## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/home/siebrenf/tdewijs/results/star/GRCg6a-GSM1481260.samtools-coordinate-unsieved.bam] OUTPUT=/home/siebrenf/tdewijs/results/star/GRCg6a-GSM1481260.samtools-coordinate-dupmarked.bam METRICS_FILE=/home/siebrenf/tdewijs/results/qc/markdup/GRCg6a-GSM1481260.samtools-coordinate.metrics.txt    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 20:46:50 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	22270441	5936960	0	0	5945965	0	0.266989	33895338

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	14813925	14813925
2.0	1.518386	867086	867086
3.0	1.78711	237799	237799
4.0	1.926412	111310	111310
5.0	1.998625	64614	64614
6.0	2.036059	42120	42120
7.0	2.055464	29999	29999
8.0	2.065523	22224	22224
9.0	2.070738	17056	17056
10.0	2.073441	13550	13550
11.0	2.074842	11210	11210
12.0	2.075569	9167	9167
13.0	2.075945	7663	7663
14.0	2.076141	6515	6515
15.0	2.076242	5560	5560
16.0	2.076294	4928	4928
17.0	2.076321	4290	4290
18.0	2.076336	3747	3747
19.0	2.076343	3313	3313
20.0	2.076347	2930	2930
21.0	2.076349	2664	2664
22.0	2.07635	2425	2425
23.0	2.07635	2260	2260
24.0	2.07635	1988	1988
25.0	2.076351	1806	1806
26.0	2.076351	1683	1683
27.0	2.076351	1646	1646
28.0	2.076351	1423	1423
29.0	2.076351	1386	1386
30.0	2.076351	1270	1270
31.0	2.076351	1156	1156
32.0	2.076351	1095	1095
33.0	2.076351	1017	1017
34.0	2.076351	930	930
35.0	2.076351	908	908
36.0	2.076351	846	846
37.0	2.076351	816	816
38.0	2.076351	724	724
39.0	2.076351	683	683
40.0	2.076351	663	663
41.0	2.076351	632	632
42.0	2.076351	581	581
43.0	2.076351	549	549
44.0	2.076351	531	531
45.0	2.076351	516	516
46.0	2.076351	490	490
47.0	2.076351	476	476
48.0	2.076351	463	463
49.0	2.076351	419	419
50.0	2.076351	394	394
51.0	2.076351	378	378
52.0	2.076351	358	358
53.0	2.076351	352	352
54.0	2.076351	328	328
55.0	2.076351	291	291
56.0	2.076351	314	314
57.0	2.076351	284	284
58.0	2.076351	295	295
59.0	2.076351	285	285
60.0	2.076351	270	270
61.0	2.076351	259	259
62.0	2.076351	226	226
63.0	2.076351	250	250
64.0	2.076351	225	225
65.0	2.076351	201	201
66.0	2.076351	208	208
67.0	2.076351	189	189
68.0	2.076351	197	197
69.0	2.076351	198	198
70.0	2.076351	176	176
71.0	2.076351	170	170
72.0	2.076351	159	159
73.0	2.076351	169	169
74.0	2.076351	140	140
75.0	2.076351	149	149
76.0	2.076351	150	150
77.0	2.076351	136	136
78.0	2.076351	138	138
79.0	2.076351	122	122
80.0	2.076351	119	119
81.0	2.076351	121	121
82.0	2.076351	165	165
83.0	2.076351	133	133
84.0	2.076351	111	111
85.0	2.076351	101	101
86.0	2.076351	120	120
87.0	2.076351	94	94
88.0	2.076351	107	107
89.0	2.076351	96	96
90.0	2.076351	89	89
91.0	2.076351	110	110
92.0	2.076351	70	70
93.0	2.076351	88	88
94.0	2.076351	70	70
95.0	2.076351	75	75
96.0	2.076351	83	83
97.0	2.076351	93	93
98.0	2.076351	85	85
99.0	2.076351	75	75
100.0	2.076351	70	70
101.0	0	91	91
102.0	0	72	72
103.0	0	65	65
104.0	0	57	57
105.0	0	59	59
106.0	0	63	63
107.0	0	71	71
108.0	0	72	72
109.0	0	51	51
110.0	0	66	66
111.0	0	75	75
112.0	0	37	37
113.0	0	52	52
114.0	0	56	56
115.0	0	44	44
116.0	0	47	47
117.0	0	52	52
118.0	0	38	38
119.0	0	52	52
120.0	0	51	51
121.0	0	44	44
122.0	0	45	45
123.0	0	40	40
124.0	0	45	45
125.0	0	45	45
126.0	0	40	40
127.0	0	41	41
128.0	0	43	43
129.0	0	43	43
130.0	0	47	47
131.0	0	36	36
132.0	0	43	43
133.0	0	45	45
134.0	0	36	36
135.0	0	27	27
136.0	0	38	38
137.0	0	49	49
138.0	0	25	25
139.0	0	34	34
140.0	0	28	28
141.0	0	30	30
142.0	0	24	24
143.0	0	28	28
144.0	0	26	26
145.0	0	38	38
146.0	0	27	27
147.0	0	20	20
148.0	0	21	21
149.0	0	30	30
150.0	0	25	25
151.0	0	17	17
152.0	0	38	38
153.0	0	25	25
154.0	0	27	27
155.0	0	23	23
156.0	0	26	26
157.0	0	19	19
158.0	0	12	12
159.0	0	27	27
160.0	0	22	22
161.0	0	22	22
162.0	0	18	18
163.0	0	28	28
164.0	0	23	23
165.0	0	20	20
166.0	0	19	19
167.0	0	18	18
168.0	0	26	26
169.0	0	15	15
170.0	0	16	16
171.0	0	24	24
172.0	0	18	18
173.0	0	13	13
174.0	0	16	16
175.0	0	14	14
176.0	0	22	22
177.0	0	20	20
178.0	0	15	15
179.0	0	16	16
180.0	0	15	15
181.0	0	13	13
182.0	0	18	18
183.0	0	18	18
184.0	0	12	12
185.0	0	15	15
186.0	0	12	12
187.0	0	15	15
188.0	0	8	8
189.0	0	13	13
190.0	0	16	16
191.0	0	17	17
192.0	0	14	14
193.0	0	14	14
194.0	0	14	14
195.0	0	13	13
196.0	0	18	18
197.0	0	11	11
198.0	0	14	14
199.0	0	7	7
200.0	0	5	5
201.0	0	10	10
202.0	0	12	12
203.0	0	10	10
204.0	0	18	18
205.0	0	11	11
206.0	0	9	9
207.0	0	10	10
208.0	0	9	9
209.0	0	13	13
210.0	0	14	14
211.0	0	15	15
212.0	0	6	6
213.0	0	11	11
214.0	0	4	4
215.0	0	10	10
216.0	0	11	11
217.0	0	6	6
218.0	0	9	9
219.0	0	9	9
220.0	0	11	11
221.0	0	5	5
222.0	0	11	11
223.0	0	9	9
224.0	0	8	8
225.0	0	6	6
226.0	0	6	6
227.0	0	8	8
228.0	0	5	5
229.0	0	13	13
230.0	0	7	7
231.0	0	4	4
232.0	0	7	7
233.0	0	15	15
234.0	0	4	4
235.0	0	4	4
236.0	0	6	6
237.0	0	12	12
238.0	0	6	6
239.0	0	7	7
240.0	0	2	2
241.0	0	7	7
242.0	0	9	9
243.0	0	9	9
244.0	0	6	6
245.0	0	7	7
246.0	0	5	5
247.0	0	6	6
248.0	0	8	8
249.0	0	9	9
250.0	0	10	10
251.0	0	7	7
252.0	0	5	5
253.0	0	8	8
254.0	0	11	11
255.0	0	7	7
256.0	0	7	7
257.0	0	6	6
258.0	0	2	2
259.0	0	7	7
260.0	0	3	3
261.0	0	6	6
262.0	0	9	9
263.0	0	5	5
264.0	0	5	5
265.0	0	9	9
266.0	0	6	6
267.0	0	7	7
268.0	0	5	5
269.0	0	6	6
270.0	0	8	8
271.0	0	6	6
272.0	0	4	4
273.0	0	10	10
274.0	0	4	4
275.0	0	11	11
276.0	0	4	4
277.0	0	3	3
278.0	0	5	5
279.0	0	3	3
280.0	0	6	6
281.0	0	7	7
282.0	0	2	2
283.0	0	5	5
284.0	0	3	3
285.0	0	3	3
286.0	0	7	7
287.0	0	7	7
288.0	0	4	4
289.0	0	1	1
290.0	0	6	6
291.0	0	5	5
292.0	0	3	3
293.0	0	1	1
294.0	0	5	5
295.0	0	3	3
296.0	0	4	4
297.0	0	4	4
298.0	0	9	9
299.0	0	5	5
300.0	0	1	1
301.0	0	3	3
302.0	0	4	4
303.0	0	4	4
305.0	0	5	5
307.0	0	7	7
308.0	0	3	3
309.0	0	4	4
310.0	0	2	2
311.0	0	4	4
312.0	0	5	5
313.0	0	2	2
314.0	0	2	2
315.0	0	2	2
316.0	0	4	4
317.0	0	2	2
318.0	0	3	3
319.0	0	2	2
320.0	0	1	1
321.0	0	5	5
322.0	0	2	2
323.0	0	2	2
324.0	0	5	5
325.0	0	5	5
326.0	0	6	6
327.0	0	1	1
328.0	0	5	5
329.0	0	2	2
330.0	0	1	1
331.0	0	3	3
332.0	0	2	2
333.0	0	4	4
334.0	0	3	3
335.0	0	3	3
336.0	0	10	10
337.0	0	3	3
338.0	0	2	2
340.0	0	2	2
341.0	0	2	2
342.0	0	3	3
343.0	0	3	3
344.0	0	3	3
345.0	0	5	5
346.0	0	2	2
347.0	0	3	3
348.0	0	4	4
349.0	0	3	3
350.0	0	2	2
351.0	0	3	3
352.0	0	4	4
353.0	0	3	3
354.0	0	2	2
355.0	0	2	2
356.0	0	4	4
357.0	0	2	2
358.0	0	2	2
359.0	0	3	3
360.0	0	5	5
361.0	0	1	1
362.0	0	5	5
363.0	0	3	3
364.0	0	2	2
365.0	0	5	5
367.0	0	1	1
368.0	0	3	3
369.0	0	2	2
370.0	0	3	3
371.0	0	2	2
372.0	0	3	3
373.0	0	1	1
374.0	0	3	3
375.0	0	6	6
376.0	0	3	3
378.0	0	3	3
379.0	0	2	2
380.0	0	1	1
381.0	0	2	2
382.0	0	3	3
383.0	0	1	1
384.0	0	5	5
385.0	0	1	1
386.0	0	2	2
387.0	0	2	2
388.0	0	1	1
390.0	0	2	2
391.0	0	1	1
393.0	0	1	1
394.0	0	1	1
395.0	0	1	1
396.0	0	1	1
397.0	0	2	2
398.0	0	1	1
399.0	0	1	1
400.0	0	1	1
401.0	0	1	1
402.0	0	2	2
403.0	0	1	1
405.0	0	1	1
406.0	0	3	3
407.0	0	1	1
408.0	0	2	2
409.0	0	3	3
410.0	0	1	1
411.0	0	3	3
412.0	0	1	1
413.0	0	1	1
414.0	0	2	2
415.0	0	2	2
416.0	0	1	1
417.0	0	1	1
418.0	0	2	2
419.0	0	1	1
420.0	0	2	2
422.0	0	2	2
425.0	0	2	2
426.0	0	1	1
428.0	0	1	1
429.0	0	3	3
430.0	0	2	2
431.0	0	1	1
432.0	0	2	2
433.0	0	1	1
434.0	0	4	4
435.0	0	1	1
437.0	0	1	1
439.0	0	1	1
440.0	0	1	1
442.0	0	2	2
443.0	0	2	2
444.0	0	2	2
445.0	0	2	2
446.0	0	1	1
447.0	0	1	1
450.0	0	2	2
451.0	0	1	1
452.0	0	2	2
454.0	0	2	2
455.0	0	1	1
456.0	0	1	1
457.0	0	2	2
461.0	0	1	1
462.0	0	2	2
463.0	0	3	3
465.0	0	1	1
466.0	0	1	1
467.0	0	1	1
468.0	0	2	2
470.0	0	2	2
473.0	0	1	1
474.0	0	1	1
476.0	0	1	1
483.0	0	2	2
484.0	0	2	2
485.0	0	1	1
487.0	0	1	1
490.0	0	1	1
491.0	0	1	1
494.0	0	1	1
495.0	0	1	1
496.0	0	2	2
497.0	0	3	3
498.0	0	2	2
499.0	0	2	2
500.0	0	1	1
504.0	0	1	1
506.0	0	1	1
509.0	0	1	1
511.0	0	1	1
512.0	0	2	2
513.0	0	1	1
515.0	0	1	1
516.0	0	1	1
517.0	0	1	1
522.0	0	2	2
523.0	0	1	1
525.0	0	1	1
527.0	0	1	1
528.0	0	2	2
533.0	0	1	1
534.0	0	2	2
541.0	0	2	2
545.0	0	1	1
546.0	0	3	3
550.0	0	2	2
559.0	0	2	2
561.0	0	1	1
562.0	0	1	1
563.0	0	1	1
564.0	0	1	1
565.0	0	1	1
566.0	0	1	1
567.0	0	1	1
570.0	0	2	2
571.0	0	1	1
578.0	0	1	1
581.0	0	1	1
587.0	0	1	1
590.0	0	1	1
593.0	0	1	1
594.0	0	1	1
596.0	0	1	1
598.0	0	2	2
601.0	0	1	1
602.0	0	1	1
603.0	0	1	1
606.0	0	1	1
620.0	0	1	1
622.0	0	1	1
623.0	0	1	1
628.0	0	1	1
630.0	0	1	1
632.0	0	2	2
634.0	0	1	1
644.0	0	1	1
654.0	0	2	2
655.0	0	1	1
657.0	0	1	1
663.0	0	1	1
665.0	0	1	1
669.0	0	1	1
670.0	0	1	1
676.0	0	1	1
679.0	0	1	1
686.0	0	1	1
687.0	0	1	1
688.0	0	2	2
689.0	0	1	1
690.0	0	1	1
694.0	0	1	1
698.0	0	1	1
704.0	0	1	1
706.0	0	1	1
707.0	0	1	1
708.0	0	2	2
711.0	0	1	1
712.0	0	1	1
713.0	0	1	1
717.0	0	1	1
728.0	0	1	1
737.0	0	1	1
747.0	0	1	1
749.0	0	1	1
750.0	0	1	1
751.0	0	1	1
762.0	0	1	1
764.0	0	1	1
783.0	0	1	1
796.0	0	1	1
812.0	0	1	1
832.0	0	1	1
841.0	0	1	1
844.0	0	1	1
846.0	0	1	1
847.0	0	1	1
849.0	0	1	1
851.0	0	1	1
859.0	0	1	1
863.0	0	1	1
881.0	0	2	2
897.0	0	1	1
905.0	0	1	1
908.0	0	1	1
932.0	0	1	1
934.0	0	1	1
943.0	0	1	1
952.0	0	1	1
969.0	0	1	1
971.0	0	1	1
979.0	0	1	1
986.0	0	1	1
989.0	0	1	1
994.0	0	1	1
1016.0	0	1	1
1081.0	0	1	1
1082.0	0	1	1
1097.0	0	1	1
1113.0	0	1	1
1140.0	0	1	1
1141.0	0	1	1
1149.0	0	1	1
1186.0	0	1	1
1289.0	0	1	1
1290.0	0	1	1
1291.0	0	1	1
1409.0	0	1	1
1439.0	0	1	1
1461.0	0	1	1
1466.0	0	1	1
1612.0	0	1	1
1727.0	0	1	1
1873.0	0	1	1
1882.0	0	1	1
1890.0	0	1	1
1949.0	0	1	1
2103.0	0	1	1
2218.0	0	1	1
7385.0	0	1	1
11057.0	0	1	1