## 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_1.Aligned.sortedByCoord.out.bam --OUTPUT U118MG_FFPE_RNA_0001_B23LG7FLT4_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: Fri Feb 27 07:06:52 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
25468215089	25137248648	13362	22459047204	1584715497	932542432	160930153	0	0	0	3940646	76438008	491787	0.049026	0.950974	0.000001	0.893457	0.063043	0.037098	0.006402	0.956499	0.944069	0	0.503006	0.619999	0.735341	0.978561			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.320064
1	0.364362
2	0.418753
3	0.486488
4	0.545792
5	0.603364
6	0.668934
7	0.733207
8	0.788948
9	0.848883
10	0.897327
11	0.94783
12	0.992961
13	1.02837
14	1.060659
15	1.098036
16	1.12741
17	1.142807
18	1.151863
19	1.154782
20	1.17287
21	1.19165
22	1.199085
23	1.213012
24	1.214932
25	1.213766
26	1.214812
27	1.211454
28	1.207424
29	1.198527
30	1.195202
31	1.193091
32	1.186796
33	1.189243
34	1.183388
35	1.185713
36	1.18202
37	1.175482
38	1.174517
39	1.171804
40	1.172635
41	1.171844
42	1.170939
43	1.169409
44	1.163846
45	1.162902
46	1.1606
47	1.159324
48	1.157444
49	1.159347
50	1.156937
51	1.159066
52	1.153748
53	1.152325
54	1.153984
55	1.15475
56	1.14864
57	1.143724
58	1.134615
59	1.123164
60	1.111655
61	1.106828
62	1.104369
63	1.100493
64	1.090729
65	1.082377
66	1.076315
67	1.064905
68	1.058461
69	1.052581
70	1.043785
71	1.033972
72	1.031721
73	1.01844
74	1.002814
75	0.993554
76	0.984146
77	0.961213
78	0.953011
79	0.945535
80	0.933701
81	0.920651
82	0.910449
83	0.893383
84	0.884458
85	0.876095
86	0.860393
87	0.843527
88	0.828438
89	0.81216
90	0.800168
91	0.77951
92	0.757135
93	0.734876
94	0.711716
95	0.688382
96	0.666536
97	0.638597
98	0.613997
99	0.586454
100	0.551591