## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/scratch/tdewijs/results/star/GRCg6a-GSM1481261.samtools-coordinate-unsieved.bam] OUTPUT=/scratch/tdewijs/results/star/GRCg6a-GSM1481261.samtools-coordinate-dupmarked.bam METRICS_FILE=/scratch/tdewijs/results/qc/markdup/GRCg6a-GSM1481261.samtools-coordinate.metrics.txt TMP_DIR=[/scratch/tdewijs/tmp]    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 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 REMOVE_DUPLICATES=false 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 VALIDATION_STRINGENCY=STRICT 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 Dec 09 17:47:07 CET 2021

## 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	0	27731543	2514446	0	0	4338267	0	0.156438	79126950

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	21386525	21386525
2.0	1.704358	1307783	1307783
3.0	2.200477	326634	326634
4.0	2.549923	136177	136177
5.0	2.796058	71794	71794
6.0	2.969425	42948	42948
7.0	3.091537	27929	27929
8.0	3.177548	19274	19274
9.0	3.23813	14007	14007
10.0	3.280802	10297	10297
11.0	3.310858	7814	7814
12.0	3.332028	6100	6100
13.0	3.34694	5013	5013
14.0	3.357443	4118	4118
15.0	3.36484	3227	3227
16.0	3.370051	2738	2738
17.0	3.373721	2253	2253
18.0	3.376307	1988	1988
19.0	3.378127	1708	1708
20.0	3.37941	1451	1451
21.0	3.380313	1205	1205
22.0	3.38095	1071	1071
23.0	3.381398	967	967
24.0	3.381713	888	888
25.0	3.381936	683	683
26.0	3.382092	693	693
27.0	3.382203	602	602
28.0	3.38228	517	517
29.0	3.382335	507	507
30.0	3.382374	420	420
31.0	3.382401	437	437
32.0	3.38242	340	340
33.0	3.382433	306	306
34.0	3.382443	274	274
35.0	3.38245	290	290
36.0	3.382454	281	281
37.0	3.382458	229	229
38.0	3.38246	206	206
39.0	3.382462	200	200
40.0	3.382463	195	195
41.0	3.382464	173	173
42.0	3.382464	157	157
43.0	3.382465	136	136
44.0	3.382465	131	131
45.0	3.382465	138	138
46.0	3.382465	111	111
47.0	3.382465	126	126
48.0	3.382465	120	120
49.0	3.382465	92	92
50.0	3.382465	89	89
51.0	3.382465	71	71
52.0	3.382466	76	76
53.0	3.382466	94	94
54.0	3.382466	78	78
55.0	3.382466	62	62
56.0	3.382466	67	67
57.0	3.382466	65	65
58.0	3.382466	59	59
59.0	3.382466	63	63
60.0	3.382466	59	59
61.0	3.382466	46	46
62.0	3.382466	61	61
63.0	3.382466	51	51
64.0	3.382466	36	36
65.0	3.382466	44	44
66.0	3.382466	24	24
67.0	3.382466	35	35
68.0	3.382466	29	29
69.0	3.382466	31	31
70.0	3.382466	33	33
71.0	3.382466	25	25
72.0	3.382466	26	26
73.0	3.382466	21	21
74.0	3.382466	24	24
75.0	3.382466	19	19
76.0	3.382466	16	16
77.0	3.382466	25	25
78.0	3.382466	22	22
79.0	3.382466	23	23
80.0	3.382466	22	22
81.0	3.382466	12	12
82.0	3.382466	22	22
83.0	3.382466	16	16
84.0	3.382466	18	18
85.0	3.382466	22	22
86.0	3.382466	13	13
87.0	3.382466	22	22
88.0	3.382466	9	9
89.0	3.382466	13	13
90.0	3.382466	17	17
91.0	3.382466	7	7
92.0	3.382466	18	18
93.0	3.382466	19	19
94.0	3.382466	11	11
95.0	3.382466	10	10
96.0	3.382466	4	4
97.0	3.382466	10	10
98.0	3.382466	3	3
99.0	3.382466	8	8
100.0	3.382466	5	5
101.0	0	10	10
102.0	0	7	7
103.0	0	8	8
104.0	0	8	8
105.0	0	4	4
106.0	0	3	3
107.0	0	6	6
108.0	0	6	6
109.0	0	6	6
110.0	0	5	5
111.0	0	6	6
112.0	0	9	9
113.0	0	11	11
114.0	0	5	5
115.0	0	7	7
116.0	0	3	3
117.0	0	2	2
118.0	0	5	5
119.0	0	6	6
120.0	0	6	6
121.0	0	3	3
122.0	0	5	5
123.0	0	4	4
124.0	0	6	6
125.0	0	4	4
127.0	0	3	3
128.0	0	6	6
129.0	0	5	5
130.0	0	7	7
131.0	0	4	4
132.0	0	3	3
133.0	0	4	4
134.0	0	4	4
135.0	0	2	2
136.0	0	1	1
137.0	0	1	1
138.0	0	4	4
139.0	0	2	2
140.0	0	3	3
141.0	0	2	2
142.0	0	3	3
143.0	0	2	2
144.0	0	3	3
146.0	0	1	1
147.0	0	3	3
148.0	0	2	2
149.0	0	2	2
150.0	0	1	1
151.0	0	2	2
152.0	0	3	3
153.0	0	2	2
154.0	0	2	2
155.0	0	4	4
156.0	0	3	3
157.0	0	2	2
158.0	0	2	2
159.0	0	3	3
160.0	0	3	3
161.0	0	2	2
162.0	0	4	4
163.0	0	1	1
164.0	0	4	4
165.0	0	1	1
167.0	0	2	2
168.0	0	2	2
169.0	0	4	4
173.0	0	1	1
174.0	0	2	2
175.0	0	1	1
176.0	0	2	2
177.0	0	3	3
178.0	0	1	1
181.0	0	3	3
182.0	0	2	2
183.0	0	2	2
184.0	0	1	1
185.0	0	1	1
187.0	0	1	1
192.0	0	1	1
193.0	0	1	1
194.0	0	1	1
195.0	0	1	1
198.0	0	1	1
199.0	0	2	2
200.0	0	2	2
204.0	0	1	1
205.0	0	2	2
207.0	0	1	1
208.0	0	1	1
209.0	0	1	1
210.0	0	1	1
212.0	0	1	1
214.0	0	1	1
216.0	0	4	4
218.0	0	1	1
219.0	0	1	1
224.0	0	1	1
226.0	0	1	1
227.0	0	1	1
228.0	0	2	2
234.0	0	1	1
236.0	0	1	1
237.0	0	1	1
240.0	0	1	1
244.0	0	1	1
249.0	0	1	1
257.0	0	1	1
262.0	0	1	1
267.0	0	1	1
268.0	0	1	1
269.0	0	1	1
271.0	0	1	1
277.0	0	1	1
280.0	0	1	1
282.0	0	1	1
283.0	0	1	1
286.0	0	1	1
313.0	0	1	1
321.0	0	2	2
324.0	0	1	1
325.0	0	1	1
339.0	0	1	1
344.0	0	1	1
348.0	0	1	1
362.0	0	1	1
374.0	0	1	1
393.0	0	1	1
422.0	0	1	1
427.0	0	1	1
439.0	0	1	1
441.0	0	1	1
466.0	0	1	1
497.0	0	1	1
506.0	0	1	1
511.0	0	1	1
527.0	0	1	1
580.0	0	1	1
584.0	0	1	1
1400.0	0	1	1