## 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_15.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_15_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 17:59:23 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
25289335687	24992531902	8974	21572393182	2064257824	1212743368	143128554	0	0	0	4019696	75377219	300695	0.050628	0.949372	0	0.863154	0.082595	0.048524	0.005727	0.945749	0.934649	0	0.522778	0.566632	0.76009	0.826286			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.280146
1	0.317634
2	0.371537
3	0.4326
4	0.497604
5	0.563361
6	0.626725
7	0.687315
8	0.739396
9	0.790224
10	0.834885
11	0.883414
12	0.93076
13	0.966398
14	0.992096
15	1.017434
16	1.042006
17	1.061691
18	1.077705
19	1.09441
20	1.106058
21	1.121901
22	1.136122
23	1.150472
24	1.157564
25	1.160194
26	1.165989
27	1.174115
28	1.181945
29	1.182236
30	1.180946
31	1.182009
32	1.173377
33	1.171287
34	1.168198
35	1.165517
36	1.163541
37	1.155919
38	1.14659
39	1.140071
40	1.129471
41	1.120567
42	1.122373
43	1.125373
44	1.123998
45	1.134004
46	1.133042
47	1.129936
48	1.129856
49	1.136138
50	1.141235
51	1.138718
52	1.135671
53	1.13528
54	1.136111
55	1.139604
56	1.142776
57	1.143068
58	1.140306
59	1.139553
60	1.137769
61	1.144046
62	1.142956
63	1.135039
64	1.132139
65	1.13322
66	1.128062
67	1.123384
68	1.116532
69	1.108797
70	1.097961
71	1.091912
72	1.091365
73	1.083631
74	1.078647
75	1.072927
76	1.061246
77	1.044686
78	1.037528
79	1.028392
80	1.011715
81	0.995692
82	0.988793
83	0.97396
84	0.962691
85	0.955819
86	0.943322
87	0.927305
88	0.907533
89	0.889583
90	0.866577
91	0.84261
92	0.819653
93	0.789546
94	0.757064
95	0.72485
96	0.687631
97	0.650255
98	0.613409
99	0.573987
100	0.530255