## 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_46.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_46_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 18:00:08 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
24414905357	24114347814	24617	20805826844	1997094789	1165420633	145980931	0	0	0	1368553	77656137	348427	0.017318	0.982682	0.000001	0.862799	0.082818	0.048329	0.006054	0.945616	0.933975	0	0.528523	0.568216	0.749297	0.833456			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.286465
1	0.321939
2	0.374825
3	0.434143
4	0.499015
5	0.565028
6	0.628123
7	0.690259
8	0.742445
9	0.79299
10	0.837737
11	0.883874
12	0.932178
13	0.972188
14	1.001024
15	1.024947
16	1.03976
17	1.054765
18	1.070748
19	1.089299
20	1.104896
21	1.126597
22	1.145316
23	1.157847
24	1.165036
25	1.16751
26	1.17552
27	1.183048
28	1.189482
29	1.187627
30	1.182758
31	1.182111
32	1.172489
33	1.170311
34	1.164001
35	1.162477
36	1.160295
37	1.15108
38	1.142133
39	1.138241
40	1.130684
41	1.126464
42	1.130757
43	1.132725
44	1.12882
45	1.135123
46	1.131491
47	1.126314
48	1.125987
49	1.132564
50	1.13886
51	1.1368
52	1.134879
53	1.135433
54	1.137267
55	1.140077
56	1.14042
57	1.138836
58	1.1365
59	1.134024
60	1.134165
61	1.138715
62	1.139398
63	1.134579
64	1.135343
65	1.13627
66	1.132616
67	1.128156
68	1.119827
69	1.111023
70	1.101594
71	1.095388
72	1.095623
73	1.084273
74	1.074737
75	1.069134
76	1.05681
77	1.037852
78	1.028585
79	1.017776
80	1.002959
81	0.986039
82	0.981385
83	0.967554
84	0.955342
85	0.951832
86	0.939921
87	0.923752
88	0.905103
89	0.887012
90	0.864274
91	0.839513
92	0.816583
93	0.789308
94	0.757781
95	0.723967
96	0.689534
97	0.652889
98	0.616244
99	0.576211
100	0.52966