## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT FFPE_HD789_02_RNA_0011_23KMKGLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_HD789_02_RNA_0011_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: Sat May 16 11:55:06 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
78450166497	77658984785	41025	69011540033	5377354346	2885385523	384663858	0	0	0	6462456	237575086	1029745	0.026481	0.973519	0.000001	0.888648	0.069243	0.037155	0.004953	0.957892	0.948231	0	0.517936	0.617132	0.732233	0.944963			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.302729
1	0.34803
2	0.403529
3	0.471413
4	0.54645
5	0.617075
6	0.683963
7	0.749721
8	0.809627
9	0.865007
10	0.908066
11	0.953274
12	1.001811
13	1.040129
14	1.068527
15	1.089111
16	1.111509
17	1.131483
18	1.140662
19	1.150016
20	1.165661
21	1.183386
22	1.192826
23	1.195432
24	1.197807
25	1.192478
26	1.18917
27	1.184804
28	1.186014
29	1.18052
30	1.175621
31	1.173977
32	1.167156
33	1.167753
34	1.160366
35	1.164442
36	1.164068
37	1.160785
38	1.158828
39	1.152384
40	1.147939
41	1.152341
42	1.150522
43	1.152558
44	1.148693
45	1.146056
46	1.140172
47	1.137528
48	1.134395
49	1.140486
50	1.143935
51	1.141691
52	1.135806
53	1.131023
54	1.134729
55	1.127148
56	1.116311
57	1.118131
58	1.120908
59	1.110603
60	1.10697
61	1.106646
62	1.106333
63	1.101386
64	1.093992
65	1.089728
66	1.09661
67	1.090914
68	1.082262
69	1.073595
70	1.060678
71	1.050044
72	1.042784
73	1.033
74	1.027333
75	1.023574
76	1.011857
77	0.995049
78	0.993749
79	0.986165
80	0.972587
81	0.956228
82	0.947088
83	0.934229
84	0.917799
85	0.900752
86	0.880984
87	0.86764
88	0.849807
89	0.830884
90	0.818058
91	0.794327
92	0.771457
93	0.747454
94	0.723963
95	0.699528
96	0.674911
97	0.646101
98	0.614763
99	0.5842
100	0.544365