## 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_13.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_13_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 17:59:22 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
25325462259	25031583134	10956	21589103804	2085241871	1207189011	150037492	0	0	0	2660860	76677903	315768	0.033538	0.966462	0	0.862475	0.083304	0.048227	0.005994	0.945779	0.934804	0	0.515153	0.579124	0.754539	0.837467			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.280161
1	0.317184
2	0.371862
3	0.433405
4	0.500667
5	0.567851
6	0.632059
7	0.692524
8	0.745211
9	0.795717
10	0.8415
11	0.889812
12	0.937648
13	0.97619
14	1.004099
15	1.027562
16	1.051536
17	1.069191
18	1.083756
19	1.100598
20	1.11838
21	1.135964
22	1.150246
23	1.163407
24	1.173452
25	1.176425
26	1.180769
27	1.18523
28	1.189753
29	1.187958
30	1.184563
31	1.185974
32	1.176415
33	1.172745
34	1.164752
35	1.16156
36	1.162008
37	1.155246
38	1.147444
39	1.143548
40	1.134826
41	1.130789
42	1.134403
43	1.133615
44	1.128462
45	1.137667
46	1.137118
47	1.135225
48	1.136193
49	1.14213
50	1.146238
51	1.142768
52	1.139253
53	1.139216
54	1.141016
55	1.144074
56	1.14627
57	1.146188
58	1.144089
59	1.14166
60	1.141301
61	1.144104
62	1.140713
63	1.135878
64	1.135852
65	1.136973
66	1.132439
67	1.128539
68	1.12088
69	1.112521
70	1.101334
71	1.093447
72	1.090316
73	1.078478
74	1.069988
75	1.063146
76	1.051993
77	1.035257
78	1.027677
79	1.016556
80	0.998935
81	0.980231
82	0.973813
83	0.962214
84	0.949729
85	0.942217
86	0.927143
87	0.910938
88	0.889266
89	0.868993
90	0.846525
91	0.822812
92	0.799269
93	0.77065
94	0.741946
95	0.710353
96	0.67443
97	0.638577
98	0.602921
99	0.562986
100	0.520257