## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[P06-male_bleached_K5.sorted.bam] OUTPUT=P06-male_bleached_K5.sorted.dedup.bam METRICS_FILE=P06-male_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 13:59:14 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	696475	17002778	0	2031905	409781	7081629	546169	0.419948	14764693

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.017729	6375141	0	6515569
2.0	1.33947	2034853	407591	2021920
3.0	1.441184	786157	48335	750302
4.0	1.473339	342427	8942	311328
5.0	1.483505	164219	2157	142617
6.0	1.486718	84515	572	70460
7.0	1.487734	46208	202	37042
8.0	1.488055	26290	102	20463
9.0	1.488157	15843	47	12570
10.0	1.488189	10073	33	8037
11.0	1.488199	6934	21	5641
12.0	1.488202	4952	14	4062
13.0	1.488203	3607	13	2986
14.0	1.488204	2836	7	2430
15.0	1.488204	2085	7	1784
16.0	1.488204	1661	2	1570
17.0	1.488204	1417	3	1265
18.0	1.488204	1183	1	1088
19.0	1.488204	1007	1	914
20.0	1.488204	900	1	822
21.0	1.488204	726	1	660
22.0	1.488204	676	1	636
23.0	1.488204	534	0	512
24.0	1.488204	524	0	487
25.0	1.488204	447	1	396
26.0	1.488204	381	0	384
27.0	1.488204	371	0	357
28.0	1.488204	335	2	288
29.0	1.488204	299	0	297
30.0	1.488204	266	0	256
31.0	1.488204	271	0	245
32.0	1.488204	207	0	184
33.0	1.488204	203	0	205
34.0	1.488204	184	0	157
35.0	1.488204	157	0	170
36.0	1.488204	165	1	154
37.0	1.488204	160	0	148
38.0	1.488204	156	0	144
39.0	1.488204	134	0	128
40.0	1.488204	126	0	118
41.0	1.488204	110	0	110
42.0	1.488204	117	0	109
43.0	1.488204	90	0	94
44.0	1.488204	110	0	108
45.0	1.488204	88	0	66
46.0	1.488204	87	0	74
47.0	1.488204	99	0	97
48.0	1.488204	72	0	75
49.0	1.488204	69	0	70
50.0	1.488204	80	0	72
51.0	1.488204	65	0	54
52.0	1.488204	55	0	56
53.0	1.488204	68	0	48
54.0	1.488204	55	0	49
55.0	1.488204	48	0	56
56.0	1.488204	45	0	46
57.0	1.488204	47	0	31
58.0	1.488204	36	0	33
59.0	1.488204	36	0	34
60.0	1.488204	32	0	30
61.0	1.488204	31	0	29
62.0	1.488204	31	0	34
63.0	1.488204	28	0	39
64.0	1.488204	38	0	38
65.0	1.488204	32	0	30
66.0	1.488204	29	0	32
67.0	1.488204	33	0	33
68.0	1.488204	34	0	25
69.0	1.488204	29	0	22
70.0	1.488204	24	0	26
71.0	1.488204	24	0	26
72.0	1.488204	29	0	11
73.0	1.488204	21	0	21
74.0	1.488204	18	0	15
75.0	1.488204	17	0	14
76.0	1.488204	20	0	11
77.0	1.488204	20	0	22
78.0	1.488204	19	0	22
79.0	1.488204	15	0	21
80.0	1.488204	19	0	8
81.0	1.488204	11	0	14
82.0	1.488204	20	0	10
83.0	1.488204	9	0	17
84.0	1.488204	10	0	18
85.0	1.488204	15	0	11
86.0	1.488204	19	0	12
87.0	1.488204	9	0	12
88.0	1.488204	12	0	11
89.0	1.488204	19	0	14
90.0	1.488204	11	0	14
91.0	1.488204	9	0	9
92.0	1.488204	13	0	12
93.0	1.488204	9	0	6
94.0	1.488204	8	0	8
95.0	1.488204	16	0	14
96.0	1.488204	10	0	4
97.0	1.488204	9	0	6
98.0	1.488204	8	0	4
99.0	1.488204	4	0	7
100.0	1.488204	9	0	9
101.0	0	3	0	9
102.0	0	6	0	3
103.0	0	5	0	5
104.0	0	6	0	4
105.0	0	4	0	5
106.0	0	5	0	7
107.0	0	9	0	6
108.0	0	3	0	8
109.0	0	6	0	5
110.0	0	6	0	8
111.0	0	12	0	7
112.0	0	6	0	5
113.0	0	5	0	1
114.0	0	6	0	4
115.0	0	4	0	3
116.0	0	3	0	3
117.0	0	0	0	8
118.0	0	6	0	4
119.0	0	6	0	3
120.0	0	6	0	4
121.0	0	2	0	4
122.0	0	3	0	7
123.0	0	2	0	6
124.0	0	6	0	4
125.0	0	2	0	2
126.0	0	4	0	2
127.0	0	3	0	2
128.0	0	3	0	3
129.0	0	6	0	3
130.0	0	3	0	1
131.0	0	4	0	1
132.0	0	2	0	4
133.0	0	3	0	4
134.0	0	1	0	3
135.0	0	3	0	1
136.0	0	1	0	2
137.0	0	1	0	4
138.0	0	4	0	2
139.0	0	2	0	3
140.0	0	5	0	1
141.0	0	2	0	3
142.0	0	1	0	2
143.0	0	1	0	0
144.0	0	2	0	1
145.0	0	2	0	5
146.0	0	4	0	3
147.0	0	5	0	2
148.0	0	3	0	2
149.0	0	4	0	6
150.0	0	4	0	1
151.0	0	3	0	2
152.0	0	4	0	7
153.0	0	1	0	2
154.0	0	4	0	2
155.0	0	6	0	1
156.0	0	2	0	2
157.0	0	0	0	3
158.0	0	3	0	0
160.0	0	1	0	1
161.0	0	1	0	1
162.0	0	1	0	0
163.0	0	0	0	1
164.0	0	1	0	2
165.0	0	1	0	0
167.0	0	1	0	1
168.0	0	3	0	2
169.0	0	0	0	3
170.0	0	2	0	0
171.0	0	3	0	2
172.0	0	0	0	5
173.0	0	3	0	1
174.0	0	2	0	0
175.0	0	2	0	3
176.0	0	0	0	1
177.0	0	1	0	6
179.0	0	3	0	3
180.0	0	4	0	1
181.0	0	3	0	3
182.0	0	1	0	1
183.0	0	2	0	0
184.0	0	4	0	3
185.0	0	2	0	2
186.0	0	2	0	2
187.0	0	0	0	5
189.0	0	0	0	2
190.0	0	6	0	1
191.0	0	0	0	1
192.0	0	2	0	1
193.0	0	1	0	3
194.0	0	1	0	1
195.0	0	2	0	1
196.0	0	3	0	3
197.0	0	2	0	0
198.0	0	3	0	2
199.0	0	1	0	2
200.0	0	4	0	1
201.0	0	0	0	2
202.0	0	0	0	1
203.0	0	1	0	1
204.0	0	3	0	0
205.0	0	1	0	2
206.0	0	2	0	2
207.0	0	2	0	1
208.0	0	1	0	1
209.0	0	2	0	0
210.0	0	0	0	3
211.0	0	0	0	1
212.0	0	2	0	2
213.0	0	1	0	1
214.0	0	1	0	2
215.0	0	2	0	1
216.0	0	3	0	1
217.0	0	0	0	1
219.0	0	2	0	1
220.0	0	0	0	1
221.0	0	0	0	1
222.0	0	1	0	1
223.0	0	1	0	2
224.0	0	1	0	2
225.0	0	0	0	1
227.0	0	1	0	0
228.0	0	3	0	0
229.0	0	1	0	2
230.0	0	1	0	0
231.0	0	1	0	0
232.0	0	2	0	0
233.0	0	0	0	2
234.0	0	1	0	1
235.0	0	0	0	2
237.0	0	1	0	2
238.0	0	2	0	0
239.0	0	0	0	1
240.0	0	1	0	1
241.0	0	2	0	0
242.0	0	1	0	0
244.0	0	3	0	0
247.0	0	1	0	0
249.0	0	0	0	1
250.0	0	0	0	1
251.0	0	0	0	1
253.0	0	1	0	0
254.0	0	0	0	1
255.0	0	1	0	1
256.0	0	0	0	1
257.0	0	1	0	1
258.0	0	1	0	0
263.0	0	1	0	0
264.0	0	0	0	1
265.0	0	0	0	1
267.0	0	1	0	0
268.0	0	0	0	1
269.0	0	1	0	0
271.0	0	0	0	1
273.0	0	0	0	2
274.0	0	1	0	0
275.0	0	2	0	0
276.0	0	1	0	0
280.0	0	1	0	0
282.0	0	1	0	0
285.0	0	0	0	1
289.0	0	1	0	0
294.0	0	0	0	1
302.0	0	0	0	1
303.0	0	0	0	1
306.0	0	0	0	1
308.0	0	1	0	0
309.0	0	0	0	1
311.0	0	1	0	0
312.0	0	1	0	0
316.0	0	1	0	0
317.0	0	1	0	0
322.0	0	0	0	1
332.0	0	1	0	0
344.0	0	0	0	1
349.0	0	0	0	1
354.0	0	1	0	0
361.0	0	0	0	1
367.0	0	0	0	1
368.0	0	2	0	0
372.0	0	0	0	1
378.0	0	1	0	1
379.0	0	1	0	0
382.0	0	0	0	2
388.0	0	1	0	0
390.0	0	1	0	0
393.0	0	1	0	0
407.0	0	0	0	1
418.0	0	1	0	0
448.0	0	0	0	1
458.0	0	1	0	0
465.0	0	0	0	1
483.0	0	1	0	0
509.0	0	0	0	1
517.0	0	0	0	1
525.0	0	1	0	0
536.0	0	1	0	0
624.0	0	0	0	1
638.0	0	1	0	0
900.0	0	0	0	1
935.0	0	1	0	0
1034.0	0	0	0	1
1061.0	0	1	0	0