## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT U118MG_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT U118MG_FFPE_RNA_0001_B23LG7FLT4_2_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 07:06:58 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
25398174740	25069940474	13125	22409843680	1578269315	925524713	156289641	0	0	0	3657766	76791373	491081	0.045467	0.954533	0.000001	0.893893	0.062955	0.036918	0.006234	0.956848	0.944482	0	0.502233	0.619143	0.746177	0.964539			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.325479
1	0.369655
2	0.423573
3	0.491076
4	0.55258
5	0.613786
6	0.678153
7	0.741194
8	0.796924
9	0.857509
10	0.903902
11	0.953365
12	1.003068
13	1.040245
14	1.073876
15	1.110261
16	1.129394
17	1.141213
18	1.150712
19	1.156931
20	1.177767
21	1.19623
22	1.203215
23	1.216729
24	1.21736
25	1.215644
26	1.218268
27	1.216062
28	1.210015
29	1.197643
30	1.195268
31	1.194055
32	1.187137
33	1.188279
34	1.181752
35	1.184287
36	1.181483
37	1.176648
38	1.176322
39	1.173288
40	1.173244
41	1.17215
42	1.170232
43	1.169413
44	1.164228
45	1.163267
46	1.159261
47	1.155114
48	1.153417
49	1.1565
50	1.155151
51	1.159433
52	1.154543
53	1.151438
54	1.155233
55	1.157303
56	1.148928
57	1.142434
58	1.133515
59	1.119817
60	1.106165
61	1.099403
62	1.095707
63	1.090964
64	1.081911
65	1.074816
66	1.070955
67	1.061848
68	1.055425
69	1.04884
70	1.037955
71	1.02615
72	1.02372
73	1.011462
74	0.996401
75	0.987235
76	0.977698
77	0.956852
78	0.94734
79	0.940553
80	0.932615
81	0.920692
82	0.9109
83	0.893499
84	0.883751
85	0.875801
86	0.860549
87	0.843592
88	0.827994
89	0.809891
90	0.797161
91	0.775962
92	0.754606
93	0.73348
94	0.709704
95	0.685802
96	0.664885
97	0.637757
98	0.613371
99	0.585718
100	0.552539