## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_20.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_20_rna_metrics.txt --TMP_DIR ./tmp --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 --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
## htsjdk.samtools.metrics.StringHeader
# Started on: Mon Mar 09 17:59:43 GMT 2026

## 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
24834336950	24533896299	16662	21270884267	2017703887	1106156511	139134972	0	0	0	2292657	77159025	316368	0.028856	0.971144	0.000001	0.867	0.082241	0.045087	0.005671	0.949241	0.937758	0	0.519994	0.578371	0.775761	0.846929			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.27852
1	0.31651
2	0.373086
3	0.435182
4	0.50225
5	0.56899
6	0.63277
7	0.692704
8	0.74648
9	0.797208
10	0.842745
11	0.89098
12	0.941752
13	0.9796
14	1.010943
15	1.038707
16	1.056115
17	1.070849
18	1.086062
19	1.102993
20	1.114238
21	1.131693
22	1.147134
23	1.159774
24	1.167
25	1.169304
26	1.174474
27	1.179161
28	1.183785
29	1.182586
30	1.178328
31	1.177072
32	1.167718
33	1.165345
34	1.162034
35	1.161242
36	1.158902
37	1.151268
38	1.142236
39	1.13826
40	1.131409
41	1.127307
42	1.129849
43	1.131559
44	1.127303
45	1.137505
46	1.137872
47	1.13536
48	1.135038
49	1.141602
50	1.146013
51	1.141988
52	1.138038
53	1.13818
54	1.140653
55	1.142806
56	1.140592
57	1.139551
58	1.136585
59	1.131501
60	1.131029
61	1.137307
62	1.135062
63	1.130293
64	1.12844
65	1.133002
66	1.133388
67	1.129032
68	1.120381
69	1.112155
70	1.099762
71	1.092783
72	1.090352
73	1.079717
74	1.07253
75	1.066085
76	1.054278
77	1.034961
78	1.026467
79	1.017892
80	1.001907
81	0.983519
82	0.976217
83	0.960989
84	0.949006
85	0.943333
86	0.93111
87	0.915008
88	0.89474
89	0.877524
90	0.859517
91	0.837146
92	0.814052
93	0.784909
94	0.752828
95	0.719991
96	0.684073
97	0.647167
98	0.609296
99	0.568388
100	0.523625