## 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_s11.Aligned.sortedByCoord.out.bam --OUTPUT V4_0001_RNA_0005_23H5VFLT4_s11_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 22:34:29 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
26244826803	25890215400	34091	20719977639	2444091782	2390123354	335988534	0	0	0	3067021	70923178	355643	0.041452	0.958548	0.000001	0.800301	0.094402	0.092318	0.012977	0.894704	0.882615	0	0.502129	0.600202	0.74648	0.869819			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.285712
1	0.327466
2	0.388036
3	0.455052
4	0.522834
5	0.5884
6	0.65303
7	0.716428
8	0.773822
9	0.828206
10	0.871814
11	0.918563
12	0.964554
13	1.007968
14	1.041006
15	1.069439
16	1.087759
17	1.105143
18	1.118634
19	1.133578
20	1.147786
21	1.162817
22	1.173775
23	1.183825
24	1.194624
25	1.198785
26	1.203114
27	1.204492
28	1.204317
29	1.203387
30	1.19697
31	1.195722
32	1.184184
33	1.180615
34	1.176307
35	1.173598
36	1.172136
37	1.162566
38	1.156631
39	1.150911
40	1.146732
41	1.143377
42	1.144841
43	1.145185
44	1.143932
45	1.148858
46	1.143703
47	1.138393
48	1.136925
49	1.138007
50	1.141451
51	1.138802
52	1.134405
53	1.135339
54	1.139498
55	1.137645
56	1.133722
57	1.12867
58	1.125013
59	1.119609
60	1.11676
61	1.120383
62	1.116021
63	1.108846
64	1.105173
65	1.102872
66	1.098203
67	1.094385
68	1.086651
69	1.079546
70	1.070207
71	1.062376
72	1.057982
73	1.04967
74	1.043487
75	1.038184
76	1.025488
77	1.008429
78	1.006687
79	0.998029
80	0.980357
81	0.959463
82	0.948461
83	0.933707
84	0.923227
85	0.918018
86	0.902944
87	0.887418
88	0.86709
89	0.848599
90	0.828116
91	0.806896
92	0.786094
93	0.761401
94	0.735784
95	0.707173
96	0.676635
97	0.643278
98	0.610623
99	0.576629
100	0.534976