## 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_17.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_17_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 18:10:57 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
25511860340	25216458537	8834	22128169205	2026613372	927427309	134239817	0	0	0	1941959	78098482	342917	0.024262	0.975738	0	0.877529	0.080369	0.036779	0.005323	0.957897	0.946806	0	0.508196	0.611664	0.742798	0.906993			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.268544
1	0.307742
2	0.369229
3	0.439273
4	0.511812
5	0.583095
6	0.64853
7	0.7119
8	0.768518
9	0.825368
10	0.875307
11	0.926079
12	0.980365
13	1.023292
14	1.056031
15	1.082403
16	1.094595
17	1.107352
18	1.127013
19	1.145192
20	1.155568
21	1.171205
22	1.181927
23	1.192779
24	1.200508
25	1.202257
26	1.203897
27	1.20477
28	1.200291
29	1.192381
30	1.185231
31	1.1796
32	1.166815
33	1.167128
34	1.164302
35	1.162392
36	1.163861
37	1.155776
38	1.147354
39	1.146029
40	1.139246
41	1.137018
42	1.139964
43	1.140488
44	1.136592
45	1.148141
46	1.145898
47	1.144438
48	1.143838
49	1.150195
50	1.157253
51	1.155894
52	1.152201
53	1.151687
54	1.150721
55	1.152185
56	1.149979
57	1.147543
58	1.143459
59	1.132656
60	1.126394
61	1.124627
62	1.119346
63	1.113285
64	1.108807
65	1.108051
66	1.105544
67	1.10229
68	1.096538
69	1.088619
70	1.07925
71	1.072285
72	1.067498
73	1.058856
74	1.050024
75	1.042399
76	1.030572
77	1.013929
78	1.008275
79	1.001259
80	0.985195
81	0.966499
82	0.957087
83	0.941371
84	0.925493
85	0.915703
86	0.899248
87	0.880274
88	0.857076
89	0.83558
90	0.819744
91	0.795919
92	0.77374
93	0.746513
94	0.721055
95	0.688174
96	0.654983
97	0.621642
98	0.58634
99	0.548015
100	0.504336