## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Kie_Kyi_1_2020-09-29/UA_Kie_Kyi_1_2020-09-29.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Kie_Kyi_1_2020-09-29/UA_Kie_Kyi_1_2020-09-29.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Kie_Kyi_1_2020-09-29/UA_Kie_Kyi_1_2020-09-29.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 Jan 18 04:21:55 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	4674013	23461474	0	0	2592498	5861403	228230	0.277445	39805327

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.007213	12926365	0	13056400
2.0	1.565871	3202256	222651	3136656
3.0	1.875735	763907	2468	722386
4.0	2.047602	177628	40	161666
5.0	2.14293	41416	9	36406
6.0	2.195804	10289	5	8925
7.0	2.225132	3234	6	2876
8.0	2.241398	1318	4	1195
9.0	2.25042	789	2	744
10.0	2.255425	462	7	445
11.0	2.2582	385	2	382
12.0	2.25974	285	1	272
13.0	2.260594	216	0	215
14.0	2.261067	218	0	214
15.0	2.26133	137	1	137
16.0	2.261476	144	0	147
17.0	2.261557	146	0	138
18.0	2.261601	81	0	85
19.0	2.261626	101	0	90
20.0	2.26164	65	1	67
21.0	2.261648	79	0	78
22.0	2.261652	56	1	59
23.0	2.261654	48	1	45
24.0	2.261656	38	0	42
25.0	2.261656	52	0	50
26.0	2.261657	41	0	39
27.0	2.261657	36	0	43
28.0	2.261657	41	0	33
29.0	2.261657	32	0	33
30.0	2.261657	25	0	26
31.0	2.261657	31	0	30
32.0	2.261657	21	0	24
33.0	2.261657	28	0	26
34.0	2.261657	23	0	23
35.0	2.261657	19	0	16
36.0	2.261657	19	0	21
37.0	2.261657	21	0	22
38.0	2.261657	23	0	25
39.0	2.261657	21	0	19
40.0	2.261657	21	0	18
41.0	2.261657	16	0	16
42.0	2.261657	11	0	14
43.0	2.261657	20	0	17
44.0	2.261657	22	0	24
45.0	2.261657	11	0	11
46.0	2.261657	14	0	14
47.0	2.261657	12	0	10
48.0	2.261657	12	0	13
49.0	2.261657	6	0	5
50.0	2.261657	10	0	10
51.0	2.261657	15	0	15
52.0	2.261657	14	0	14
53.0	2.261657	6	0	6
54.0	2.261657	16	0	15
55.0	2.261657	13	0	16
56.0	2.261657	8	0	6
57.0	2.261657	8	0	7
58.0	2.261657	3	0	3
59.0	2.261657	8	0	9
60.0	2.261657	8	0	8
61.0	2.261657	6	0	6
62.0	2.261657	10	0	10
63.0	2.261657	3	0	4
64.0	2.261657	10	1	10
65.0	2.261657	8	0	8
66.0	2.261657	6	0	4
67.0	2.261657	7	0	11
68.0	2.261657	7	0	5
69.0	2.261657	5	0	7
70.0	2.261657	6	0	5
71.0	2.261657	5	0	4
72.0	2.261657	5	0	3
73.0	2.261657	3	0	3
74.0	2.261657	2	0	2
75.0	2.261657	3	0	3
76.0	2.261657	2	0	4
77.0	2.261657	6	0	7
78.0	2.261657	6	0	8
79.0	2.261657	7	0	8
80.0	2.261657	5	0	3
81.0	2.261657	9	0	6
82.0	2.261657	5	0	4
83.0	2.261657	4	0	4
84.0	2.261657	3	0	4
85.0	2.261657	6	0	6
86.0	2.261657	5	0	4
87.0	2.261657	3	0	4
88.0	2.261657	4	0	3
89.0	2.261657	0	0	0
90.0	2.261657	2	0	5
91.0	2.261657	8	0	7
92.0	2.261657	3	0	2
93.0	2.261657	3	0	5
94.0	2.261657	4	0	3
95.0	2.261657	3	0	2
96.0	2.261657	4	0	5
97.0	2.261657	4	0	3
98.0	2.261657	2	0	2
99.0	2.261657	2	0	1
100.0	2.261657	3	0	3
101.0	0	1	0	2
102.0	0	2	0	1
103.0	0	1	0	1
104.0	0	2	0	2
106.0	0	3	0	3
107.0	0	1	0	2
108.0	0	3	0	3
109.0	0	1	0	0
112.0	0	3	0	4
113.0	0	1	0	3
114.0	0	4	0	2
115.0	0	2	0	1
116.0	0	1	0	2
117.0	0	1	0	1
118.0	0	4	0	3
119.0	0	1	0	2
120.0	0	1	0	0
121.0	0	2	0	2
122.0	0	1	0	1
123.0	0	0	0	1
124.0	0	4	0	5
125.0	0	3	0	2
126.0	0	4	0	4
127.0	0	2	0	2
128.0	0	2	0	1
130.0	0	1	0	2
131.0	0	2	0	3
132.0	0	4	0	2
133.0	0	2	0	2
134.0	0	3	0	3
135.0	0	3	0	3
137.0	0	1	0	2
138.0	0	1	0	0
139.0	0	3	0	4
140.0	0	1	0	1
141.0	0	3	0	4
142.0	0	1	0	0
143.0	0	4	0	3
144.0	0	2	0	3
145.0	0	4	0	3
146.0	0	4	0	4
147.0	0	1	0	1
148.0	0	2	0	3
149.0	0	1	0	0
150.0	0	1	1	1
151.0	0	1	0	1
152.0	0	2	0	2
153.0	0	2	0	3
154.0	0	2	0	2
155.0	0	1	0	2
156.0	0	2	0	1
157.0	0	2	0	1
158.0	0	2	0	2
159.0	0	0	0	1
160.0	0	1	0	1
161.0	0	1	0	1
162.0	0	2	0	1
163.0	0	2	0	2
164.0	0	1	0	1
165.0	0	2	0	3
166.0	0	3	0	2
167.0	0	2	0	2
168.0	0	1	0	1
169.0	0	1	0	1
171.0	0	1	0	1
172.0	0	4	0	5
173.0	0	1	0	1
174.0	0	1	0	1
175.0	0	4	0	3
176.0	0	1	0	1
177.0	0	2	0	2
179.0	0	3	0	3
180.0	0	1	0	1
181.0	0	1	0	1
182.0	0	2	0	2
183.0	0	3	0	3
184.0	0	1	0	1
185.0	0	2	0	3
186.0	0	2	0	1
187.0	0	2	0	2
188.0	0	1	0	2
189.0	0	1	0	0
190.0	0	1	0	1
191.0	0	0	0	1
192.0	0	1	0	0
194.0	0	3	0	3
195.0	0	1	0	1
196.0	0	1	0	1
199.0	0	2	0	3
200.0	0	1	0	1
201.0	0	1	0	0
202.0	0	1	0	1
203.0	0	1	0	1
205.0	0	0	0	1
206.0	0	2	0	1
208.0	0	2	0	2
209.0	0	3	0	4
210.0	0	1	0	0
211.0	0	1	0	1
212.0	0	1	0	1
213.0	0	0	0	1
214.0	0	3	0	3
215.0	0	0	0	1
216.0	0	2	0	2
217.0	0	0	0	1
218.0	0	3	0	1
219.0	0	3	0	2
222.0	0	1	0	1
223.0	0	1	0	2
224.0	0	1	0	1
225.0	0	1	0	1
226.0	0	1	0	1
227.0	0	0	0	2
228.0	0	2	0	0
229.0	0	1	0	1
230.0	0	1	0	0
231.0	0	1	0	1
233.0	0	1	0	1
236.0	0	0	0	1
237.0	0	1	0	3
238.0	0	2	0	0
240.0	0	3	0	2
241.0	0	1	0	1
242.0	0	2	0	2
245.0	0	0	0	1
246.0	0	2	0	1
249.0	0	1	0	1
252.0	0	0	0	1
253.0	0	2	0	1
256.0	0	1	0	1
261.0	0	1	0	1
264.0	0	1	0	1
266.0	0	1	0	1
268.0	0	1	0	2
269.0	0	2	0	2
270.0	0	2	0	1
271.0	0	1	0	2
272.0	0	2	0	1
273.0	0	1	0	1
274.0	0	0	0	1
275.0	0	1	0	2
277.0	0	1	0	1
278.0	0	2	0	0
281.0	0	2	0	2
282.0	0	1	0	1
285.0	0	1	0	1
290.0	0	0	0	1
291.0	0	1	0	0
293.0	0	1	0	2
294.0	0	1	0	0
297.0	0	1	0	1
298.0	0	0	0	1
299.0	0	1	0	0
300.0	0	1	0	1
301.0	0	1	0	1
304.0	0	0	0	1
305.0	0	1	0	0
306.0	0	1	0	1
307.0	0	1	0	1
309.0	0	3	0	3
310.0	0	1	0	1
313.0	0	1	0	1
316.0	0	0	0	1
317.0	0	2	0	1
319.0	0	1	0	1
324.0	0	1	0	1
331.0	0	0	0	1
333.0	0	1	0	1
335.0	0	1	0	0
339.0	0	1	0	1
345.0	0	1	0	1
348.0	0	1	0	1
355.0	0	1	0	1
356.0	0	2	0	2
359.0	0	1	0	1
361.0	0	1	0	1
369.0	0	0	0	1
370.0	0	1	0	0
375.0	0	1	0	1
379.0	0	1	0	1
387.0	0	1	0	1
391.0	0	0	0	1
394.0	0	0	0	2
395.0	0	1	0	1
396.0	0	1	0	0
397.0	0	1	0	0
398.0	0	2	0	1
402.0	0	1	0	1
409.0	0	1	0	1
414.0	0	1	0	1
417.0	0	0	0	1
418.0	0	1	0	1
419.0	0	1	0	1
420.0	0	1	0	0
426.0	0	1	0	2
427.0	0	1	0	1
428.0	0	2	0	1
429.0	0	1	0	1
437.0	0	1	0	1
439.0	0	1	0	1
440.0	0	1	0	1
442.0	0	1	0	1
444.0	0	1	0	1
445.0	0	2	0	2
446.0	0	0	0	1
447.0	0	1	0	1
448.0	0	1	0	0
451.0	0	1	0	1
455.0	0	0	0	1
461.0	0	1	0	0
463.0	0	1	0	1
464.0	0	0	0	1
465.0	0	1	0	0
467.0	0	1	0	1
481.0	0	0	0	1
482.0	0	1	0	0
486.0	0	1	0	1
489.0	0	1	0	1
499.0	0	1	0	1
500.0	0	0	0	1
501.0	0	0	0	1
502.0	0	2	0	0
511.0	0	1	0	1
516.0	0	1	0	1
531.0	0	1	0	1
534.0	0	1	0	2
539.0	0	2	0	1
556.0	0	1	0	1
557.0	0	0	0	1
558.0	0	1	0	0
561.0	0	0	0	1
563.0	0	1	0	1
565.0	0	1	0	1
572.0	0	1	0	0
578.0	0	1	0	1
581.0	0	1	0	1
585.0	0	2	0	2
589.0	0	0	0	1
592.0	0	1	0	1
596.0	0	0	0	1
597.0	0	1	0	0
598.0	0	2	0	1
601.0	0	1	0	1
607.0	0	0	0	1
608.0	0	1	0	0
621.0	0	1	0	1
627.0	0	0	0	1
628.0	0	1	0	0
635.0	0	0	0	1
636.0	0	1	0	0
638.0	0	0	0	1
639.0	0	1	0	0
650.0	0	0	0	1
652.0	0	0	0	1
653.0	0	1	0	1
654.0	0	1	0	0
658.0	0	1	0	1
660.0	0	1	0	0
663.0	0	1	0	1
665.0	0	1	0	1
666.0	0	1	0	1
685.0	0	1	0	1
695.0	0	1	0	1
703.0	0	1	0	1
705.0	0	1	0	1
713.0	0	1	0	1
721.0	0	0	0	1
727.0	0	1	0	0
741.0	0	1	0	1
745.0	0	1	0	1
746.0	0	0	0	1
748.0	0	1	0	1
750.0	0	1	0	1
753.0	0	1	0	0
772.0	0	1	0	1
821.0	0	0	0	1
830.0	0	1	0	0
837.0	0	0	0	1
838.0	0	1	0	0
842.0	0	0	0	1
844.0	0	0	0	1
847.0	0	2	0	0
849.0	0	1	0	1
856.0	0	1	0	2
858.0	0	1	0	0
860.0	0	0	0	1
863.0	0	1	0	1
864.0	0	1	0	1
867.0	0	1	0	0
870.0	0	0	0	1
872.0	0	1	0	1
873.0	0	1	0	0
874.0	0	1	0	1
890.0	0	0	0	1
892.0	0	1	0	0
912.0	0	0	0	1
921.0	0	1	0	0
924.0	0	0	0	1
928.0	0	1	0	0
938.0	0	1	0	1
945.0	0	0	0	1
946.0	0	1	0	0
956.0	0	1	0	1
991.0	0	0	0	1
993.0	0	1	0	1
995.0	0	0	0	1
996.0	0	1	0	0
998.0	0	0	0	1
1001.0	0	1	0	0
1004.0	0	1	0	0
1009.0	0	0	0	1
1015.0	0	1	0	0
1019.0	0	1	0	1
1022.0	0	1	0	1
1044.0	0	0	0	1
1048.0	0	1	0	0
1049.0	0	1	0	1
1130.0	0	0	0	1
1135.0	0	1	0	0
1156.0	0	0	0	1
1158.0	0	1	0	0
1289.0	0	0	0	1
1293.0	0	1	0	1
1302.0	0	1	0	1
1308.0	0	1	0	0
1335.0	0	1	0	1
1346.0	0	0	0	1
1347.0	0	1	0	0
1437.0	0	0	0	1
1446.0	0	1	0	0
1555.0	0	1	0	1
1757.0	0	1	0	1
1780.0	0	0	0	1
1781.0	0	1	0	0
1801.0	0	0	0	1
1809.0	0	1	0	0
1858.0	0	0	0	1
1864.0	0	1	0	0
2007.0	0	0	0	1
2013.0	0	1	0	0
2097.0	0	0	0	1
2100.0	0	1	0	0
2104.0	0	0	0	1
2111.0	0	1	0	0
2259.0	0	0	0	1
2265.0	0	1	0	0
2301.0	0	0	0	1
2302.0	0	1	0	0
2315.0	0	0	0	1
2323.0	0	1	0	0
2402.0	0	0	0	1
2411.0	0	1	0	0
2618.0	0	0	0	1
2622.0	0	0	0	1
2623.0	0	1	0	0
2625.0	0	1	0	0
2663.0	0	0	0	1
2673.0	0	1	0	0
2928.0	0	0	0	1
2937.0	0	1	0	0
2956.0	0	1	0	1
3619.0	0	0	0	1
3640.0	0	1	0	0
4642.0	0	0	0	1
4651.0	0	1	0	0
5175.0	0	0	0	1
5180.0	0	1	0	0
11794.0	0	0	0	1
11816.0	0	1	0	0
12058.0	0	0	0	1
12072.0	0	1	0	0
19531.0	0	0	0	1
19594.0	0	1	0	0
48139.0	0	0	0	1
48288.0	0	1	0	0