## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT tih_rna_sample_00457_23KMKGLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00457_23KMKGLT4_1_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 23:26:31 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
25259263871	24903801877	9676	22301015235	1630215960	877976884	94584122	0	0	0	3432414	78151397	264688	0.042072	0.957928	0	0.895486	0.065461	0.035255	0.003798	0.960947	0.947424	0	0.557172	0.553211	0.687977	0.913042			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.307441
1	0.349496
2	0.405681
3	0.46867
4	0.520992
5	0.573948
6	0.637357
7	0.704956
8	0.765917
9	0.820124
10	0.867166
11	0.920491
12	0.976834
13	1.021205
14	1.056573
15	1.084496
16	1.101245
17	1.122081
18	1.129147
19	1.135189
20	1.146044
21	1.155897
22	1.171494
23	1.189447
24	1.196571
25	1.191185
26	1.186973
27	1.186885
28	1.19152
29	1.188835
30	1.198795
31	1.195961
32	1.187997
33	1.194298
34	1.193944
35	1.202471
36	1.202904
37	1.200137
38	1.191902
39	1.182251
40	1.173147
41	1.165181
42	1.176493
43	1.186909
44	1.18432
45	1.196094
46	1.201125
47	1.19624
48	1.191926
49	1.187342
50	1.174633
51	1.170567
52	1.159965
53	1.14614
54	1.138541
55	1.139707
56	1.129935
57	1.126194
58	1.119299
59	1.103468
60	1.091486
61	1.096937
62	1.10117
63	1.096192
64	1.089434
65	1.08143
66	1.074086
67	1.061331
68	1.060608
69	1.051392
70	1.04242
71	1.030812
72	1.023703
73	1.019148
74	1.007868
75	1.002682
76	1.001503
77	0.992707
78	0.991649
79	0.988102
80	0.971833
81	0.958344
82	0.951403
83	0.93864
84	0.929399
85	0.919525
86	0.899483
87	0.882898
88	0.862642
89	0.840408
90	0.817448
91	0.789023
92	0.760813
93	0.732831
94	0.70342
95	0.676432
96	0.650094
97	0.622604
98	0.589788
99	0.561249
100	0.525955