## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[P01-male_bleached_K5.sorted.bam] OUTPUT=P01-male_bleached_K5.sorted.dedup.bam METRICS_FILE=P01-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 10:52:26 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	944593	23233066	0	2283111	631301	9613021	761317	0.418837	20400182

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.018235	8553720	0	8740327
2.0	1.344256	2896214	569018	2890215
3.0	1.448642	1147118	68781	1101158
4.0	1.482064	503846	12561	460179
5.0	1.492766	238913	2828	207603
6.0	1.496192	120166	703	98115
7.0	1.497289	63343	216	49321
8.0	1.49764	34913	63	26026
9.0	1.497753	20070	34	14384
10.0	1.497789	12069	13	8795
11.0	1.4978	7544	4	5498
12.0	1.497804	4893	1	3727
13.0	1.497805	3366	2	2679
14.0	1.497806	2508	2	2037
15.0	1.497806	1842	0	1486
16.0	1.497806	1413	0	1173
17.0	1.497806	1114	0	947
18.0	1.497806	907	0	856
19.0	1.497806	752	0	682
20.0	1.497806	618	0	565
21.0	1.497806	547	0	460
22.0	1.497806	450	0	431
23.0	1.497806	399	0	339
24.0	1.497806	338	0	327
25.0	1.497806	294	0	252
26.0	1.497806	248	0	208
27.0	1.497806	195	0	183
28.0	1.497806	201	0	179
29.0	1.497806	162	0	182
30.0	1.497806	148	0	136
31.0	1.497806	143	0	124
32.0	1.497806	144	0	125
33.0	1.497806	105	0	96
34.0	1.497806	94	0	84
35.0	1.497806	77	0	62
36.0	1.497806	77	0	71
37.0	1.497806	63	0	67
38.0	1.497806	83	0	66
39.0	1.497806	66	0	65
40.0	1.497806	65	0	47
41.0	1.497806	45	0	42
42.0	1.497806	41	0	42
43.0	1.497806	35	0	33
44.0	1.497806	39	0	44
45.0	1.497806	28	0	30
46.0	1.497806	36	0	36
47.0	1.497806	36	0	27
48.0	1.497806	30	0	19
49.0	1.497806	24	0	21
50.0	1.497806	20	0	20
51.0	1.497806	24	0	22
52.0	1.497806	16	0	24
53.0	1.497806	20	0	21
54.0	1.497806	21	0	20
55.0	1.497806	17	0	22
56.0	1.497806	14	0	9
57.0	1.497806	17	0	13
58.0	1.497806	18	0	18
59.0	1.497806	19	0	12
60.0	1.497806	16	0	11
61.0	1.497806	10	0	10
62.0	1.497806	11	0	14
63.0	1.497806	11	0	10
64.0	1.497806	15	0	13
65.0	1.497806	9	0	10
66.0	1.497806	6	0	13
67.0	1.497806	14	0	7
68.0	1.497806	14	0	17
69.0	1.497806	13	0	13
70.0	1.497806	8	0	9
71.0	1.497806	17	0	8
72.0	1.497806	5	0	5
73.0	1.497806	7	0	2
74.0	1.497806	3	0	6
75.0	1.497806	5	0	1
76.0	1.497806	2	0	2
77.0	1.497806	6	0	4
78.0	1.497806	3	0	9
79.0	1.497806	4	0	2
80.0	1.497806	5	0	2
81.0	1.497806	6	0	3
82.0	1.497806	6	0	4
83.0	1.497806	0	0	2
84.0	1.497806	1	0	5
85.0	1.497806	5	0	7
86.0	1.497806	2	0	3
87.0	1.497806	5	0	3
88.0	1.497806	5	0	3
89.0	1.497806	4	0	3
90.0	1.497806	5	0	1
91.0	1.497806	2	0	1
92.0	1.497806	3	0	3
93.0	1.497806	1	0	4
94.0	1.497806	4	0	5
95.0	1.497806	2	0	1
96.0	1.497806	2	0	1
97.0	1.497806	4	0	1
98.0	1.497806	0	0	1
99.0	1.497806	0	0	1
100.0	1.497806	1	0	0
101.0	0	0	0	1
102.0	0	1	0	1
103.0	0	1	0	3
104.0	0	0	0	1
105.0	0	2	0	0
106.0	0	1	0	2
107.0	0	0	0	1
108.0	0	3	0	4
109.0	0	3	0	1
110.0	0	1	0	2
111.0	0	2	0	1
112.0	0	2	0	1
113.0	0	1	0	2
114.0	0	3	0	0
116.0	0	1	0	0
117.0	0	1	0	1
118.0	0	0	0	2
120.0	0	3	0	2
121.0	0	1	0	0
124.0	0	0	0	1
125.0	0	1	0	0
126.0	0	1	0	0
127.0	0	0	0	4
130.0	0	2	0	2
131.0	0	1	0	1
132.0	0	2	0	0
133.0	0	1	0	1
139.0	0	0	0	1
140.0	0	1	0	1
141.0	0	0	0	3
142.0	0	1	0	1
143.0	0	2	0	1
144.0	0	1	0	1
146.0	0	1	0	0
147.0	0	2	0	0
148.0	0	2	0	2
150.0	0	1	0	0
151.0	0	1	0	1
154.0	0	1	0	1
157.0	0	1	0	2
158.0	0	0	0	1
160.0	0	1	0	0
161.0	0	0	0	1
162.0	0	2	0	0
163.0	0	0	0	1
164.0	0	1	0	0
169.0	0	0	0	1
170.0	0	1	0	2
174.0	0	0	0	1
175.0	0	0	0	1
176.0	0	1	0	0
177.0	0	1	0	0
178.0	0	1	0	0
180.0	0	1	0	0
181.0	0	1	0	0
184.0	0	0	0	1
185.0	0	0	0	1
186.0	0	0	0	1
190.0	0	0	0	1
191.0	0	2	0	0
192.0	0	1	0	0
193.0	0	1	0	0
195.0	0	0	0	1
204.0	0	1	0	0
205.0	0	0	0	1
208.0	0	1	0	0
210.0	0	0	0	1
213.0	0	0	0	1
216.0	0	1	0	0
217.0	0	1	0	0
222.0	0	1	0	2
226.0	0	1	0	0
233.0	0	0	0	1
239.0	0	1	0	0
246.0	0	0	0	1
248.0	0	1	0	0
258.0	0	0	0	1
267.0	0	1	0	0
286.0	0	0	0	1
293.0	0	1	0	0
300.0	0	0	0	1
301.0	0	1	0	0
333.0	0	1	0	1
370.0	0	1	0	1