## 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_s26.Aligned.sortedByCoord.out.bam --OUTPUT V4_0001_RNA_0005_23H5VFLT4_s26_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 May 19 19:38:49 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
77908703542	76949443698	193789	62467633405	7076377316	6506388837	898850351	0	0	0	5451737	217792677	1212683	0.02442	0.97558	0.000003	0.811801	0.091961	0.084554	0.011681	0.903762	0.892635	0	0.492934	0.596404	0.757139	0.863174			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.279986
1	0.320806
2	0.380707
3	0.449177
4	0.51892
5	0.586558
6	0.648189
7	0.710427
8	0.76458
9	0.818036
10	0.861045
11	0.906994
12	0.950514
13	0.991979
14	1.023176
15	1.050975
16	1.076662
17	1.093948
18	1.106106
19	1.120157
20	1.133505
21	1.150798
22	1.163117
23	1.173722
24	1.185411
25	1.192088
26	1.199114
27	1.202871
28	1.201387
29	1.197834
30	1.191994
31	1.189801
32	1.184276
33	1.181067
34	1.178542
35	1.178471
36	1.177148
37	1.170177
38	1.163329
39	1.163818
40	1.162292
41	1.159621
42	1.159434
43	1.16093
44	1.158542
45	1.158813
46	1.154401
47	1.151909
48	1.15122
49	1.152973
50	1.158351
51	1.157403
52	1.15447
53	1.154691
54	1.156472
55	1.154167
56	1.148279
57	1.143797
58	1.137674
59	1.128249
60	1.125969
61	1.130054
62	1.126431
63	1.118644
64	1.114585
65	1.113086
66	1.109302
67	1.102494
68	1.094041
69	1.084149
70	1.073638
71	1.064787
72	1.059068
73	1.048843
74	1.040362
75	1.033121
76	1.020184
77	1.001315
78	0.999164
79	0.993651
80	0.975527
81	0.955264
82	0.945456
83	0.928447
84	0.914586
85	0.907857
86	0.894088
87	0.876505
88	0.856942
89	0.838912
90	0.822911
91	0.803196
92	0.781127
93	0.755865
94	0.728974
95	0.70143
96	0.672472
97	0.639909
98	0.608513
99	0.574996
100	0.534056