## 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_9.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_9_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 18:00:03 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
25671852182	25381092140	8638	22268117480	2060952737	917637149	134376136	0	0	0	3542817	76687892	303726	0.044158	0.955842	0	0.877351	0.0812	0.036154	0.005294	0.958551	0.947694	0	0.503531	0.605523	0.746336	0.864543			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.266516
1	0.30804
2	0.369615
3	0.440909
4	0.514164
5	0.583543
6	0.648089
7	0.710712
8	0.768421
9	0.822745
10	0.869452
11	0.919343
12	0.970622
13	1.014377
14	1.045931
15	1.073801
16	1.092826
17	1.107731
18	1.121349
19	1.13776
20	1.152882
21	1.168005
22	1.177089
23	1.185459
24	1.191567
25	1.193679
26	1.198813
27	1.202603
28	1.199263
29	1.194327
30	1.188618
31	1.183841
32	1.170476
33	1.164967
34	1.161032
35	1.160786
36	1.161622
37	1.152209
38	1.143339
39	1.140576
40	1.13412
41	1.131639
42	1.133154
43	1.13494
44	1.132574
45	1.141798
46	1.141929
47	1.141057
48	1.140353
49	1.148173
50	1.15708
51	1.157446
52	1.153741
53	1.15267
54	1.151569
55	1.152701
56	1.149313
57	1.146634
58	1.143288
59	1.135115
60	1.131577
61	1.130994
62	1.124619
63	1.117022
64	1.114949
65	1.114793
66	1.113186
67	1.110129
68	1.103097
69	1.094706
70	1.085261
71	1.079269
72	1.074991
73	1.066066
74	1.059843
75	1.052686
76	1.038729
77	1.020388
78	1.012323
79	1.000887
80	0.981715
81	0.961924
82	0.952699
83	0.938922
84	0.925688
85	0.918136
86	0.900539
87	0.882619
88	0.861054
89	0.841572
90	0.825924
91	0.801508
92	0.778811
93	0.750325
94	0.721682
95	0.689042
96	0.655962
97	0.621718
98	0.586747
99	0.549351
100	0.508039