## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND INPUT=G221_M79_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/G221_M79_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 11:57:43 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
2142234300	2000024692	9718694	1397158742	392029286	77477852	123640118	0	12426080	24397	10912	6115107	103113	0.001781	0.998219	0.004859	0.698571	0.196012	0.038738	0.061819	0.894583	0.835197	0.99804	0.531391	0.358525	0.154586	2.088895			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.109197
1	0.193
2	0.337629
3	0.487505
4	0.599822
5	0.71409
6	0.808498
7	0.875812
8	0.927022
9	0.963098
10	0.987855
11	1.014772
12	1.044113
13	1.066892
14	1.088748
15	1.110379
16	1.126246
17	1.141766
18	1.158629
19	1.175642
20	1.191108
21	1.200759
22	1.210257
23	1.215067
24	1.216474
25	1.219839
26	1.220122
27	1.226637
28	1.238334
29	1.257
30	1.262232
31	1.259459
32	1.254324
33	1.249198
34	1.253562
35	1.257798
36	1.254642
37	1.253272
38	1.256711
39	1.263591
40	1.265343
41	1.260214
42	1.264728
43	1.268727
44	1.266029
45	1.258712
46	1.25409
47	1.248539
48	1.243531
49	1.238859
50	1.230707
51	1.22397
52	1.217361
53	1.22225
54	1.219699
55	1.213558
56	1.211324
57	1.212715
58	1.218162
59	1.213724
60	1.211051
61	1.19962
62	1.181595
63	1.170688
64	1.161646
65	1.148954
66	1.135679
67	1.129541
68	1.120884
69	1.109623
70	1.095976
71	1.08519
72	1.072006
73	1.061271
74	1.046878
75	1.033032
76	1.018554
77	0.998163
78	0.98593
79	0.970312
80	0.943526
81	0.91798
82	0.893827
83	0.864747
84	0.840203
85	0.816417
86	0.7902
87	0.761671
88	0.729796
89	0.686108
90	0.634475
91	0.577635
92	0.515669
93	0.450946
94	0.381225
95	0.309368
96	0.242272
97	0.177834
98	0.120333
99	0.072959
100	0.039286

