## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT rna_s1221_S42.Aligned.sortedByCoord.out.bam --OUTPUT rna_s1221_S42_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: Wed Feb 25 18:53:53 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
27545664	27291792	26490	24057884	1937564	945718	324136	0	0	0	838	80369	436	0.010319	0.989681	0.000971	0.881506	0.070994	0.034652	0.011877	0.952501	0.943722	0	0.763821	0.471534	0.612925	0.241379			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.301096
1	0.34047
2	0.406363
3	0.480831
4	0.542785
5	0.60968
6	0.670995
7	0.718686
8	0.76922
9	0.806237
10	0.852448
11	0.900502
12	0.947025
13	0.988721
14	1.015661
15	1.050632
16	1.082561
17	1.098514
18	1.096227
19	1.108466
20	1.126817
21	1.141923
22	1.142395
23	1.1511
24	1.156132
25	1.156154
26	1.161838
27	1.170075
28	1.169936
29	1.166436
30	1.151995
31	1.143909
32	1.135556
33	1.134257
34	1.133371
35	1.135132
36	1.133212
37	1.123909
38	1.111071
39	1.107147
40	1.096941
41	1.107875
42	1.114978
43	1.107362
44	1.102193
45	1.113212
46	1.119729
47	1.117717
48	1.116708
49	1.121051
50	1.127536
51	1.124689
52	1.124772
53	1.122841
54	1.128102
55	1.131244
56	1.136352
57	1.1381
58	1.137639
59	1.139893
60	1.142183
61	1.154297
62	1.153019
63	1.149028
64	1.141034
65	1.134207
66	1.132555
67	1.127662
68	1.11782
69	1.118687
70	1.106737
71	1.094694
72	1.097875
73	1.092107
74	1.089547
75	1.083927
76	1.07706
77	1.071762
78	1.059821
79	1.046751
80	1.015139
81	0.995112
82	0.980466
83	0.972198
84	0.965269
85	0.942239
86	0.930509
87	0.923402
88	0.905272
89	0.876932
90	0.855858
91	0.832257
92	0.806001
93	0.768235
94	0.736454
95	0.711658
96	0.676074
97	0.64703
98	0.599085
99	0.556378
100	0.511034