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aih-tih-sc-96d0f6-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-96d0f6-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:54 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-96d0f6-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-96d0f6-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 20:42:59 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
70166807455	69345558730	5508	62621679006	4803708472	1704879830	215285914	0	0	0	5676833	243975396	1049689	0.022739	0.977261	0	0.903038	0.069272	0.024585	0.003105	0.97231	0.96093	0	0.54704	0.495882	0.725092	0.788557			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.279072
1	0.309991
2	0.357791
3	0.415464
4	0.466857
5	0.514662
6	0.579704
7	0.634341
8	0.693062
9	0.74461
10	0.791972
11	0.843608
12	0.892739
13	0.933672
14	0.96696
15	0.99456
16	1.024803
17	1.051889
18	1.068872
19	1.086323
20	1.104138
21	1.121831
22	1.138272
23	1.149184
24	1.154585
25	1.159427
26	1.164585
27	1.16587
28	1.173717
29	1.178211
30	1.182489
31	1.18703
32	1.178368
33	1.178426
34	1.177939
35	1.18171
36	1.179359
37	1.182323
38	1.184382
39	1.177744
40	1.172162
41	1.169216
42	1.175246
43	1.181329
44	1.171977
45	1.180157
46	1.182877
47	1.180716
48	1.179092
49	1.18183
50	1.185436
51	1.181592
52	1.175627
53	1.171074
54	1.168841
55	1.16807
56	1.159001
57	1.153527
58	1.144244
59	1.129875
60	1.125378
61	1.126358
62	1.13128
63	1.131275
64	1.129922
65	1.128246
66	1.121079
67	1.113835
68	1.107792
69	1.103333
70	1.093554
71	1.085149
72	1.081611
73	1.07787
74	1.069153
75	1.055508
76	1.046374
77	1.038713
78	1.034596
79	1.024546
80	1.010281
81	0.995795
82	0.983739
83	0.967263
84	0.960437
85	0.948332
86	0.926872
87	0.917982
88	0.901089
89	0.880626
90	0.855675
91	0.831111
92	0.804989
93	0.777536
94	0.745421
95	0.712413
96	0.678784
97	0.644449
98	0.606627
99	0.571405
100	0.536888