.0	0	12	0	5
198.0	0	13	0	11
199.0	0	14	0	11
200.0	0	13	1	11
201.0	0	12	0	4
202.0	0	19	3	6
203.0	0	18	0	8
204.0	0	10	1	9
205.0	0	17	1	9
206.0	0	16	1	9
207.0	0	4	1	9
208.0	0	10	1	9
209.0	0	19	1	12
210.0	0	12	1	10
211.0	0	13	0	12
212.0	0	6	0	10
213.0	0	10	0	4
214.0	0	16	2	11
215.0	0	17	2	10
216.0	0	10	0	2
217.0	0	10	0	12
218.0	0	12	2	14
219.0	0	7	4	4
220.0	0	12	0	10
221.0	0	11	2	11
222.0	0	11	0	6
223.0	0	7	1	6
224.0	0	8	2	9
225.0	0	7	2	5
226.0	0	14	0	10
227.0	0	8	0	10
228.0	0	5	1	8
229.0	0	8	1	9
230.0	0	12	0	8
231.0	0	16	0	7
232.0	0	14	1	10
233.0	0	11	1	8
234.0	0	13	1	6
235.0	0	11	1	7
236.0	0	14	0	10
237.0	0	9	0	12
238.0	0	6	1	3
239.0	0	6	1	13
240.0	0	7	0	5
241.0	0	13	0	9
242.0	0	9	0	3
243.0	0	9	2	5
244.0	0	5	0	8
245.0	0	6	1	9
246.0	0	3	0	10
247.0	0	11	1	6
248.0	0	8	0	12
249.0	0	11	1	5
250.0	0	12	0	6
251.0	0	7	0	6
252.0	0	6	0	4
253.0	0	6	0	9
254.0	0	11	0	7
255.0	0	14	0	4
256.0	0	10	1	2
257.0	0	7	0	1
258.0	0	1	0	6
259.0	0	8	1	3
260.0	0	9	0	9
261.0	0	7	2	4
262.0	0	7	1	9
263.0	0	9	1	6
264.0	0	5	0	6
265.0	0	6	1	7
266.0	0	7	0	7
267.0	0	4	0	5
268.0	0	9	0	3
269.0	0	7	0	3
270.0	0	10	0	4
271.0	0	7	1	10
272.0	0	6	0	5
273.0	0	8	0	2
274.0	0	10	0	6
275.0	0	7	0	5
276.0	0	7	0	3
277.0	0	6	0	5
278.0	0	4	0	9
279.0	0	7	1	4
280.0	0	7	0	3
281.0	0	7	0	3
282.0	0	8	2	6
283.0	0	4	0	4
284.0	0	4	1	4
285.0	0	8	0	2
286.0	0	2	0	2
287.0	0	9	0	5
288.0	0	1	0	2
289.0	0	5	0	5
290.0	0	6	0	3
291.0	0	5	0	4
292.0	0	6	0	7
293.0	0	7	1	3
294.0	0	7	1	6
295.0	0	6	0	3
296.0	0	7	0	6
297.0	0	7	0	3
298.0	0	3	1	4
299.0	0	4	1	2
300.0	0	7	0	2
301.0	0	8	0	5
302.0	0	7	0	2
303.0	0	7	0	3
304.0	0	5	0	2
305.0	0	5	0	4
306.0	0	4	0	1
307.0	0	4	0	4
308.0	0	4	0	2
309.0	0	3	0	2
310.0	0	7	0	3
311.0	0	2	0	5
312.0	0	4	0	3
313.0	0	9	1	3
314.0	0	8	0	2
315.0	0	6	0	3
316.0	0	4	0	0
317.0	0	3	0	4
318.0	0	5	0	4
319.0	0	8	0	6
320.0	0	6	0	3
321.0	0	5	0	1
322.0	0	4	0	4
323.0	0	5	0	1
324.0	0	5	0	3
325.0	0	5	0	1
326.0	0	4	0	2
327.0	0	3	0	5
328.0	0	4	0	4
329.0	0	5	0	6
330.0	0	4	0	2
331.0	0	6	0	4
332.0	0	6	0	1
333.0	0	5	0	1
334.0	0	5	0	1
335.0	0	4	1	2
336.0	0	4	1	2
337.0	0	3	1	2
338.0	0	8	0	3
339.0	0	4	0	5
340.0	0	4	0	2
341.0	0	2	0	1
342.0	0	3	0	2
343.0	0	5	0	8
344.0	0	5	0	2
345.0	0	1	1	1
346.0	0	2	0	4
347.0	0	5	0	3
348.0	0	3	0	0
349.0	0	3	0	1
350.0	0	6	0	0
351.0	0	4	1	6
352.0	0	0	0	3
353.0	0	3	0	3
354.0	0	4	0	1
355.0	0	3	0	3
356.0	0	4	0	1
357.0	0	4	0	1
358.0	0	3	0	0
359.0	0	3	0	5
360.0	0	3	1	2
361.0	0	1	0	6
362.0	0	6	0	1
363.0	0	4	1	3
364.0	0	1	0	1
365.0	0	1	1	2
366.0	0	4	0	2
367.0	0	3	0	3
368.0	0	3	0	2
369.0	0	5	0	1
370.0	0	1	0	2
371.0	0	1	1	0
372.0	0	2	0	2
373.0	0	9	0	1
374.0	0	5	0	2
375.0	0	3	0	1
376.0	0	5	0	3
377.0	0	3	0	3
379.0	0	4	0	2
380.0	0	3	0	2
381.0	0	2	1	3
382.0	0	3	0	2
383.0	0	8	0	1
384.0	0	5	0	4
385.0	0	4	0	2
386.0	0	2	0	1
387.0	0	3	0	4
388.0	0	1	0	1
389.0	0	1	0	4
390.0	0	1	2	0
391.0	0	0	0	4
392.0	0	2	0	1
393.0	0	2	0	1
394.0	0	4	0	2
395.0	0	1	0	0
396.0	0	2	0	3
397.0	0	3	0	3
398.0	0	0	0	1
399.0	0	3	0	2
400.0	0	1	0	0
401.0	0	4	0	2
402.0	0	0	1	2
403.0	0	1	1	3
404.0	0	3	2	0
405.0	0	1	0	0
406.0	0	3	0	1
407.0	0	3	0	3
408.0	0	3	0	0
409.0	0	1	0	1
410.0	0	0	0	1
411.0	0	0	0	2
412.0	0	4	0	1
413.0	0	2	0	1
414.0	0	3	0	2
415.0	0	2	0	3
416.0	0	2	0	1
417.0	0	2	0	0
418.0	0	5	1	3
419.0	0	1	0	1
420.0	0	4	0	1
421.0	0	1	0	3
422.0	0	1	0	0
423.0	0	3	0	3
424.0	0	1	0	1
425.0	0	0	1	2
426.0	0	1	0	0
427.0	0	2	0	0
428.0	0	2	0	1
429.0	0	0	0	2
430.0	0	2	0	3
431.0	0	1	0	2
432.0	0	1	0	1
433.0	0	2	0	0
434.0	0	0	0	2
435.0	0	1	0	5
436.0	0	0	0	1
437.0	0	3	0	1
438.0	0	1	0	0
439.0	0	4	0	1
440.0	0	2	0	2
441.0	0	3	0	0
442.0	0	3	0	0
443.0	0	3	1	1
444.0	0	1	0	4
445.0	0	1	0	1
446.0	0	2	0	1
447.0	0	1	0	1
448.0	0	2	0	1
449.0	0	2	0	0
450.0	0	1	1	0
451.0	0	1	0	0
452.0	0	0	0	1
453.0	0	1	0	2
454.0	0	0	0	1
455.0	0	1	0	1
456.0	0	3	0	1
457.0	0	2	0	1
458.0	0	2	0	3
460.0	0	3	0	1
461.0	0	4	0	1
462.0	0	3	0	1
463.0	0	2	0	0
464.0	0	1	0	2
465.0	0	1	0	1
466.0	0	2	0	3
467.0	0	4	0	2
468.0	0	1	0	2
469.0	0	1	0	4
470.0	0	0	0	3
471.0	0	2	0	2
472.0	0	4	0	0
473.0	0	1	1	2
474.0	0	4	0	3
475.0	0	2	1	3
476.0	0	0	0	1
477.0	0	1	0	1
478.0	0	2	0	1
479.0	0	0	0	1
480.0	0	1	0	1
481.0	0	0	1	0
482.0	0	0	0	1
483.0	0	1	0	0
484.0	0	2	0	0
486.0	0	1	0	2
487.0	0	1	0	0
488.0	0	2	0	1
489.0	0	1	0	1
490.0	0	3	0	0
491.0	0	1	0	0
492.0	0	0	0	2
493.0	0	1	0	1
494.0	0	0	0	1
495.0	0	1	0	2
496.0	0	1	0	1
497.0	0	1	0	1
498.0	0	1	0	2
499.0	0	1	0	0
501.0	0	1	0	0
503.0	0	4	0	2
504.0	0	0	0	1
505.0	0	1	0	0
506.0	0	3	0	1
507.0	0	1	0	1
509.0	0	2	0	1
510.0	0	1	1	1
511.0	0	1	0	1
512.0	0	2	0	1
513.0	0	2	0	1
517.0	0	1	0	1
518.0	0	1	0	1
519.0	0	2	0	1
520.0	0	1	0	1
521.0	0	1	0	0
524.0	0	3	0	1
525.0	0	0	0	1
526.0	0	2	0	0
528.0	0	4	0	0
529.0	0	3	0	1
530.0	0	3	0	0
531.0	0	1	0	1
534.0	0	1	0	1
535.0	0	1	0	0
536.0	0	1	0	0
538.0	0	2	0	1
540.0	0	1	0	0
541.0	0	1	0	1
542.0	0	2	0	0
543.0	0	0	0	1
545.0	0	0	0	2
546.0	0	1	0	1
547.0	0	0	1	2
548.0	0	1	0	1
549.0	0	0	0	1
550.0	0	0	0	2
551.0	0	0	0	1
552.0	0	2	0	2
554.0	0	1	0	0
555.0	0	0	0	1
556.0	0	2	0	1
558.0	0	2	0	1
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