## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT NTC_0001_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT NTC_0001_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: Tue Mar 03 22:04:42 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
341866160	1584361	10228	147103	52955	882040	492035	0	0	0	233	587	6	0.284146	0.715854	0.006456	0.092847	0.033424	0.556717	0.310557	0.12627	0.000585	0	2.434436	0	0	0			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.386544
1	0.820578
2	0.884067
3	0.884067
4	0.884067
5	0.884067
6	0.884067
7	0.938234
8	0.715054
9	0.645717
10	0.645717
11	0.645717
12	0.457007
13	0.354214
14	0.237937
15	0.318954
16	0.441726
17	0.514045
18	1.091645
19	1.125193
20	1.083866
21	0.891587
22	0.514197
23	0.514634
24	0.514634
25	0.514634
26	0.553625
27	0.70959
28	1.017426
29	1.182338
30	1.094768
31	0.887943
32	0.898445
33	0.991096
34	0.772196
35	0.838966
36	0.844839
37	0.844619
38	0.872719
39	0.993719
40	0.823001
41	1.491911
42	1.960146
43	1.590092
44	0.938145
45	0.897978
46	0.77474
47	0.726063
48	0.667872
49	0.79046
50	0.877603
51	0.942322
52	0.963359
53	1.075676
54	1.143955
55	1.390536
56	1.764803
57	2.118063
58	1.999694
59	1.608697
60	1.622295
61	1.698695
62	1.788553
63	1.478708
64	1.429642
65	1.67342
66	1.669885
67	1.53917
68	1.838603
69	1.695923
70	1.439945
71	1.306669
72	1.207805
73	1.227016
74	1.166242
75	1.062807
76	0.729506
77	0.752099
78	0.694209
79	0.628231
80	0.626939
81	0.617889
82	0.575006
83	0.568879
84	0.547345
85	0.4526
86	0.690363
87	1.28676
88	1.507157
89	1.47624
90	1.422424
91	1.086714
92	1.01343
93	0.982203
94	0.982203
95	0.943782
96	0.881938
97	0.945633
98	0.892153
99	0.892153
100	0.834236