## 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_19.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_19_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
25227920886	24928632471	12376	21638908959	2057119920	1089190371	143400845	0	0	0	2005620	77518873	320337	0.02522	0.97478	0	0.868034	0.08252	0.043692	0.005752	0.950555	0.939278	0	0.514687	0.578613	0.765575	0.843871			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.277899
1	0.317093
2	0.374938
3	0.437986
4	0.504585
5	0.571985
6	0.636876
7	0.69801
8	0.751963
9	0.803094
10	0.847264
11	0.892873
12	0.941823
13	0.980202
14	1.008591
15	1.034616
16	1.060427
17	1.078036
18	1.09056
19	1.105073
20	1.119092
21	1.135339
22	1.145181
23	1.154423
24	1.163959
25	1.167119
26	1.172614
27	1.17849
28	1.180739
29	1.179948
30	1.176608
31	1.175061
32	1.164742
33	1.162844
34	1.156877
35	1.156409
36	1.157404
37	1.149125
38	1.140671
39	1.139041
40	1.133614
41	1.133582
42	1.138309
43	1.140517
44	1.137128
45	1.145841
46	1.145623
47	1.146886
48	1.145315
49	1.151354
50	1.15735
51	1.153329
52	1.149489
53	1.147567
54	1.147828
55	1.147425
56	1.14416
57	1.141913
58	1.137349
59	1.130395
60	1.128783
61	1.132836
62	1.129102
63	1.124444
64	1.122863
65	1.125177
66	1.125448
67	1.121694
68	1.114045
69	1.107744
70	1.097176
71	1.089005
72	1.086617
73	1.076254
74	1.067765
75	1.061337
76	1.050286
77	1.033584
78	1.027984
79	1.018505
80	1.000776
81	0.98028
82	0.97195
83	0.959222
84	0.947043
85	0.940723
86	0.925592
87	0.908402
88	0.887949
89	0.868727
90	0.850103
91	0.82731
92	0.80458
93	0.778323
94	0.750454
95	0.719467
96	0.685347
97	0.648727
98	0.611911
99	0.570851
100	0.524675