## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_supernatant_TA_2.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_supernatant_TA_2.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/markdup/GRCh38.p13-D12_supernatant_TA_2.samtools-coordinate.metrics.txt TMP_DIR=[/scratch/slrinzema/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 FLOW_MODE=false FLOW_QUALITY_SUM_STRATEGY=false USE_END_IN_UNPAIRED_READS=false USE_UNPAIRED_CLIPPED_END=false UNPAIRED_END_UNCERTAINTY=0 FLOW_SKIP_FIRST_N_FLOWS=0 FLOW_Q_IS_KNOWN_END=false FLOW_EFFECTIVE_QUALITY_THRESHOLD=15 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 USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri Oct 06 01:59:30 CEST 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
Unknown Library	1822	24079780	31523368	0	1702	4909200	0	0.2039	50722304

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	17537379	17537379
2.0	1.622048	1108058	1108058
3.0	2.008992	217150	217150
4.0	2.24969	92802	92802
5.0	2.399416	52061	52061
6.0	2.492553	33227	33227
7.0	2.550488	22576	22576
8.0	2.586527	16448	16448
9.0	2.608945	12683	12683
10.0	2.62289	9734	9734
11.0	2.631564	7762	7762
12.0	2.63696	6348	6348
13.0	2.640317	5242	5242
14.0	2.642404	4415	4415
15.0	2.643703	3744	3744
16.0	2.644511	3227	3227
17.0	2.645014	2848	2848
18.0	2.645326	2600	2600
19.0	2.645521	2139	2139
20.0	2.645642	1946	1946
21.0	2.645717	1723	1723
22.0	2.645764	1583	1583
23.0	2.645793	1466	1466
24.0	2.645811	1290	1290
25.0	2.645822	1111	1111
26.0	2.645829	1034	1034
27.0	2.645834	958	958
28.0	2.645836	866	866
29.0	2.645838	835	835
30.0	2.645839	693	693
31.0	2.64584	725	725
32.0	2.64584	641	641
33.0	2.64584	585	585
34.0	2.645841	571	571
35.0	2.645841	532	532
36.0	2.645841	487	487
37.0	2.645841	468	468
38.0	2.645841	482	482
39.0	2.645841	454	454
40.0	2.645841	397	397
41.0	2.645841	355	355
42.0	2.645841	329	329
43.0	2.645841	344	344
44.0	2.645841	326	326
45.0	2.645841	283	283
46.0	2.645841	279	279
47.0	2.645841	246	246
48.0	2.645841	252	252
49.0	2.645841	245	245
50.0	2.645841	201	201
51.0	2.645841	197	197
52.0	2.645841	190	190
53.0	2.645841	246	246
54.0	2.645841	189	189
55.0	2.645841	186	186
56.0	2.645841	194	194
57.0	2.645841	161	161
58.0	2.645841	175	175
59.0	2.645841	168	168
60.0	2.645841	152	152
61.0	2.645841	149	149
62.0	2.645841	133	133
63.0	2.645841	125	125
64.0	2.645841	139	139
65.0	2.645841	126	126
66.0	2.645841	96	96
67.0	2.645841	107	107
68.0	2.645841	102	102
69.0	2.645841	111	111
70.0	2.645841	84	84
71.0	2.645841	113	113
72.0	2.645841	123	123
73.0	2.645841	89	89
74.0	2.645841	104	104
75.0	2.645841	77	77
76.0	2.645841	93	93
77.0	2.645841	86	86
78.0	2.645841	85	85
79.0	2.645841	68	68
80.0	2.645841	74	74
81.0	2.645841	75	75
82.0	2.645841	61	61
83.0	2.645841	71	71
84.0	2.645841	82	82
85.0	2.645841	72	72
86.0	2.645841	64	64
87.0	2.645841	79	79
88.0	2.645841	66	66
89.0	2.645841	62	62
90.0	2.645841	72	72
91.0	2.645841	58	58
92.0	2.645841	52	52
93.0	2.645841	42	42
94.0	2.645841	39	39
95.0	2.645841	43	43
96.0	2.645841	57	57
97.0	2.645841	55	55
98.0	2.645841	45	45
99.0	2.645841	58	58
100.0	2.645841	39	39
101.0	0	57	57
102.0	0	46	46
103.0	0	41	41
104.0	0	53	53
105.0	0	40	40
106.0	0	44	44
107.0	0	32	32
108.0	0	46	46
109.0	0	45	45
110.0	0	35	35
111.0	0	46	46
112.0	0	40	40
113.0	0	38	38
114.0	0	32	32
115.0	0	29	29
116.0	0	36	36
117.0	0	33	33
118.0	0	23	23
119.0	0	34	34
120.0	0	33	33
121.0	0	31	31
122.0	0	26	26
123.0	0	36	36
124.0	0	24	24
125.0	0	25	25
126.0	0	21	21
127.0	0	28	28
128.0	0	21	21
129.0	0	18	18
130.0	0	18	18
131.0	0	27	27
132.0	0	24	24
133.0	0	15	15
134.0	0	17	17
135.0	0	27	27
136.0	0	21	21
137.0	0	23	23
138.0	0	19	19
139.0	0	21	21
140.0	0	25	25
141.0	0	15	15
142.0	0	14	14
143.0	0	21	21
144.0	0	18	18
145.0	0	17	17
146.0	0	23	23
147.0	0	18	18
148.0	0	24	24
149.0	0	22	22
150.0	0	11	11
151.0	0	19	19
152.0	0	12	12
153.0	0	18	18
154.0	0	10	10
155.0	0	15	15
156.0	0	14	14
157.0	0	13	13
158.0	0	17	17
159.0	0	23	23
160.0	0	10	10
161.0	0	9	9
162.0	0	18	18
163.0	0	10	10
164.0	0	9	9
165.0	0	15	15
166.0	0	16	16
167.0	0	7	7
168.0	0	13	13
169.0	0	16	16
170.0	0	6	6
171.0	0	11	11
172.0	0	11	11
173.0	0	17	17
174.0	0	5	5
175.0	0	15	15
176.0	0	12	12
177.0	0	15	15
178.0	0	13	13
179.0	0	15	15
180.0	0	17	17
181.0	0	18	18
182.0	0	10	10
183.0	0	8	8
184.0	0	11	11
185.0	0	11	11
186.0	0	16	16
187.0	0	13	13
188.0	0	3	3
189.0	0	7	7
190.0	0	9	9
191.0	0	5	5
192.0	0	9	9
193.0	0	10	10
194.0	0	7	7
195.0	0	12	12
196.0	0	8	8
197.0	0	7	7
198.0	0	13	13
199.0	0	16	16
200.0	0	8	8
201.0	0	6	6
202.0	0	6	6
203.0	0	13	13
204.0	0	11	11
205.0	0	11	11
206.0	0	10	10
207.0	0	14	14
208.0	0	6	6
209.0	0	2	2
210.0	0	7	7
211.0	0	6	6
212.0	0	10	10
213.0	0	9	9
214.0	0	7	7
215.0	0	4	4
216.0	0	13	13
217.0	0	8	8
218.0	0	3	3
219.0	0	5	5
220.0	0	10	10
221.0	0	4	4
222.0	0	7	7
223.0	0	6	6
224.0	0	4	4
225.0	0	4	4
226.0	0	5	5
227.0	0	5	5
228.0	0	8	8
229.0	0	8	8
230.0	0	12	12
231.0	0	6	6
232.0	0	6	6
233.0	0	7	7
234.0	0	10	10
235.0	0	5	5
236.0	0	11	11
237.0	0	8	8
238.0	0	8	8
239.0	0	7	7
240.0	0	6	6
241.0	0	4	4
242.0	0	11	11
243.0	0	9	9
244.0	0	7	7
245.0	0	12	12
246.0	0	6	6
247.0	0	6	6
248.0	0	9	9
249.0	0	7	7
250.0	0	7	7
251.0	0	7	7
252.0	0	4	4
253.0	0	7	7
254.0	0	3	3
255.0	0	3	3
256.0	0	8	8
257.0	0	4	4
258.0	0	5	5
259.0	0	2	2
260.0	0	5	5
261.0	0	9	9
262.0	0	3	3
263.0	0	6	6
264.0	0	3	3
265.0	0	1	1
266.0	0	2	2
267.0	0	3	3
268.0	0	9	9
269.0	0	4	4
270.0	0	6	6
271.0	0	1	1
272.0	0	8	8
273.0	0	8	8
274.0	0	5	5
275.0	0	2	2
276.0	0	9	9
277.0	0	5	5
278.0	0	7	7
279.0	0	4	4
280.0	0	5	5
281.0	0	1	1
282.0	0	4	4
283.0	0	6	6
284.0	0	4	4
285.0	0	3	3
286.0	0	3	3
287.0	0	6	6
288.0	0	8	8
289.0	0	8	8
290.0	0	5	5
291.0	0	6	6
292.0	0	5	5
293.0	0	3	3
294.0	0	2	2
295.0	0	3	3
296.0	0	5	5
297.0	0	5	5
298.0	0	6	6
299.0	0	1	1
300.0	0	6	6
301.0	0	4	4
302.0	0	1	1
303.0	0	1	1
304.0	0	7	7
305.0	0	5	5
306.0	0	4	4
307.0	0	7	7
308.0	0	5	5
309.0	0	2	2
310.0	0	5	5
311.0	0	2	2
312.0	0	4	4
313.0	0	4	4
314.0	0	2	2
315.0	0	5	5
316.0	0	6	6
317.0	0	4	4
318.0	0	2	2
319.0	0	1	1
320.0	0	4	4
321.0	0	7	7
322.0	0	4	4
323.0	0	5	5
324.0	0	3	3
325.0	0	5	5
326.0	0	2	2
327.0	0	1	1
328.0	0	4	4
329.0	0	3	3
330.0	0	4	4
331.0	0	4	4
332.0	0	4	4
333.0	0	2	2
334.0	0	2	2
335.0	0	2	2
336.0	0	3	3
337.0	0	3	3
338.0	0	2	2
340.0	0	2	2
341.0	0	5	5
342.0	0	2	2
343.0	0	3	3
344.0	0	4	4
345.0	0	3	3
346.0	0	2	2
347.0	0	5	5
348.0	0	3	3
349.0	0	2	2
350.0	0	4	4
351.0	0	3	3
352.0	0	2	2
353.0	0	3	3
356.0	0	2	2
357.0	0	3	3
358.0	0	4	4
359.0	0	7	7
360.0	0	4	4
361.0	0	2	2
362.0	0	2	2
363.0	0	4	4
364.0	0	3	3
366.0	0	2	2
369.0	0	3	3
370.0	0	1	1
371.0	0	2	2
372.0	0	1	1
373.0	0	1	1
374.0	0	3	3
375.0	0	4	4
376.0	0	2	2
377.0	0	1	1
379.0	0	1	1
380.0	0	3	3
381.0	0	1	1
383.0	0	3	3
384.0	0	5	5
385.0	0	2	2
386.0	0	4	4
389.0	0	3	3
390.0	0	2	2
393.0	0	2	2
394.0	0	3	3
395.0	0	2	2
396.0	0	6	6
398.0	0	3	3
399.0	0	2	2
400.0	0	1	1
401.0	0	1	1
402.0	0	1	1
403.0	0	3	3
405.0	0	2	2
407.0	0	1	1
408.0	0	2	2
411.0	0	2	2
415.0	0	5	5
416.0	0	3	3
417.0	0	3	3
420.0	0	4	4
421.0	0	1	1
422.0	0	2	2
423.0	0	4	4
424.0	0	4	4
425.0	0	1	1
426.0	0	2	2
427.0	0	3	3
428.0	0	1	1
429.0	0	1	1
430.0	0	2	2
433.0	0	5	5
434.0	0	1	1
439.0	0	1	1
440.0	0	1	1
442.0	0	2	2
443.0	0	1	1
446.0	0	1	1
448.0	0	2	2
449.0	0	2	2
450.0	0	1	1
451.0	0	5	5
452.0	0	3	3
453.0	0	3	3
454.0	0	3	3
455.0	0	1	1
456.0	0	3	3
457.0	0	1	1
459.0	0	3	3
461.0	0	1	1
464.0	0	1	1
466.0	0	1	1
468.0	0	6	6
471.0	0	2	2
472.0	0	2	2
473.0	0	2	2
474.0	0	3	3
476.0	0	1	1
477.0	0	1	1
478.0	0	1	1
479.0	0	3	3
480.0	0	2	2
481.0	0	1	1
484.0	0	3	3
486.0	0	3	3
487.0	0	1	1
489.0	0	2	2
491.0	0	2	2
492.0	0	2	2
493.0	0	2	2
494.0	0	1	1
495.0	0	2	2
496.0	0	3	3
497.0	0	1	1
498.0	0	2	2
499.0	0	1	1
500.0	0	1	1
501.0	0	1	1
503.0	0	1	1
504.0	0	2	2
506.0	0	1	1
507.0	0	1	1
508.0	0	1	1
509.0	0	1	1
512.0	0	2	2
513.0	0	1	1
514.0	0	1	1
515.0	0	2	2
516.0	0	2	2
517.0	0	1	1
518.0	0	1	1
519.0	0	1	1
520.0	0	1	1
521.0	0	1	1
523.0	0	1	1
524.0	0	2	2
526.0	0	1	1
527.0	0	1	1
530.0	0	2	2
534.0	0	3	3
535.0	0	1	1
537.0	0	1	1
539.0	0	1	1
540.0	0	1	1
541.0	0	1	1
545.0	0	1	1
546.0	0	2	2
549.0	0	1	1
550.0	0	2	2
551.0	0	3	3
558.0	0	1	1
559.0	0	2	2
563.0	0	2	2
564.0	0	2	2
565.0	0	1	1
568.0	0	1	1
569.0	0	2	2
573.0	0	2	2
576.0	0	1	1
578.0	0	1	1
580.0	0	1	1
582.0	0	1	1
583.0	0	1	1
585.0	0	2	2
586.0	0	1	1
587.0	0	1	1
590.0	0	1	1
591.0	0	1	1
593.0	0	1	1
595.0	0	1	1
597.0	0	1	1
599.0	0	4	4
600.0	0	1	1
609.0	0	2	2
611.0	0	1	1
613.0	0	1	1
614.0	0	2	2
615.0	0	2	2
618.0	0	1	1
620.0	0	1	1
624.0	0	1	1
625.0	0	1	1
626.0	0	1	1
630.0	0	1	1
632.0	0	1	1
633.0	0	1	1
635.0	0	1	1
640.0	0	1	1
644.0	0	1	1
646.0	0	1	1
647.0	0	1	1
649.0	0	1	1
651.0	0	2	2
653.0	0	3	3
656.0	0	3	3
657.0	0	1	1
660.0	0	1	1
663.0	0	2	2
669.0	0	1	1
673.0	0	1	1
679.0	0	1	1
680.0	0	1	1
681.0	0	1	1
684.0	0	1	1
688.0	0	1	1
689.0	0	1	1
690.0	0	2	2
693.0	0	1	1
701.0	0	1	1
703.0	0	1	1
705.0	0	2	2
709.0	0	2	2
712.0	0	1	1
714.0	0	1	1
725.0	0	1	1
727.0	0	1	1
730.0	0	1	1
736.0	0	1	1
743.0	0	1	1
745.0	0	1	1
750.0	0	1	1
755.0	0	1	1
767.0	0	1	1
770.0	0	1	1
771.0	0	1	1
773.0	0	1	1
774.0	0	2	2
778.0	0	1	1
781.0	0	1	1
784.0	0	1	1
791.0	0	1	1
795.0	0	1	1
797.0	0	1	1
799.0	0	1	1
813.0	0	1	1
829.0	0	1	1
832.0	0	1	1
841.0	0	1	1
844.0	0	1	1
856.0	0	1	1
857.0	0	1	1
863.0	0	1	1
866.0	0	1	1
868.0	0	1	1
870.0	0	1	1
899.0	0	1	1
910.0	0	1	1
917.0	0	1	1
923.0	0	1	1
924.0	0	1	1
928.0	0	1	1
931.0	0	1	1
943.0	0	1	1
977.0	0	1	1
995.0	0	1	1
999.0	0	1	1
1006.0	0	1	1
1030.0	0	1	1
1031.0	0	1	1
1038.0	0	1	1
1043.0	0	1	1
1052.0	0	1	1
1057.0	0	1	1
1059.0	0	1	1
1084.0	0	1	1
1090.0	0	1	1
1094.0	0	1	1
1106.0	0	1	1
1119.0	0	1	1
1127.0	0	1	1
1132.0	0	1	1
1174.0	0	1	1
1176.0	0	1	1
1187.0	0	1	1
1196.0	0	1	1
1197.0	0	1	1
1212.0	0	1	1
1230.0	0	1	1
1239.0	0	1	1
1324.0	0	1	1
1350.0	0	1	1
1365.0	0	1	1
1375.0	0	1	1
1417.0	0	1	1
1423.0	0	1	1
1481.0	0	1	1
1556.0	0	1	1
1563.0	0	1	1
1679.0	0	1	1
1696.0	0	1	1
1733.0	0	1	1
1770.0	0	1	1
1795.0	0	1	1
1887.0	0	1	1
1900.0	0	1	1
1936.0	0	1	1
1960.0	0	1	1
1975.0	0	1	1
1989.0	0	1	1
2108.0	0	1	1
2221.0	0	1	1
2298.0	0	1	1
2312.0	0	1	1
2397.0	0	1	1
2400.0	0	1	1
2493.0	0	1	1
2495.0	0	1	1
2583.0	0	1	1
2594.0	0	1	1
2624.0	0	1	1
2700.0	0	1	1
2831.0	0	1	1
2911.0	0	1	1
2974.0	0	1	1
3097.0	0	1	1
3160.0	0	1	1
6198.0	0	1	1
7328.0	0	1	1