## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT tih_rna_sample_00157_23KMKGLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00157_23KMKGLT4_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: Wed Mar 04 23:42:18 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
24329509470	23973944513	12408	21229473299	1662006826	976121667	106330313	0	0	0	1686947	78346549	256119	0.021078	0.978922	0.000001	0.885523	0.069326	0.040716	0.004435	0.954848	0.940894	0	0.550463	0.559691	0.745135	0.860623			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.263506
1	0.301501
2	0.354994
3	0.421587
4	0.492442
5	0.566526
6	0.63179
7	0.688762
8	0.743725
9	0.790617
10	0.837401
11	0.885124
12	0.933997
13	0.970848
14	1.003096
15	1.028615
16	1.055937
17	1.07914
18	1.096268
19	1.11388
20	1.123401
21	1.142373
22	1.155509
23	1.173259
24	1.180826
25	1.182731
26	1.185907
27	1.185227
28	1.186062
29	1.185272
30	1.183864
31	1.179601
32	1.174005
33	1.167035
34	1.162693
35	1.159487
36	1.155352
37	1.147494
38	1.139765
39	1.135528
40	1.134705
41	1.132915
42	1.131154
43	1.132647
44	1.135005
45	1.142201
46	1.136192
47	1.131101
48	1.133333
49	1.139868
50	1.140186
51	1.13712
52	1.131207
53	1.134794
54	1.142605
55	1.142479
56	1.1433
57	1.144409
58	1.140142
59	1.130013
60	1.123981
61	1.12701
62	1.131787
63	1.127938
64	1.128382
65	1.1288
66	1.122539
67	1.11265
68	1.112225
69	1.10885
70	1.095256
71	1.091058
72	1.088043
73	1.081886
74	1.081182
75	1.081777
76	1.070858
77	1.055108
78	1.050529
79	1.039355
80	1.022977
81	1.003718
82	0.992182
83	0.973198
84	0.962606
85	0.95642
86	0.936735
87	0.918721
88	0.896805
89	0.880017
90	0.85853
91	0.830168
92	0.803202
93	0.77212
94	0.736471
95	0.69879
96	0.666964
97	0.63326
98	0.592662
99	0.550609
100	0.504993