## 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_00473_23KMKGLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00473_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 23:37:28 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
24947748593	24632701822	14024	22111785523	1707228300	721342493	92331482	0	0	0	2880331	79352055	289801	0.035027	0.964973	0.000001	0.89766	0.069307	0.029284	0.003748	0.966967	0.954756	0	0.540307	0.570027	0.708221	0.903654			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.300895
1	0.343846
2	0.406853
3	0.483172
4	0.548708
5	0.60258
6	0.66604
7	0.721468
8	0.776722
9	0.824301
10	0.874286
11	0.926
12	0.968085
13	1.004774
14	1.029576
15	1.04961
16	1.070191
17	1.094121
18	1.107001
19	1.115558
20	1.131576
21	1.150458
22	1.165389
23	1.176964
24	1.181642
25	1.186788
26	1.192545
27	1.196044
28	1.199995
29	1.202807
30	1.204986
31	1.202521
32	1.204423
33	1.200682
34	1.206571
35	1.204789
36	1.195892
37	1.184554
38	1.181288
39	1.188629
40	1.194892
41	1.193453
42	1.19398
43	1.199457
44	1.192913
45	1.188159
46	1.17682
47	1.169567
48	1.159178
49	1.168047
50	1.16667
51	1.16417
52	1.165097
53	1.153606
54	1.152025
55	1.145259
56	1.138281
57	1.140349
58	1.131387
59	1.112674
60	1.108557
61	1.10966
62	1.113248
63	1.113187
64	1.108825
65	1.107467
66	1.092652
67	1.080527
68	1.067929
69	1.064272
70	1.058531
71	1.050045
72	1.045575
73	1.034342
74	1.022641
75	1.00995
76	0.998913
77	0.989505
78	0.986942
79	0.984517
80	0.963224
81	0.946398
82	0.933161
83	0.917794
84	0.904008
85	0.896018
86	0.879495
87	0.863813
88	0.84578
89	0.825839
90	0.808572
91	0.784626
92	0.755941
93	0.726554
94	0.712976
95	0.684029
96	0.642878
97	0.615823
98	0.582644
99	0.546587
100	0.509979