## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2_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 00:18:10 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
15320795090	14685801339	69925	12501011652	1204561539	782432581	197725642	0	0	0	5118262	57161443	336563	0.082182	0.917818	0.000005	0.851231	0.082022	0.053278	0.013464	0.933253	0.894573	0	0.891572	0.354418	0.446786	0.690367			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.269641
1	0.309783
2	0.379051
3	0.462351
4	0.54795
5	0.6305
6	0.708902
7	0.785893
8	0.853722
9	0.902689
10	0.936436
11	0.966074
12	1.002096
13	1.04469
14	1.080221
15	1.106179
16	1.121459
17	1.136319
18	1.12406
19	1.110685
20	1.116293
21	1.117862
22	1.124997
23	1.13499
24	1.145638
25	1.13868
26	1.128286
27	1.136435
28	1.154424
29	1.151193
30	1.151832
31	1.162451
32	1.146027
33	1.152544
34	1.144087
35	1.129855
36	1.130885
37	1.129833
38	1.127093
39	1.125206
40	1.128391
41	1.147963
42	1.157169
43	1.158504
44	1.164396
45	1.175636
46	1.166541
47	1.15196
48	1.1383
49	1.131302
50	1.136128
51	1.130118
52	1.122816
53	1.1197
54	1.118508
55	1.118432
56	1.105688
57	1.099111
58	1.096434
59	1.074729
60	1.075701
61	1.092983
62	1.110452
63	1.105363
64	1.103853
65	1.102895
66	1.11037
67	1.088842
68	1.084297
69	1.082284
70	1.068479
71	1.056255
72	1.053898
73	1.056303
74	1.055556
75	1.06466
76	1.076837
77	1.063123
78	1.046082
79	1.041917
80	1.037411
81	1.021248
82	0.998989
83	0.99092
84	0.978944
85	0.965015
86	0.948477
87	0.928654
88	0.90646
89	0.873788
90	0.854858
91	0.825775
92	0.77814
93	0.743217
94	0.710428
95	0.675106
96	0.635344
97	0.598447
98	0.561202
99	0.520815
100	0.474394