## 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_42.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_42_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 17:59:54 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
25097340316	24810676087	14142	21666385681	2007020030	1005280030	131976204	0	0	0	1131846	78573369	342379	0.0142	0.9858	0.000001	0.873269	0.080893	0.040518	0.005319	0.954162	0.943264	0	0.514239	0.559989	0.761969	0.823531			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.269639
1	0.307991
2	0.364435
3	0.429336
4	0.49766
5	0.564622
6	0.626455
7	0.686077
8	0.74224
9	0.795916
10	0.84175
11	0.892121
12	0.945699
13	0.986935
14	1.017585
15	1.043558
16	1.059291
17	1.071999
18	1.08481
19	1.099048
20	1.109357
21	1.128422
22	1.140445
23	1.152568
24	1.162303
25	1.165221
26	1.171129
27	1.177534
28	1.179141
29	1.175384
30	1.169421
31	1.167265
32	1.155617
33	1.152797
34	1.147737
35	1.146227
36	1.147614
37	1.140086
38	1.133021
39	1.132004
40	1.127661
41	1.126799
42	1.13119
43	1.134228
44	1.135767
45	1.145445
46	1.146732
47	1.147703
48	1.147152
49	1.154033
50	1.16217
51	1.16351
52	1.161357
53	1.161385
54	1.162549
55	1.16389
56	1.160377
57	1.160466
58	1.157982
59	1.150252
60	1.14519
61	1.144184
62	1.14148
63	1.136899
64	1.135249
65	1.137128
66	1.133856
67	1.129426
68	1.121547
69	1.114537
70	1.10516
71	1.099648
72	1.095795
73	1.085734
74	1.077186
75	1.069813
76	1.056957
77	1.038095
78	1.031082
79	1.020418
80	1.002662
81	0.981551
82	0.972473
83	0.958709
84	0.9452
85	0.938073
86	0.923634
87	0.906608
88	0.882158
89	0.862204
90	0.843493
91	0.821932
92	0.800393
93	0.773292
94	0.741772
95	0.707471
96	0.673634
97	0.639735
98	0.603395
99	0.563645
100	0.518438