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aih-tih-sc-e08fa3-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-e08fa3-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:59 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-e08fa3-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-e08fa3-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 20:47:08 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
74452321102	73595029625	4316	67262446746	4510590012	1619945354	202043197	0	0	0	6864544	241037261	1235522	0.027691	0.972309	0	0.913954	0.061289	0.022012	0.002745	0.975243	0.964013	0	0.508515	0.57789	0.742335	0.89424			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.267599
1	0.310294
2	0.362979
3	0.42899
4	0.495094
5	0.559254
6	0.622878
7	0.682079
8	0.738409
9	0.792397
10	0.840173
11	0.883537
12	0.926884
13	0.9686
14	1.004796
15	1.030656
16	1.054667
17	1.0795
18	1.099755
19	1.115737
20	1.132374
21	1.147972
22	1.154046
23	1.164773
24	1.171796
25	1.175068
26	1.17954
27	1.180693
28	1.185652
29	1.187114
30	1.18397
31	1.182144
32	1.179555
33	1.178558
34	1.174706
35	1.179425
36	1.182559
37	1.178999
38	1.180976
39	1.18113
40	1.174241
41	1.176082
42	1.179499
43	1.179266
44	1.172905
45	1.180575
46	1.169872
47	1.165777
48	1.164061
49	1.160494
50	1.165391
51	1.156709
52	1.153691
53	1.161031
54	1.167835
55	1.170016
56	1.166538
57	1.163256
58	1.157051
59	1.143674
60	1.133538
61	1.128867
62	1.126889
63	1.124807
64	1.124012
65	1.117079
66	1.113279
67	1.106035
68	1.103603
69	1.096315
70	1.087038
71	1.073961
72	1.067717
73	1.064579
74	1.058134
75	1.048532
76	1.041234
77	1.031605
78	1.029271
79	1.021417
80	1.001171
81	0.987395
82	0.971999
83	0.953583
84	0.941252
85	0.922316
86	0.900478
87	0.884635
88	0.861134
89	0.84084
90	0.815589
91	0.792788
92	0.768942
93	0.740983
94	0.710738
95	0.679825
96	0.649439
97	0.617491
98	0.58311
99	0.548573
100	0.511725