## 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_22.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_22_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 17:59:36 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
24839416276	24536207295	18125	21222216894	2018635509	1156370772	138965995	0	0	0	3180175	76197907	317455	0.040064	0.959936	0.000001	0.864935	0.082272	0.047129	0.005664	0.947206	0.935644	0	0.52478	0.562496	0.760916	0.835034			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.279124
1	0.314561
2	0.368731
3	0.429341
4	0.494055
5	0.560463
6	0.624559
7	0.684957
8	0.737389
9	0.788198
10	0.834231
11	0.882693
12	0.929096
13	0.966858
14	0.996298
15	1.021037
16	1.046058
17	1.06461
18	1.07909
19	1.097012
20	1.109489
21	1.127009
22	1.14139
23	1.153763
24	1.159894
25	1.162728
26	1.169003
27	1.174476
28	1.179485
29	1.178714
30	1.174395
31	1.17269
32	1.164054
33	1.162042
34	1.159004
35	1.157052
36	1.154224
37	1.144869
38	1.136639
39	1.134367
40	1.125411
41	1.12304
42	1.127907
43	1.130857
44	1.126179
45	1.134723
46	1.131708
47	1.130192
48	1.132121
49	1.139647
50	1.145146
51	1.142694
52	1.140008
53	1.139965
54	1.142407
55	1.145952
56	1.146841
57	1.146076
58	1.143565
59	1.141655
60	1.14091
61	1.146503
62	1.144906
63	1.138525
64	1.136669
65	1.137195
66	1.132315
67	1.1264
68	1.119811
69	1.113351
70	1.100997
71	1.094886
72	1.092982
73	1.083556
74	1.077006
75	1.07192
76	1.061691
77	1.045407
78	1.037776
79	1.028513
80	1.013301
81	0.995679
82	0.989253
83	0.975232
84	0.963536
85	0.956602
86	0.943851
87	0.926205
88	0.905287
89	0.887575
90	0.863497
91	0.838547
92	0.815829
93	0.78692
94	0.754871
95	0.72226
96	0.685694
97	0.649509
98	0.612572
99	0.573289
100	0.528627