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A673_FFPE_RNA_0001_B23LG7FLT4_1_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/A673_FFPE_RNA_0001_B23LG7FLT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0008_exp0011-e7be3c7a_b
Published
May 28, 2026 6:25 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 A673_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT A673_FFPE_RNA_0001_B23LG7FLT4_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: Thu May 28 22:28:57 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
75073905894	74237085342	49845	64761235662	5038798762	3849276793	587724280	0	0	0	4832977	232742082	1430561	0.020343	0.979657	0.000001	0.872357	0.067874	0.051851	0.007917	0.940231	0.929751	0	0.516854	0.57091	0.72931	0.870973			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.262125
1	0.301291
2	0.356363
3	0.42178
4	0.495339
5	0.561599
6	0.62714
7	0.69178
8	0.75248
9	0.806833
10	0.856988
11	0.902247
12	0.948204
13	0.988273
14	1.023745
15	1.04818
16	1.080165
17	1.104602
18	1.11208
19	1.123638
20	1.137124
21	1.153915
22	1.163711
23	1.178192
24	1.181736
25	1.185196
26	1.186423
27	1.19107
28	1.18789
29	1.180754
30	1.171454
31	1.163209
32	1.166676
33	1.161096
34	1.15475
35	1.154334
36	1.15231
37	1.144389
38	1.143947
39	1.147476
40	1.148759
41	1.151248
42	1.15712
43	1.158835
44	1.153968
45	1.147495
46	1.133067
47	1.127708
48	1.12871
49	1.132537
50	1.137754
51	1.132902
52	1.139248
53	1.141702
54	1.146108
55	1.146206
56	1.139775
57	1.139578
58	1.140878
59	1.138575
60	1.134617
61	1.135616
62	1.134231
63	1.127473
64	1.123839
65	1.116093
66	1.109961
67	1.106998
68	1.106669
69	1.10794
70	1.096912
71	1.087741
72	1.080597
73	1.071814
74	1.069493
75	1.063914
76	1.051868
77	1.039428
78	1.03395
79	1.027326
80	1.017999
81	1.006475
82	0.993429
83	0.967384
84	0.951921
85	0.941193
86	0.927203
87	0.910577
88	0.890361
89	0.868394
90	0.845863
91	0.820432
92	0.792351
93	0.760633
94	0.721403
95	0.692715
96	0.659615
97	0.622294
98	0.581534
99	0.53969
100	0.497697