## 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_41.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_41_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 17:59:53 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
25473070713	25191184060	7702	22048465809	2045678621	966175273	130856655	0	0	0	1022546	78942391	345928	0.012787	0.987213	0	0.875245	0.081206	0.038354	0.005195	0.956451	0.945867	0	0.499657	0.589416	0.756094	0.8603			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.264704
1	0.307407
2	0.369343
3	0.438364
4	0.509752
5	0.579517
6	0.643981
7	0.704494
8	0.760106
9	0.813361
10	0.859084
11	0.905277
12	0.953685
13	0.994871
14	1.024687
15	1.051073
16	1.07474
17	1.092087
18	1.108174
19	1.123279
20	1.136627
21	1.149402
22	1.159051
23	1.166675
24	1.174582
25	1.175994
26	1.180529
27	1.184627
28	1.181429
29	1.178065
30	1.172948
31	1.168774
32	1.155808
33	1.153678
34	1.149892
35	1.149018
36	1.153181
37	1.146226
38	1.140595
39	1.140625
40	1.135832
41	1.136558
42	1.139274
43	1.142844
44	1.144228
45	1.153336
46	1.152152
47	1.151695
48	1.150643
49	1.156912
50	1.16443
51	1.16146
52	1.158816
53	1.156207
54	1.155619
55	1.158831
56	1.157108
57	1.155337
58	1.150717
59	1.141416
60	1.135804
61	1.134689
62	1.129579
63	1.124709
64	1.122194
65	1.122652
66	1.119824
67	1.118192
68	1.111964
69	1.104568
70	1.096407
71	1.090764
72	1.086998
73	1.079405
74	1.074888
75	1.063952
76	1.050875
77	1.032506
78	1.025026
79	1.012526
80	0.993575
81	0.97527
82	0.966303
83	0.951254
84	0.93518
85	0.927845
86	0.912662
87	0.893307
88	0.869604
89	0.848505
90	0.830031
91	0.806478
92	0.784753
93	0.755259
94	0.724616
95	0.691007
96	0.658995
97	0.625331
98	0.589746
99	0.551319
100	0.505999