## 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_25.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_25_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 17:59:38 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
25332132072	25047683973	13054	22023797379	2008654031	886749053	128470456	0	0	0	1573536	78452494	335961	0.019663	0.980337	0.000001	0.879275	0.080193	0.035402	0.005129	0.959468	0.948694	0	0.515606	0.579707	0.736452	0.893054			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.268195
1	0.308258
2	0.369509
3	0.437091
4	0.506341
5	0.576077
6	0.639995
7	0.701337
8	0.756246
9	0.811048
10	0.856592
11	0.901998
12	0.952308
13	1.000443
14	1.035152
15	1.063584
16	1.089769
17	1.105091
18	1.117663
19	1.134243
20	1.146631
21	1.164539
22	1.17382
23	1.183231
24	1.18903
25	1.19087
26	1.197013
27	1.203363
28	1.203417
29	1.195244
30	1.187651
31	1.181245
32	1.168309
33	1.164037
34	1.157904
35	1.155244
36	1.152812
37	1.146509
38	1.139408
39	1.140253
40	1.137003
41	1.137353
42	1.139554
43	1.143388
44	1.141085
45	1.150171
46	1.150364
47	1.149119
48	1.146649
49	1.152971
50	1.159797
51	1.161145
52	1.161374
53	1.159876
54	1.160274
55	1.159598
56	1.153469
57	1.150888
58	1.147456
59	1.138487
60	1.132618
61	1.134817
62	1.134656
63	1.126631
64	1.119491
65	1.116918
66	1.113887
67	1.11028
68	1.101917
69	1.091112
70	1.084557
71	1.077253
72	1.071106
73	1.060847
74	1.052832
75	1.04698
76	1.035447
77	1.015339
78	1.00811
79	1.001618
80	0.984141
81	0.967282
82	0.959896
83	0.942822
84	0.929565
85	0.922412
86	0.910157
87	0.891761
88	0.868773
89	0.84713
90	0.830411
91	0.807436
92	0.785965
93	0.758512
94	0.723965
95	0.690093
96	0.657561
97	0.62393
98	0.589082
99	0.551182
100	0.507316