## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-245-TP4.bam --OUTPUT POR-245-TP4.md.bam --METRICS_FILE POR-245-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 18:15:17 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	516	13981685	6240788	0	270	8492449	3222341	0.607397	6987555

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.100842	3134489	0	3954584
2.0	1.249685	1160476	782544	954737
3.0	1.269809	490899	294866	253605
4.0	1.27253	239297	141580	94147
5.0	1.272898	131434	75663	50001
6.0	1.272948	79575	42233	32538
7.0	1.272955	51246	24493	23051
8.0	1.272956	34597	14856	17214
9.0	1.272956	24740	9644	13238
10.0	1.272956	18486	6651	10836
11.0	1.272956	14462	4558	8765
12.0	1.272956	11564	3306	7304
13.0	1.272956	9399	2470	6210
14.0	1.272956	7779	1928	5215
15.0	1.272956	6617	1607	4519
16.0	1.272956	5732	1252	4050
17.0	1.272956	5188	1119	3518
18.0	1.272956	4334	953	2971
19.0	1.272956	3855	815	2690
20.0	1.272956	3437	642	2423
21.0	1.272956	3119	605	2269
22.0	1.272956	2750	548	2025
23.0	1.272956	2516	430	1827
24.0	1.272956	2195	396	1645
25.0	1.272956	2141	390	1516
26.0	1.272956	1886	354	1454
27.0	1.272956	1860	289	1319
28.0	1.272956	1706	303	1211
29.0	1.272956	1493	233	1103
30.0	1.272956	1456	222	1050
31.0	1.272956	1273	194	896
32.0	1.272956	1202	203	901
33.0	1.272956	1079	188	812
34.0	1.272956	1112	169	766
35.0	1.272956	1007	159	718
36.0	1.272956	910	144	720
37.0	1.272956	861	141	624
38.0	1.272956	824	139	623
39.0	1.272956	803	117	537
40.0	1.272956	726	104	577
41.0	1.272956	677	83	513
42.0	1.272956	649	95	459
43.0	1.272956	658	68	454
44.0	1.272956	581	68	462
45.0	1.272956	610	76	392
46.0	1.272956	573	71	344
47.0	1.272956	513	64	392
48.0	1.272956	505	69	333
49.0	1.272956	435	44	311
50.0	1.272956	451	41	335
51.0	1.272956	413	45	305
52.0	1.272956	404	49	276
53.0	1.272956	369	55	308
54.0	1.272956	370	46	265
55.0	1.272956	383	35	259
56.0	1.272956	340	47	239
57.0	1.272956	325	32	215
58.0	1.272956	307	36	228
59.0	1.272956	299	32	219
60.0	1.272956	309	25	208
61.0	1.272956	253	33	208
62.0	1.272956	284	31	199
63.0	1.272956	264	21	171
64.0	1.272956	218	31	179
65.0	1.272956	253	19	170
66.0	1.272956	225	24	163
67.0	1.272956	226	24	153
68.0	1.272956	203	28	152
69.0	1.272956	217	14	142
70.0	1.272956	174	22	141
71.0	1.272956	208	17	145
72.0	1.272956	181	15	127
73.0	1.272956	174	21	155
74.0	1.272956	155	13	107
75.0	1.272956	166	15	135
76.0	1.272956	159	11	129
77.0	1.272956	167	15	117
78.0	1.272956	157	16	126
79.0	1.272956	156	15	109
80.0	1.272956	148	10	108
81.0	1.272956	134	11	101
82.0	1.272956	135	13	118
83.0	1.272956	111	12	81
84.0	1.272956	146	14	98
85.0	1.272956	135	17	101
86.0	1.272956	108	9	93
87.0	1.272956	102	11	84
88.0	1.272956	103	10	98
89.0	1.272956	95	7	84
90.0	1.272956	120	10	81
91.0	1.272956	103	8	67
92.0	1.272956	101	6	81
93.0	1.272956	117	6	76
94.0	1.272956	98	5	56
95.0	1.272956	104	6	62
96.0	1.272956	102	13	64
97.0	1.272956	96	5	73
98.0	1.272956	85	9	73
99.0	1.272956	102	6	73
100.0	1.272956	71	10	65
101.0	0	93	10	75
102.0	0	93	5	79
103.0	0	91	1	68
104.0	0	89	4	51
105.0	0	82	8	60
106.0	0	85	8	56
107.0	0	91	10	49
108.0	0	62	8	60
109.0	0	67	3	45
110.0	0	58	4	56
111.0	0	67	2	49
112.0	0	78	7	50
113.0	0	58	6	47
114.0	0	78	5	39
115.0	0	50	5	59
116.0	0	54	3	57
117.0	0	58	5	40
118.0	0	53	3	47
119.0	0	58	5	36
120.0	0	62	3	51
121.0	0	55	6	46
122.0	0	51	4	38
123.0	0	42	2	45
124.0	0	51	4	41
125.0	0	53	2	34
126.0	0	47	3	45
127.0	0	50	2	31
128.0	0	38	3	28
129.0	0	59	5	35
130.0	0	46	1	34
131.0	0	45	8	38
132.0	0	42	5	42
133.0	0	55	1	35
134.0	0	54	4	25
135.0	0	37	1	35
136.0	0	53	2	34
137.0	0	37	0	25
138.0	0	41	1	28
139.0	0	33	0	39
140.0	0	30	6	28
141.0	0	43	3	28
142.0	0	49	0	27
143.0	0	32	0	17
144.0	0	26	3	35
145.0	0	32	4	25
146.0	0	43	3	23
147.0	0	29	1	16
148.0	0	39	3	16
149.0	0	35	4	14
150.0	0	34	5	33
151.0	0	30	4	21
152.0	0	32	2	27
153.0	0	27	2	29
154.0	0	33	2	19
155.0	0	39	0	16
156.0	0	18	1	13
157.0	0	25	3	26
158.0	0	31	1	16
159.0	0	25	1	22
160.0	0	28	2	20
161.0	0	20	3	32
162.0	0	30	0	15
163.0	0	20	2	19
164.0	0	17	0	15
165.0	0	25	1	19
166.0	0	24	2	23
167.0	0	26	1	20
168.0	0	27	3	19
169.0	0	28	0	16
170.0	0	28	0	18
171.0	0	21	2	18
172.0	0	24	1	13
173.0	0	23	1	15
174.0	0	13	1	18
175.0	0	15	0	12
176.0	0	23	1	22
177.0	0	27	0	7
178.0	0	21	0	12
179.0	0	23	4	18
180.0	0	19	3	10
181.0	0	19	1	13
182.0	0	17	1	13
183.0	0	21	3	15
184.0	0	13	0	10
185.0	0	24	1	14
186.0	0	25	2	8
187.0	0	19	2	17
188.0	0	20	1	13
189.0	0	23	0	15
190.0	0	16	0	16
191.0	0	7	2	10
192.0	0	20	0	14
193.0	0	15	2	6
194.0	0	21	0	18
195.0	0	14	2	15
196.0	0	11	0	12
197.0	0	10	0	9
198.0	0	20	0	9
199.0	0	18	0	11
200.0	0	16	1	11
201.0	0	13	0	8
202.0	0	20	1	5
203.0	0	16	0	13
204.0	0	19	2	12
205.0	0	8	0	5
206.0	0	21	0	6
207.0	0	12	1	6
208.0	0	16	1	9
209.0	0	7	1	13
210.0	0	16	0	9
211.0	0	12	0	6
212.0	0	15	0	6
213.0	0	10	2	15
214.0	0	11	0	6
215.0	0	16	0	8
216.0	0	12	0	9
217.0	0	9	1	9
218.0	0	12	0	6
219.0	0	12	0	3
220.0	0	16	0	7
221.0	0	12	0	10
222.0	0	8	1	13
223.0	0	11	2	6
224.0	0	10	0	7
225.0	0	12	1	6
226.0	0	7	1	7
227.0	0	7	0	7
228.0	0	7	0	5
229.0	0	10	0	10
230.0	0	13	0	6
231.0	0	9	2	6
232.0	0	9	0	7
233.0	0	7	2	7
234.0	0	9	0	8
235.0	0	8	0	10
236.0	0	9	0	0
237.0	0	6	1	7
238.0	0	9	1	9
239.0	0	13	2	3
240.0	0	12	1	4
241.0	0	3	0	8
242.0	0	12	0	9
243.0	0	4	0	4
244.0	0	8	0	6
245.0	0	11	0	5
246.0	0	16	1	15
247.0	0	11	0	4
248.0	0	10	0	6
249.0	0	3	0	4
250.0	0	7	0	6
251.0	0	9	0	13
252.0	0	9	0	7
253.0	0	4	0	9
254.0	0	5	1	5
255.0	0	10	0	1
256.0	0	6	0	6
257.0	0	8	1	6
258.0	0	4	0	7
259.0	0	7	0	6
260.0	0	14	0	8
261.0	0	6	1	7
262.0	0	5	0	2
263.0	0	8	0	8
264.0	0	7	0	3
265.0	0	11	0	6
266.0	0	5	0	5
267.0	0	5	0	4
268.0	0	6	1	3
269.0	0	5	0	2
270.0	0	9	0	7
271.0	0	4	1	6
272.0	0	5	0	2
273.0	0	6	0	4
274.0	0	8	0	3
275.0	0	10	0	3
276.0	0	5	0	4
277.0	0	5	0	1
278.0	0	2	0	5
279.0	0	5	0	5
280.0	0	5	1	7
281.0	0	4	2	1
282.0	0	6	1	4
283.0	0	5	0	2
284.0	0	2	0	5
285.0	0	6	0	5
286.0	0	4	0	3
287.0	0	8	0	6
288.0	0	5	0	5
289.0	0	3	0	6
290.0	0	8	0	7
291.0	0	10	0	2
292.0	0	6	0	3
293.0	0	3	0	2
294.0	0	7	0	6
295.0	0	5	0	6
296.0	0	7	0	5
297.0	0	2	0	7
298.0	0	4	0	0
299.0	0	2	0	2
300.0	0	3	0	3
301.0	0	3	1	5
302.0	0	7	0	3
303.0	0	10	0	2
304.0	0	6	0	3
305.0	0	4	0	4
306.0	0	6	0	6
307.0	0	5	0	4
308.0	0	4	0	4
309.0	0	9	1	6
310.0	0	3	1	4
311.0	0	4	0	4
312.0	0	5	0	1
313.0	0	7	0	5
314.0	0	2	1	5
315.0	0	3	0	3
316.0	0	4	0	2
317.0	0	7	0	2
318.0	0	6	1	3
319.0	0	6	0	8
320.0	0	1	0	2
321.0	0	6	0	3
322.0	0	4	0	1
323.0	0	4	0	2
324.0	0	6	0	4
325.0	0	2	0	3
326.0	0	3	0	2
327.0	0	2	1	4
328.0	0	6	0	4
329.0	0	3	0	0
330.0	0	5	0	1
331.0	0	2	0	3
332.0	0	0	0	3
333.0	0	2	0	0
334.0	0	2	0	3
335.0	0	6	0	2
336.0	0	3	1	1
337.0	0	4	0	5
338.0	0	3	0	1
339.0	0	2	0	1
340.0	0	1	1	2
341.0	0	2	0	2
342.0	0	2	0	3
343.0	0	4	0	2
344.0	0	3	0	1
345.0	0	4	0	1
346.0	0	2	0	2
347.0	0	3	0	0
348.0	0	6	0	1
349.0	0	3	0	3
350.0	0	2	0	0
351.0	0	3	0	0
352.0	0	1	1	2
353.0	0	3	0	2
354.0	0	2	0	6
355.0	0	1	0	0
356.0	0	5	0	2
357.0	0	1	0	1
358.0	0	3	0	3
359.0	0	5	0	1
360.0	0	2	0	1
361.0	0	2	0	0
362.0	0	4	0	2
363.0	0	3	0	2
364.0	0	2	0	0
365.0	0	2	0	2
366.0	0	1	0	3
367.0	0	1	0	1
368.0	0	1	0	4
369.0	0	1	0	3
370.0	0	2	1	3
371.0	0	3	1	0
372.0	0	3	0	2
373.0	0	1	0	3
374.0	0	2	0	1
375.0	0	0	0	4
376.0	0	0	0	4
377.0	0	2	0	1
378.0	0	2	0	2
379.0	0	1	0	1
380.0	0	2	1	3
381.0	0	2	1	1
382.0	0	3	0	1
383.0	0	1	0	0
384.0	0	5	0	4
385.0	0	3	0	5
386.0	0	3	0	2
387.0	0	2	0	2
388.0	0	5	0	0
389.0	0	4	0	0
390.0	0	2	1	1
392.0	0	1	0	2
394.0	0	0	0	3
395.0	0	2	0	2
396.0	0	4	0	3
397.0	0	5	0	1
398.0	0	3	0	2
399.0	0	1	0	0
400.0	0	5	0	1
401.0	0	2	0	1
402.0	0	4	0	2
403.0	0	2	0	4
404.0	0	0	0	3
405.0	0	5	0	1
406.0	0	0	0	1
407.0	0	3	0	2
408.0	0	5	0	1
409.0	0	3	0	3
410.0	0	3	0	3
411.0	0	6	0	1
412.0	0	3	1	2
413.0	0	3	0	3
414.0	0	3	0	1
415.0	0	3	0	0
417.0	0	0	0	1
418.0	0	1	0	1
419.0	0	2	0	2
420.0	0	2	0	1
421.0	0	1	0	0
422.0	0	1	0	3
423.0	0	4	0	1
424.0	0	2	0	1
425.0	0	0	0	2
426.0	0	2	0	0
427.0	0	0	0	2
428.0	0	2	0	1
429.0	0	2	0	0
430.0	0	5	0	1
431.0	0	0	0	2
432.0	0	3	0	1
433.0	0	1	0	4
435.0	0	4	0	2
436.0	0	2	0	1
437.0	0	2	0	3
438.0	0	4	0	3
439.0	0	1	0	2
440.0	0	0	0	2
441.0	0	8	0	3
442.0	0	2	0	1
444.0	0	1	0	1
445.0	0	3	0	1
446.0	0	1	0	2
447.0	0	3	0	1
448.0	0	2	0	1
449.0	0	0	0	2
450.0	0	1	0	3
451.0	0	2	0	2
452.0	0	2	0	2
453.0	0	5	0	1
454.0	0	0	0	2
455.0	0	1	0	1
456.0	0	2	0	2
457.0	0	1	0	4
458.0	0	2	0	1
459.0	0	1	0	1
460.0	0	2	0	0
461.0	0	1	0	0
462.0	0	2	0	1
463.0	0	5	0	1
464.0	0	1	0	3
465.0	0	2	0	0
467.0	0	0	0	1
468.0	0	2	0	1
469.0	0	2	0	1
470.0	0	2	0	1
471.0	0	2	0	0
472.0	0	2	0	0
475.0	0	1	0	0
476.0	0	0	0	3
478.0	0	1	0	2
479.0	0	1	0	0
480.0	0	2	0	2
482.0	0	1	0	2
483.0	0	0	0	1
485.0	0	4	0	2
486.0	0	2	0	2
487.0	0	1	0	2
489.0	0	1	0	1
490.0	0	2	0	0
491.0	0	0	0	3
492.0	0	1	0	2
493.0	0	1	0	1
494.0	0	0	0	1
495.0	0	1	0	1
496.0	0	2	0	1
497.0	0	1	0	0
498.0	0	1	0	1
499.0	0	2	0	0
500.0	0	1	0	3
501.0	0	2	0	0
504.0	0	2	0	0
505.0	0	1	0	2
507.0	0	2	0	1
508.0	0	1	0	0
509.0	0	3	0	0
510.0	0	2	0	2
511.0	0	5	0	1
512.0	0	1	0	1
514.0	0	1	0	1
516.0	0	1	0	0
517.0	0	1	0	1
518.0	0	2	0	0
519.0	0	1	0	2
520.0	0	2	0	1
521.0	0	4	0	0
522.0	0	3	0	0
523.0	0	0	0	1
524.0	0	2	0	1
526.0	0	0	0	2
527.0	0	1	0	0
528.0	0	2	0	1
529.0	0	2	0	0
530.0	0	1	0	0
531.0	0	1	0	1
532.0	0	1	0	0
535.0	0	1	0	1
536.0	0	4	0	0
538.0	0	0	0	1
539.0	0	1	0	2
540.0	0	1	0	1
541.0	0	2	0	1
543.0	0	1	0	0
544.0	0	3	0	0
545.0	0	1	0	2
546.0	0	2	0	0
547.0	0	1	0	0
548.0	0	0	0	1
549.0	0	1	0	0
550.0	0	3	0	0
551.0	0	0	0	2
552.0	0	0	0	1
553.0	0	1	0	1
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