## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND INPUT=G221_M74_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/G221_M74_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 11:58:01 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
3812065200	3642163851	22510676	2549132437	726161842	85405535	258953361	0	22007019	212742	102457	10809794	197668	0.009389	0.990611	0.006181	0.699895	0.199376	0.023449	0.071099	0.899272	0.859192	0.990426	0.46826	0.310065	0.222205	1.347362			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.097857
1	0.162776
2	0.271164
3	0.390118
4	0.47819
5	0.577283
6	0.663466
7	0.729771
8	0.789451
9	0.838361
10	0.879699
11	0.917138
12	0.954618
13	0.983128
14	1.003844
15	1.026512
16	1.047125
17	1.066155
18	1.087187
19	1.104024
20	1.120537
21	1.133402
22	1.144094
23	1.153469
24	1.165308
25	1.178802
26	1.185525
27	1.197953
28	1.214594
29	1.233479
30	1.244562
31	1.251235
32	1.251601
33	1.249788
34	1.247092
35	1.246098
36	1.242379
37	1.24292
38	1.250689
39	1.258609
40	1.264122
41	1.265406
42	1.267823
43	1.267079
44	1.264271
45	1.254667
46	1.250037
47	1.248153
48	1.240918
49	1.238023
50	1.23652
51	1.236725
52	1.237465
53	1.241158
54	1.242281
55	1.237038
56	1.233688
57	1.234843
58	1.240111
59	1.24
60	1.237047
61	1.228197
62	1.210737
63	1.19726
64	1.192744
65	1.18232
66	1.172604
67	1.17122
68	1.165705
69	1.149315
70	1.138845
71	1.132249
72	1.122653
73	1.116306
74	1.10106
75	1.083287
76	1.067392
77	1.048396
78	1.034187
79	1.019049
80	0.995359
81	0.979612
82	0.957973
83	0.933501
84	0.913951
85	0.888274
86	0.860565
87	0.828725
88	0.791136
89	0.749095
90	0.70526
91	0.655616
92	0.600636
93	0.539021
94	0.46753
95	0.394781
96	0.321468
97	0.244695
98	0.169898
99	0.10467
100	0.055875

