## 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_00166_23KMKGLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00166_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 23:38:09 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
24358289193	23982202708	12470	21337945523	1595385913	933932723	114926079	0	0	0	1406020	77275802	273708	0.01787	0.98213	0.000001	0.889741	0.066524	0.038943	0.004792	0.956265	0.9415	0	0.60136	0.518327	0.672277	0.909853			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.291264
1	0.331069
2	0.386755
3	0.45328
4	0.511931
5	0.563326
6	0.626617
7	0.688812
8	0.7484
9	0.806829
10	0.862584
11	0.915181
12	0.964698
13	1.007564
14	1.044022
15	1.073592
16	1.094493
17	1.115838
18	1.121935
19	1.127307
20	1.142782
21	1.160413
22	1.185594
23	1.20325
24	1.211281
25	1.209211
26	1.205506
27	1.207794
28	1.218678
29	1.215745
30	1.214091
31	1.206893
32	1.202218
33	1.196131
34	1.186868
35	1.186112
36	1.184572
37	1.176017
38	1.1642
39	1.154239
40	1.146145
41	1.145138
42	1.148984
43	1.146722
44	1.143243
45	1.149071
46	1.147449
47	1.149952
48	1.158563
49	1.161394
50	1.161505
51	1.16072
52	1.158265
53	1.155319
54	1.157011
55	1.154285
56	1.151385
57	1.148365
58	1.141776
59	1.132429
60	1.128873
61	1.124277
62	1.123894
63	1.1137
64	1.104044
65	1.100871
66	1.098207
67	1.092911
68	1.086263
69	1.078196
70	1.068733
71	1.056273
72	1.051093
73	1.041919
74	1.027992
75	1.017852
76	1.007054
77	1.001805
78	0.998158
79	0.994093
80	0.985714
81	0.971035
82	0.956185
83	0.942222
84	0.924859
85	0.912299
86	0.892258
87	0.879474
88	0.859935
89	0.840151
90	0.818944
91	0.78792
92	0.764418
93	0.736729
94	0.706025
95	0.678479
96	0.649126
97	0.620117
98	0.58457
99	0.547431
100	0.505594