## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-72-TP2.bam --OUTPUT POR-72-TP2.md.bam --METRICS_FILE POR-72-TP2.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 18:17:47 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	298	12007776	6262592	0	199	8761394	3085642	0.729643	3527602

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.050504	1157412	0	1542938
2.0	1.085425	779560	554812	874961
3.0	1.086586	477631	240698	404379
4.0	1.086624	278522	127619	170369
5.0	1.086626	163642	72855	74621
6.0	1.086626	100716	44350	38151
7.0	1.086626	64265	27656	23251
8.0	1.086626	43204	17831	16226
9.0	1.086626	30195	11891	12238
10.0	1.086626	21922	8219	9849
11.0	1.086626	16816	5769	8031
12.0	1.086626	13012	4236	6653
13.0	1.086626	10233	3206	5624
14.0	1.086626	8434	2458	4897
15.0	1.086626	6995	1958	4145
16.0	1.086626	5804	1516	3607
17.0	1.086626	5089	1239	3275
18.0	1.086626	4361	1208	2834
19.0	1.086626	3851	931	2554
20.0	1.086626	3435	854	2233
21.0	1.086626	3073	748	2018
22.0	1.086626	2650	666	1945
23.0	1.086626	2441	559	1745
24.0	1.086626	2280	529	1597
25.0	1.086626	2058	441	1410
26.0	1.086626	1969	440	1294
27.0	1.086626	1698	355	1241
28.0	1.086626	1595	331	1104
29.0	1.086626	1489	318	1049
30.0	1.086626	1389	270	927
31.0	1.086626	1212	248	885
32.0	1.086626	1130	259	863
33.0	1.086626	1078	213	788
34.0	1.086626	1035	189	733
35.0	1.086626	970	176	677
36.0	1.086626	934	159	651
37.0	1.086626	879	155	558
38.0	1.086626	870	159	598
39.0	1.086626	751	123	520
40.0	1.086626	784	145	484
41.0	1.086626	732	131	467
42.0	1.086626	616	139	436
43.0	1.086626	608	114	441
44.0	1.086626	574	106	407
45.0	1.086626	574	98	371
46.0	1.086626	536	91	422
47.0	1.086626	537	84	360
48.0	1.086626	485	85	339
49.0	1.086626	417	94	276
50.0	1.086626	453	78	280
51.0	1.086626	412	66	304
52.0	1.086626	378	59	257
53.0	1.086626	399	68	280
54.0	1.086626	395	64	271
55.0	1.086626	318	42	272
56.0	1.086626	340	66	253
57.0	1.086626	332	64	253
58.0	1.086626	342	58	218
59.0	1.086626	271	40	214
60.0	1.086626	310	43	206
61.0	1.086626	277	49	170
62.0	1.086626	276	49	214
63.0	1.086626	272	40	173
64.0	1.086626	249	33	175
65.0	1.086626	235	21	152
66.0	1.086626	234	29	149
67.0	1.086626	216	34	164
68.0	1.086626	192	31	161
69.0	1.086626	183	35	157
70.0	1.086626	199	28	147
71.0	1.086626	208	30	147
72.0	1.086626	206	32	109
73.0	1.086626	216	26	120
74.0	1.086626	228	21	107
75.0	1.086626	153	10	109
76.0	1.086626	178	35	117
77.0	1.086626	166	31	110
78.0	1.086626	167	20	113
79.0	1.086626	143	23	107
80.0	1.086626	147	18	109
81.0	1.086626	153	18	97
82.0	1.086626	158	21	113
83.0	1.086626	126	17	95
84.0	1.086626	142	16	87
85.0	1.086626	121	19	113
86.0	1.086626	121	15	99
87.0	1.086626	145	20	82
88.0	1.086626	114	14	81
89.0	1.086626	105	15	87
90.0	1.086626	109	19	72
91.0	1.086626	105	8	59
92.0	1.086626	120	15	89
93.0	1.086626	117	7	76
94.0	1.086626	78	8	84
95.0	1.086626	88	8	83
96.0	1.086626	110	16	65
97.0	1.086626	116	14	63
98.0	1.086626	90	11	74
99.0	1.086626	99	13	44
100.0	1.086626	92	6	54
101.0	0	93	7	56
102.0	0	81	11	58
103.0	0	81	16	55
104.0	0	66	8	60
105.0	0	75	4	65
106.0	0	69	12	57
107.0	0	75	8	60
108.0	0	76	6	49
109.0	0	78	13	49
110.0	0	58	5	49
111.0	0	63	8	43
112.0	0	59	7	42
113.0	0	60	9	58
114.0	0	68	9	42
115.0	0	54	9	41
116.0	0	74	6	40
117.0	0	74	8	38
118.0	0	59	7	39
119.0	0	47	9	33
120.0	0	65	4	45
121.0	0	46	9	44
122.0	0	61	6	32
123.0	0	49	7	33
124.0	0	52	2	45
125.0	0	65	2	34
126.0	0	54	2	27
127.0	0	45	5	33
128.0	0	44	9	31
129.0	0	62	3	30
130.0	0	51	7	36
131.0	0	56	5	32
132.0	0	41	4	27
133.0	0	45	3	28
134.0	0	55	5	35
135.0	0	45	4	27
136.0	0	50	3	23
137.0	0	50	3	28
138.0	0	42	8	32
139.0	0	48	3	21
140.0	0	39	3	27
141.0	0	38	3	18
142.0	0	34	4	38
143.0	0	32	4	27
144.0	0	37	2	22
145.0	0	41	5	21
146.0	0	39	6	29
147.0	0	32	4	24
148.0	0	20	1	19
149.0	0	41	4	26
150.0	0	45	3	18
151.0	0	34	2	22
152.0	0	32	3	29
153.0	0	39	1	14
154.0	0	26	3	19
155.0	0	29	2	16
156.0	0	25	3	27
157.0	0	27	6	18
158.0	0	20	3	23
159.0	0	24	3	21
160.0	0	27	3	16
161.0	0	31	2	16
162.0	0	30	2	19
163.0	0	29	3	27
164.0	0	24	2	17
165.0	0	27	5	7
166.0	0	28	3	23
167.0	0	19	3	18
168.0	0	17	1	13
169.0	0	25	1	16
170.0	0	24	1	12
171.0	0	14	2	11
172.0	0	22	3	15
173.0	0	27	1	14
174.0	0	18	2	17
175.0	0	19	5	10
176.0	0	21	1	16
177.0	0	22	0	15
178.0	0	19	3	20
179.0	0	22	0	13
180.0	0	25	3	19
181.0	0	24	3	16
182.0	0	23	3	17
183.0	0	16	0	14
184.0	0	14	4	17
185.0	0	27	2	16
186.0	0	16	0	15
187.0	0	21	0	18
188.0	0	16	1	10
189.0	0	25	1	12
190.0	0	19	1	11
191.0	0	14	0	19
192.0	0	15	2	6
193.0	0	20	3	10
194.0	0	18	0	6
195.0	0	18	2	10
196.0	0	14	1	9
197.0	0	19	3	4
198.0	0	16	2	9
199.0	0	23	1	11
200.0	0	18	2	8
201.0	0	10	0	8
202.0	0	10	1	13
203.0	0	14	0	13
204.0	0	20	1	10
205.0	0	18	2	11
206.0	0	10	0	10
207.0	0	17	0	10
208.0	0	15	1	9
209.0	0	9	0	4
210.0	0	16	0	10
211.0	0	12	2	11
212.0	0	11	1	12
213.0	0	8	0	13
214.0	0	17	1	3
215.0	0	18	0	12
216.0	0	16	0	6
217.0	0	13	1	4
218.0	0	15	0	11
219.0	0	10	1	4
220.0	0	11	0	7
221.0	0	8	0	5
222.0	0	9	1	8
223.0	0	11	0	7
224.0	0	17	0	4
225.0	0	8	0	6
226.0	0	7	0	7
227.0	0	11	2	6
228.0	0	5	1	8
229.0	0	9	2	8
230.0	0	9	0	6
231.0	0	8	0	8
232.0	0	2	1	12
233.0	0	7	1	7
234.0	0	6	0	6
235.0	0	6	1	4
236.0	0	10	1	3
237.0	0	14	0	4
238.0	0	17	0	12
239.0	0	9	0	1
240.0	0	9	1	8
241.0	0	13	1	10
242.0	0	9	0	8
243.0	0	10	1	2
244.0	0	6	3	2
245.0	0	7	1	5
246.0	0	9	1	4
247.0	0	10	1	11
248.0	0	5	2	10
249.0	0	5	2	6
250.0	0	10	0	7
251.0	0	5	0	7
252.0	0	7	1	1
253.0	0	6	1	3
254.0	0	11	1	6
255.0	0	5	0	6
256.0	0	8	0	4
257.0	0	8	1	4
258.0	0	11	1	8
259.0	0	10	1	5
260.0	0	8	0	6
261.0	0	3	2	4
262.0	0	7	0	2
263.0	0	2	2	3
264.0	0	8	1	5
265.0	0	5	0	6
266.0	0	7	0	7
267.0	0	3	1	10
268.0	0	9	0	1
269.0	0	7	0	4
270.0	0	12	0	6
271.0	0	8	0	3
272.0	0	8	0	6
273.0	0	4	1	4
274.0	0	3	0	5
275.0	0	6	0	5
276.0	0	5	2	9
277.0	0	12	1	6
278.0	0	9	0	4
279.0	0	2	0	8
280.0	0	3	0	6
281.0	0	7	0	6
282.0	0	9	0	3
283.0	0	5	0	6
284.0	0	5	0	3
285.0	0	6	1	6
286.0	0	6	0	5
287.0	0	3	0	3
288.0	0	7	1	3
289.0	0	5	1	4
290.0	0	8	1	5
291.0	0	6	1	5
292.0	0	7	0	2
293.0	0	9	0	3
294.0	0	8	0	3
295.0	0	4	0	0
296.0	0	3	0	5
297.0	0	6	0	4
298.0	0	5	0	3
299.0	0	4	0	2
300.0	0	5	0	0
301.0	0	4	1	2
302.0	0	8	1	1
303.0	0	4	0	3
304.0	0	6	0	6
305.0	0	11	0	1
306.0	0	6	0	1
307.0	0	5	1	2
308.0	0	6	0	2
309.0	0	3	1	9
310.0	0	9	0	2
311.0	0	6	0	1
312.0	0	6	0	3
313.0	0	10	1	1
314.0	0	5	0	6
315.0	0	3	0	4
316.0	0	3	0	6
317.0	0	4	0	4
318.0	0	10	0	3
319.0	0	5	0	2
320.0	0	4	0	2
321.0	0	3	0	1
322.0	0	6	1	4
323.0	0	1	0	2
324.0	0	5	1	1
325.0	0	4	0	2
326.0	0	7	0	2
327.0	0	1	0	1
328.0	0	4	0	3
329.0	0	7	0	5
330.0	0	2	1	3
331.0	0	4	0	5
332.0	0	9	0	1
333.0	0	4	0	1
334.0	0	3	1	5
335.0	0	4	0	1
336.0	0	1	0	1
337.0	0	4	1	2
338.0	0	2	0	0
339.0	0	7	0	3
340.0	0	1	0	2
341.0	0	8	0	2
342.0	0	4	0	0
343.0	0	4	1	3
344.0	0	5	0	2
345.0	0	4	0	3
346.0	0	6	0	3
347.0	0	1	0	0
348.0	0	3	0	1
349.0	0	4	0	1
350.0	0	5	0	1
351.0	0	8	0	4
352.0	0	2	0	3
353.0	0	5	0	2
354.0	0	4	0	1
355.0	0	4	0	3
356.0	0	4	0	2
357.0	0	1	0	4
358.0	0	6	0	3
359.0	0	2	0	3
360.0	0	3	0	3
361.0	0	3	1	1
362.0	0	3	0	3
363.0	0	1	0	0
364.0	0	0	1	2
365.0	0	7	0	5
366.0	0	1	0	1
367.0	0	1	0	1
368.0	0	2	0	1
369.0	0	3	0	0
370.0	0	1	0	1
371.0	0	0	0	3
372.0	0	1	0	2
373.0	0	4	0	0
374.0	0	6	0	3
375.0	0	3	0	2
376.0	0	3	1	3
377.0	0	0	1	1
378.0	0	2	0	2
379.0	0	1	0	2
380.0	0	5	0	1
381.0	0	4	0	3
382.0	0	5	0	1
383.0	0	1	1	1
384.0	0	1	1	1
385.0	0	4	0	0
386.0	0	3	1	3
387.0	0	3	0	3
388.0	0	1	0	1
389.0	0	3	1	2
390.0	0	4	0	1
391.0	0	3	0	1
392.0	0	2	0	2
393.0	0	1	0	2
394.0	0	5	1	2
395.0	0	5	1	2
396.0	0	1	0	0
397.0	0	2	0	1
398.0	0	3	1	2
399.0	0	2	0	2
400.0	0	1	0	0
401.0	0	1	0	2
402.0	0	2	0	1
403.0	0	5	0	2
404.0	0	2	0	0
405.0	0	5	0	1
406.0	0	1	0	1
407.0	0	1	0	2
408.0	0	2	1	1
409.0	0	3	0	0
410.0	0	3	0	1
411.0	0	4	0	2
412.0	0	2	0	3
413.0	0	3	0	2
414.0	0	4	0	6
415.0	0	0	0	1
416.0	0	0	0	1
417.0	0	3	0	2
418.0	0	1	0	2
419.0	0	1	0	4
420.0	0	3	0	0
421.0	0	3	0	1
422.0	0	2	0	0
423.0	0	1	0	2
424.0	0	1	0	1
425.0	0	2	1	2
426.0	0	3	0	3
427.0	0	1	0	0
428.0	0	0	0	1
429.0	0	3	0	1
431.0	0	1	0	3
433.0	0	2	0	2
434.0	0	2	0	1
435.0	0	1	0	0
436.0	0	3	0	1
437.0	0	3	0	2
438.0	0	1	0	1
439.0	0	4	1	0
440.0	0	3	0	1
441.0	0	3	0	1
442.0	0	1	1	1
443.0	0	3	0	2
444.0	0	1	0	1
445.0	0	1	0	0
446.0	0	2	0	1
447.0	0	1	0	1
448.0	0	1	0	0
449.0	0	2	0	1
450.0	0	1	0	3
451.0	0	0	0	1
452.0	0	0	0	1
453.0	0	0	0	1
454.0	0	1	0	2
455.0	0	2	0	0
456.0	0	1	0	0
457.0	0	2	0	2
458.0	0	4	1	1
459.0	0	0	0	1
460.0	0	1	0	3
461.0	0	1	0	0
462.0	0	1	0	1
463.0	0	2	0	1
464.0	0	1	0	1
465.0	0	3	0	1
467.0	0	1	0	0
468.0	0	3	0	2
469.0	0	0	0	2
470.0	0	3	1	0
471.0	0	0	0	1
472.0	0	1	0	1
473.0	0	0	1	0
474.0	0	1	0	1
475.0	0	1	0	1
476.0	0	1	0	1
477.0	0	2	0	0
478.0	0	2	0	1
479.0	0	1	0	0
480.0	0	0	0	1
481.0	0	1	0	2
482.0	0	1	0	0
483.0	0	2	0	1
484.0	0	1	0	2
485.0	0	1	0	0
486.0	0	1	0	0
487.0	0	0	0	2
488.0	0	4	0	1
489.0	0	0	0	4
490.0	0	4	0	0
492.0	0	1	0	0
493.0	0	1	0	0
494.0	0	2	0	0
495.0	0	1	0	1
496.0	0	2	0	0
498.0	0	2	0	0
499.0	0	4	0	0
500.0	0	2	0	0
501.0	0	2	0	0
502.0	0	0	0	1
503.0	0	2	0	1
504.0	0	1	0	0
505.0	0	2	0	1
506.0	0	1	0	1
507.0	0	2	1	0
508.0	0	3	0	0
509.0	0	1	0	0
510.0	0	2	0	2
511.0	0	0	0	2
512.0	0	1	0	1
513.0	0	2	0	0
514.0	0	0	0	3
515.0	0	1	0	1
516.0	0	2	0	1
517.0	0	2	0	0
518.0	0	1	0	1
519.0	0	1	0	1
520.0	0	0	0	2
521.0	0	0	0	2
523.0	0	0	0	1
524.0	0	0	0	1
527.0	0	2	0	0
528.0	0	0	0	1
529.0	0	0	0	1
530.0	0	1	0	0
531.0	0	0	0	1
532.0	0	2	0	1
534.0	0	1	0	0
535.0	0	3	0	0
536.0	0	1	0	0
537.0	0	1	0	0
539.0	0	1	0	0
541.0	0	1	0	1
542.0	0	0	0	2
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