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NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0008_exp0011/B23LG7FLT4/nfcore_rnafusion__e7be3c7a--20260528-111100/QC/picard/NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3_rna_metrics.txt
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2.9 KB
Workflow Run
dev_rna_exp0008_exp0011-e7be3c7a_b
Published
May 28, 2026 6:09 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 NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam --OUTPUT NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3_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: Thu May 28 22:48:56 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
73313962819	72484022515	43706	64374786940	4696329490	2997690758	415171621	0	0	0	3188145	235884320	1423524	0.013335	0.986665	0.000001	0.888124	0.064791	0.041357	0.005728	0.952915	0.942128	0	0.537139	0.554605	0.76717	0.857342			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.261638
1	0.301166
2	0.353124
3	0.412815
4	0.474807
5	0.540675
6	0.607173
7	0.667497
8	0.725217
9	0.776869
10	0.827732
11	0.880753
12	0.92987
13	0.967166
14	0.994405
15	1.022197
16	1.055691
17	1.078748
18	1.087855
19	1.10766
20	1.122499
21	1.13339
22	1.142496
23	1.154933
24	1.157164
25	1.154909
26	1.161497
27	1.171606
28	1.18405
29	1.181742
30	1.174367
31	1.167749
32	1.169506
33	1.168378
34	1.163783
35	1.155917
36	1.154366
37	1.146368
38	1.141532
39	1.142677
40	1.148227
41	1.152581
42	1.159789
43	1.164407
44	1.163619
45	1.169711
46	1.164506
47	1.159082
48	1.154331
49	1.165807
50	1.173694
51	1.174615
52	1.168744
53	1.161235
54	1.162948
55	1.149828
56	1.146207
57	1.142857
58	1.13984
59	1.135737
60	1.13008
61	1.137785
62	1.145126
63	1.138896
64	1.128953
65	1.124984
66	1.117353
67	1.109633
68	1.096622
69	1.087291
70	1.072026
71	1.065948
72	1.06091
73	1.050626
74	1.049037
75	1.047411
76	1.042748
77	1.034455
78	1.032265
79	1.028471
80	1.016537
81	1.002346
82	0.993667
83	0.979261
84	0.963079
85	0.951946
86	0.935401
87	0.922731
88	0.905593
89	0.887358
90	0.864436
91	0.839285
92	0.81197
93	0.782747
94	0.7497
95	0.71531
96	0.683237
97	0.651602
98	0.615187
99	0.577101
100	0.53384