## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND INPUT=G221_M75_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/G221_M75_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 11:58:13 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
5502522300	5209403972	18001270	3693091407	1013291781	125491322	359528192	0	32166644	89533	41260	15846817	247820	0.002597	0.997403	0.003456	0.708928	0.194512	0.024089	0.069015	0.90344	0.855314	0.997224	0.469072	0.348034	0.199901	1.614437			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.10218
1	0.176248
2	0.303734
3	0.439127
4	0.53887
5	0.643366
6	0.734392
7	0.80308
8	0.857688
9	0.903127
10	0.937177
11	0.97239
12	1.006842
13	1.033924
14	1.055881
15	1.075777
16	1.093807
17	1.110258
18	1.127092
19	1.141868
20	1.156949
21	1.165139
22	1.176981
23	1.187699
24	1.198598
25	1.207751
26	1.213255
27	1.21925
28	1.229336
29	1.244677
30	1.253163
31	1.255591
32	1.255034
33	1.253377
34	1.263575
35	1.271321
36	1.26674
37	1.266043
38	1.267821
39	1.27131
40	1.269747
41	1.263282
42	1.266969
43	1.266362
44	1.261388
45	1.249226
46	1.242873
47	1.236362
48	1.228633
49	1.22916
50	1.227936
51	1.225954
52	1.227998
53	1.232106
54	1.229721
55	1.223629
56	1.220959
57	1.224121
58	1.227543
59	1.226121
60	1.22404
61	1.214867
62	1.198719
63	1.184849
64	1.177266
65	1.167329
66	1.159328
67	1.157166
68	1.1505
69	1.135999
70	1.120851
71	1.106701
72	1.096277
73	1.084239
74	1.068922
75	1.049476
76	1.031565
77	1.010822
78	0.99436
79	0.978096
80	0.95456
81	0.930219
82	0.907881
83	0.884429
84	0.863985
85	0.840374
86	0.813956
87	0.785577
88	0.753883
89	0.712599
90	0.665184
91	0.614139
92	0.557102
93	0.494414
94	0.425741
95	0.354879
96	0.286173
97	0.219822
98	0.15625
99	0.100168
100	0.05557

