## 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_45.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_45_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 17:59:55 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
24572535665	24284540361	14540	20949040959	1993420211	1200658343	141406308	0	0	0	1265506	77880248	325447	0.01599	0.98401	0.000001	0.862649	0.082086	0.049441	0.005823	0.944735	0.933663	0	0.531923	0.547149	0.763857	0.784944			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.278778
1	0.313744
2	0.364944
3	0.424199
4	0.489429
5	0.554544
6	0.617139
7	0.677805
8	0.730591
9	0.780337
10	0.824142
11	0.872626
12	0.91845
13	0.952951
14	0.980493
15	1.00421
16	1.027506
17	1.04509
18	1.059111
19	1.075791
20	1.090968
21	1.111643
22	1.129059
23	1.143953
24	1.152561
25	1.154979
26	1.162809
27	1.170823
28	1.177739
29	1.178633
30	1.176224
31	1.175467
32	1.166494
33	1.165038
34	1.158218
35	1.158033
36	1.158777
37	1.15184
38	1.141354
39	1.137337
40	1.131877
41	1.1303
42	1.131921
43	1.132954
44	1.128208
45	1.136544
46	1.134831
47	1.13204
48	1.133916
49	1.141738
50	1.147494
51	1.146888
52	1.145361
53	1.146267
54	1.149104
55	1.15161
56	1.152552
57	1.150498
58	1.146214
59	1.143519
60	1.14131
61	1.14492
62	1.145034
63	1.139972
64	1.137319
65	1.140411
66	1.136488
67	1.131207
68	1.121447
69	1.113888
70	1.103639
71	1.098676
72	1.098165
73	1.090556
74	1.085958
75	1.080679
76	1.069577
77	1.052114
78	1.04386
79	1.031726
80	1.015836
81	0.999176
82	0.99246
83	0.979825
84	0.969013
85	0.962918
86	0.948523
87	0.93242
88	0.911704
89	0.892718
90	0.868554
91	0.845207
92	0.822083
93	0.791858
94	0.76113
95	0.727982
96	0.691471
97	0.654515
98	0.617259
99	0.578001
100	0.533507