## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT SRX7354065.sorted.bam --OUTPUT SRX7354065.markdup.sorted.bam --METRICS_FILE SRX7354065.markdup.sorted.MarkDuplicates.metrics.txt --REMOVE_DUPLICATES false --ASSUME_SORTED true --TMP_DIR tmp --VALIDATION_STRINGENCY LENIENT --REFERENCE_SEQUENCE Homo_sapiens_assembly38_noALT_noHLA_noDecoy_patched_ERCC92.fasta --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 --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 --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 --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri Oct 27 17:03:12 GMT 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	42587	32677521	5396443	5318069	33581	15552433	0	0.47614	22244967

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	12870920	12870920
2.0	1.230159	2469925	2469925
3.0	1.283132	694888	694888
4.0	1.295324	305035	305035
5.0	1.298131	174488	174488
6.0	1.298776	113635	113635
7.0	1.298925	80136	80136
8.0	1.298959	59240	59240
9.0	1.298967	45957	45957
10.0	1.298969	36297	36297
11.0	1.298969	29599	29599
12.0	1.298969	24572	24572
13.0	1.298969	20469	20469
14.0	1.298969	17619	17619
15.0	1.298969	15082	15082
16.0	1.29897	13193	13193
17.0	1.29897	11444	11444
18.0	1.29897	9922	9922
19.0	1.29897	8998	8998
20.0	1.29897	8023	8023
21.0	1.29897	7126	7126
22.0	1.29897	6554	6554
23.0	1.29897	5933	5933
24.0	1.29897	5329	5329
25.0	1.29897	4936	4936
26.0	1.29897	4424	4424
27.0	1.29897	4004	4004
28.0	1.29897	3785	3785
29.0	1.29897	3528	3528
30.0	1.29897	3145	3145
31.0	1.29897	3027	3027
32.0	1.29897	2735	2735
33.0	1.29897	2680	2680
34.0	1.29897	2460	2460
35.0	1.29897	2373	2373
36.0	1.29897	2154	2154
37.0	1.29897	2010	2010
38.0	1.29897	1842	1842
39.0	1.29897	1792	1792
40.0	1.29897	1700	1700
41.0	1.29897	1561	1561
42.0	1.29897	1502	1502
43.0	1.29897	1404	1404
44.0	1.29897	1351	1351
45.0	1.29897	1288	1288
46.0	1.29897	1231	1231
47.0	1.29897	1189	1189
48.0	1.29897	1073	1073
49.0	1.29897	1069	1069
50.0	1.29897	1030	1030
51.0	1.29897	919	919
52.0	1.29897	893	893
53.0	1.29897	912	912
54.0	1.29897	810	810
55.0	1.29897	772	772
56.0	1.29897	709	709
57.0	1.29897	726	726
58.0	1.29897	704	704
59.0	1.29897	649	649
60.0	1.29897	621	621
61.0	1.29897	623	623
62.0	1.29897	618	618
63.0	1.29897	579	579
64.0	1.29897	543	543
65.0	1.29897	537	537
66.0	1.29897	521	521
67.0	1.29897	474	474
68.0	1.29897	487	487
69.0	1.29897	467	467
70.0	1.29897	428	428
71.0	1.29897	443	443
72.0	1.29897	408	408
73.0	1.29897	408	408
74.0	1.29897	370	370
75.0	1.29897	350	350
76.0	1.29897	371	371
77.0	1.29897	352	352
78.0	1.29897	348	348
79.0	1.29897	308	308
80.0	1.29897	334	334
81.0	1.29897	301	301
82.0	1.29897	310	310
83.0	1.29897	287	287
84.0	1.29897	275	275
85.0	1.29897	260	260
86.0	1.29897	224	224
87.0	1.29897	278	278
88.0	1.29897	255	255
89.0	1.29897	249	249
90.0	1.29897	234	234
91.0	1.29897	228	228
92.0	1.29897	237	237
93.0	1.29897	201	201
94.0	1.29897	231	231
95.0	1.29897	232	232
96.0	1.29897	203	203
97.0	1.29897	197	197
98.0	1.29897	171	171
99.0	1.29897	213	213
100.0	1.29897	202	202
101.0	0	171	171
102.0	0	196	196
103.0	0	166	166
104.0	0	161	161
105.0	0	154	154
106.0	0	157	157
107.0	0	146	146
108.0	0	148	148
109.0	0	143	143
110.0	0	143	143
111.0	0	131	131
112.0	0	115	115
113.0	0	125	125
114.0	0	148	148
115.0	0	108	108
116.0	0	127	127
117.0	0	126	126
118.0	0	99	99
119.0	0	126	126
120.0	0	123	123
121.0	0	99	99
122.0	0	115	115
123.0	0	96	96
124.0	0	103	103
125.0	0	106	106
126.0	0	84	84
127.0	0	97	97
128.0	0	88	88
129.0	0	104	104
130.0	0	87	87
131.0	0	87	87
132.0	0	89	89
133.0	0	98	98
134.0	0	82	82
135.0	0	94	94
136.0	0	69	69
137.0	0	82	82
138.0	0	76	76
139.0	0	79	79
140.0	0	78	78
141.0	0	82	82
142.0	0	76	76
143.0	0	52	52
144.0	0	66	66
145.0	0	68	68
146.0	0	77	77
147.0	0	63	63
148.0	0	79	79
149.0	0	52	52
150.0	0	54	54
151.0	0	67	67
152.0	0	49	49
153.0	0	74	74
154.0	0	51	51
155.0	0	52	52
156.0	0	50	50
157.0	0	54	54
158.0	0	46	46
159.0	0	51	51
160.0	0	53	53
161.0	0	50	50
162.0	0	45	45
163.0	0	50	50
164.0	0	41	41
165.0	0	62	62
166.0	0	44	44
167.0	0	42	42
168.0	0	47	47
169.0	0	51	51
170.0	0	37	37
171.0	0	45	45
172.0	0	49	49
173.0	0	33	33
174.0	0	39	39
175.0	0	48	48
176.0	0	44	44
177.0	0	38	38
178.0	0	34	34
179.0	0	43	43
180.0	0	40	40
181.0	0	37	37
182.0	0	29	29
183.0	0	38	38
184.0	0	33	33
185.0	0	40	40
186.0	0	37	37
187.0	0	44	44
188.0	0	36	36
189.0	0	33	33
190.0	0	28	28
191.0	0	34	34
192.0	0	33	33
193.0	0	27	27
194.0	0	31	31
195.0	0	37	37
196.0	0	20	20
197.0	0	15	15
198.0	0	23	23
199.0	0	30	30
200.0	0	30	30
201.0	0	25	25
202.0	0	26	26
203.0	0	23	23
204.0	0	16	16
205.0	0	21	21
206.0	0	21	21
207.0	0	19	19
208.0	0	17	17
209.0	0	21	21
210.0	0	32	32
211.0	0	20	20
212.0	0	18	18
213.0	0	14	14
214.0	0	23	23
215.0	0	23	23
216.0	0	18	18
217.0	0	22	22
218.0	0	21	21
219.0	0	23	23
220.0	0	17	17
221.0	0	21	21
222.0	0	23	23
223.0	0	29	29
224.0	0	17	17
225.0	0	25	25
226.0	0	18	18
227.0	0	16	16
228.0	0	20	20
229.0	0	17	17
230.0	0	12	12
231.0	0	15	15
232.0	0	22	22
233.0	0	25	25
234.0	0	19	19
235.0	0	21	21
236.0	0	17	17
237.0	0	24	24
238.0	0	11	11
239.0	0	19	19
240.0	0	16	16
241.0	0	16	16
242.0	0	14	14
243.0	0	10	10
244.0	0	16	16
245.0	0	18	18
246.0	0	11	11
247.0	0	13	13
248.0	0	9	9
249.0	0	18	18
250.0	0	21	21
251.0	0	16	16
252.0	0	13	13
253.0	0	9	9
254.0	0	16	16
255.0	0	8	8
256.0	0	13	13
257.0	0	14	14
258.0	0	7	7
259.0	0	16	16
260.0	0	10	10
261.0	0	7	7
262.0	0	9	9
263.0	0	8	8
264.0	0	6	6
265.0	0	5	5
266.0	0	10	10
267.0	0	16	16
268.0	0	12	12
269.0	0	9	9
270.0	0	13	13
271.0	0	10	10
272.0	0	14	14
273.0	0	15	15
274.0	0	8	8
275.0	0	7	7
276.0	0	6	6
277.0	0	16	16
278.0	0	13	13
279.0	0	13	13
280.0	0	8	8
281.0	0	15	15
282.0	0	11	11
283.0	0	11	11
284.0	0	6	6
285.0	0	10	10
286.0	0	5	5
287.0	0	13	13
288.0	0	7	7
289.0	0	8	8
290.0	0	9	9
291.0	0	11	11
292.0	0	10	10
293.0	0	16	16
294.0	0	10	10
295.0	0	12	12
296.0	0	8	8
297.0	0	11	11
298.0	0	6	6
299.0	0	11	11
300.0	0	9	9
301.0	0	11	11
302.0	0	9	9
303.0	0	11	11
304.0	0	8	8
305.0	0	5	5
306.0	0	10	10
307.0	0	10	10
308.0	0	9	9
309.0	0	10	10
310.0	0	5	5
311.0	0	4	4
312.0	0	8	8
313.0	0	3	3
314.0	0	8	8
315.0	0	9	9
316.0	0	8	8
317.0	0	10	10
318.0	0	6	6
319.0	0	4	4
320.0	0	6	6
321.0	0	14	14
322.0	0	4	4
323.0	0	9	9
324.0	0	7	7
325.0	0	5	5
326.0	0	8	8
327.0	0	11	11
328.0	0	4	4
329.0	0	10	10
330.0	0	6	6
331.0	0	4	4
332.0	0	5	5
333.0	0	3	3
334.0	0	4	4
335.0	0	4	4
336.0	0	2	2
337.0	0	7	7
338.0	0	8	8
339.0	0	5	5
340.0	0	4	4
341.0	0	8	8
342.0	0	6	6
343.0	0	7	7
344.0	0	6	6
345.0	0	4	4
346.0	0	8	8
347.0	0	6	6
348.0	0	5	5
349.0	0	6	6
350.0	0	6	6
351.0	0	10	10
352.0	0	1	1
353.0	0	5	5
354.0	0	11	11
355.0	0	9	9
356.0	0	7	7
357.0	0	3	3
358.0	0	3	3
359.0	0	5	5
360.0	0	1	1
361.0	0	5	5
362.0	0	5	5
363.0	0	9	9
364.0	0	4	4
365.0	0	6	6
366.0	0	5	5
367.0	0	5	5
368.0	0	4	4
369.0	0	5	5
370.0	0	6	6
371.0	0	2	2
372.0	0	3	3
373.0	0	8	8
374.0	0	3	3
375.0	0	3	3
376.0	0	7	7
377.0	0	2	2
378.0	0	2	2
379.0	0	5	5
380.0	0	5	5
381.0	0	4	4
382.0	0	6	6
383.0	0	3	3
384.0	0	2	2
385.0	0	5	5
386.0	0	4	4
387.0	0	4	4
388.0	0	1	1
389.0	0	5	5
390.0	0	6	6
391.0	0	7	7
392.0	0	4	4
393.0	0	5	5
394.0	0	5	5
395.0	0	3	3
396.0	0	4	4
397.0	0	4	4
399.0	0	8	8
400.0	0	2	2
401.0	0	4	4
402.0	0	4	4
403.0	0	3	3
404.0	0	3	3
405.0	0	8	8
406.0	0	3	3
407.0	0	3	3
408.0	0	4	4
409.0	0	3	3
410.0	0	6	6
411.0	0	5	5
412.0	0	2	2
413.0	0	4	4
414.0	0	3	3
415.0	0	3	3
416.0	0	5	5
417.0	0	2	2
418.0	0	3	3
419.0	0	1	1
420.0	0	4	4
421.0	0	2	2
422.0	0	2	2
423.0	0	4	4
424.0	0	2	2
425.0	0	5	5
426.0	0	1	1
427.0	0	3	3
429.0	0	1	1
430.0	0	2	2
431.0	0	1	1
432.0	0	4	4
433.0	0	4	4
434.0	0	3	3
436.0	0	1	1
437.0	0	6	6
438.0	0	4	4
439.0	0	2	2
440.0	0	1	1
441.0	0	2	2
442.0	0	2	2
443.0	0	1	1
444.0	0	1	1
445.0	0	1	1
446.0	0	5	5
447.0	0	3	3
448.0	0	4	4
449.0	0	5	5
450.0	0	2	2
451.0	0	4	4
452.0	0	1	1
453.0	0	2	2
454.0	0	3	3
455.0	0	2	2
456.0	0	2	2
458.0	0	3	3
459.0	0	2	2
460.0	0	2	2
461.0	0	2	2
462.0	0	1	1
463.0	0	2	2
464.0	0	2	2
465.0	0	1	1
466.0	0	3	3
467.0	0	2	2
468.0	0	4	4
470.0	0	3	3
471.0	0	1	1
472.0	0	1	1
473.0	0	2	2
474.0	0	3	3
475.0	0	2	2
476.0	0	3	3
477.0	0	2	2
478.0	0	3	3
479.0	0	1	1
480.0	0	4	4
481.0	0	6	6
482.0	0	2	2
484.0	0	1	1
485.0	0	1	1
487.0	0	4	4
488.0	0	2	2
489.0	0	2	2
491.0	0	3	3
492.0	0	1	1
494.0	0	1	1
495.0	0	3	3
496.0	0	1	1
497.0	0	1	1
498.0	0	1	1
499.0	0	3	3
500.0	0	4	4
501.0	0	2	2
502.0	0	2	2
503.0	0	1	1
504.0	0	1	1
506.0	0	2	2
507.0	0	4	4
508.0	0	2	2
509.0	0	2	2
511.0	0	1	1
512.0	0	2	2
514.0	0	2	2
515.0	0	1	1
516.0	0	1	1
517.0	0	1	1
518.0	0	1	1
520.0	0	1	1
521.0	0	3	3
522.0	0	2	2
523.0	0	1	1
524.0	0	1	1
525.0	0	1	1
526.0	0	2	2
527.0	0	1	1
528.0	0	2	2
529.0	0	2	2
530.0	0	1	1
531.0	0	2	2
533.0	0	1	1
535.0	0	1	1
537.0	0	1	1
538.0	0	1	1
539.0	0	2	2
540.0	0	5	5
541.0	0	1	1
542.0	0	2	2
544.0	0	2	2
545.0	0	4	4
546.0	0	1	1
547.0	0	3	3
549.0	0	1	1
550.0	0	1	1
553.0	0	2	2
554.0	0	1	1
555.0	0	2	2
556.0	0	1	1
557.0	0	1	1
558.0	0	3	3
562.0	0	1	1
565.0	0	2	2
566.0	0	1	1
568.0	0	2	2
569.0	0	1	1
573.0	0	1	1
577.0	0	2	2
578.0	0	3	3
582.0	0	3	3
583.0	0	1	1
584.0	0	1	1
586.0	0	3	3
588.0	0	1	1
589.0	0	1	1
590.0	0	1	1
591.0	0	4	4
594.0	0	1	1
597.0	0	1	1
598.0	0	2	2
601.0	0	1	1
602.0	0	1	1
605.0	0	1	1
606.0	0	1	1
608.0	0	1	1
610.0	0	1	1
611.0	0	1	1
612.0	0	1	1
616.0	0	2	2
621.0	0	2	2
622.0	0	2	2
625.0	0	1	1
627.0	0	1	1
628.0	0	2	2
634.0	0	1	1
636.0	0	1	1
638.0	0	3	3
639.0	0	1	1
640.0	0	1	1
642.0	0	1	1
645.0	0	1	1
647.0	0	1	1
649.0	0	2	2
653.0	0	2	2
655.0	0	2	2
658.0	0	1	1
660.0	0	2	2
662.0	0	2	2
663.0	0	2	2
664.0	0	2	2
667.0	0	1	1
669.0	0	1	1
670.0	0	1	1
671.0	0	1	1
672.0	0	1	1
674.0	0	1	1
677.0	0	1	1
682.0	0	1	1
684.0	0	1	1
690.0	0	1	1
693.0	0	1	1
696.0	0	1	1
697.0	0	1	1
700.0	0	1	1
703.0	0	2	2
704.0	0	1	1
707.0	0	1	1
709.0	0	2	2
711.0	0	3	3
712.0	0	1	1
713.0	0	1	1
714.0	0	1	1
716.0	0	1	1
719.0	0	1	1
720.0	0	1	1
721.0	0	1	1
723.0	0	1	1
724.0	0	1	1
730.0	0	1	1
736.0	0	1	1
744.0	0	1	1
746.0	0	1	1
747.0	0	2	2
748.0	0	1	1
752.0	0	1	1
753.0	0	1	1
755.0	0	2	2
758.0	0	1	1
760.0	0	3	3
762.0	0	1	1
767.0	0	1	1
769.0	0	1	1
770.0	0	1	1
774.0	0	1	1
777.0	0	1	1
779.0	0	2	2
781.0	0	1	1
786.0	0	1	1
790.0	0	2	2
792.0	0	1	1
799.0	0	1	1
806.0	0	1	1
812.0	0	1	1
814.0	0	1	1
815.0	0	1	1
819.0	0	1	1
821.0	0	1	1
823.0	0	1	1
832.0	0	1	1
835.0	0	1	1
843.0	0	1	1
851.0	0	1	1
852.0	0	1	1
853.0	0	1	1
860.0	0	1	1
873.0	0	1	1
875.0	0	1	1
897.0	0	1	1
902.0	0	1	1
904.0	0	1	1
915.0	0	1	1
926.0	0	1	1
930.0	0	1	1
931.0	0	1	1
942.0	0	1	1
952.0	0	1	1
956.0	0	1	1
977.0	0	1	1
981.0	0	1	1
984.0	0	1	1
988.0	0	1	1
995.0	0	1	1
996.0	0	1	1
1007.0	0	1	1
1012.0	0	1	1
1032.0	0	1	1
1034.0	0	1	1
1043.0	0	1	1
1062.0	0	1	1
1064.0	0	1	1
1079.0	0	1	1
1090.0	0	1	1
1098.0	0	1	1
1106.0	0	1	1
1136.0	0	1	1
1150.0	0	1	1
1160.0	0	1	1
1165.0	0	2	2
1168.0	0	1	1
1192.0	0	1	1
1206.0	0	1	1
1234.0	0	1	1
1261.0	0	1	1
1279.0	0	1	1
1300.0	0	1	1
1307.0	0	1	1
1309.0	0	1	1
1313.0	0	1	1
1395.0	0	1	1
1478.0	0	1	1
1508.0	0	1	1
1622.0	0	1	1
1687.0	0	1	1
1702.0	0	1	1
1802.0	0	1	1
1806.0	0	1	1
1890.0	0	1	1
1992.0	0	1	1