## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT U118MG_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam --OUTPUT U118MG_FFPE_RNA_0001_B23LG7FLT4_3_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: Fri Feb 27 07:06:09 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
25318608506	25002969966	11440	22333503691	1561639789	951741643	156073403	0	0	0	2015266	78379102	491090	0.025067	0.974933	0	0.893234	0.062458	0.038065	0.006242	0.955692	0.943778	0	0.502844	0.618884	0.740758	0.973814			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.321514
1	0.365031
2	0.420761
3	0.488574
4	0.548612
5	0.607177
6	0.671907
7	0.734991
8	0.791354
9	0.850589
10	0.899077
11	0.948822
12	0.994233
13	1.033858
14	1.067325
15	1.102185
16	1.130707
17	1.143909
18	1.1503
19	1.153967
20	1.168677
21	1.187835
22	1.195544
23	1.210082
24	1.211016
25	1.212355
26	1.212732
27	1.206637
28	1.200222
29	1.188973
30	1.18515
31	1.180954
32	1.176781
33	1.179105
34	1.17301
35	1.174331
36	1.16984
37	1.164249
38	1.164788
39	1.164784
40	1.165119
41	1.166223
42	1.163392
43	1.163369
44	1.159247
45	1.158913
46	1.158527
47	1.156061
48	1.152123
49	1.154099
50	1.152989
51	1.157164
52	1.154535
53	1.151476
54	1.154733
55	1.155815
56	1.14873
57	1.142673
58	1.135632
59	1.119973
60	1.107706
61	1.102896
62	1.104135
63	1.102082
64	1.092219
65	1.08496
66	1.080868
67	1.069785
68	1.062151
69	1.056343
70	1.04888
71	1.038734
72	1.035819
73	1.022121
74	1.007831
75	0.999813
76	0.99094
77	0.973712
78	0.96531
79	0.956284
80	0.944088
81	0.931972
82	0.92185
83	0.903961
84	0.89301
85	0.88454
86	0.869642
87	0.854389
88	0.838026
89	0.821892
90	0.807174
91	0.780879
92	0.75724
93	0.732814
94	0.705902
95	0.682748
96	0.660938
97	0.633734
98	0.609597
99	0.582778
100	0.550841