## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT rna_s1221_S42.Aligned.sortedByCoord.out.bam --OUTPUT rna_s1221_S42_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 13:03:09 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
2753045385	2726986315	2363782	2400056821	197304400	95147272	32114040	0	0	0	81857	8016197	43628	0.010108	0.989892	0.000867	0.880113	0.072353	0.034891	0.011776	0.952466	0.94345	0	0.581228	0.568749	0.689316	0.702081			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.305117
1	0.3486
2	0.425254
3	0.509418
4	0.583762
5	0.657586
6	0.7227
7	0.77956
8	0.8315
9	0.873191
10	0.910129
11	0.943316
12	0.981913
13	1.019771
14	1.041487
15	1.065191
16	1.084804
17	1.100733
18	1.107508
19	1.126124
20	1.144831
21	1.157485
22	1.165038
23	1.171752
24	1.182159
25	1.188534
26	1.1936
27	1.190999
28	1.18753
29	1.178973
30	1.159768
31	1.151127
32	1.140343
33	1.14628
34	1.148843
35	1.150857
36	1.150068
37	1.138666
38	1.12906
39	1.123164
40	1.116789
41	1.116372
42	1.121102
43	1.121147
44	1.124293
45	1.126468
46	1.127464
47	1.127205
48	1.121889
49	1.12373
50	1.131492
51	1.129519
52	1.127463
53	1.122715
54	1.125738
55	1.119596
56	1.120203
57	1.120997
58	1.116352
59	1.114047
60	1.111116
61	1.11498
62	1.110051
63	1.104107
64	1.095655
65	1.092734
66	1.093156
67	1.086263
68	1.079283
69	1.077461
70	1.072148
71	1.067889
72	1.060795
73	1.059012
74	1.049544
75	1.041122
76	1.038193
77	1.028362
78	1.0224
79	1.018519
80	1.000316
81	0.983386
82	0.969363
83	0.958842
84	0.94282
85	0.928191
86	0.901964
87	0.890334
88	0.888513
89	0.867842
90	0.8493
91	0.81884
92	0.796875
93	0.772358
94	0.742109
95	0.708753
96	0.669549
97	0.637767
98	0.588826
99	0.546923
100	0.507449