## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-72-TP4.bam --OUTPUT POR-72-TP4.md.bam --METRICS_FILE POR-72-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 18:19:54 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	557	19128011	10166311	0	380	13306553	3886114	0.695658	6418735

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.046597	3264183	0	4032289
2.0	1.099755	1249420	808052	1055634
3.0	1.102455	516770	291954	291682
4.0	1.102592	244320	137432	109149
5.0	1.102599	131821	73110	58429
6.0	1.102599	79682	41510	38788
7.0	1.102599	52619	25096	28979
8.0	1.102599	37264	16068	22836
9.0	1.102599	27594	10965	17899
10.0	1.102599	21692	7942	15224
11.0	1.102599	17379	6063	12502
12.0	1.102599	14376	4654	10498
13.0	1.102599	12194	3848	9407
14.0	1.102599	10494	2984	8228
15.0	1.102599	9187	2567	7087
16.0	1.102599	8207	2174	6279
17.0	1.102599	7306	1891	5701
18.0	1.102599	6577	1632	5063
19.0	1.102599	5831	1440	4518
20.0	1.102599	5347	1261	4103
21.0	1.102599	4666	1162	3821
22.0	1.102599	4477	1002	3386
23.0	1.102599	4091	896	3136
24.0	1.102599	3744	820	2904
25.0	1.102599	3447	714	2735
26.0	1.102599	3171	652	2493
27.0	1.102599	3111	655	2403
28.0	1.102599	2740	531	2175
29.0	1.102599	2695	502	2094
30.0	1.102599	2487	479	1889
31.0	1.102599	2286	435	1789
32.0	1.102599	2128	411	1700
33.0	1.102599	2053	354	1554
34.0	1.102599	1907	357	1469
35.0	1.102599	1892	312	1482
36.0	1.102599	1619	298	1315
37.0	1.102599	1643	282	1207
38.0	1.102599	1514	256	1180
39.0	1.102599	1464	233	1108
40.0	1.102599	1361	243	1082
41.0	1.102599	1326	225	1046
42.0	1.102599	1227	187	961
43.0	1.102599	1142	213	958
44.0	1.102599	1109	196	863
45.0	1.102599	1118	172	809
46.0	1.102599	988	196	780
47.0	1.102599	982	163	817
48.0	1.102599	972	145	766
49.0	1.102599	870	147	671
50.0	1.102599	839	131	736
51.0	1.102599	810	136	695
52.0	1.102599	813	139	584
53.0	1.102599	802	124	631
54.0	1.102599	713	103	543
55.0	1.102599	736	103	589
56.0	1.102599	706	91	510
57.0	1.102599	657	88	537
58.0	1.102599	675	92	485
59.0	1.102599	637	88	482
60.0	1.102599	643	95	467
61.0	1.102599	620	83	448
62.0	1.102599	546	82	429
63.0	1.102599	561	76	425
64.0	1.102599	537	76	460
65.0	1.102599	506	74	401
66.0	1.102599	508	73	380
67.0	1.102599	456	81	352
68.0	1.102599	452	54	360
69.0	1.102599	437	48	361
70.0	1.102599	424	54	374
71.0	1.102599	389	58	344
72.0	1.102599	463	51	292
73.0	1.102599	449	48	310
74.0	1.102599	400	59	293
75.0	1.102599	399	53	298
76.0	1.102599	357	56	288
77.0	1.102599	361	41	277
78.0	1.102599	364	38	260
79.0	1.102599	349	52	261
80.0	1.102599	322	42	259
81.0	1.102599	302	38	243
82.0	1.102599	329	35	233
83.0	1.102599	251	34	232
84.0	1.102599	314	33	238
85.0	1.102599	288	31	220
86.0	1.102599	260	22	222
87.0	1.102599	280	22	236
88.0	1.102599	285	37	201
89.0	1.102599	265	22	169
90.0	1.102599	230	28	211
91.0	1.102599	259	27	196
92.0	1.102599	222	33	205
93.0	1.102599	237	30	175
94.0	1.102599	245	28	185
95.0	1.102599	223	26	166
96.0	1.102599	193	26	175
97.0	1.102599	224	25	140
98.0	1.102599	220	28	161
99.0	1.102599	198	19	157
100.0	1.102599	200	19	144
101.0	0	175	25	157
102.0	0	176	28	159
103.0	0	188	19	139
104.0	0	146	16	148
105.0	0	164	18	139
106.0	0	194	26	110
107.0	0	173	17	131
108.0	0	189	26	142
109.0	0	174	23	127
110.0	0	169	18	126
111.0	0	159	13	137
112.0	0	158	8	133
113.0	0	142	18	126
114.0	0	181	17	127
115.0	0	158	12	124
116.0	0	136	16	107
117.0	0	150	19	129
118.0	0	160	14	96
119.0	0	142	14	106
120.0	0	133	17	115
121.0	0	167	11	109
122.0	0	135	16	101
123.0	0	134	16	95
124.0	0	108	7	90
125.0	0	143	14	99
126.0	0	131	12	103
127.0	0	124	14	106
128.0	0	126	18	85
129.0	0	118	9	74
130.0	0	109	6	87
131.0	0	110	4	85
132.0	0	107	4	89
133.0	0	96	11	79
134.0	0	119	12	95
135.0	0	90	9	91
136.0	0	116	11	76
137.0	0	89	5	71
138.0	0	86	13	72
139.0	0	100	13	76
140.0	0	90	7	59
141.0	0	102	11	69
142.0	0	96	13	71
143.0	0	89	14	70
144.0	0	85	11	82
145.0	0	92	10	69
146.0	0	63	4	75
147.0	0	96	8	78
148.0	0	85	5	67
149.0	0	90	10	55
150.0	0	89	4	54
151.0	0	77	5	56
152.0	0	92	6	66
153.0	0	73	6	56
154.0	0	82	7	58
155.0	0	76	10	50
156.0	0	90	10	63
157.0	0	72	11	53
158.0	0	82	6	55
159.0	0	72	9	41
160.0	0	62	7	56
161.0	0	80	6	53
162.0	0	80	5	68
163.0	0	69	6	59
164.0	0	64	7	50
165.0	0	64	4	45
166.0	0	68	4	49
167.0	0	55	8	64
168.0	0	57	9	45
169.0	0	63	7	43
170.0	0	62	7	46
171.0	0	66	6	55
172.0	0	53	3	53
173.0	0	56	2	35
174.0	0	61	4	43
175.0	0	57	3	56
176.0	0	61	2	45
177.0	0	65	7	41
178.0	0	58	3	37
179.0	0	46	4	42
180.0	0	57	1	41
181.0	0	55	6	35
182.0	0	57	7	40
183.0	0	55	4	47
184.0	0	48	3	30
185.0	0	44	2	37
186.0	0	44	5	49
187.0	0	49	7	41
188.0	0	46	4	31
189.0	0	50	4	36
190.0	0	46	4	39
191.0	0	50	7	41
192.0	0	41	4	41
193.0	0	42	1	23
194.0	0	41	2	34
195.0	0	50	4	36
196.0	0	47	4	38
197.0	0	39	3	35
198.0	0	32	2	26
199.0	0	47	6	26
200.0	0	34	5	24
201.0	0	30	8	38
202.0	0	49	0	29
203.0	0	43	1	32
204.0	0	41	5	33
205.0	0	42	0	25
206.0	0	39	3	26
207.0	0	43	4	29
208.0	0	34	5	21
209.0	0	37	4	26
210.0	0	39	5	30
211.0	0	40	4	22
212.0	0	31	6	22
213.0	0	32	1	23
214.0	0	31	0	36
215.0	0	36	0	35
216.0	0	39	6	23
217.0	0	34	2	35
218.0	0	27	2	21
219.0	0	30	3	20
220.0	0	35	2	18
221.0	0	43	1	19
222.0	0	29	1	29
223.0	0	35	6	20
224.0	0	33	5	38
225.0	0	35	4	21
226.0	0	36	2	20
227.0	0	29	2	35
228.0	0	23	2	18
229.0	0	40	0	20
230.0	0	32	2	22
231.0	0	23	2	24
232.0	0	27	0	28
233.0	0	36	2	32
234.0	0	20	2	27
235.0	0	38	3	27
236.0	0	28	3	21
237.0	0	19	2	16
238.0	0	32	1	22
239.0	0	29	1	15
240.0	0	32	4	19
241.0	0	25	1	22
242.0	0	21	1	21
243.0	0	31	6	22
244.0	0	21	3	9
245.0	0	24	0	16
246.0	0	25	4	26
247.0	0	25	2	25
248.0	0	14	1	13
249.0	0	23	0	15
250.0	0	32	0	21
251.0	0	23	3	26
252.0	0	35	3	14
253.0	0	21	3	18
254.0	0	18	6	17
255.0	0	25	2	21
256.0	0	19	1	21
257.0	0	18	2	23
258.0	0	28	1	22
259.0	0	19	1	19
260.0	0	21	3	17
261.0	0	26	1	11
262.0	0	22	0	12
263.0	0	26	2	15
264.0	0	16	1	20
265.0	0	19	4	13
266.0	0	30	1	21
267.0	0	26	1	13
268.0	0	27	0	19
269.0	0	23	1	17
270.0	0	22	2	23
271.0	0	10	3	14
272.0	0	24	2	12
273.0	0	18	3	19
274.0	0	24	0	26
275.0	0	27	1	16
276.0	0	17	1	17
277.0	0	17	1	10
278.0	0	23	0	15
279.0	0	14	1	12
280.0	0	24	2	15
281.0	0	17	1	20
282.0	0	13	2	19
283.0	0	23	1	9
284.0	0	22	3	14
285.0	0	24	1	13
286.0	0	15	1	9
287.0	0	24	3	12
288.0	0	19	1	15
289.0	0	18	1	17
290.0	0	18	1	15
291.0	0	25	1	15
292.0	0	13	3	12
293.0	0	22	0	14
294.0	0	20	0	10
295.0	0	14	0	12
296.0	0	12	0	18
297.0	0	19	0	12
298.0	0	23	0	10
299.0	0	18	1	15
300.0	0	16	0	12
301.0	0	22	0	8
302.0	0	22	0	16
303.0	0	12	2	12
304.0	0	11	0	13
305.0	0	9	2	11
306.0	0	15	2	13
307.0	0	17	1	17
308.0	0	16	0	11
309.0	0	16	1	11
310.0	0	22	0	12
311.0	0	14	2	12
312.0	0	8	2	7
313.0	0	15	2	10
314.0	0	13	1	10
315.0	0	17	3	6
316.0	0	12	2	17
317.0	0	10	1	10
318.0	0	11	0	4
319.0	0	12	0	8
320.0	0	16	0	8
321.0	0	12	0	10
322.0	0	13	1	8
323.0	0	6	1	14
324.0	0	10	1	13
325.0	0	10	1	14
326.0	0	14	0	13
327.0	0	12	0	7
328.0	0	14	1	6
329.0	0	16	1	8
330.0	0	14	0	4
331.0	0	16	1	12
332.0	0	8	0	9
333.0	0	8	0	10
334.0	0	9	1	9
335.0	0	10	3	15
336.0	0	12	0	13
337.0	0	11	1	11
338.0	0	14	3	10
339.0	0	15	0	7
340.0	0	15	0	8
341.0	0	11	2	6
342.0	0	10	3	13
343.0	0	11	1	5
344.0	0	10	0	12
345.0	0	11	0	7
346.0	0	12	2	11
347.0	0	14	1	9
348.0	0	9	1	9
349.0	0	11	0	11
350.0	0	9	0	5
351.0	0	15	1	11
352.0	0	10	1	10
353.0	0	6	0	5
354.0	0	8	0	7
355.0	0	11	0	5
356.0	0	8	0	8
357.0	0	7	0	10
358.0	0	9	1	5
359.0	0	9	0	11
360.0	0	10	2	12
361.0	0	5	0	5
362.0	0	6	0	9
363.0	0	11	1	11
364.0	0	13	0	11
365.0	0	8	0	4
366.0	0	14	0	10
367.0	0	11	0	5
368.0	0	11	0	3
369.0	0	15	1	5
370.0	0	11	1	8
371.0	0	6	0	6
372.0	0	13	0	4
373.0	0	12	0	5
374.0	0	17	0	8
375.0	0	11	0	10
376.0	0	9	0	7
377.0	0	9	0	7
378.0	0	10	1	2
379.0	0	6	0	7
380.0	0	17	0	6
381.0	0	11	0	4
382.0	0	7	1	13
383.0	0	12	2	9
384.0	0	11	0	10
385.0	0	6	0	7
386.0	0	7	0	8
387.0	0	5	0	10
388.0	0	8	0	7
389.0	0	6	0	6
390.0	0	6	0	10
391.0	0	10	0	4
392.0	0	9	1	14
393.0	0	10	0	10
394.0	0	11	3	8
395.0	0	8	0	3
396.0	0	9	0	5
397.0	0	5	0	6
398.0	0	8	0	6
399.0	0	6	0	5
400.0	0	8	1	6
401.0	0	9	0	2
402.0	0	5	2	5
403.0	0	4	2	6
404.0	0	6	0	3
405.0	0	7	0	9
406.0	0	11	0	7
407.0	0	8	0	7
408.0	0	5	0	6
409.0	0	8	0	4
410.0	0	5	0	3
411.0	0	7	0	3
412.0	0	7	3	5
413.0	0	3	0	8
414.0	0	11	0	5
415.0	0	5	0	7
416.0	0	9	0	3
417.0	0	14	0	5
418.0	0	7	0	7
419.0	0	4	0	7
420.0	0	7	2	3
421.0	0	6	1	7
422.0	0	6	1	9
423.0	0	6	0	8
424.0	0	8	1	4
425.0	0	5	2	8
426.0	0	6	1	0
427.0	0	4	0	4
428.0	0	7	0	3
429.0	0	6	0	6
430.0	0	9	1	9
431.0	0	11	0	4
432.0	0	3	0	3
433.0	0	11	2	4
434.0	0	11	2	5
435.0	0	7	1	5
436.0	0	5	0	4
437.0	0	7	0	9
438.0	0	3	0	4
439.0	0	11	0	2
440.0	0	6	0	3
441.0	0	0	0	8
442.0	0	6	0	9
443.0	0	6	0	3
444.0	0	6	0	9
445.0	0	6	0	4
446.0	0	3	0	4
447.0	0	4	0	6
448.0	0	2	0	6
449.0	0	8	0	7
450.0	0	4	1	6
451.0	0	8	0	8
452.0	0	8	0	5
453.0	0	4	1	4
454.0	0	6	0	3
455.0	0	6	0	9
456.0	0	4	1	4
457.0	0	10	0	9
458.0	0	7	0	4
459.0	0	10	1	6
460.0	0	5	1	9
461.0	0	7	0	2
462.0	0	4	0	2
463.0	0	5	0	3
464.0	0	7	1	5
465.0	0	4	0	4
466.0	0	6	0	6
467.0	0	7	0	7
468.0	0	5	1	4
469.0	0	8	0	4
470.0	0	5	0	7
471.0	0	6	0	3
472.0	0	7	1	2
473.0	0	1	0	2
474.0	0	6	0	2
475.0	0	6	1	3
476.0	0	7	0	5
477.0	0	2	1	7
478.0	0	5	0	3
479.0	0	11	0	6
480.0	0	6	0	7
481.0	0	7	1	3
482.0	0	3	0	6
483.0	0	8	0	2
484.0	0	4	0	9
485.0	0	7	0	3
486.0	0	6	0	4
487.0	0	3	0	3
488.0	0	7	0	1
489.0	0	7	1	5
490.0	0	4	1	6
491.0	0	7	0	2
492.0	0	5	0	3
493.0	0	4	0	2
494.0	0	7	1	1
495.0	0	4	0	1
496.0	0	6	0	2
497.0	0	4	0	2
498.0	0	8	0	7
499.0	0	8	0	0
500.0	0	6	0	5
501.0	0	2	0	5
502.0	0	4	0	1
503.0	0	5	0	4
504.0	0	2	0	5
505.0	0	5	1	1
506.0	0	4	0	3
507.0	0	8	1	8
508.0	0	1	0	3
509.0	0	5	0	4
510.0	0	6	1	5
511.0	0	7	0	2
512.0	0	6	0	2
513.0	0	4	0	2
514.0	0	4	0	4
515.0	0	5	0	4
516.0	0	3	1	5
517.0	0	8	0	6
518.0	0	7	2	4
519.0	0	3	0	2
520.0	0	5	0	3
521.0	0	5	1	6
522.0	0	3	0	3
523.0	0	5	0	7
524.0	0	2	0	4
525.0	0	5	0	3
526.0	0	3	1	0
527.0	0	4	0	2
528.0	0	4	0	4
529.0	0	3	0	4
530.0	0	3	0	5
531.0	0	5	0	1
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