## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[P02-female_nonbleached_K5.sorted.bam] OUTPUT=P02-female_nonbleached_K5.sorted.dedup.bam METRICS_FILE=P02-female_nonbleached_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 11:30:56 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	656710	22795982	0	1480100	448822	10660805	623781	0.470726	16344878

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.01299	7130589	0	7247955
2.0	1.264121	2646362	462417	2654545
3.0	1.326379	1145312	56099	1123236
4.0	1.341813	544322	10818	519467
5.0	1.345639	278661	2574	256740
6.0	1.346588	150880	733	134400
7.0	1.346823	85635	217	73562
8.0	1.346881	50593	90	41669
9.0	1.346896	30779	30	24792
10.0	1.346899	19351	20	15153
11.0	1.3469	12691	8	9801
12.0	1.346901	8459	5	6717
13.0	1.346901	5909	2	4683
14.0	1.346901	4293	2	3421
15.0	1.346901	3169	3	2627
16.0	1.346901	2456	2	2113
17.0	1.346901	1990	1	1706
18.0	1.346901	1541	2	1366
19.0	1.346901	1316	1	1143
20.0	1.346901	1126	0	973
21.0	1.346901	917	0	871
22.0	1.346901	860	1	791
23.0	1.346901	707	0	668
24.0	1.346901	637	1	566
25.0	1.346901	511	0	498
26.0	1.346901	488	0	445
27.0	1.346901	419	0	401
28.0	1.346901	397	0	325
29.0	1.346901	331	0	311
30.0	1.346901	277	0	275
31.0	1.346901	246	1	246
32.0	1.346901	285	0	249
33.0	1.346901	229	0	211
34.0	1.346901	200	0	175
35.0	1.346901	164	0	175
36.0	1.346901	176	0	160
37.0	1.346901	154	0	137
38.0	1.346901	144	0	151
39.0	1.346901	149	0	142
40.0	1.346901	126	0	111
41.0	1.346901	110	0	102
42.0	1.346901	102	0	91
43.0	1.346901	100	0	95
44.0	1.346901	84	0	102
45.0	1.346901	94	0	81
46.0	1.346901	87	0	70
47.0	1.346901	87	0	80
48.0	1.346901	64	0	83
49.0	1.346901	79	0	69
50.0	1.346901	62	0	56
51.0	1.346901	51	0	58
52.0	1.346901	69	0	53
53.0	1.346901	54	0	51
54.0	1.346901	50	0	51
55.0	1.346901	55	0	63
56.0	1.346901	52	0	48
57.0	1.346901	54	0	28
58.0	1.346901	44	0	43
59.0	1.346901	38	0	36
60.0	1.346901	25	0	24
61.0	1.346901	25	0	34
62.0	1.346901	48	0	26
63.0	1.346901	20	0	24
64.0	1.346901	32	0	26
65.0	1.346901	18	0	21
66.0	1.346901	23	0	27
67.0	1.346901	27	0	23
68.0	1.346901	27	0	24
69.0	1.346901	18	0	20
70.0	1.346901	24	0	13
71.0	1.346901	20	0	23
72.0	1.346901	13	0	16
73.0	1.346901	16	0	21
74.0	1.346901	18	0	13
75.0	1.346901	13	0	10
76.0	1.346901	15	0	17
77.0	1.346901	15	0	11
78.0	1.346901	15	0	16
79.0	1.346901	12	0	7
80.0	1.346901	11	0	11
81.0	1.346901	11	0	10
82.0	1.346901	19	0	16
83.0	1.346901	15	0	13
84.0	1.346901	9	0	10
85.0	1.346901	8	0	7
86.0	1.346901	10	0	15
87.0	1.346901	13	0	11
88.0	1.346901	8	0	8
89.0	1.346901	13	0	13
90.0	1.346901	9	0	6
91.0	1.346901	6	0	9
92.0	1.346901	12	0	10
93.0	1.346901	11	0	11
94.0	1.346901	9	0	12
95.0	1.346901	11	0	13
96.0	1.346901	9	0	8
97.0	1.346901	13	0	7
98.0	1.346901	5	0	12
99.0	1.346901	9	0	8
100.0	1.346901	11	0	7
101.0	0	7	0	11
102.0	0	10	0	4
103.0	0	9	0	6
104.0	0	2	0	2
105.0	0	8	0	6
106.0	0	2	0	6
107.0	0	7	0	8
108.0	0	6	0	8
109.0	0	4	0	7
110.0	0	9	0	5
111.0	0	7	0	10
112.0	0	6	0	2
113.0	0	7	0	6
114.0	0	4	0	4
115.0	0	9	0	9
116.0	0	5	0	5
117.0	0	3	0	7
118.0	0	11	0	5
119.0	0	5	0	7
120.0	0	5	0	4
121.0	0	5	0	4
122.0	0	6	0	5
123.0	0	3	0	0
124.0	0	5	0	1
125.0	0	3	0	4
126.0	0	2	0	4
127.0	0	2	0	4
128.0	0	1	0	5
129.0	0	4	0	4
130.0	0	5	0	2
131.0	0	4	0	4
132.0	0	4	0	2
133.0	0	6	0	4
134.0	0	1	0	4
135.0	0	2	0	1
136.0	0	2	0	2
137.0	0	3	0	1
138.0	0	2	0	1
139.0	0	5	0	1
140.0	0	1	0	5
141.0	0	1	0	3
142.0	0	4	0	3
143.0	0	4	0	3
144.0	0	2	0	3
145.0	0	1	0	1
146.0	0	3	0	0
147.0	0	2	0	6
148.0	0	0	0	2
149.0	0	3	0	1
150.0	0	1	0	0
151.0	0	2	0	3
152.0	0	0	0	3
153.0	0	4	0	2
154.0	0	3	0	3
155.0	0	2	0	3
156.0	0	3	0	3
157.0	0	0	0	3
158.0	0	2	0	1
159.0	0	3	0	1
160.0	0	1	0	0
161.0	0	2	0	0
163.0	0	3	0	1
164.0	0	2	0	1
165.0	0	1	0	2
166.0	0	2	0	3
167.0	0	0	0	4
168.0	0	1	0	1
169.0	0	1	0	3
170.0	0	2	0	0
172.0	0	3	0	2
173.0	0	1	0	1
174.0	0	0	0	1
175.0	0	3	0	0
177.0	0	1	0	1
178.0	0	0	0	1
179.0	0	3	0	0
180.0	0	3	0	1
182.0	0	1	0	2
183.0	0	0	0	1
185.0	0	3	0	2
186.0	0	1	0	1
187.0	0	1	0	1
188.0	0	0	0	1
189.0	0	0	0	2
190.0	0	1	0	0
191.0	0	1	0	0
192.0	0	1	0	2
194.0	0	3	0	0
197.0	0	1	0	1
201.0	0	1	0	0
203.0	0	0	0	1
204.0	0	0	0	1
205.0	0	1	0	1
206.0	0	2	0	0
207.0	0	0	0	1
209.0	0	0	0	1
211.0	0	2	0	0
215.0	0	1	0	1
218.0	0	0	0	1
219.0	0	1	0	1
221.0	0	1	0	0
223.0	0	1	0	0
224.0	0	1	0	1
226.0	0	0	0	1
227.0	0	1	0	0
229.0	0	0	0	1
231.0	0	1	0	0
232.0	0	0	0	1
233.0	0	1	0	0
239.0	0	0	0	1
242.0	0	1	0	0
244.0	0	0	0	2
246.0	0	1	0	1
253.0	0	1	0	1
255.0	0	1	0	0
256.0	0	1	0	0
257.0	0	0	0	1
260.0	0	1	0	0
261.0	0	0	0	2
263.0	0	1	0	0
265.0	0	1	0	2
268.0	0	1	0	0
269.0	0	1	0	0
273.0	0	0	0	1
275.0	0	1	0	3
276.0	0	0	0	1
278.0	0	0	0	2
279.0	0	2	0	0
280.0	0	1	0	0
284.0	0	1	0	0
287.0	0	0	0	1
288.0	0	0	0	1
289.0	0	0	0	2
290.0	0	0	0	1
291.0	0	2	0	1
292.0	0	1	0	1
293.0	0	2	0	0
295.0	0	1	0	2
296.0	0	1	0	0
298.0	0	1	0	0
299.0	0	1	0	0
300.0	0	1	0	0
305.0	0	1	0	1
308.0	0	1	0	0
313.0	0	0	0	1
316.0	0	1	0	0
319.0	0	0	0	1
322.0	0	0	0	1
327.0	0	1	0	0
328.0	0	1	0	0
329.0	0	0	0	1
335.0	0	1	0	1
337.0	0	0	0	1
339.0	0	1	0	0
341.0	0	1	0	0
348.0	0	0	0	1
351.0	0	1	0	0
357.0	0	0	0	1
358.0	0	0	0	2
361.0	0	2	0	0
362.0	0	1	0	0
369.0	0	0	0	1
376.0	0	1	0	0
377.0	0	0	0	1
381.0	0	0	0	1
385.0	0	1	0	0
386.0	0	1	0	0
405.0	0	0	0	1
406.0	0	0	0	1
409.0	0	1	0	0
418.0	0	0	0	1
419.0	0	0	0	1
421.0	0	1	0	0
429.0	0	1	0	0
431.0	0	1	0	0
487.0	0	0	0	1
505.0	0	1	0	0
611.0	0	0	0	1
628.0	0	1	0	0
659.0	0	0	0	1
663.0	0	1	0	0
686.0	0	0	0	1
689.0	0	1	0	0
753.0	0	0	0	1
761.0	0	1	0	0
786.0	0	0	0	1
787.0	0	0	0	1
794.0	0	1	0	0
796.0	0	1	0	0
3000.0	0	0	0	1
3002.0	0	1	0	0
3828.0	0	0	0	1
3831.0	0	1	0	0
11196.0	0	0	0	1
11217.0	0	1	0	0
11225.0	0	0	0	1
11255.0	0	1	0	0
11284.0	0	0	0	1
11307.0	0	1	0	0