## 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_s12.Aligned.sortedByCoord.out.bam --OUTPUT V4_0001_RNA_0005_23H5VFLT4_s12_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 22:55:19 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
25533998285	25149975735	32703	19886279261	2422542516	2471554768	369566487	0	0	0	3511482	69376778	339726	0.048176	0.951824	0.000001	0.790708	0.096324	0.098273	0.014695	0.887032	0.873691	0	0.511863	0.599008	0.732733	0.906176			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.29414
1	0.334981
2	0.402491
3	0.471265
4	0.540601
5	0.607375
6	0.671556
7	0.73369
8	0.790934
9	0.844288
10	0.888238
11	0.935325
12	0.980073
13	1.020362
14	1.052044
15	1.076725
16	1.10028
17	1.116728
18	1.123824
19	1.137505
20	1.15325
21	1.168401
22	1.183488
23	1.19528
24	1.204802
25	1.208416
26	1.21123
27	1.210088
28	1.206637
29	1.202639
30	1.198513
31	1.198207
32	1.185845
33	1.18178
34	1.174572
35	1.170326
36	1.169506
37	1.161575
38	1.153093
39	1.148584
40	1.144976
41	1.14067
42	1.140036
43	1.136585
44	1.132384
45	1.137128
46	1.132475
47	1.126931
48	1.126999
49	1.125824
50	1.127297
51	1.125023
52	1.122116
53	1.121464
54	1.12256
55	1.122695
56	1.123124
57	1.118693
58	1.118903
59	1.115677
60	1.11655
61	1.121024
62	1.116263
63	1.112086
64	1.109958
65	1.110482
66	1.104769
67	1.097967
68	1.088013
69	1.080345
70	1.070751
71	1.06202
72	1.058434
73	1.047741
74	1.042734
75	1.033814
76	1.022367
77	1.007542
78	1.002414
79	0.991355
80	0.972776
81	0.953422
82	0.943081
83	0.928471
84	0.915499
85	0.910771
86	0.895741
87	0.877488
88	0.857958
89	0.839273
90	0.819082
91	0.79931
92	0.781747
93	0.757607
94	0.732601
95	0.704219
96	0.672495
97	0.640304
98	0.606993
99	0.570765
100	0.528297