## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND INPUT=G221_M69_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/G221_M69_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
1867152600	1748930620	7126859	1216770649	336544885	61748039	126740188	0	10762745	25669	11737	5278944	103808	0.002218	0.997782	0.004075	0.695723	0.192429	0.035306	0.072467	0.888152	0.831917	0.997621	0.51244	0.371234	0.164323	1.987355			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.10817
1	0.190987
2	0.335082
3	0.487382
4	0.598162
5	0.712691
6	0.804032
7	0.867762
8	0.919449
9	0.955303
10	0.986406
11	1.014251
12	1.047818
13	1.070683
14	1.088374
15	1.10751
16	1.120724
17	1.1364
18	1.149776
19	1.163642
20	1.176443
21	1.184266
22	1.190943
23	1.199691
24	1.206127
25	1.215534
26	1.219743
27	1.225782
28	1.23453
29	1.250055
30	1.257128
31	1.256381
32	1.250299
33	1.247099
34	1.257645
35	1.265787
36	1.264745
37	1.263616
38	1.266899
39	1.273937
40	1.269376
41	1.261273
42	1.265514
43	1.263543
44	1.258369
45	1.24856
46	1.241773
47	1.237443
48	1.23254
49	1.23241
50	1.226243
51	1.224911
52	1.226924
53	1.233873
54	1.232775
55	1.23113
56	1.226138
57	1.222491
58	1.223203
59	1.219478
60	1.217634
61	1.205252
62	1.182424
63	1.167862
64	1.156552
65	1.143499
66	1.131594
67	1.124316
68	1.116803
69	1.107403
70	1.093381
71	1.083334
72	1.074463
73	1.063308
74	1.045638
75	1.027821
76	1.013415
77	0.995217
78	0.984989
79	0.971632
80	0.946529
81	0.924293
82	0.896655
83	0.871727
84	0.847715
85	0.81979
86	0.792446
87	0.764473
88	0.728045
89	0.681246
90	0.632858
91	0.581697
92	0.52244
93	0.463068
94	0.395837
95	0.326383
96	0.258826
97	0.190402
98	0.12868
99	0.077242
100	0.040853

