## 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_26.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_26_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 17:59:42 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
25658779609	25367974575	8218	22083552196	2075741935	1071060764	137611462	0	0	0	1581154	78017200	340664	0.019864	0.980136	0	0.870529	0.081825	0.042221	0.005425	0.952354	0.941561	0	0.495582	0.574534	0.765254	0.828145			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.269685
1	0.307878
2	0.36513
3	0.432268
4	0.499606
5	0.564646
6	0.625484
7	0.684477
8	0.738187
9	0.791588
10	0.835825
11	0.882216
12	0.929851
13	0.969638
14	0.999996
15	1.025359
16	1.051313
17	1.070409
18	1.090476
19	1.107511
20	1.12154
21	1.136533
22	1.147759
23	1.155272
24	1.164312
25	1.167912
26	1.172371
27	1.179012
28	1.179144
29	1.176395
30	1.170442
31	1.167344
32	1.154604
33	1.151984
34	1.146909
35	1.145333
36	1.148648
37	1.141255
38	1.133796
39	1.134115
40	1.128768
41	1.128064
42	1.134556
43	1.141225
44	1.141016
45	1.153463
46	1.153174
47	1.153986
48	1.15106
49	1.157233
50	1.164971
51	1.16555
52	1.162899
53	1.16151
54	1.161711
55	1.163435
56	1.162168
57	1.161062
58	1.159936
59	1.152973
60	1.148228
61	1.14908
62	1.144702
63	1.138417
64	1.135567
65	1.136026
66	1.135096
67	1.130962
68	1.122327
69	1.114016
70	1.106024
71	1.098615
72	1.093175
73	1.082564
74	1.077297
75	1.06763
76	1.05414
77	1.035001
78	1.02805
79	1.017826
80	0.998528
81	0.98004
82	0.971535
83	0.958686
84	0.946572
85	0.93947
86	0.925037
87	0.908561
88	0.884966
89	0.865546
90	0.845207
91	0.821184
92	0.799073
93	0.770226
94	0.740796
95	0.708181
96	0.672962
97	0.636675
98	0.600005
99	0.5607
100	0.515015