## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/scratch/tdewijs/results/star/GRCg6a-GSM1481262.samtools-coordinate-unsieved.bam] OUTPUT=/scratch/tdewijs/results/star/GRCg6a-GSM1481262.samtools-coordinate-dupmarked.bam METRICS_FILE=/scratch/tdewijs/results/qc/markdup/GRCg6a-GSM1481262.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 17:37:56 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	19973054	1480636	0	0	3493706	0	0.174921	50219336

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	14927853	14927853
2.0	1.671853	1003917	1003917
3.0	2.123238	250169	250169
4.0	2.426503	105981	105981
5.0	2.630252	56401	56401
6.0	2.767142	34219	34219
7.0	2.859111	22191	22191
8.0	2.920901	15608	15608
9.0	2.962415	11269	11269
10.0	2.990306	8516	8516
11.0	3.009045	6545	6545
12.0	3.021634	5062	5062
13.0	3.030093	4174	4174
14.0	3.035775	3302	3302
15.0	3.039593	2853	2853
16.0	3.042158	2369	2369
17.0	3.043882	1994	1994
18.0	3.04504	1698	1698
19.0	3.045818	1470	1470
20.0	3.04634	1246	1246
21.0	3.046691	1092	1092
22.0	3.046927	1028	1028
23.0	3.047086	876	876
24.0	3.047192	783	783
25.0	3.047264	627	627
26.0	3.047312	611	611
27.0	3.047344	497	497
28.0	3.047366	485	485
29.0	3.047381	410	410
30.0	3.04739	406	406
31.0	3.047397	333	333
32.0	3.047401	350	350
33.0	3.047404	288	288
34.0	3.047406	289	289
35.0	3.047408	243	243
36.0	3.047409	224	224
37.0	3.047409	242	242
38.0	3.04741	209	209
39.0	3.04741	180	180
40.0	3.04741	147	147
41.0	3.04741	183	183
42.0	3.04741	147	147
43.0	3.04741	130	130
44.0	3.04741	140	140
45.0	3.04741	131	131
46.0	3.04741	107	107
47.0	3.04741	94	94
48.0	3.04741	105	105
49.0	3.04741	89	89
50.0	3.04741	82	82
51.0	3.04741	89	89
52.0	3.04741	93	93
53.0	3.04741	68	68
54.0	3.04741	67	67
55.0	3.04741	63	63
56.0	3.04741	78	78
57.0	3.04741	65	65
58.0	3.04741	54	54
59.0	3.04741	51	51
60.0	3.04741	50	50
61.0	3.04741	62	62
62.0	3.04741	40	40
63.0	3.04741	39	39
64.0	3.04741	40	40
65.0	3.04741	29	29
66.0	3.04741	44	44
67.0	3.04741	30	30
68.0	3.04741	30	30
69.0	3.04741	43	43
70.0	3.04741	24	24
71.0	3.04741	35	35
72.0	3.04741	34	34
73.0	3.04741	27	27
74.0	3.04741	29	29
75.0	3.04741	22	22
76.0	3.04741	31	31
77.0	3.04741	28	28
78.0	3.04741	26	26
79.0	3.04741	19	19
80.0	3.04741	21	21
81.0	3.04741	23	23
82.0	3.04741	15	15
83.0	3.04741	14	14
84.0	3.04741	25	25
85.0	3.04741	15	15
86.0	3.04741	17	17
87.0	3.04741	11	11
88.0	3.04741	15	15
89.0	3.04741	19	19
90.0	3.04741	12	12
91.0	3.04741	9	9
92.0	3.04741	17	17
93.0	3.04741	10	10
94.0	3.04741	13	13
95.0	3.04741	12	12
96.0	3.04741	21	21
97.0	3.04741	9	9
98.0	3.04741	8	8
99.0	3.04741	8	8
100.0	3.04741	11	11
101.0	0	6	6
102.0	0	6	6
103.0	0	8	8
104.0	0	10	10
105.0	0	9	9
106.0	0	11	11
107.0	0	6	6
108.0	0	11	11
109.0	0	5	5
110.0	0	6	6
111.0	0	6	6
112.0	0	4	4
113.0	0	3	3
114.0	0	6	6
115.0	0	2	2
116.0	0	7	7
117.0	0	5	5
118.0	0	4	4
119.0	0	7	7
120.0	0	3	3
121.0	0	6	6
122.0	0	5	5
123.0	0	5	5
124.0	0	2	2
125.0	0	1	1
126.0	0	5	5
127.0	0	5	5
128.0	0	7	7
129.0	0	8	8
130.0	0	2	2
131.0	0	4	4
132.0	0	3	3
133.0	0	2	2
134.0	0	2	2
135.0	0	8	8
136.0	0	4	4
137.0	0	6	6
138.0	0	6	6
139.0	0	2	2
140.0	0	2	2
141.0	0	1	1
142.0	0	5	5
143.0	0	6	6
144.0	0	2	2
145.0	0	1	1
146.0	0	4	4
147.0	0	3	3
148.0	0	4	4
149.0	0	2	2
150.0	0	2	2
151.0	0	3	3
152.0	0	3	3
154.0	0	2	2
156.0	0	2	2
157.0	0	5	5
158.0	0	5	5
163.0	0	1	1
165.0	0	2	2
166.0	0	2	2
168.0	0	1	1
169.0	0	1	1
170.0	0	3	3
172.0	0	1	1
174.0	0	3	3
175.0	0	3	3
176.0	0	2	2
177.0	0	2	2
178.0	0	3	3
179.0	0	2	2
180.0	0	4	4
181.0	0	1	1
182.0	0	1	1
183.0	0	2	2
187.0	0	1	1
189.0	0	1	1
194.0	0	1	1
201.0	0	2	2
202.0	0	1	1
203.0	0	1	1
206.0	0	1	1
207.0	0	1	1
212.0	0	1	1
214.0	0	1	1
215.0	0	1	1
216.0	0	1	1
218.0	0	1	1
219.0	0	1	1
223.0	0	1	1
229.0	0	1	1
230.0	0	1	1
234.0	0	1	1
237.0	0	1	1
239.0	0	1	1
240.0	0	1	1
243.0	0	2	2
244.0	0	2	2
246.0	0	3	3
249.0	0	1	1
252.0	0	1	1
255.0	0	1	1
258.0	0	1	1
260.0	0	1	1
266.0	0	1	1
268.0	0	1	1
269.0	0	1	1
270.0	0	3	3
271.0	0	1	1
275.0	0	1	1
277.0	0	1	1
278.0	0	1	1
280.0	0	2	2
281.0	0	2	2
288.0	0	1	1
296.0	0	2	2
297.0	0	1	1
323.0	0	1	1
326.0	0	1	1
329.0	0	1	1
349.0	0	1	1
350.0	0	3	3
357.0	0	1	1
368.0	0	1	1
369.0	0	1	1
372.0	0	1	1
385.0	0	1	1
436.0	0	1	1
549.0	0	1	1
552.0	0	1	1
577.0	0	1	1
636.0	0	1	1
652.0	0	1	1
664.0	0	1	1
668.0	0	1	1
681.0	0	1	1
777.0	0	1	1