## 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_s22.Aligned.sortedByCoord.out.bam --OUTPUT V4_0001_RNA_0005_23H5VFLT4_s22_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 22:56:37 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
25401980097	24994021654	41389	19540116939	2447409437	2627365663	379088226	0	0	0	3131330	69057107	355454	0.043377	0.956623	0.000002	0.781792	0.09792	0.10512	0.015167	0.879711	0.865583	0	0.520831	0.572035	0.737087	0.838328			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.291151
1	0.329944
2	0.393528
3	0.461308
4	0.52929
5	0.596259
6	0.6614
7	0.722143
8	0.776253
9	0.828478
10	0.868421
11	0.913298
12	0.959357
13	0.997248
14	1.027561
15	1.056047
16	1.073501
17	1.089361
18	1.095779
19	1.112538
20	1.131202
21	1.148846
22	1.168144
23	1.182419
24	1.192831
25	1.198149
26	1.199571
27	1.199969
28	1.200056
29	1.19912
30	1.194048
31	1.194264
32	1.182866
33	1.178929
34	1.172652
35	1.168154
36	1.166586
37	1.159439
38	1.150306
39	1.144181
40	1.137646
41	1.133796
42	1.133098
43	1.129382
44	1.128343
45	1.135363
46	1.13124
47	1.124712
48	1.126474
49	1.127347
50	1.130618
51	1.127457
52	1.124599
53	1.127449
54	1.129474
55	1.129002
56	1.130621
57	1.125773
58	1.12386
59	1.120298
60	1.120622
61	1.125113
62	1.122409
63	1.119032
64	1.115951
65	1.117107
66	1.111858
67	1.106583
68	1.098047
69	1.089909
70	1.079152
71	1.070102
72	1.066755
73	1.057454
74	1.054487
75	1.045387
76	1.036098
77	1.022174
78	1.015592
79	1.004468
80	0.987077
81	0.9707
82	0.962277
83	0.946519
84	0.933449
85	0.927342
86	0.912165
87	0.892945
88	0.871721
89	0.850879
90	0.830904
91	0.810448
92	0.792464
93	0.771116
94	0.746417
95	0.719333
96	0.687383
97	0.654375
98	0.620487
99	0.581935
100	0.535956