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aih-tih-sc-eecf9f-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-eecf9f-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:34 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-eecf9f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-eecf9f-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 20:35:04 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
74037648398	72999954690	5215	67479631909	3852380408	1416163796	251773362	0	0	0	5137139	251016362	1205053	0.020055	0.979945	0	0.924379	0.052772	0.0194	0.003449	0.977151	0.963456	0	0.667744	0.511977	0.499856	0.948791			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.352004
1	0.399527
2	0.468129
3	0.536815
4	0.59169
5	0.645603
6	0.700304
7	0.753894
8	0.813617
9	0.873406
10	0.929456
11	0.98228
12	1.029698
13	1.073924
14	1.105067
15	1.120086
16	1.123792
17	1.138865
18	1.155486
19	1.16936
20	1.188336
21	1.202692
22	1.220616
23	1.232877
24	1.249921
25	1.260707
26	1.264292
27	1.265455
28	1.266529
29	1.262285
30	1.256169
31	1.251829
32	1.240336
33	1.246509
34	1.242023
35	1.241572
36	1.238435
37	1.228782
38	1.218329
39	1.202573
40	1.197739
41	1.194361
42	1.199871
43	1.208459
44	1.206839
45	1.206497
46	1.189183
47	1.176552
48	1.162481
49	1.153501
50	1.149795
51	1.143763
52	1.13935
53	1.135744
54	1.130563
55	1.122039
56	1.116629
57	1.0993
58	1.087801
59	1.076362
60	1.072738
61	1.076179
62	1.076885
63	1.056698
64	1.05383
65	1.049165
66	1.037031
67	1.031137
68	1.029697
69	1.022474
70	1.010853
71	0.997497
72	0.993719
73	0.989204
74	0.979511
75	0.967641
76	0.964634
77	0.961152
78	0.953065
79	0.936139
80	0.92603
81	0.90969
82	0.893971
83	0.882008
84	0.871345
85	0.847522
86	0.815508
87	0.800854
88	0.785118
89	0.764512
90	0.743229
91	0.728177
92	0.700218
93	0.674232
94	0.653338
95	0.631455
96	0.608073
97	0.581693
98	0.550471
99	0.52435
100	0.492181