## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT V4_0001_RNA_0005_23H5VFLT4_s38.Aligned.sortedByCoord.out.bam --OUTPUT V4_0001_RNA_0005_23H5VFLT4_s38_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 Mar 04 22:03:03 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
24687210416	24271510187	91698	18956527969	2365767419	2575468068	373655033	0	0	0	1783379	69504412	348931	0.025017	0.974983	0.000004	0.78102	0.097471	0.106111	0.015395	0.878491	0.863698	0	0.526541	0.550824	0.723429	0.83599			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.290998
1	0.330475
2	0.39486
3	0.461421
4	0.52642
5	0.592941
6	0.657372
7	0.716713
8	0.770415
9	0.826514
10	0.866479
11	0.912832
12	0.959371
13	0.998167
14	1.025932
15	1.052938
16	1.071161
17	1.085147
18	1.089705
19	1.100841
20	1.11746
21	1.135012
22	1.15364
23	1.168146
24	1.179598
25	1.184757
26	1.187207
27	1.187947
28	1.185892
29	1.184306
30	1.181247
31	1.181269
32	1.171185
33	1.172322
34	1.164434
35	1.159111
36	1.160521
37	1.154608
38	1.145079
39	1.140729
40	1.136239
41	1.136279
42	1.137519
43	1.13486
44	1.134799
45	1.143432
46	1.138734
47	1.13483
48	1.134799
49	1.1353
50	1.137967
51	1.135895
52	1.133847
53	1.135221
54	1.135228
55	1.134668
56	1.134327
57	1.130893
58	1.128853
59	1.12678
60	1.129711
61	1.135591
62	1.133416
63	1.126293
64	1.123669
65	1.123437
66	1.118725
67	1.114578
68	1.103402
69	1.096441
70	1.088383
71	1.08092
72	1.078047
73	1.070652
74	1.066601
75	1.056137
76	1.043801
77	1.028461
78	1.018791
79	1.007251
80	0.99223
81	0.972868
82	0.961506
83	0.947214
84	0.933942
85	0.92588
86	0.910044
87	0.891632
88	0.870676
89	0.85036
90	0.82997
91	0.811619
92	0.794019
93	0.771138
94	0.745797
95	0.717516
96	0.685455
97	0.651456
98	0.615409
99	0.575643
100	0.527852