## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND INPUT=G221_M70_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/G221_M70_metrics    MINIMUM_LENGTH=500 RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] END_BIAS_BASES=100 ASSUME_SORTED=true STOP_AFTER=0 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: Fri Feb 23 11:57:48 EST 2024

## METRICS CLASS	picard.analysis.RnaSeqMetrics
PF_BASES	PF_ALIGNED_BASES	RIBOSOMAL_BASES	CODING_BASES	UTR_BASES	INTRONIC_BASES	INTERGENIC_BASES	IGNORED_READS	CORRECT_STRAND_READS	INCORRECT_STRAND_READS	NUM_R1_TRANSCRIPT_STRAND_READS	NUM_R2_TRANSCRIPT_STRAND_READS	NUM_UNEXPLAINED_READS	PCT_R1_TRANSCRIPT_STRAND_READS	PCT_R2_TRANSCRIPT_STRAND_READS	PCT_RIBOSOMAL_BASES	PCT_CODING_BASES	PCT_UTR_BASES	PCT_INTRONIC_BASES	PCT_INTERGENIC_BASES	PCT_MRNA_BASES	PCT_USABLE_BASES	PCT_CORRECT_STRAND_READS	MEDIAN_CV_COVERAGE	MEDIAN_5PRIME_BIAS	MEDIAN_3PRIME_BIAS	MEDIAN_5PRIME_TO_3PRIME_BIAS	SAMPLE	LIBRARY	READ_GROUP
2143225500	1989050102	7399432	1429204795	367768185	53032686	131645004	0	12548813	24652	11192	6152341	124342	0.001816	0.998184	0.00372	0.718536	0.184896	0.026662	0.066185	0.903433	0.838443	0.998039	0.525097	0.356169	0.15464	2.062114			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.104301
1	0.185542
2	0.325441
3	0.473852
4	0.584597
5	0.698244
6	0.791144
7	0.856282
8	0.912119
9	0.954268
10	0.983794
11	1.015491
12	1.048495
13	1.076087
14	1.098529
15	1.121643
16	1.139277
17	1.153694
18	1.168548
19	1.182204
20	1.199674
21	1.209064
22	1.21774
23	1.223646
24	1.231264
25	1.240752
26	1.2445
27	1.248263
28	1.258188
29	1.272521
30	1.276717
31	1.280468
32	1.277938
33	1.272595
34	1.281427
35	1.284238
36	1.279352
37	1.278776
38	1.284126
39	1.289561
40	1.283521
41	1.274295
42	1.277241
43	1.278782
44	1.275277
45	1.261741
46	1.252055
47	1.243893
48	1.231267
49	1.229559
50	1.22059
51	1.215075
52	1.214227
53	1.221436
54	1.222474
55	1.218476
56	1.216103
57	1.219967
58	1.227424
59	1.225915
60	1.224034
61	1.210837
62	1.188878
63	1.174076
64	1.162862
65	1.148627
66	1.135006
67	1.127152
68	1.116183
69	1.101355
70	1.084783
71	1.071611
72	1.060011
73	1.046863
74	1.031553
75	1.013547
76	0.997507
77	0.976999
78	0.965913
79	0.950891
80	0.924055
81	0.896447
82	0.870632
83	0.845791
84	0.822743
85	0.797547
86	0.770081
87	0.742757
88	0.710973
89	0.668128
90	0.618123
91	0.563652
92	0.506652
93	0.4463
94	0.379844
95	0.310579
96	0.244724
97	0.178233
98	0.117832
99	0.068465
100	0.035673

