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U118MG_FFPE_RNA_0001_B23LG7FLT4_3_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0008_exp0011/B23LG7FLT4/nfcore_rnafusion__e7be3c7a--20260528-111100/QC/picard/U118MG_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 5:10 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 U118MG_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam --OUTPUT U118MG_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 21:28:54 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
75950584146	75034671496	40858	67026170969	4682201275	2854676242	471582152	0	0	0	6044080	235298213	1430493	0.025044	0.974956	0.000001	0.893269	0.062401	0.038045	0.006285	0.95567	0.944145	0	0.503627	0.619251	0.731669	0.973209			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.320534
1	0.363183
2	0.418348
3	0.487379
4	0.548037
5	0.607746
6	0.674132
7	0.737447
8	0.793459
9	0.852395
10	0.899537
11	0.948746
12	0.995101
13	1.033465
14	1.065958
15	1.100358
16	1.126982
17	1.140089
18	1.146208
19	1.150115
20	1.167129
21	1.186693
22	1.195265
23	1.208936
24	1.211672
25	1.213698
26	1.213906
27	1.209211
28	1.203974
29	1.193432
30	1.189854
31	1.185067
32	1.179542
33	1.181192
34	1.174609
35	1.176198
36	1.173534
37	1.166942
38	1.168696
39	1.16762
40	1.166423
41	1.166047
42	1.162518
43	1.162185
44	1.156251
45	1.156429
46	1.155388
47	1.153598
48	1.151338
49	1.152239
50	1.15122
51	1.155977
52	1.152356
53	1.149902
54	1.150534
55	1.151786
56	1.145931
57	1.141463
58	1.133873
59	1.118735
60	1.10753
61	1.10342
62	1.105404
63	1.103136
64	1.092278
65	1.084913
66	1.083089
67	1.074832
68	1.067629
69	1.061441
70	1.052733
71	1.041305
72	1.036699
73	1.022968
74	1.008703
75	1.001213
76	0.993402
77	0.976537
78	0.96793
79	0.959159
80	0.944568
81	0.930979
82	0.920624
83	0.901878
84	0.891242
85	0.881854
86	0.867644
87	0.852884
88	0.837132
89	0.820898
90	0.806532
91	0.781118
92	0.756467
93	0.731579
94	0.703027
95	0.679956
96	0.658294
97	0.632318
98	0.608365
99	0.581036
100	0.549536