## 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_27.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_27_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 17:59:53 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
25371409783	25086504404	13480	21753949794	2052992347	1135366919	144181864	0	0	0	1905419	77486358	369277	0.024	0.976	0.000001	0.867157	0.081837	0.045258	0.005747	0.948994	0.938337	0	0.510351	0.573951	0.763571	0.834812			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.271413
1	0.308804
2	0.363898
3	0.425415
4	0.491279
5	0.555944
6	0.618402
7	0.679975
8	0.735352
9	0.787616
10	0.831389
11	0.877628
12	0.92712
13	0.967907
14	0.995547
15	1.022225
16	1.046424
17	1.063363
18	1.082077
19	1.098787
20	1.111218
21	1.129084
22	1.142421
23	1.152264
24	1.159834
25	1.16366
26	1.170708
27	1.177061
28	1.178867
29	1.175172
30	1.170755
31	1.167841
32	1.158511
33	1.156612
34	1.154272
35	1.153968
36	1.153921
37	1.149871
38	1.143053
39	1.142451
40	1.135789
41	1.135531
42	1.139198
43	1.141448
44	1.137721
45	1.147239
46	1.148834
47	1.147744
48	1.146482
49	1.152431
50	1.160625
51	1.159726
52	1.157493
53	1.157813
54	1.158276
55	1.160126
56	1.157724
57	1.1561
58	1.152265
59	1.145334
60	1.145795
61	1.149919
62	1.147079
63	1.140874
64	1.138638
65	1.140185
66	1.138915
67	1.134508
68	1.126162
69	1.117853
70	1.109245
71	1.101938
72	1.098925
73	1.088104
74	1.077299
75	1.068691
76	1.057426
77	1.039169
78	1.031518
79	1.020986
80	1.001254
81	0.9814
82	0.974147
83	0.959861
84	0.9478
85	0.941335
86	0.92834
87	0.910186
88	0.887962
89	0.867349
90	0.847576
91	0.825746
92	0.803594
93	0.77684
94	0.746004
95	0.713734
96	0.678409
97	0.641876
98	0.606113
99	0.566501
100	0.522834