## 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_34.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_34_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 18:00:04 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
25341940272	25054976028	14190	21861905447	2028604637	1031288090	133163664	0	0	0	1425137	78274252	346594	0.017881	0.982119	0.000001	0.872557	0.080966	0.041161	0.005315	0.953524	0.942726	0	0.502471	0.562602	0.768224	0.845299			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.261707
1	0.300897
2	0.35916
3	0.425166
4	0.492654
5	0.558933
6	0.619893
7	0.677749
8	0.731976
9	0.785482
10	0.829885
11	0.87528
12	0.926396
13	0.969801
14	1.000244
15	1.027491
16	1.053655
17	1.071311
18	1.090375
19	1.106783
20	1.118418
21	1.133888
22	1.147107
23	1.156816
24	1.162339
25	1.165261
26	1.169312
27	1.176182
28	1.177455
29	1.174222
30	1.168763
31	1.165971
32	1.154302
33	1.152852
34	1.149655
35	1.147483
36	1.147824
37	1.139861
38	1.133335
39	1.136358
40	1.133537
41	1.133046
42	1.136645
43	1.139773
44	1.139809
45	1.150075
46	1.14987
47	1.150363
48	1.149162
49	1.155017
50	1.163374
51	1.16304
52	1.161283
53	1.160461
54	1.160489
55	1.162719
56	1.1591
57	1.158359
58	1.156594
59	1.148227
60	1.14388
61	1.146291
62	1.143785
63	1.138948
64	1.137567
65	1.137911
66	1.136907
67	1.131645
68	1.123189
69	1.114576
70	1.103744
71	1.097584
72	1.092943
73	1.083375
74	1.078661
75	1.07152
76	1.059123
77	1.039095
78	1.032137
79	1.024244
80	1.007515
81	0.98908
82	0.980429
83	0.965119
84	0.951028
85	0.944946
86	0.933106
87	0.914946
88	0.890241
89	0.871114
90	0.852536
91	0.827896
92	0.804257
93	0.774541
94	0.740543
95	0.706941
96	0.673707
97	0.638676
98	0.601605
99	0.561829
100	0.515635