## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kha_Kha_1_2015-08-20/UA_Kha_Kha_1_2015-08-20.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kha_Kha_1_2015-08-20/UA_Kha_Kha_1_2015-08-20.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kha_Kha_1_2015-08-20/UA_Kha_Kha_1_2015-08-20.mark_duplicates_report.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT    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: Fri Jan 20 09:40:01 UTC 2023

## 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
lib1	11217142	38362427	0	0	4682965	3989870	0	0.143989	171404181

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	30377246	30377246
2.0	1.799465	3143152	3143152
3.0	2.438609	288266	288266
4.0	2.949582	27396	27396
5.0	3.358087	3543	3543
6.0	3.684673	1085	1085
7.0	3.945767	616	616
8.0	4.154502	490	490
9.0	4.321378	314	314
10.0	4.45479	290	290
11.0	4.561448	235	235
12.0	4.646718	213	213
13.0	4.714888	174	174
14.0	4.769387	132	132
15.0	4.812958	126	126
16.0	4.847791	119	119
17.0	4.875638	108	108
18.0	4.897902	104	104
19.0	4.9157	89	89
20.0	4.92993	98	98
21.0	4.941306	98	98
22.0	4.9504	85	85
23.0	4.957671	84	84
24.0	4.963484	79	79
25.0	4.968131	81	81
26.0	4.971847	63	63
27.0	4.974817	63	63
28.0	4.977191	59	59
29.0	4.97909	61	61
30.0	4.980607	48	48
31.0	4.981821	59	59
32.0	4.982791	65	65
33.0	4.983566	65	65
34.0	4.984186	63	63
35.0	4.984682	43	43
36.0	4.985078	49	49
37.0	4.985395	47	47
38.0	4.985648	37	37
39.0	4.985851	30	30
40.0	4.986013	40	40
41.0	4.986142	32	32
42.0	4.986245	33	33
43.0	4.986328	29	29
44.0	4.986394	27	27
45.0	4.986447	29	29
46.0	4.986489	26	26
47.0	4.986523	24	24
48.0	4.98655	32	32
49.0	4.986572	30	30
50.0	4.986589	24	24
51.0	4.986603	26	26
52.0	4.986614	18	18
53.0	4.986623	21	21
54.0	4.98663	26	26
55.0	4.986635	16	16
56.0	4.98664	18	18
57.0	4.986643	23	23
58.0	4.986646	15	15
59.0	4.986649	14	14
60.0	4.986651	16	16
61.0	4.986652	12	12
62.0	4.986653	17	17
63.0	4.986654	16	16
64.0	4.986655	12	12
65.0	4.986655	11	11
66.0	4.986656	19	19
67.0	4.986656	9	9
68.0	4.986657	22	22
69.0	4.986657	14	14
70.0	4.986657	9	9
71.0	4.986657	14	14
72.0	4.986657	14	14
73.0	4.986657	7	7
74.0	4.986658	11	11
75.0	4.986658	11	11
76.0	4.986658	15	15
77.0	4.986658	10	10
78.0	4.986658	11	11
79.0	4.986658	7	7
80.0	4.986658	9	9
81.0	4.986658	7	7
82.0	4.986658	10	10
83.0	4.986658	10	10
84.0	4.986658	13	13
85.0	4.986658	9	9
86.0	4.986658	13	13
87.0	4.986658	7	7
88.0	4.986658	8	8
89.0	4.986658	10	10
90.0	4.986658	10	10
91.0	4.986658	13	13
92.0	4.986658	7	7
93.0	4.986658	6	6
94.0	4.986658	8	8
95.0	4.986658	0	0
96.0	4.986658	8	8
97.0	4.986658	4	4
98.0	4.986658	5	5
99.0	4.986658	7	7
100.0	4.986658	6	6
101.0	0	11	11
102.0	0	8	8
103.0	0	6	6
104.0	0	7	7
105.0	0	5	5
106.0	0	3	3
107.0	0	3	3
108.0	0	5	5
109.0	0	6	6
110.0	0	5	5
111.0	0	3	3
112.0	0	5	5
114.0	0	2	2
115.0	0	2	2
116.0	0	5	5
117.0	0	4	4
118.0	0	4	4
119.0	0	6	6
121.0	0	4	4
122.0	0	8	8
123.0	0	1	1
124.0	0	2	2
125.0	0	2	2
126.0	0	1	1
127.0	0	3	3
128.0	0	1	1
129.0	0	1	1
130.0	0	4	4
131.0	0	4	4
132.0	0	4	4
134.0	0	2	2
135.0	0	5	5
136.0	0	3	3
137.0	0	4	4
138.0	0	1	1
139.0	0	1	1
140.0	0	4	4
141.0	0	3	3
142.0	0	2	2
144.0	0	4	4
145.0	0	3	3
146.0	0	2	2
147.0	0	4	4
148.0	0	4	4
149.0	0	2	2
150.0	0	1	1
151.0	0	3	3
152.0	0	1	1
154.0	0	1	1
155.0	0	2	2
156.0	0	4	4
157.0	0	1	1
158.0	0	1	1
159.0	0	1	1
160.0	0	4	4
161.0	0	2	2
163.0	0	1	1
165.0	0	2	2
166.0	0	1	1
167.0	0	3	3
168.0	0	1	1
170.0	0	1	1
171.0	0	1	1
172.0	0	1	1
173.0	0	1	1
174.0	0	4	4
176.0	0	2	2
177.0	0	6	6
178.0	0	4	4
179.0	0	1	1
182.0	0	1	1
184.0	0	4	4
185.0	0	1	1
187.0	0	2	2
188.0	0	1	1
189.0	0	1	1
190.0	0	1	1
191.0	0	1	1
192.0	0	1	1
194.0	0	1	1
196.0	0	1	1
198.0	0	1	1
200.0	0	1	1
201.0	0	2	2
203.0	0	1	1
204.0	0	1	1
205.0	0	1	1
206.0	0	2	2
208.0	0	1	1
209.0	0	2	2
210.0	0	2	2
213.0	0	2	2
215.0	0	1	1
219.0	0	1	1
220.0	0	2	2
230.0	0	2	2
232.0	0	2	2
233.0	0	1	1
234.0	0	1	1
235.0	0	1	1
237.0	0	2	2
239.0	0	1	1
242.0	0	2	2
243.0	0	1	1
248.0	0	2	2
250.0	0	1	1
251.0	0	1	1
253.0	0	1	1
255.0	0	2	2
261.0	0	2	2
262.0	0	1	1
267.0	0	1	1
276.0	0	1	1
280.0	0	1	1
281.0	0	1	1
290.0	0	1	1
293.0	0	1	1
300.0	0	1	1
301.0	0	1	1
303.0	0	1	1
307.0	0	1	1
312.0	0	1	1
314.0	0	1	1
316.0	0	1	1
319.0	0	2	2
324.0	0	1	1
345.0	0	1	1
349.0	0	2	2
362.0	0	1	1
409.0	0	1	1
420.0	0	1	1
469.0	0	1	1