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aih-tih-sc-da06ce-R1_A23YTGFLT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0021/A23YTGFLT4/nfcore_rnafusion__d2190e45--20260603-105009/QC/picard/aih-tih-sc-da06ce-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 4:11 PM

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## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT aih-tih-sc-da06ce-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-da06ce-R1_A23YTGFLT4_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 Jun 03 20:58:54 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
74693009773	73598652817	2938	66105101342	4897980956	2244676617	350890964	0	0	0	18233558	232668084	1282797	0.072672	0.927328	0	0.898184	0.06655	0.030499	0.004768	0.964733	0.950599	0	0.645577	0.577132	0.563869	1.111426			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.360914
1	0.404187
2	0.468974
3	0.541829
4	0.610996
5	0.666408
6	0.727796
7	0.781991
8	0.836292
9	0.88685
10	0.939498
11	0.996505
12	1.046013
13	1.090419
14	1.116996
15	1.145575
16	1.160141
17	1.177079
18	1.191919
19	1.201366
20	1.203394
21	1.214665
22	1.23043
23	1.238324
24	1.246894
25	1.252454
26	1.253789
27	1.250801
28	1.24049
29	1.241905
30	1.239035
31	1.232595
32	1.225256
33	1.215764
34	1.205114
35	1.20714
36	1.20774
37	1.201453
38	1.186547
39	1.171679
40	1.171075
41	1.165218
42	1.163852
43	1.165745
44	1.162944
45	1.164894
46	1.155058
47	1.153502
48	1.144973
49	1.142955
50	1.136712
51	1.137391
52	1.135139
53	1.138531
54	1.136388
55	1.124053
56	1.104349
57	1.085275
58	1.068861
59	1.059997
60	1.05876
61	1.069427
62	1.071031
63	1.058844
64	1.05735
65	1.057441
66	1.058519
67	1.062932
68	1.062714
69	1.053293
70	1.039044
71	1.026872
72	1.020097
73	1.014344
74	1.004536
75	0.995181
76	0.980362
77	0.962393
78	0.945873
79	0.936288
80	0.925565
81	0.914224
82	0.904084
83	0.889304
84	0.872702
85	0.85853
86	0.833364
87	0.814007
88	0.792968
89	0.770107
90	0.748242
91	0.726909
92	0.702045
93	0.67593
94	0.645031
95	0.62146
96	0.599452
97	0.574185
98	0.542515
99	0.518061
100	0.488337