## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND INPUT=G221_M77_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/G221_M77_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 11:57:42 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
2048699100	1916767431	14675583	1317239169	412824387	56626342	115401950	0	11932839	38244	17765	5873710	99327	0.003015	0.996985	0.007656	0.687219	0.215375	0.029543	0.060207	0.902594	0.844469	0.996805	0.545323	0.266683	0.236595	1.026895			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.088191
1	0.143283
2	0.233742
3	0.333465
4	0.411811
5	0.498805
6	0.578812
7	0.640304
8	0.695929
9	0.742457
10	0.778843
11	0.815757
12	0.853612
13	0.880669
14	0.9039
15	0.929781
16	0.950625
17	0.971714
18	0.993305
19	1.017039
20	1.037602
21	1.052501
22	1.067256
23	1.080357
24	1.097279
25	1.109601
26	1.119071
27	1.132142
28	1.146339
29	1.161465
30	1.172052
31	1.181064
32	1.184457
33	1.184171
34	1.184867
35	1.18745
36	1.190032
37	1.192573
38	1.200376
39	1.21338
40	1.218786
41	1.219793
42	1.227017
43	1.232379
44	1.234166
45	1.235737
46	1.243612
47	1.246963
48	1.244662
49	1.248512
50	1.24531
51	1.242667
52	1.239874
53	1.245338
54	1.245858
55	1.246488
56	1.25324
57	1.262552
58	1.269345
59	1.270431
60	1.273911
61	1.269047
62	1.258774
63	1.251166
64	1.249431
65	1.238632
66	1.227982
67	1.22371
68	1.217197
69	1.210328
70	1.204995
71	1.20238
72	1.199992
73	1.197162
74	1.185304
75	1.174011
76	1.164806
77	1.146583
78	1.129916
79	1.118243
80	1.098763
81	1.078767
82	1.064036
83	1.043386
84	1.024247
85	0.997893
86	0.97437
87	0.942842
88	0.915325
89	0.869943
90	0.809907
91	0.747453
92	0.678426
93	0.605596
94	0.528395
95	0.442197
96	0.35762
97	0.268108
98	0.176417
99	0.098996
100	0.048782

