## 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_7.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_7_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 17:59:59 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
24695884199	24393010033	11314	21054770497	2034807522	1149467078	153953622	0	0	0	5804536	73486677	300001	0.073205	0.926795	0	0.863148	0.083418	0.047123	0.006311	0.946565	0.934957	0	0.532459	0.589957	0.739273	0.870839			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.279185
1	0.3156
2	0.372225
3	0.435409
4	0.503657
5	0.571759
6	0.638792
7	0.702732
8	0.757126
9	0.807366
10	0.853814
11	0.901523
12	0.949843
13	0.988563
14	1.017534
15	1.041633
16	1.0667
17	1.084529
18	1.098653
19	1.11621
20	1.131173
21	1.149067
22	1.1618
23	1.177089
24	1.185288
25	1.190139
26	1.197158
27	1.202319
28	1.205719
29	1.206024
30	1.201169
31	1.198975
32	1.189088
33	1.184876
34	1.177755
35	1.173348
36	1.170183
37	1.159539
38	1.147113
39	1.142508
40	1.130488
41	1.124809
42	1.130367
43	1.131253
44	1.125467
45	1.132889
46	1.130411
47	1.125623
48	1.124048
49	1.129024
50	1.133209
51	1.129678
52	1.12907
53	1.129316
54	1.13124
55	1.134843
56	1.135804
57	1.135185
58	1.133928
59	1.129423
60	1.13082
61	1.135119
62	1.1329
63	1.128069
64	1.126426
65	1.12633
66	1.122756
67	1.117317
68	1.109895
69	1.102756
70	1.091636
71	1.082845
72	1.08045
73	1.069709
74	1.061858
75	1.056176
76	1.043903
77	1.02282
78	1.015472
79	1.00682
80	0.991431
81	0.973901
82	0.968268
83	0.954036
84	0.943212
85	0.938043
86	0.923854
87	0.905951
88	0.885526
89	0.865851
90	0.845563
91	0.822693
92	0.801145
93	0.774061
94	0.74378
95	0.711823
96	0.675356
97	0.638303
98	0.601688
99	0.561001
100	0.516548