## 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_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0001_B23LG7FLT4_1_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: Fri Feb 27 08:05:06 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
25707036773	25367655839	19185	21092884976	2747854175	1353680564	173216939	0	0	0	2164155	73988345	519484	0.028419	0.971581	0.000001	0.831487	0.108321	0.053362	0.006828	0.939809	0.927401	0	0.519447	0.571776	0.743782	0.848222			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.273003
1	0.312334
2	0.375387
3	0.44211
4	0.512152
5	0.581619
6	0.65018
7	0.713851
8	0.768893
9	0.819083
10	0.864718
11	0.917466
12	0.967319
13	1.008106
14	1.041205
15	1.074025
16	1.095705
17	1.107242
18	1.119516
19	1.134735
20	1.151561
21	1.16653
22	1.174471
23	1.181021
24	1.189375
25	1.196973
26	1.200469
27	1.202662
28	1.199713
29	1.1982
30	1.187757
31	1.185084
32	1.174042
33	1.174352
34	1.17208
35	1.175604
36	1.176251
37	1.16747
38	1.159525
39	1.15891
40	1.157571
41	1.15546
42	1.155567
43	1.153844
44	1.148159
45	1.157038
46	1.157929
47	1.15676
48	1.150694
49	1.152296
50	1.155891
51	1.152418
52	1.147319
53	1.147269
54	1.145173
55	1.141671
56	1.138573
57	1.136885
58	1.128795
59	1.122445
60	1.122587
61	1.125076
62	1.124112
63	1.117009
64	1.114925
65	1.108993
66	1.100483
67	1.093677
68	1.080674
69	1.071263
70	1.060197
71	1.049109
72	1.04457
73	1.036995
74	1.03117
75	1.021796
76	1.011041
77	0.999104
78	0.992668
79	0.985939
80	0.969929
81	0.951241
82	0.944557
83	0.928992
84	0.918029
85	0.910939
86	0.899121
87	0.889134
88	0.872808
89	0.854703
90	0.833981
91	0.807477
92	0.78679
93	0.763284
94	0.738519
95	0.709558
96	0.679166
97	0.649025
98	0.616281
99	0.580699
100	0.537465