## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[P04-female_nonbleached_44.sorted.bam] OUTPUT=P04-female_nonbleached_44.sorted.dedup.bam METRICS_FILE=P04-female_nonbleached_44-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 12:45:26 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	886178	21124432	0	1858658	616444	8661251	588576	0.415879	18697490

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.015501	7884132	0	8026193
2.0	1.343607	2641375	452665	2639027
3.0	1.449617	1040036	49756	1005259
4.0	1.483869	450847	8357	417406
5.0	1.494936	210094	1794	184595
6.0	1.498511	103527	451	86698
7.0	1.499667	53990	143	42664
8.0	1.50004	28765	44	21781
9.0	1.500161	16277	25	12072
10.0	1.5002	9488	13	7081
11.0	1.500212	5923	9	4428
12.0	1.500216	3843	4	3004
13.0	1.500217	2688	3	2156
14.0	1.500218	1926	5	1506
15.0	1.500218	1440	1	1241
16.0	1.500218	1134	2	965
17.0	1.500218	940	1	820
18.0	1.500218	708	1	688
19.0	1.500218	628	1	555
20.0	1.500218	533	1	494
21.0	1.500218	453	0	424
22.0	1.500218	395	1	343
23.0	1.500218	331	2	327
24.0	1.500218	306	0	277
25.0	1.500218	280	0	248
26.0	1.500218	230	0	222
27.0	1.500218	216	0	210
28.0	1.500218	183	0	156
29.0	1.500218	165	0	155
30.0	1.500218	143	0	129
31.0	1.500218	138	0	137
32.0	1.500218	144	0	139
33.0	1.500218	120	0	115
34.0	1.500218	111	0	105
35.0	1.500218	88	0	72
36.0	1.500218	92	0	78
37.0	1.500218	87	0	89
38.0	1.500218	73	0	72
39.0	1.500218	59	0	60
40.0	1.500218	77	0	70
41.0	1.500218	54	0	53
42.0	1.500218	57	0	35
43.0	1.500218	46	0	54
44.0	1.500218	33	0	49
45.0	1.500218	54	0	44
46.0	1.500218	46	0	35
47.0	1.500218	50	0	35
48.0	1.500218	30	0	32
49.0	1.500218	27	0	35
50.0	1.500218	39	0	31
51.0	1.500218	37	0	40
52.0	1.500218	25	0	19
53.0	1.500218	27	0	37
54.0	1.500218	32	0	18
55.0	1.500218	25	0	21
56.0	1.500218	16	0	18
57.0	1.500218	30	0	26
58.0	1.500218	23	0	21
59.0	1.500218	10	0	12
60.0	1.500218	12	0	17
61.0	1.500218	13	0	18
62.0	1.500218	18	0	15
63.0	1.500218	18	0	12
64.0	1.500218	18	0	21
65.0	1.500218	14	0	16
66.0	1.500218	17	0	19
67.0	1.500218	14	0	12
68.0	1.500218	14	0	6
69.0	1.500218	18	0	7
70.0	1.500218	11	0	13
71.0	1.500218	9	0	10
72.0	1.500218	6	0	6
73.0	1.500218	14	0	6
74.0	1.500218	6	0	7
75.0	1.500218	13	0	9
76.0	1.500218	6	0	7
77.0	1.500218	4	0	7
78.0	1.500218	8	0	6
79.0	1.500218	6	0	8
80.0	1.500218	5	0	10
81.0	1.500218	6	0	8
82.0	1.500218	7	0	1
83.0	1.500218	4	0	6
84.0	1.500218	7	0	6
85.0	1.500218	7	0	4
86.0	1.500218	6	0	4
87.0	1.500218	6	0	7
88.0	1.500218	4	0	5
89.0	1.500218	4	0	8
90.0	1.500218	6	0	5
91.0	1.500218	6	0	7
92.0	1.500218	6	0	3
93.0	1.500218	1	0	2
94.0	1.500218	3	0	1
95.0	1.500218	5	0	3
96.0	1.500218	4	0	2
97.0	1.500218	4	0	4
98.0	1.500218	1	0	4
99.0	1.500218	3	0	9
100.0	1.500218	4	0	4
101.0	0	1	0	4
102.0	0	8	0	2
103.0	0	4	0	3
104.0	0	3	0	2
105.0	0	3	0	3
106.0	0	3	0	1
107.0	0	3	0	3
108.0	0	3	0	2
109.0	0	2	0	2
110.0	0	2	0	8
111.0	0	3	0	2
112.0	0	4	0	2
113.0	0	2	0	5
114.0	0	3	0	3
115.0	0	2	0	2
116.0	0	5	0	3
117.0	0	4	0	1
118.0	0	4	0	3
119.0	0	3	0	2
120.0	0	1	0	0
121.0	0	1	0	0
122.0	0	3	0	4
123.0	0	5	0	3
124.0	0	1	0	0
125.0	0	0	0	1
126.0	0	2	0	2
127.0	0	0	0	4
128.0	0	1	0	0
129.0	0	3	0	1
130.0	0	2	0	2
131.0	0	1	0	3
132.0	0	4	0	0
133.0	0	1	0	2
134.0	0	3	0	2
135.0	0	1	0	2
136.0	0	0	0	2
137.0	0	2	0	1
138.0	0	1	0	1
140.0	0	1	0	1
141.0	0	1	0	2
142.0	0	1	0	0
143.0	0	2	0	1
144.0	0	1	0	0
145.0	0	2	0	2
146.0	0	2	0	1
147.0	0	0	0	1
148.0	0	1	0	2
149.0	0	0	0	1
150.0	0	0	0	1
151.0	0	5	0	3
152.0	0	1	0	1
153.0	0	1	0	0
154.0	0	1	0	0
156.0	0	1	0	3
157.0	0	1	0	1
159.0	0	1	0	1
162.0	0	2	0	0
163.0	0	1	0	1
164.0	0	2	0	1
166.0	0	0	0	3
167.0	0	2	0	0
168.0	0	0	0	3
169.0	0	1	0	1
171.0	0	2	0	0
172.0	0	3	0	1
176.0	0	1	0	1
177.0	0	0	0	3
178.0	0	1	0	0
179.0	0	1	0	0
182.0	0	1	0	3
183.0	0	1	0	0
185.0	0	1	0	0
186.0	0	2	0	0
187.0	0	1	0	0
188.0	0	0	0	1
192.0	0	0	0	1
194.0	0	1	0	0
197.0	0	2	0	3
198.0	0	1	0	0
202.0	0	1	0	2
203.0	0	1	0	0
205.0	0	0	0	2
208.0	0	0	0	1
209.0	0	1	0	0
210.0	0	1	0	0
211.0	0	1	0	1
214.0	0	0	0	1
215.0	0	0	0	1
216.0	0	0	0	1
218.0	0	1	0	1
219.0	0	1	0	1
220.0	0	3	0	2
222.0	0	2	0	0
224.0	0	1	0	1
225.0	0	0	0	2
226.0	0	0	0	1
228.0	0	1	0	0
229.0	0	3	0	0
232.0	0	0	0	1
233.0	0	0	0	1
236.0	0	1	0	0
239.0	0	1	0	0
242.0	0	0	0	1
247.0	0	1	0	0
248.0	0	1	0	0
252.0	0	0	0	1
259.0	0	1	0	0
266.0	0	0	0	1
270.0	0	0	0	1
273.0	0	1	0	0
279.0	0	1	0	0
290.0	0	0	0	2
296.0	0	1	0	0
300.0	0	0	0	1
302.0	0	2	0	1
309.0	0	1	0	1
310.0	0	1	0	0
316.0	0	1	0	1
333.0	0	1	0	1
340.0	0	0	0	1
346.0	0	1	0	1
352.0	0	2	0	1
371.0	0	0	0	1
393.0	0	1	0	0
414.0	0	0	0	2
425.0	0	1	0	0
432.0	0	1	0	0
435.0	0	0	0	1
445.0	0	0	0	1
448.0	0	1	0	0
464.0	0	1	0	0
481.0	0	0	0	1
483.0	0	1	0	0
526.0	0	0	0	1
537.0	0	0	0	1
538.0	0	1	0	0
542.0	0	1	0	0
547.0	0	0	0	1
562.0	0	1	0	0
742.0	0	0	0	1
763.0	0	1	0	0
872.0	0	0	0	1
894.0	0	1	0	0
5015.0	0	0	0	1
5020.0	0	1	0	0
5125.0	0	0	0	1
5130.0	0	1	0	0
5546.0	0	0	0	1
5550.0	0	1	0	0
5588.0	0	0	0	1
5590.0	0	0	0	1
5591.0	0	1	0	0
5595.0	0	1	0	0
5633.0	0	0	0	1
5640.0	0	1	0	0
5698.0	0	0	0	1
5709.0	0	1	0	0
5790.0	0	0	0	1
5794.0	0	1	0	0
6833.0	0	0	0	1
6843.0	0	1	0	0
6968.0	0	0	0	1
6978.0	0	1	0	0