## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Kop_6_Sep_2019/UA_Kop_6_Sep_2019.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Kop_6_Sep_2019/UA_Kop_6_Sep_2019.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Kop_6_Sep_2019/UA_Kop_6_Sep_2019.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: Wed Dec 21 04:04:33 UTC 2022

## 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	2762792	23669522	0	0	1490836	6478191	260521	0.288357	35858281

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.00786	12187549	0	12324957
2.0	1.52873	3366137	253836	3305147
3.0	1.797919	901957	3130	856052
4.0	1.937038	235681	53	215804
5.0	2.008936	61336	10	53975
6.0	2.046093	16307	3	14112
7.0	2.065296	4781	9	4047
8.0	2.07522	1602	3	1393
9.0	2.080349	697	1	619
10.0	2.083	399	1	372
11.0	2.08437	285	0	279
12.0	2.085078	203	0	190
13.0	2.085444	172	0	175
14.0	2.085633	152	0	151
15.0	2.085731	93	0	87
16.0	2.085781	87	0	84
17.0	2.085807	76	0	74
18.0	2.085821	82	1	81
19.0	2.085828	67	0	71
20.0	2.085831	50	0	46
21.0	2.085833	46	0	51
22.0	2.085834	41	0	38
23.0	2.085835	39	0	40
24.0	2.085835	33	0	30
25.0	2.085835	39	0	43
26.0	2.085835	35	0	32
27.0	2.085835	37	0	37
28.0	2.085835	28	0	29
29.0	2.085835	25	0	21
30.0	2.085835	26	0	28
31.0	2.085835	22	0	21
32.0	2.085835	18	0	16
33.0	2.085835	17	0	17
34.0	2.085835	13	1	14
35.0	2.085835	13	0	17
36.0	2.085835	18	0	15
37.0	2.085835	11	0	12
38.0	2.085835	10	0	9
39.0	2.085835	13	0	13
40.0	2.085835	11	0	9
41.0	2.085835	8	0	8
42.0	2.085835	18	0	20
43.0	2.085835	15	0	13
44.0	2.085835	12	0	14
45.0	2.085835	7	0	9
46.0	2.085835	14	0	11
47.0	2.085835	10	0	10
48.0	2.085835	15	0	16
49.0	2.085835	10	0	8
50.0	2.085835	7	0	10
51.0	2.085835	11	0	8
52.0	2.085835	6	0	7
53.0	2.085835	4	0	3
54.0	2.085835	6	0	8
55.0	2.085835	4	0	3
56.0	2.085835	9	0	8
57.0	2.085835	4	0	5
58.0	2.085835	8	0	10
59.0	2.085835	7	0	6
60.0	2.085835	8	0	8
61.0	2.085835	6	0	5
62.0	2.085835	5	0	5
63.0	2.085835	3	0	2
64.0	2.085835	7	0	9
65.0	2.085835	7	0	7
66.0	2.085835	6	0	5
67.0	2.085835	7	0	8
68.0	2.085835	7	0	6
69.0	2.085835	5	0	4
70.0	2.085835	2	1	2
71.0	2.085835	0	0	0
72.0	2.085835	4	0	4
73.0	2.085835	1	0	1
74.0	2.085835	4	0	5
75.0	2.085835	10	0	10
76.0	2.085835	8	0	8
77.0	2.085835	4	0	6
78.0	2.085835	2	0	1
79.0	2.085835	5	0	3
80.0	2.085835	3	0	4
81.0	2.085835	3	0	3
82.0	2.085835	4	0	3
83.0	2.085835	2	0	3
84.0	2.085835	1	0	2
85.0	2.085835	7	0	7
86.0	2.085835	5	0	4
87.0	2.085835	4	0	3
88.0	2.085835	4	0	6
89.0	2.085835	9	0	10
90.0	2.085835	8	0	8
91.0	2.085835	8	0	6
92.0	2.085835	1	0	1
93.0	2.085835	4	0	4
94.0	2.085835	3	0	3
95.0	2.085835	2	0	3
96.0	2.085835	6	0	5
97.0	2.085835	3	0	2
98.0	2.085835	2	0	2
99.0	2.085835	0	0	0
100.0	2.085835	4	0	5
101.0	0	5	0	5
102.0	0	2	0	1
103.0	0	1	0	2
104.0	0	5	0	5
105.0	0	3	0	2
106.0	0	2	0	2
107.0	0	4	0	6
108.0	0	3	0	2
109.0	0	1	0	0
110.0	0	0	0	1
111.0	0	2	0	1
112.0	0	1	0	2
113.0	0	7	0	6
114.0	0	2	0	2
115.0	0	1	0	2
116.0	0	3	0	3
117.0	0	3	0	2
118.0	0	2	0	4
119.0	0	4	0	2
120.0	0	2	0	3
121.0	0	4	0	4
122.0	0	1	0	2
123.0	0	3	0	1
125.0	0	2	0	4
126.0	0	4	0	2
127.0	0	1	0	2
128.0	0	4	0	4
129.0	0	2	0	1
130.0	0	5	0	5
132.0	0	3	0	3
133.0	0	1	0	1
134.0	0	2	0	2
135.0	0	2	0	2
136.0	0	1	0	1
137.0	0	1	0	2
138.0	0	2	0	2
139.0	0	1	0	0
141.0	0	3	0	3
143.0	0	1	0	1
144.0	0	0	0	2
145.0	0	3	0	2
146.0	0	1	0	2
147.0	0	1	0	0
148.0	0	1	0	0
149.0	0	2	0	2
150.0	0	0	0	1
151.0	0	2	0	2
152.0	0	1	0	0
153.0	0	2	0	2
154.0	0	1	0	2
155.0	0	1	0	1
156.0	0	2	0	1
157.0	0	1	0	1
158.0	0	1	0	1
159.0	0	1	0	1
160.0	0	3	0	3
161.0	0	2	0	2
162.0	0	2	0	2
163.0	0	4	0	4
164.0	0	2	0	2
166.0	0	1	0	2
167.0	0	2	0	1
172.0	0	2	0	2
174.0	0	1	0	2
176.0	0	1	0	0
177.0	0	1	0	1
178.0	0	1	0	1
179.0	0	1	0	1
180.0	0	2	0	2
181.0	0	1	0	1
182.0	0	1	0	1
183.0	0	2	0	2
184.0	0	2	0	2
185.0	0	1	0	1
186.0	0	1	0	1
187.0	0	2	0	2
190.0	0	1	0	2
191.0	0	1	0	0
192.0	0	1	0	1
193.0	0	1	0	1
194.0	0	0	0	1
195.0	0	1	0	1
196.0	0	1	0	0
197.0	0	0	0	1
198.0	0	2	0	2
199.0	0	1	0	1
200.0	0	0	0	1
201.0	0	2	0	2
202.0	0	1	0	0
203.0	0	0	0	1
204.0	0	1	0	2
205.0	0	2	0	0
206.0	0	1	0	0
207.0	0	1	0	1
210.0	0	1	0	2
211.0	0	1	0	1
212.0	0	1	0	1
213.0	0	2	0	1
216.0	0	1	0	1
217.0	0	0	0	1
218.0	0	1	0	1
219.0	0	1	0	2
220.0	0	2	0	1
221.0	0	2	0	1
222.0	0	1	0	2
224.0	0	1	0	0
227.0	0	1	0	2
228.0	0	1	0	0
229.0	0	1	0	1
232.0	0	1	0	1
233.0	0	1	0	1
234.0	0	1	0	1
235.0	0	2	0	2
240.0	0	1	0	1
241.0	0	1	0	1
245.0	0	2	0	2
247.0	0	1	0	1
249.0	0	0	0	1
250.0	0	1	0	0
253.0	0	1	0	1
255.0	0	1	0	1
258.0	0	1	0	1
259.0	0	0	0	1
260.0	0	1	0	0
261.0	0	0	0	1
265.0	0	1	0	1
267.0	0	4	0	3
269.0	0	1	0	1
273.0	0	1	0	1
275.0	0	2	0	2
278.0	0	1	0	1
280.0	0	1	0	2
281.0	0	1	0	0
282.0	0	1	0	1
283.0	0	1	0	1
285.0	0	0	0	1
286.0	0	2	0	1
287.0	0	1	0	1
289.0	0	2	0	2
291.0	0	1	0	1
293.0	0	0	0	1
295.0	0	1	0	1
296.0	0	0	0	1
297.0	0	3	0	1
299.0	0	1	0	1
302.0	0	0	0	1
303.0	0	1	0	1
305.0	0	2	0	3
307.0	0	2	0	0
309.0	0	2	0	2
312.0	0	1	0	1
315.0	0	1	0	1
316.0	0	1	0	1
319.0	0	1	0	1
329.0	0	0	0	1
330.0	0	2	0	1
331.0	0	1	0	1
334.0	0	1	0	1
339.0	0	0	0	1
340.0	0	2	0	1
345.0	0	0	0	1
346.0	0	1	0	0
351.0	0	0	0	1
354.0	0	1	0	0
355.0	0	0	0	1
356.0	0	0	0	1
358.0	0	1	0	0
359.0	0	1	0	0
364.0	0	1	0	1
367.0	0	1	0	1
370.0	0	2	0	2
371.0	0	1	0	1
374.0	0	1	0	1
379.0	0	1	0	1
383.0	0	0	0	2
384.0	0	1	0	1
385.0	0	2	0	0
392.0	0	1	0	1
396.0	0	0	0	1
397.0	0	2	0	2
398.0	0	2	0	2
400.0	0	1	0	0
404.0	0	0	0	1
409.0	0	1	0	0
410.0	0	1	0	1
413.0	0	0	0	1
414.0	0	1	0	0
421.0	0	1	0	1
423.0	0	1	0	1
427.0	0	0	0	1
432.0	0	1	0	1
433.0	0	1	0	0
435.0	0	1	0	1
439.0	0	0	0	1
444.0	0	1	0	1
445.0	0	1	0	0
446.0	0	1	0	1
447.0	0	1	0	1
454.0	0	1	0	1
471.0	0	0	0	1
476.0	0	0	0	1
477.0	0	1	0	0
478.0	0	1	0	0
485.0	0	1	0	1
487.0	0	2	0	2
495.0	0	1	0	1
506.0	0	1	0	1
509.0	0	0	0	1
511.0	0	1	0	1
512.0	0	1	0	1
513.0	0	1	0	0
515.0	0	1	0	1
516.0	0	0	0	1
517.0	0	3	0	2
532.0	0	1	0	1
533.0	0	1	0	1
536.0	0	1	0	1
543.0	0	0	0	1
544.0	0	1	0	0
546.0	0	1	0	1
550.0	0	0	0	1
551.0	0	1	0	0
553.0	0	0	0	1
555.0	0	1	0	0
563.0	0	1	0	1
564.0	0	1	0	2
565.0	0	1	0	0
584.0	0	1	0	1
587.0	0	1	0	1
588.0	0	1	0	1
590.0	0	0	0	1
591.0	0	1	0	0
600.0	0	0	0	1
603.0	0	1	0	0
610.0	0	1	0	1
612.0	0	0	0	1
616.0	0	1	0	0
620.0	0	1	0	2
621.0	0	1	0	0
624.0	0	0	0	1
626.0	0	1	0	0
648.0	0	1	0	1
658.0	0	1	0	1
671.0	0	1	0	1
678.0	0	0	0	1
681.0	0	0	0	1
682.0	0	2	0	0
687.0	0	0	0	1
691.0	0	1	0	0
720.0	0	0	0	1
722.0	0	1	0	0
741.0	0	1	0	1
744.0	0	1	0	1
745.0	0	0	0	1
748.0	0	0	0	1
749.0	0	1	0	0
751.0	0	1	0	0
774.0	0	1	0	1
797.0	0	1	0	1
805.0	0	0	0	1
806.0	0	1	0	0
812.0	0	1	0	1
820.0	0	0	0	1
823.0	0	1	0	0
829.0	0	0	0	1
835.0	0	1	0	0
889.0	0	0	0	1
894.0	0	1	0	0
903.0	0	0	0	1
905.0	0	1	0	0
926.0	0	1	0	1
1040.0	0	0	0	1
1045.0	0	1	0	0
1058.0	0	0	0	1
1060.0	0	1	0	0
1117.0	0	1	0	1
1258.0	0	0	0	1
1260.0	0	0	0	1
1261.0	0	1	0	0
1264.0	0	1	0	0
1277.0	0	0	0	1
1280.0	0	1	0	0
1402.0	0	0	0	1
1403.0	0	1	0	0
1447.0	0	0	0	1
1455.0	0	1	0	1
1458.0	0	0	0	1
1461.0	0	1	0	0
1475.0	0	1	0	0
1484.0	0	0	0	1
1485.0	0	1	0	0
1555.0	0	0	0	1
1556.0	0	1	0	0
1577.0	0	0	0	1
1579.0	0	1	0	0
1600.0	0	1	0	1
1686.0	0	0	0	1
1692.0	0	1	0	0
1714.0	0	0	0	1
1720.0	0	1	0	0
1742.0	0	0	0	1
1744.0	0	1	0	0
1902.0	0	0	0	1
1909.0	0	1	0	0
2749.0	0	0	0	1
2750.0	0	1	0	0
2820.0	0	0	0	1
2827.0	0	1	0	0
6099.0	0	0	0	1
6108.0	0	1	0	0
7154.0	0	0	0	1
7157.0	0	1	0	0
11801.0	0	0	0	1
11834.0	0	1	0	0
25568.0	0	0	0	1
25637.0	0	1	0	0