## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[P08-female_bleached_K5.sorted.bam] OUTPUT=P08-female_bleached_K5.sorted.dedup.bam METRICS_FILE=P08-female_bleached_K5-picard_metrics.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT    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 ADD_PG_TAG_TO_READS=true ASSUME_SORTED=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 GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Thu Jul 18 15:20:36 PDT 2019

## 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	809104	27142801	0	1551384	503977	7175181	905318	0.269615	45750815

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.0253	15763057	0	16197894
2.0	1.591794	2908188	709941	2703046
3.0	1.90479	770368	72165	647218
4.0	2.077725	260346	11452	203455
5.0	2.173274	106962	2458	82114
6.0	2.226067	52076	691	40512
7.0	2.255235	28796	212	23647
8.0	2.271352	17758	104	15019
9.0	2.280256	12056	45	10545
10.0	2.285176	8577	31	7721
11.0	2.287894	6437	19	5853
12.0	2.289396	4856	5	4385
13.0	2.290226	3874	5	3629
14.0	2.290684	3073	7	2856
15.0	2.290938	2514	5	2322
16.0	2.291077	2123	3	1941
17.0	2.291155	1762	3	1656
18.0	2.291198	1520	1	1417
19.0	2.291221	1278	0	1208
20.0	2.291234	1158	2	1040
21.0	2.291241	961	0	902
22.0	2.291245	795	3	745
23.0	2.291248	776	0	690
24.0	2.291249	656	0	621
25.0	2.291249	556	0	573
26.0	2.29125	534	0	519
27.0	2.29125	482	2	459
28.0	2.29125	455	0	390
29.0	2.29125	372	0	370
30.0	2.29125	365	0	314
31.0	2.29125	317	0	317
32.0	2.29125	287	0	226
33.0	2.29125	271	0	268
34.0	2.29125	243	0	236
35.0	2.29125	215	0	201
36.0	2.29125	201	0	167
37.0	2.29125	163	1	144
38.0	2.29125	169	0	168
39.0	2.29125	161	0	151
40.0	2.29125	129	0	137
41.0	2.29125	121	0	117
42.0	2.29125	143	0	132
43.0	2.29125	124	0	97
44.0	2.29125	96	0	96
45.0	2.29125	113	0	93
46.0	2.29125	96	0	85
47.0	2.29125	93	0	84
48.0	2.29125	81	0	83
49.0	2.29125	62	0	76
50.0	2.29125	72	0	81
51.0	2.29125	72	0	50
52.0	2.29125	67	0	58
53.0	2.29125	61	0	46
54.0	2.29125	51	0	56
55.0	2.29125	53	0	46
56.0	2.29125	47	0	43
57.0	2.29125	52	0	53
58.0	2.29125	38	0	59
59.0	2.29125	51	0	45
60.0	2.29125	50	0	39
61.0	2.29125	41	0	31
62.0	2.29125	42	0	43
63.0	2.29125	31	0	32
64.0	2.29125	33	0	31
65.0	2.29125	33	0	30
66.0	2.29125	32	0	29
67.0	2.29125	31	0	26
68.0	2.29125	32	0	29
69.0	2.29125	26	0	26
70.0	2.29125	34	0	37
71.0	2.29125	32	0	24
72.0	2.29125	28	0	24
73.0	2.29125	27	0	21
74.0	2.29125	33	0	27
75.0	2.29125	10	0	11
76.0	2.29125	13	0	15
77.0	2.29125	22	0	15
78.0	2.29125	20	0	14
79.0	2.29125	11	0	22
80.0	2.29125	17	0	15
81.0	2.29125	18	0	20
82.0	2.29125	12	0	17
83.0	2.29125	18	0	12
84.0	2.29125	20	0	17
85.0	2.29125	13	0	14
86.0	2.29125	15	0	16
87.0	2.29125	12	0	12
88.0	2.29125	11	0	14
89.0	2.29125	17	0	16
90.0	2.29125	14	0	13
91.0	2.29125	17	0	10
92.0	2.29125	12	0	11
93.0	2.29125	12	0	2
94.0	2.29125	14	0	13
95.0	2.29125	14	0	17
96.0	2.29125	6	0	4
97.0	2.29125	9	0	6
98.0	2.29125	9	0	3
99.0	2.29125	7	0	8
100.0	2.29125	0	0	9
101.0	0	4	0	15
102.0	0	8	0	3
103.0	0	6	0	4
104.0	0	8	0	7
105.0	0	5	0	9
106.0	0	8	0	4
107.0	0	7	0	4
108.0	0	7	0	3
109.0	0	10	0	10
110.0	0	8	0	9
111.0	0	9	0	5
112.0	0	5	0	6
113.0	0	3	0	4
114.0	0	5	0	7
115.0	0	7	0	3
116.0	0	2	0	3
117.0	0	6	0	5
118.0	0	6	0	7
119.0	0	5	0	3
120.0	0	2	0	4
121.0	0	5	0	8
122.0	0	5	0	3
123.0	0	4	0	3
124.0	0	6	0	6
125.0	0	4	0	2
126.0	0	6	0	6
127.0	0	3	0	7
128.0	0	6	0	5
129.0	0	4	0	2
130.0	0	3	0	3
131.0	0	3	0	2
132.0	0	0	0	5
133.0	0	7	0	9
134.0	0	4	0	3
135.0	0	6	0	2
136.0	0	6	0	1
137.0	0	4	0	1
138.0	0	2	0	2
139.0	0	2	0	0
140.0	0	2	0	4
141.0	0	3	0	3
142.0	0	4	0	5
143.0	0	3	0	4
144.0	0	2	0	3
145.0	0	3	0	3
146.0	0	5	0	2
147.0	0	3	0	1
148.0	0	4	0	4
149.0	0	1	0	5
150.0	0	1	0	3
151.0	0	3	0	4
152.0	0	3	0	1
153.0	0	2	0	3
154.0	0	2	0	1
155.0	0	5	0	1
156.0	0	4	0	4
157.0	0	3	0	2
158.0	0	3	0	1
159.0	0	0	0	3
160.0	0	2	0	4
161.0	0	1	0	0
162.0	0	2	0	2
163.0	0	0	0	3
164.0	0	2	0	2
166.0	0	2	0	3
167.0	0	4	0	0
168.0	0	2	0	0
169.0	0	1	0	1
170.0	0	1	0	0
171.0	0	3	0	0
172.0	0	0	0	2
173.0	0	0	0	1
174.0	0	1	0	1
175.0	0	1	0	1
176.0	0	2	0	0
177.0	0	1	0	1
178.0	0	1	0	0
179.0	0	1	0	0
180.0	0	0	0	1
181.0	0	0	0	2
182.0	0	2	0	0
183.0	0	1	0	1
184.0	0	1	0	1
186.0	0	0	0	1
187.0	0	1	0	3
189.0	0	3	0	0
190.0	0	0	0	2
191.0	0	1	0	0
192.0	0	1	0	0
194.0	0	0	0	1
195.0	0	1	0	1
197.0	0	1	0	0
198.0	0	1	0	2
199.0	0	1	0	1
200.0	0	3	0	0
201.0	0	1	0	1
202.0	0	0	0	1
204.0	0	1	0	0
206.0	0	1	0	0
207.0	0	0	0	1
209.0	0	0	0	1
210.0	0	0	0	2
212.0	0	0	0	1
213.0	0	1	0	1
214.0	0	1	0	0
215.0	0	0	0	1
216.0	0	1	0	1
217.0	0	3	0	0
218.0	0	1	0	0
219.0	0	0	0	2
222.0	0	0	0	1
223.0	0	1	0	2
224.0	0	1	0	0
225.0	0	0	0	1
226.0	0	1	0	0
227.0	0	0	0	1
228.0	0	1	0	1
229.0	0	1	0	1
230.0	0	2	0	0
231.0	0	0	0	1
232.0	0	0	0	1
233.0	0	1	0	1
234.0	0	0	0	2
235.0	0	1	0	0
236.0	0	1	0	0
237.0	0	1	0	1
239.0	0	1	0	1
240.0	0	1	0	1
241.0	0	1	0	1
242.0	0	1	0	1
243.0	0	0	0	2
244.0	0	2	0	0
246.0	0	2	0	1
248.0	0	0	0	2
249.0	0	1	0	1
250.0	0	1	0	0
252.0	0	0	0	1
253.0	0	1	0	0
254.0	0	0	0	1
256.0	0	1	0	0
257.0	0	1	0	1
258.0	0	2	0	1
259.0	0	0	0	1
261.0	0	0	0	2
262.0	0	1	0	0
263.0	0	0	0	1
264.0	0	1	0	0
265.0	0	0	0	2
266.0	0	1	0	0
267.0	0	1	0	0
268.0	0	1	0	1
269.0	0	1	0	1
271.0	0	1	0	2
272.0	0	1	0	0
273.0	0	1	0	0
277.0	0	0	0	1
278.0	0	1	0	0
280.0	0	1	0	1
284.0	0	2	0	1
286.0	0	0	0	1
288.0	0	1	0	0
289.0	0	1	0	0
290.0	0	2	0	0
291.0	0	1	0	0
292.0	0	0	0	2
296.0	0	0	0	2
297.0	0	0	0	1
298.0	0	1	0	0
301.0	0	2	0	0
302.0	0	1	0	0
304.0	0	0	0	1
306.0	0	1	0	0
307.0	0	0	0	1
309.0	0	1	0	0
312.0	0	0	0	1
316.0	0	1	0	0
319.0	0	0	0	1
320.0	0	0	0	1
321.0	0	1	0	0
328.0	0	1	0	0
329.0	0	1	0	0
333.0	0	0	0	1
341.0	0	0	0	1
344.0	0	0	0	2
346.0	0	1	0	0
348.0	0	1	0	0
350.0	0	0	0	1
354.0	0	0	0	1
357.0	0	1	0	0
358.0	0	1	0	0
360.0	0	2	0	0
365.0	0	0	0	2
371.0	0	1	0	0
373.0	0	1	0	0
376.0	0	0	0	1
386.0	0	1	0	0
396.0	0	0	0	1
401.0	0	1	0	0
408.0	0	0	0	1
411.0	0	0	0	1
416.0	0	1	0	0
417.0	0	0	0	1
420.0	0	1	0	0
421.0	0	0	0	1
423.0	0	1	0	0
424.0	0	1	0	0
426.0	0	0	0	1
432.0	0	1	0	0
438.0	0	0	0	1
447.0	0	1	0	0
463.0	0	0	0	1
478.0	0	1	0	0
519.0	0	0	0	1
531.0	0	1	0	0
544.0	0	0	0	1
556.0	0	1	0	0
561.0	0	0	0	1
564.0	0	0	0	1
566.0	0	1	0	0
568.0	0	1	0	0
592.0	0	0	0	1
604.0	0	1	0	0
627.0	0	0	0	1
641.0	0	1	0	0
827.0	0	0	0	1
846.0	0	1	0	0
931.0	0	0	0	1
952.0	0	1	0	0
1132.0	0	0	0	1
1168.0	0	1	0	0
1187.0	0	0	0	1
1213.0	0	1	0	0