## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/AT_Kar_See_1_2014-08-17/AT_Kar_See_1_2014-08-17.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/AT_Kar_See_1_2014-08-17/AT_Kar_See_1_2014-08-17.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/AT_Kar_See_1_2014-08-17/AT_Kar_See_1_2014-08-17.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 09:10:43 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	6116568	23930774	0	0	1500707	853981	0	0.059444	327276045

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	21982362	21982362
2.0	1.929488	524990	524990
3.0	2.793437	11975	11975
4.0	3.596467	1266	1266
5.0	4.342874	609	609
6.0	5.03665	466	466
7.0	5.681507	305	305
8.0	6.280895	226	226
9.0	6.838018	204	204
10.0	7.355858	185	185
11.0	7.837184	149	149
12.0	8.28457	115	115
13.0	8.700411	103	103
14.0	9.08693	100	100
15.0	9.446195	94	94
16.0	9.780128	92	92
17.0	10.090514	68	68
18.0	10.379015	89	89
19.0	10.647173	68	68
20.0	10.896423	54	54
21.0	11.128097	52	52
22.0	11.343436	60	60
23.0	11.543591	46	46
24.0	11.729633	47	47
25.0	11.902556	40	40
26.0	12.063287	52	52
27.0	12.212684	44	44
28.0	12.351547	37	37
29.0	12.480618	42	42
30.0	12.600588	37	37
31.0	12.712099	45	45
32.0	12.815747	29	29
33.0	12.912087	43	43
34.0	13.001634	40	40
35.0	13.084866	29	29
36.0	13.16223	22	22
37.0	13.234139	26	26
38.0	13.300977	26	26
39.0	13.363102	25	25
40.0	13.420847	21	21
41.0	13.47452	18	18
42.0	13.524409	20	20
43.0	13.57078	25	25
44.0	13.613881	18	18
45.0	13.653943	17	17
46.0	13.69118	16	16
47.0	13.725792	20	20
48.0	13.757963	14	14
49.0	13.787865	15	15
50.0	13.815659	16	16
51.0	13.841493	17	17
52.0	13.865506	13	13
53.0	13.887826	11	11
54.0	13.908571	11	11
55.0	13.927854	13	13
56.0	13.945777	22	22
57.0	13.962437	9	9
58.0	13.977922	10	10
59.0	13.992314	23	23
60.0	14.005692	10	10
61.0	14.018127	12	12
62.0	14.029685	10	10
63.0	14.040428	19	19
64.0	14.050413	16	16
65.0	14.059695	8	8
66.0	14.068322	12	12
67.0	14.07634	16	16
68.0	14.083793	11	11
69.0	14.090721	8	8
70.0	14.09716	8	8
71.0	14.103145	14	14
72.0	14.108709	14	14
73.0	14.113879	6	6
74.0	14.118686	11	11
75.0	14.123153	11	11
76.0	14.127305	12	12
77.0	14.131165	8	8
78.0	14.134752	8	8
79.0	14.138087	11	11
80.0	14.141186	9	9
81.0	14.144067	10	10
82.0	14.146745	8	8
83.0	14.149234	12	12
84.0	14.151547	12	12
85.0	14.153697	11	11
86.0	14.155696	9	9
87.0	14.157554	6	6
88.0	14.15928	8	8
89.0	14.160885	7	7
90.0	14.162377	6	6
91.0	14.163764	7	7
92.0	14.165052	9	9
93.0	14.16625	5	5
94.0	14.167364	7	7
95.0	14.168399	1	1
96.0	14.169361	3	3
97.0	14.170255	5	5
98.0	14.171086	3	3
99.0	14.171859	3	3
100.0	14.172577	6	6
101.0	0	5	5
102.0	0	5	5
103.0	0	3	3
104.0	0	10	10
105.0	0	7	7
106.0	0	7	7
107.0	0	4	4
108.0	0	8	8
109.0	0	4	4
110.0	0	5	5
111.0	0	3	3
112.0	0	5	5
113.0	0	3	3
114.0	0	5	5
115.0	0	8	8
116.0	0	6	6
117.0	0	2	2
118.0	0	3	3
119.0	0	5	5
120.0	0	2	2
121.0	0	6	6
122.0	0	8	8
123.0	0	5	5
124.0	0	5	5
125.0	0	9	9
126.0	0	7	7
127.0	0	2	2
128.0	0	9	9
129.0	0	4	4
130.0	0	5	5
131.0	0	5	5
132.0	0	2	2
133.0	0	1	1
134.0	0	4	4
135.0	0	1	1
137.0	0	2	2
138.0	0	6	6
139.0	0	4	4
140.0	0	2	2
141.0	0	4	4
142.0	0	3	3
143.0	0	5	5
144.0	0	4	4
145.0	0	2	2
146.0	0	2	2
147.0	0	1	1
148.0	0	4	4
149.0	0	3	3
150.0	0	5	5
151.0	0	1	1
152.0	0	5	5
153.0	0	5	5
154.0	0	3	3
155.0	0	5	5
156.0	0	2	2
157.0	0	4	4
158.0	0	1	1
159.0	0	3	3
160.0	0	6	6
161.0	0	5	5
162.0	0	2	2
163.0	0	3	3
164.0	0	5	5
165.0	0	4	4
166.0	0	1	1
167.0	0	4	4
168.0	0	2	2
169.0	0	2	2
170.0	0	3	3
172.0	0	3	3
173.0	0	2	2
174.0	0	2	2
175.0	0	2	2
176.0	0	5	5
177.0	0	3	3
178.0	0	5	5
179.0	0	1	1
180.0	0	4	4
181.0	0	2	2
182.0	0	5	5
183.0	0	1	1
184.0	0	2	2
185.0	0	2	2
186.0	0	1	1
187.0	0	2	2
188.0	0	3	3
189.0	0	1	1
190.0	0	1	1
191.0	0	2	2
192.0	0	2	2
194.0	0	2	2
195.0	0	1	1
196.0	0	4	4
198.0	0	4	4
199.0	0	2	2
200.0	0	1	1
202.0	0	1	1
203.0	0	1	1
204.0	0	1	1
206.0	0	3	3
207.0	0	6	6
208.0	0	2	2
209.0	0	3	3
211.0	0	5	5
212.0	0	3	3
213.0	0	2	2
214.0	0	5	5
215.0	0	2	2
216.0	0	1	1
217.0	0	1	1
218.0	0	4	4
219.0	0	1	1
221.0	0	3	3
222.0	0	4	4
223.0	0	1	1
224.0	0	3	3
225.0	0	2	2
227.0	0	1	1
229.0	0	6	6
230.0	0	1	1
231.0	0	2	2
234.0	0	2	2
236.0	0	4	4
237.0	0	1	1
238.0	0	1	1
239.0	0	3	3
242.0	0	2	2
243.0	0	2	2
244.0	0	2	2
245.0	0	1	1
246.0	0	2	2
247.0	0	1	1
248.0	0	1	1
249.0	0	2	2
250.0	0	2	2
252.0	0	1	1
253.0	0	2	2
254.0	0	3	3
255.0	0	3	3
256.0	0	1	1
258.0	0	2	2
259.0	0	1	1
260.0	0	1	1
261.0	0	1	1
263.0	0	2	2
264.0	0	1	1
265.0	0	1	1
266.0	0	3	3
267.0	0	1	1
268.0	0	1	1
269.0	0	2	2
270.0	0	3	3
271.0	0	2	2
274.0	0	3	3
275.0	0	3	3
277.0	0	1	1
278.0	0	1	1
279.0	0	2	2
280.0	0	1	1
283.0	0	1	1
284.0	0	1	1
285.0	0	1	1
286.0	0	1	1
287.0	0	1	1
288.0	0	2	2
290.0	0	1	1
291.0	0	2	2
292.0	0	1	1
293.0	0	2	2
294.0	0	1	1
295.0	0	1	1
296.0	0	3	3
297.0	0	1	1
298.0	0	4	4
299.0	0	2	2
300.0	0	2	2
301.0	0	2	2
303.0	0	3	3
304.0	0	1	1
307.0	0	1	1
309.0	0	1	1
310.0	0	1	1
311.0	0	1	1
317.0	0	1	1
320.0	0	1	1
321.0	0	3	3
322.0	0	1	1
324.0	0	4	4
325.0	0	1	1
326.0	0	3	3
330.0	0	1	1
332.0	0	2	2
334.0	0	2	2
335.0	0	2	2
336.0	0	2	2
338.0	0	1	1
339.0	0	1	1
343.0	0	1	1
345.0	0	1	1
346.0	0	1	1
347.0	0	2	2
351.0	0	2	2
353.0	0	1	1
354.0	0	1	1
356.0	0	1	1
359.0	0	1	1
360.0	0	1	1
362.0	0	1	1
363.0	0	1	1
364.0	0	3	3
367.0	0	1	1
369.0	0	1	1
370.0	0	1	1
371.0	0	1	1
372.0	0	1	1
375.0	0	1	1
378.0	0	1	1
379.0	0	1	1
381.0	0	1	1
383.0	0	1	1
385.0	0	1	1
386.0	0	1	1
388.0	0	1	1
393.0	0	4	4
397.0	0	1	1
398.0	0	1	1
400.0	0	1	1
401.0	0	1	1
402.0	0	1	1
404.0	0	1	1
405.0	0	1	1
406.0	0	1	1
409.0	0	1	1
412.0	0	1	1
413.0	0	1	1
415.0	0	1	1
417.0	0	1	1
420.0	0	1	1
421.0	0	1	1
422.0	0	1	1
424.0	0	1	1
426.0	0	2	2
428.0	0	1	1
432.0	0	2	2
433.0	0	1	1
434.0	0	2	2
436.0	0	1	1
442.0	0	1	1
452.0	0	1	1
454.0	0	1	1
459.0	0	2	2
462.0	0	1	1
466.0	0	1	1
471.0	0	1	1
475.0	0	1	1
476.0	0	1	1
481.0	0	1	1
485.0	0	1	1
486.0	0	1	1
490.0	0	1	1
496.0	0	2	2
498.0	0	1	1
499.0	0	1	1
502.0	0	1	1
504.0	0	1	1
507.0	0	1	1
508.0	0	1	1
510.0	0	1	1
515.0	0	1	1
516.0	0	1	1
517.0	0	2	2
518.0	0	1	1
520.0	0	1	1
527.0	0	1	1
528.0	0	1	1
530.0	0	1	1
534.0	0	1	1
535.0	0	1	1
538.0	0	1	1
539.0	0	1	1
541.0	0	1	1
542.0	0	1	1
549.0	0	1	1
551.0	0	1	1
553.0	0	1	1
554.0	0	1	1
555.0	0	1	1
556.0	0	1	1
558.0	0	1	1
560.0	0	1	1
561.0	0	1	1
566.0	0	2	2
568.0	0	1	1
572.0	0	1	1
573.0	0	1	1
574.0	0	1	1
583.0	0	1	1
586.0	0	1	1
590.0	0	1	1
595.0	0	1	1
604.0	0	1	1
609.0	0	1	1
612.0	0	1	1
613.0	0	3	3
615.0	0	1	1
619.0	0	1	1
622.0	0	1	1
629.0	0	1	1
655.0	0	1	1
665.0	0	1	1
675.0	0	1	1
682.0	0	1	1
683.0	0	1	1
686.0	0	2	2
697.0	0	1	1
700.0	0	1	1
701.0	0	1	1
709.0	0	1	1
712.0	0	1	1
725.0	0	1	1
730.0	0	1	1
732.0	0	1	1
744.0	0	1	1
752.0	0	1	1
758.0	0	1	1
766.0	0	1	1
774.0	0	2	2
779.0	0	1	1
795.0	0	1	1
813.0	0	1	1
821.0	0	1	1
823.0	0	1	1
831.0	0	1	1
840.0	0	1	1
850.0	0	1	1
854.0	0	1	1
871.0	0	1	1
873.0	0	1	1
877.0	0	1	1
890.0	0	1	1
906.0	0	1	1
936.0	0	1	1
949.0	0	1	1
972.0	0	1	1
979.0	0	1	1
982.0	0	1	1
1001.0	0	1	1
1003.0	0	1	1
1004.0	0	1	1
1021.0	0	1	1
1028.0	0	1	1
1038.0	0	1	1
1048.0	0	1	1
1059.0	0	1	1
1064.0	0	1	1
1099.0	0	1	1
1114.0	0	1	1
1133.0	0	1	1
1158.0	0	1	1
1183.0	0	1	1
1211.0	0	1	1
1511.0	0	1	1
1528.0	0	1	1
1552.0	0	1	1
1661.0	0	1	1