## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND INPUT=G221_M73_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/G221_M73_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 11:58:37 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
5566425000	5301447106	15878510	3693450604	1081114601	148122471	362880920	0	32486910	94164	43497	15970250	277840	0.002716	0.997284	0.002995	0.696687	0.203928	0.02794	0.068449	0.900615	0.857744	0.99711	0.46413	0.335237	0.211187	1.544441			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.099518
1	0.173725
2	0.298719
3	0.430114
4	0.523455
5	0.627391
6	0.717447
7	0.787378
8	0.844437
9	0.88791
10	0.925375
11	0.960477
12	0.993531
13	1.018688
14	1.040207
15	1.062679
16	1.080188
17	1.097102
18	1.115504
19	1.130835
20	1.146329
21	1.155372
22	1.164896
23	1.175826
24	1.185041
25	1.191604
26	1.196783
27	1.202658
28	1.21511
29	1.231677
30	1.241742
31	1.246266
32	1.244718
33	1.246931
34	1.25828
35	1.268633
36	1.267023
37	1.263507
38	1.267142
39	1.271225
40	1.270264
41	1.265833
42	1.271093
43	1.271004
44	1.266592
45	1.25745
46	1.253052
47	1.249126
48	1.240766
49	1.235485
50	1.229652
51	1.225555
52	1.224327
53	1.227721
54	1.225858
55	1.220411
56	1.222526
57	1.22962
58	1.233336
59	1.230948
60	1.229479
61	1.220247
62	1.201794
63	1.184885
64	1.177658
65	1.164595
66	1.152713
67	1.149063
68	1.143297
69	1.129568
70	1.117581
71	1.106881
72	1.096011
73	1.085922
74	1.072039
75	1.058378
76	1.044545
77	1.028052
78	1.014683
79	0.999538
80	0.973624
81	0.950166
82	0.925603
83	0.899283
84	0.879612
85	0.854669
86	0.827485
87	0.797338
88	0.766376
89	0.725896
90	0.67828
91	0.627797
92	0.57073
93	0.512397
94	0.443868
95	0.372962
96	0.30252
97	0.231566
98	0.164479
99	0.10466
100	0.057064

