## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND INPUT=G221_M76_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/G221_M76_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 11:57:45 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
2142751800	2014003868	25553523	1384889241	399946317	73301429	130313358	0	12263360	71188	33890	6035748	102164	0.005584	0.994416	0.012688	0.68763	0.198583	0.036396	0.064704	0.886213	0.832964	0.994229	0.495582	0.366371	0.179528	1.916297			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.107587
1	0.189856
2	0.329781
3	0.476078
4	0.585264
5	0.696276
6	0.790429
7	0.855281
8	0.906036
9	0.945457
10	0.974464
11	1.002036
12	1.035201
13	1.059285
14	1.075704
15	1.092331
16	1.102777
17	1.116305
18	1.134058
19	1.151724
20	1.166271
21	1.176814
22	1.187763
23	1.196463
24	1.20309
25	1.211776
26	1.215418
27	1.222107
28	1.230979
29	1.243937
30	1.249187
31	1.252316
32	1.248963
33	1.246854
34	1.24927
35	1.25514
36	1.253877
37	1.25001
38	1.253183
39	1.259485
40	1.260988
41	1.258036
42	1.259175
43	1.259438
44	1.255293
45	1.248421
46	1.242345
47	1.23887
48	1.231769
49	1.228212
50	1.222214
51	1.219359
52	1.215863
53	1.217667
54	1.213905
55	1.208511
56	1.209325
57	1.214369
58	1.217622
59	1.216558
60	1.214516
61	1.201752
62	1.179258
63	1.164735
64	1.158645
65	1.148208
66	1.137201
67	1.135332
68	1.128848
69	1.116533
70	1.105593
71	1.096958
72	1.08837
73	1.079203
74	1.063563
75	1.048457
76	1.034345
77	1.016189
78	1.003258
79	0.988664
80	0.962649
81	0.938649
82	0.915153
83	0.888887
84	0.863946
85	0.837134
86	0.809808
87	0.781794
88	0.750081
89	0.705756
90	0.656632
91	0.601682
92	0.540632
93	0.477031
94	0.409885
95	0.336087
96	0.265306
97	0.198053
98	0.135454
99	0.081963
100	0.043897

