## 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_8.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_8_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 18:00:12 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
24487986920	24181920661	16254	20909042942	2004021113	1124049985	144790367	0	0	0	4814806	74531377	318038	0.060681	0.939319	0.000001	0.864656	0.082873	0.046483	0.005988	0.947529	0.935686	0	0.535546	0.56092	0.751884	0.826859			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.285061
1	0.320828
2	0.374056
3	0.434534
4	0.499406
5	0.564223
6	0.627569
7	0.68854
8	0.741464
9	0.792411
10	0.838772
11	0.888044
12	0.936283
13	0.976448
14	1.003265
15	1.027436
16	1.052609
17	1.070436
18	1.079413
19	1.095281
20	1.108126
21	1.123922
22	1.140001
23	1.1569
24	1.162886
25	1.165714
26	1.171477
27	1.178737
28	1.186885
29	1.188764
30	1.184849
31	1.185194
32	1.176706
33	1.17508
34	1.171352
35	1.170649
36	1.169794
37	1.16107
38	1.150854
39	1.143873
40	1.134871
41	1.1305
42	1.13316
43	1.1356
44	1.130552
45	1.137244
46	1.134082
47	1.129912
48	1.131289
49	1.136409
50	1.138583
51	1.134307
52	1.13373
53	1.136085
54	1.141595
55	1.145283
56	1.145918
57	1.145342
58	1.144624
59	1.141287
60	1.139718
61	1.145065
62	1.144196
63	1.138242
64	1.135378
65	1.135576
66	1.128922
67	1.122333
68	1.113793
69	1.107179
70	1.095417
71	1.08765
72	1.086505
73	1.07537
74	1.067239
75	1.060517
76	1.049654
77	1.031909
78	1.025266
79	1.015308
80	0.999625
81	0.984015
82	0.97639
83	0.961452
84	0.950362
85	0.945543
86	0.932564
87	0.915359
88	0.896478
89	0.878844
90	0.856088
91	0.833936
92	0.812213
93	0.786069
94	0.754598
95	0.721884
96	0.68523
97	0.648499
98	0.612898
99	0.574522
100	0.530712