## 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_43.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_43_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 17:59:56 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
24694149901	24412351155	16310	21222103777	1973779328	1081462161	134989579	0	0	0	1222885	78302780	312945	0.015377	0.984623	0.000001	0.869318	0.080852	0.0443	0.00553	0.95017	0.939327	0	0.522528	0.564258	0.762056	0.829108			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.269319
1	0.308197
2	0.363423
3	0.425365
4	0.490858
5	0.557597
6	0.620837
7	0.681265
8	0.736772
9	0.788549
10	0.831336
11	0.879865
12	0.931384
13	0.971004
14	1.001613
15	1.026425
16	1.05155
17	1.069041
18	1.085592
19	1.098703
20	1.108496
21	1.124932
22	1.139148
23	1.148538
24	1.157325
25	1.159569
26	1.166198
27	1.172482
28	1.175786
29	1.172324
30	1.167334
31	1.164172
32	1.152756
33	1.152334
34	1.148221
35	1.149623
36	1.15101
37	1.143336
38	1.134994
39	1.133437
40	1.129659
41	1.128907
42	1.130786
43	1.135739
44	1.133731
45	1.141916
46	1.144323
47	1.14502
48	1.146576
49	1.155612
50	1.16281
51	1.161967
52	1.160376
53	1.159802
54	1.160196
55	1.161891
56	1.160321
57	1.158534
58	1.153925
59	1.148833
60	1.14745
61	1.148377
62	1.145776
63	1.140737
64	1.138175
65	1.139337
66	1.135856
67	1.129051
68	1.119398
69	1.11228
70	1.102602
71	1.096887
72	1.095149
73	1.087419
74	1.08169
75	1.075385
76	1.062756
77	1.043912
78	1.035701
79	1.022089
80	1.003984
81	0.984661
82	0.977087
83	0.964971
84	0.952782
85	0.947358
86	0.933679
87	0.916176
88	0.893252
89	0.873966
90	0.853489
91	0.829919
92	0.807688
93	0.779233
94	0.749882
95	0.717321
96	0.682456
97	0.646106
98	0.608334
99	0.56698
100	0.522478