## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_6.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_6_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: Mon Mar 09 18:00:00 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
24813495286	24514369815	9196	21155242726	2050520218	1154665488	153932187	0	0	0	4810555	74520788	298483	0.060639	0.939361	0	0.862973	0.083646	0.047102	0.006279	0.946619	0.935207	0	0.530138	0.578732	0.727274	0.85967			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.280753
1	0.318627
2	0.374749
3	0.438027
4	0.50599
5	0.574104
6	0.639898
7	0.704253
8	0.758356
9	0.809591
10	0.855155
11	0.902223
12	0.948972
13	0.986561
14	1.014803
15	1.039666
16	1.064963
17	1.081214
18	1.0943
19	1.111585
20	1.125744
21	1.142437
22	1.156768
23	1.170556
24	1.177934
25	1.181187
26	1.189544
27	1.196054
28	1.201632
29	1.200993
30	1.196661
31	1.194425
32	1.183188
33	1.179557
34	1.172904
35	1.167776
36	1.165097
37	1.154666
38	1.144521
39	1.141559
40	1.132386
41	1.125658
42	1.129645
43	1.129513
44	1.124511
45	1.132166
46	1.128917
47	1.123725
48	1.123212
49	1.128976
50	1.134396
51	1.131974
52	1.129145
53	1.131017
54	1.134283
55	1.137844
56	1.13989
57	1.139846
58	1.140239
59	1.134748
60	1.136653
61	1.141442
62	1.139502
63	1.13402
64	1.131714
65	1.134151
66	1.131598
67	1.126088
68	1.118143
69	1.109443
70	1.099521
71	1.090153
72	1.087568
73	1.077159
74	1.070881
75	1.064452
76	1.050593
77	1.029065
78	1.020912
79	1.0109
80	0.993445
81	0.975265
82	0.96779
83	0.953909
84	0.941504
85	0.935058
86	0.920866
87	0.904325
88	0.881743
89	0.862558
90	0.843589
91	0.818809
92	0.795403
93	0.76896
94	0.737706
95	0.705945
96	0.670745
97	0.634488
98	0.597326
99	0.557821
100	0.513577