## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POR-73-TP4.bam --OUTPUT POR-73-TP4.md.bam --METRICS_FILE POR-73-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 18:17:57 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	3036	16277939	9824536	0	2922	13246051	3872299	0.813756	3087420

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.01309	1519297	0	1938697
2.0	1.018289	600566	445746	521859
3.0	1.018316	273964	188167	167192
4.0	1.018316	147929	100117	78714
5.0	1.018316	90664	59147	49017
6.0	1.018316	60035	37010	35062
7.0	1.018316	42847	24792	26876
8.0	1.018316	32886	17354	21466
9.0	1.018316	25680	12780	17617
10.0	1.018316	20920	9561	14848
11.0	1.018316	17242	7652	12600
12.0	1.018316	14903	5990	10633
13.0	1.018316	12729	5130	9482
14.0	1.018316	11155	4217	8179
15.0	1.018316	9670	3641	7290
16.0	1.018316	8772	3114	6586
17.0	1.018316	7830	2695	5831
18.0	1.018316	6982	2406	5374
19.0	1.018316	6297	2070	4792
20.0	1.018316	5792	1875	4272
21.0	1.018316	5424	1686	3939
22.0	1.018316	4875	1514	3611
23.0	1.018316	4528	1271	3322
24.0	1.018316	4191	1227	3226
25.0	1.018316	3847	1179	2919
26.0	1.018316	3632	982	2765
27.0	1.018316	3367	912	2449
28.0	1.018316	3158	830	2378
29.0	1.018316	3043	727	2234
30.0	1.018316	2768	759	2076
31.0	1.018316	2724	677	1856
32.0	1.018316	2472	626	1846
33.0	1.018316	2219	603	1728
34.0	1.018316	2213	556	1616
35.0	1.018316	2135	515	1629
36.0	1.018316	1917	446	1464
37.0	1.018316	1766	436	1342
38.0	1.018316	1764	417	1338
39.0	1.018316	1691	391	1271
40.0	1.018316	1608	373	1199
41.0	1.018316	1542	351	1080
42.0	1.018316	1450	317	1068
43.0	1.018316	1362	308	1031
44.0	1.018316	1323	309	983
45.0	1.018316	1282	261	981
46.0	1.018316	1190	293	868
47.0	1.018316	1181	258	880
48.0	1.018316	1081	253	811
49.0	1.018316	1045	237	796
50.0	1.018316	1030	241	795
51.0	1.018316	985	214	723
52.0	1.018316	937	200	668
53.0	1.018316	923	188	697
54.0	1.018316	883	167	652
55.0	1.018316	843	191	627
56.0	1.018316	831	176	564
57.0	1.018316	815	156	563
58.0	1.018316	782	134	523
59.0	1.018316	732	156	580
60.0	1.018316	653	122	523
61.0	1.018316	698	132	554
62.0	1.018316	672	128	481
63.0	1.018316	601	129	479
64.0	1.018316	645	116	478
65.0	1.018316	671	101	437
66.0	1.018316	586	122	470
67.0	1.018316	577	128	410
68.0	1.018316	573	100	417
69.0	1.018316	538	80	409
70.0	1.018316	503	101	359
71.0	1.018316	492	91	378
72.0	1.018316	481	90	376
73.0	1.018316	469	90	365
74.0	1.018316	471	89	344
75.0	1.018316	409	94	328
76.0	1.018316	415	91	307
77.0	1.018316	436	71	327
78.0	1.018316	377	78	291
79.0	1.018316	400	77	303
80.0	1.018316	414	69	285
81.0	1.018316	401	71	275
82.0	1.018316	394	60	275
83.0	1.018316	393	55	255
84.0	1.018316	347	78	278
85.0	1.018316	347	62	243
86.0	1.018316	342	51	279
87.0	1.018316	343	57	243
88.0	1.018316	330	55	262
89.0	1.018316	315	56	243
90.0	1.018316	306	57	227
91.0	1.018316	314	60	251
92.0	1.018316	297	50	224
93.0	1.018316	300	38	224
94.0	1.018316	296	55	203
95.0	1.018316	280	51	201
96.0	1.018316	276	44	186
97.0	1.018316	237	41	182
98.0	1.018316	216	48	165
99.0	1.018316	261	43	185
100.0	1.018316	252	41	157
101.0	0	254	43	167
102.0	0	253	36	167
103.0	0	272	47	177
104.0	0	237	45	174
105.0	0	184	44	176
106.0	0	226	46	163
107.0	0	230	26	120
108.0	0	205	22	183
109.0	0	207	28	126
110.0	0	211	32	142
111.0	0	202	33	144
112.0	0	182	27	145
113.0	0	184	26	122
114.0	0	180	31	130
115.0	0	205	29	133
116.0	0	181	29	145
117.0	0	174	27	109
118.0	0	160	23	115
119.0	0	168	23	140
120.0	0	174	22	124
121.0	0	146	21	124
122.0	0	136	27	132
123.0	0	153	24	137
124.0	0	149	26	98
125.0	0	153	24	114
126.0	0	149	12	107
127.0	0	156	25	105
128.0	0	154	23	104
129.0	0	147	18	94
130.0	0	131	15	98
131.0	0	144	20	105
132.0	0	134	17	118
133.0	0	153	23	88
134.0	0	141	18	98
135.0	0	136	27	103
136.0	0	123	17	90
137.0	0	124	17	92
138.0	0	137	14	94
139.0	0	113	15	87
140.0	0	128	16	89
141.0	0	107	11	83
142.0	0	133	15	98
143.0	0	126	11	91
144.0	0	115	14	66
145.0	0	106	12	76
146.0	0	109	14	79
147.0	0	107	18	74
148.0	0	103	17	67
149.0	0	114	15	72
150.0	0	93	20	85
151.0	0	97	13	76
152.0	0	120	15	75
153.0	0	98	7	70
154.0	0	98	11	57
155.0	0	105	15	64
156.0	0	73	12	54
157.0	0	78	13	57
158.0	0	93	15	69
159.0	0	104	9	63
160.0	0	91	9	70
161.0	0	74	10	68
162.0	0	97	13	56
163.0	0	84	16	58
164.0	0	74	16	56
165.0	0	74	8	62
166.0	0	90	10	70
167.0	0	66	14	50
168.0	0	95	14	50
169.0	0	66	13	52
170.0	0	71	15	63
171.0	0	76	5	57
172.0	0	79	12	53
173.0	0	89	7	49
174.0	0	64	5	53
175.0	0	63	6	50
176.0	0	65	6	46
177.0	0	70	11	45
178.0	0	63	11	48
179.0	0	62	5	37
180.0	0	76	6	61
181.0	0	65	7	49
182.0	0	61	10	48
183.0	0	61	8	31
184.0	0	54	8	51
185.0	0	65	7	36
186.0	0	59	7	36
187.0	0	69	9	36
188.0	0	64	4	41
189.0	0	44	10	42
190.0	0	40	9	49
191.0	0	61	4	35
192.0	0	56	9	38
193.0	0	70	0	37
194.0	0	58	2	50
195.0	0	45	11	45
196.0	0	60	2	33
197.0	0	40	11	22
198.0	0	41	6	43
199.0	0	59	10	47
200.0	0	46	5	34
201.0	0	60	2	36
202.0	0	56	6	36
203.0	0	56	7	39
204.0	0	53	1	40
205.0	0	57	4	37
206.0	0	48	6	36
207.0	0	52	9	34
208.0	0	55	7	41
209.0	0	38	7	38
210.0	0	52	5	33
211.0	0	52	8	36
212.0	0	45	6	38
213.0	0	49	6	36
214.0	0	37	6	33
215.0	0	36	8	31
216.0	0	39	4	38
217.0	0	47	11	30
218.0	0	52	3	32
219.0	0	36	5	29
220.0	0	52	3	34
221.0	0	46	5	33
222.0	0	47	5	31
223.0	0	47	6	28
224.0	0	37	3	30
225.0	0	48	2	27
226.0	0	29	5	22
227.0	0	38	7	28
228.0	0	38	7	28
229.0	0	33	2	31
230.0	0	37	5	30
231.0	0	41	4	25
232.0	0	40	5	43
233.0	0	27	6	25
234.0	0	37	3	23
235.0	0	39	7	26
236.0	0	40	2	18
237.0	0	33	5	27
238.0	0	32	2	19
239.0	0	37	4	22
240.0	0	33	2	28
241.0	0	37	5	25
242.0	0	42	6	19
243.0	0	30	2	28
244.0	0	41	6	20
245.0	0	28	5	28
246.0	0	32	4	25
247.0	0	32	2	28
248.0	0	33	3	21
249.0	0	36	1	19
250.0	0	29	2	23
251.0	0	36	0	26
252.0	0	32	4	19
253.0	0	26	5	27
254.0	0	33	2	24
255.0	0	37	3	23
256.0	0	24	5	22
257.0	0	28	5	27
258.0	0	33	2	16
259.0	0	34	3	19
260.0	0	26	1	29
261.0	0	22	6	19
262.0	0	27	4	21
263.0	0	23	4	20
264.0	0	34	2	26
265.0	0	35	3	22
266.0	0	23	2	18
267.0	0	34	4	21
268.0	0	25	2	10
269.0	0	27	0	19
270.0	0	26	2	11
271.0	0	21	2	19
272.0	0	22	1	16
273.0	0	22	2	28
274.0	0	23	0	15
275.0	0	14	6	17
276.0	0	21	3	14
277.0	0	28	1	11
278.0	0	37	4	13
279.0	0	28	1	15
280.0	0	30	3	15
281.0	0	28	3	16
282.0	0	24	3	25
283.0	0	24	1	12
284.0	0	18	4	21
285.0	0	29	5	26
286.0	0	19	3	13
287.0	0	22	1	15
288.0	0	27	3	17
289.0	0	20	7	19
290.0	0	19	5	18
291.0	0	14	2	21
292.0	0	20	5	14
293.0	0	19	1	15
294.0	0	32	2	17
295.0	0	26	0	21
296.0	0	21	4	14
297.0	0	24	1	12
298.0	0	16	4	15
299.0	0	23	3	12
300.0	0	24	1	15
301.0	0	29	2	19
302.0	0	16	0	14
303.0	0	19	2	13
304.0	0	23	2	16
305.0	0	15	5	6
306.0	0	29	5	12
307.0	0	17	4	12
308.0	0	19	2	12
309.0	0	20	3	15
310.0	0	11	2	18
311.0	0	12	2	12
312.0	0	20	3	18
313.0	0	15	1	12
314.0	0	20	2	11
315.0	0	15	1	11
316.0	0	11	0	11
317.0	0	17	0	14
318.0	0	17	3	13
319.0	0	18	3	13
320.0	0	15	1	14
321.0	0	19	3	8
322.0	0	10	2	11
323.0	0	21	2	16
324.0	0	17	2	8
325.0	0	17	3	16
326.0	0	21	4	7
327.0	0	13	3	12
328.0	0	15	2	5
329.0	0	18	3	10
330.0	0	10	1	7
331.0	0	13	0	16
332.0	0	15	2	13
333.0	0	11	3	15
334.0	0	15	2	15
335.0	0	16	1	12
336.0	0	17	0	10
337.0	0	14	1	11
338.0	0	12	2	10
339.0	0	20	0	12
340.0	0	18	0	9
341.0	0	17	1	16
342.0	0	13	2	10
343.0	0	11	0	18
344.0	0	11	5	10
345.0	0	16	1	13
346.0	0	9	0	15
347.0	0	13	1	13
348.0	0	7	5	10
349.0	0	12	2	8
350.0	0	18	1	8
351.0	0	15	2	9
352.0	0	14	1	11
353.0	0	10	1	12
354.0	0	18	2	20
355.0	0	14	1	12
356.0	0	10	1	5
357.0	0	9	1	9
358.0	0	17	1	5
359.0	0	11	1	10
360.0	0	15	0	17
361.0	0	13	3	11
362.0	0	16	0	14
363.0	0	11	0	9
364.0	0	12	1	12
365.0	0	15	2	6
366.0	0	14	3	4
367.0	0	10	0	8
368.0	0	20	2	7
369.0	0	13	1	7
370.0	0	13	2	10
371.0	0	13	2	10
372.0	0	9	1	3
373.0	0	11	2	16
374.0	0	18	2	13
375.0	0	10	2	10
376.0	0	14	1	8
377.0	0	10	2	8
378.0	0	11	4	6
379.0	0	11	1	3
380.0	0	9	2	9
381.0	0	23	3	10
382.0	0	13	1	9
383.0	0	5	1	8
384.0	0	8	0	10
385.0	0	9	1	10
386.0	0	7	0	8
387.0	0	13	1	8
388.0	0	8	0	6
389.0	0	11	2	8
390.0	0	16	1	6
391.0	0	9	0	5
392.0	0	11	0	16
393.0	0	11	2	10
394.0	0	17	0	5
395.0	0	16	1	8
396.0	0	7	1	8
397.0	0	9	0	6
398.0	0	6	1	9
399.0	0	11	0	10
400.0	0	11	1	6
401.0	0	11	0	4
402.0	0	7	1	5
403.0	0	8	1	12
404.0	0	17	0	8
405.0	0	13	1	7
406.0	0	10	0	8
407.0	0	12	1	10
408.0	0	6	1	6
409.0	0	11	0	6
410.0	0	7	1	6
411.0	0	11	0	7
412.0	0	16	2	5
413.0	0	8	1	3
414.0	0	10	2	5
415.0	0	8	0	8
416.0	0	8	4	6
417.0	0	14	1	11
418.0	0	8	0	1
419.0	0	14	1	7
420.0	0	13	2	6
421.0	0	8	0	3
422.0	0	8	0	1
423.0	0	8	0	12
424.0	0	6	0	7
425.0	0	2	2	11
426.0	0	16	1	6
427.0	0	11	0	5
428.0	0	12	0	3
429.0	0	11	1	8
430.0	0	2	0	4
431.0	0	7	1	6
432.0	0	10	1	4
433.0	0	7	0	4
434.0	0	6	0	4
435.0	0	8	1	6
436.0	0	6	0	4
437.0	0	6	1	3
438.0	0	9	0	9
439.0	0	5	3	6
440.0	0	8	3	5
441.0	0	8	2	3
442.0	0	6	0	4
443.0	0	6	1	0
444.0	0	6	0	7
445.0	0	3	0	6
446.0	0	7	0	5
447.0	0	14	2	4
448.0	0	8	0	5
449.0	0	6	1	7
450.0	0	5	1	2
451.0	0	7	2	4
452.0	0	5	1	7
453.0	0	6	0	6
454.0	0	8	1	4
455.0	0	7	1	6
456.0	0	3	0	5
457.0	0	14	0	7
458.0	0	16	1	4
459.0	0	4	0	9
460.0	0	3	0	7
461.0	0	6	0	6
462.0	0	7	0	4
463.0	0	10	2	5
464.0	0	6	0	9
465.0	0	9	0	5
466.0	0	9	0	4
467.0	0	10	0	8
468.0	0	6	0	8
469.0	0	8	0	6
470.0	0	3	2	5
471.0	0	7	1	5
472.0	0	6	0	4
473.0	0	10	1	7
474.0	0	5	0	3
475.0	0	2	0	3
476.0	0	6	1	5
477.0	0	8	0	4
478.0	0	4	0	4
479.0	0	8	0	2
480.0	0	8	1	6
481.0	0	7	0	3
482.0	0	4	0	5
483.0	0	5	0	5
484.0	0	8	1	6
485.0	0	10	1	1
486.0	0	6	1	2
487.0	0	5	0	7
488.0	0	7	1	8
489.0	0	7	0	2
490.0	0	6	0	2
491.0	0	4	0	3
492.0	0	2	0	6
493.0	0	4	0	4
494.0	0	2	2	3
495.0	0	7	0	3
496.0	0	5	2	3
497.0	0	6	0	2
498.0	0	4	0	4
499.0	0	5	0	6
500.0	0	2	0	3
501.0	0	3	0	3
502.0	0	8	0	3
503.0	0	7	0	7
504.0	0	8	0	3
505.0	0	4	1	2
506.0	0	6	0	4
507.0	0	6	0	7
508.0	0	6	0	4
509.0	0	6	0	4
510.0	0	5	1	6
511.0	0	4	0	7
512.0	0	6	0	2
513.0	0	7	1	5
514.0	0	4	0	3
515.0	0	5	0	5
516.0	0	7	1	4
517.0	0	5	0	2
518.0	0	5	2	1
519.0	0	4	2	8
520.0	0	7	0	7
521.0	0	8	1	6
522.0	0	4	0	4
523.0	0	5	1	9
524.0	0	5	0	2
525.0	0	8	0	6
526.0	0	8	2	4
527.0	0	6	0	6
528.0	0	3	0	2
529.0	0	9	0	2
530.0	0	5	0	2
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