## 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_16.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_16_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 17:59:30 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
24779912484	24478287293	12562	21123960671	2021151572	1188402126	144760362	0	0	0	4040428	75212560	308352	0.050981	0.949019	0.000001	0.862967	0.082569	0.048549	0.005914	0.945536	0.934027	0	0.522113	0.569008	0.756587	0.830113			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.282572
1	0.318577
2	0.372255
3	0.430716
4	0.494664
5	0.560894
6	0.624417
7	0.685561
8	0.73758
9	0.787871
10	0.835248
11	0.8849
12	0.933566
13	0.970489
14	0.997478
15	1.019487
16	1.042373
17	1.058453
18	1.072464
19	1.090353
20	1.103868
21	1.120315
22	1.134654
23	1.148679
24	1.155717
25	1.16106
26	1.167916
27	1.176204
28	1.181875
29	1.181896
30	1.179603
31	1.180726
32	1.173937
33	1.172302
34	1.168263
35	1.16509
36	1.162323
37	1.154252
38	1.145751
39	1.142522
40	1.131126
41	1.126335
42	1.13097
43	1.132919
44	1.128843
45	1.137356
46	1.134916
47	1.131195
48	1.131699
49	1.137692
50	1.141955
51	1.138039
52	1.134815
53	1.135534
54	1.139341
55	1.143442
56	1.143726
57	1.143169
58	1.141267
59	1.138425
60	1.137345
61	1.141768
62	1.14012
63	1.13502
64	1.133372
65	1.134185
66	1.129325
67	1.124923
68	1.1172
69	1.10974
70	1.097323
71	1.090582
72	1.089392
73	1.080263
74	1.075123
75	1.069639
76	1.058647
77	1.042567
78	1.036104
79	1.026321
80	1.009222
81	0.992467
82	0.988113
83	0.974737
84	0.962841
85	0.956461
86	0.944081
87	0.927243
88	0.90774
89	0.889027
90	0.865094
91	0.841394
92	0.818518
93	0.789668
94	0.756666
95	0.723578
96	0.687353
97	0.650976
98	0.614612
99	0.574087
100	0.528823