## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT aih-tih-sc-5519ab-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-5519ab-R1_A23YTGFLT4_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 Jun 03 20:16:00 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
71746182788	70992748228	8528	63649217002	4905076654	2061225983	377220061	0	0	0	13249398	237046611	1083167	0.052935	0.947065	0	0.896559	0.069093	0.029034	0.005314	0.965652	0.955511	0	0.569759	0.542086	0.725766	0.826679			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.321555
1	0.369274
2	0.430649
3	0.496235
4	0.561008
5	0.622133
6	0.681227
7	0.734374
8	0.791478
9	0.835484
10	0.876836
11	0.921704
12	0.964504
13	1.005
14	1.038561
15	1.052281
16	1.070496
17	1.088138
18	1.099488
19	1.116687
20	1.134323
21	1.148142
22	1.162251
23	1.17166
24	1.173756
25	1.174444
26	1.181751
27	1.19026
28	1.191343
29	1.183776
30	1.174116
31	1.174128
32	1.167122
33	1.16576
34	1.153637
35	1.145485
36	1.135974
37	1.130987
38	1.130246
39	1.1324
40	1.130893
41	1.134603
42	1.134235
43	1.135467
44	1.127845
45	1.130212
46	1.130015
47	1.12956
48	1.122995
49	1.126014
50	1.128906
51	1.121857
52	1.121174
53	1.11902
54	1.120185
55	1.121693
56	1.120581
57	1.118048
58	1.111763
59	1.109379
60	1.112374
61	1.113028
62	1.110139
63	1.102236
64	1.101082
65	1.103199
66	1.099957
67	1.094626
68	1.089735
69	1.083157
70	1.075559
71	1.065584
72	1.060485
73	1.055382
74	1.054091
75	1.048005
76	1.037091
77	1.02505
78	1.020448
79	1.010344
80	0.993924
81	0.976195
82	0.9673
83	0.959276
84	0.952654
85	0.943443
86	0.923221
87	0.913695
88	0.898434
89	0.87861
90	0.858125
91	0.831876
92	0.809031
93	0.779526
94	0.745866
95	0.717142
96	0.686005
97	0.652916
98	0.6192
99	0.5842
100	0.546519