## 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_23.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_23_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 17:59:37 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
25193876655	24891848253	13977	21506117335	2052177050	1194549424	138990467	0	0	0	2843291	76568688	331860	0.035804	0.964196	0.000001	0.863982	0.082444	0.04799	0.005584	0.946426	0.93508	0	0.517033	0.558932	0.76704	0.795294			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.280497
1	0.313793
2	0.364921
3	0.421493
4	0.483753
5	0.546755
6	0.609605
7	0.669338
8	0.720964
9	0.771054
10	0.816595
11	0.8654
12	0.91565
13	0.956048
14	0.989199
15	1.011763
16	1.03481
17	1.054137
18	1.069879
19	1.088042
20	1.100309
21	1.116761
22	1.130995
23	1.145404
24	1.156293
25	1.161111
26	1.168441
27	1.174351
28	1.179193
29	1.178609
30	1.176882
31	1.176541
32	1.167083
33	1.165409
34	1.16324
35	1.16324
36	1.162506
37	1.154114
38	1.145832
39	1.139529
40	1.129513
41	1.126571
42	1.130515
43	1.133497
44	1.130513
45	1.140088
46	1.140136
47	1.138712
48	1.140575
49	1.149363
50	1.155584
51	1.154884
52	1.152897
53	1.152024
54	1.152868
55	1.155733
56	1.156328
57	1.157364
58	1.154252
59	1.152654
60	1.149651
61	1.150925
62	1.146784
63	1.138492
64	1.136182
65	1.137076
66	1.133137
67	1.130446
68	1.125305
69	1.118823
70	1.107441
71	1.101224
72	1.099206
73	1.090965
74	1.084593
75	1.078151
76	1.067246
77	1.050321
78	1.042132
79	1.029106
80	1.011463
81	0.99454
82	0.988323
83	0.97653
84	0.964119
85	0.95619
86	0.942343
87	0.924602
88	0.906078
89	0.885841
90	0.86086
91	0.835757
92	0.811656
93	0.781688
94	0.751244
95	0.71765
96	0.681553
97	0.644588
98	0.608398
99	0.569813
100	0.526521