## 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_0001_23KMKGLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0001_23KMKGLT4_1_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: Thu Mar 05 00:14:38 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
26056583885	25761725305	13356	22383179056	2237452068	988673135	152407690	0	0	0	4005396	75565956	379903	0.050337	0.949663	0.000001	0.868854	0.086852	0.038378	0.005916	0.955706	0.944891	0	0.537661	0.603524	0.70804	0.908441			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.26446
1	0.308022
2	0.382655
3	0.459142
4	0.532383
5	0.603819
6	0.678321
7	0.749704
8	0.811561
9	0.869181
10	0.913945
11	0.963187
12	1.008206
13	1.051132
14	1.081468
15	1.107167
16	1.131293
17	1.146798
18	1.164914
19	1.182059
20	1.198676
21	1.212223
22	1.228037
23	1.23811
24	1.246504
25	1.248948
26	1.256857
27	1.263371
28	1.263088
29	1.260078
30	1.249515
31	1.239517
32	1.219193
33	1.211707
34	1.20191
35	1.194952
36	1.189226
37	1.172876
38	1.157494
39	1.153789
40	1.146473
41	1.14104
42	1.143842
43	1.143888
44	1.138774
45	1.146285
46	1.145812
47	1.144391
48	1.138616
49	1.139246
50	1.143682
51	1.144738
52	1.140686
53	1.136675
54	1.136935
55	1.136115
56	1.134692
57	1.129509
58	1.121363
59	1.109078
60	1.105395
61	1.104102
62	1.098576
63	1.089827
64	1.086288
65	1.08466
66	1.083178
67	1.079117
68	1.068098
69	1.054418
70	1.046629
71	1.034727
72	1.029264
73	1.016354
74	1.007003
75	0.996755
76	0.983018
77	0.965793
78	0.961249
79	0.958947
80	0.935537
81	0.913832
82	0.902624
83	0.887859
84	0.874616
85	0.86713
86	0.851654
87	0.844223
88	0.832488
89	0.811153
90	0.792395
91	0.765766
92	0.74383
93	0.721744
94	0.69927
95	0.674844
96	0.648453
97	0.617514
98	0.581657
99	0.546763
100	0.509885