## 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_30.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_30_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 17:59:45 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
24687358998	24389095993	30636	21077925903	2000827338	1169578559	140733557	0	0	0	2630280	76636561	338231	0.033183	0.966817	0.000001	0.864236	0.082038	0.047955	0.00577	0.946273	0.934841	0	0.528227	0.551521	0.764174	0.802392			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.281114
1	0.31688
2	0.368274
3	0.425625
4	0.48907
5	0.554015
6	0.615326
7	0.673552
8	0.722364
9	0.769764
10	0.81429
11	0.861209
12	0.909971
13	0.951289
14	0.981538
15	1.006895
16	1.030126
17	1.047621
18	1.063716
19	1.081684
20	1.0966
21	1.115017
22	1.131936
23	1.146892
24	1.155445
25	1.159281
26	1.166993
27	1.174715
28	1.182354
29	1.182244
30	1.181051
31	1.181802
32	1.17192
33	1.169837
34	1.166302
35	1.164938
36	1.162895
37	1.155287
38	1.147573
39	1.142789
40	1.135506
41	1.131473
42	1.133519
43	1.135627
44	1.132011
45	1.139778
46	1.137129
47	1.133485
48	1.134722
49	1.140042
50	1.14675
51	1.145926
52	1.144004
53	1.144118
54	1.147949
55	1.151456
56	1.152763
57	1.15231
58	1.153092
59	1.146801
60	1.145103
61	1.148626
62	1.146897
63	1.141794
64	1.140838
65	1.141235
66	1.136854
67	1.130103
68	1.121574
69	1.114385
70	1.105187
71	1.098778
72	1.097257
73	1.086914
74	1.077984
75	1.073118
76	1.063067
77	1.042947
78	1.034483
79	1.024397
80	1.010194
81	0.993848
82	0.989029
83	0.974916
84	0.961927
85	0.956712
86	0.943788
87	0.925867
88	0.906898
89	0.888513
90	0.868259
91	0.844448
92	0.822112
93	0.793532
94	0.761221
95	0.726644
96	0.690782
97	0.654264
98	0.617653
99	0.57816
100	0.534373