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Filename
FFPE_V4_0002_RNA_0002_A23YTGFLT4_1_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0021/A23YTGFLT4/nfcore_rnafusion__d2190e45--20260603-105009/QC/picard/FFPE_V4_0002_RNA_0002_A23YTGFLT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:34 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 FFPE_V4_0002_RNA_0002_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0002_RNA_0002_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 20:22:59 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
74993541745	74193265091	6070	64727053895	6687803564	2381432751	396968811	0	0	0	4873703	228493977	1303743	0.020884	0.979116	0	0.872411	0.09014	0.032098	0.00535	0.962552	0.95228	0	0.535428	0.570095	0.691461	0.863836			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.264469
1	0.303999
2	0.367704
3	0.435222
4	0.5049
5	0.575561
6	0.642785
7	0.705725
8	0.763187
9	0.81859
10	0.869474
11	0.920436
12	0.970605
13	1.014493
14	1.043253
15	1.068185
16	1.091005
17	1.10611
18	1.120294
19	1.139463
20	1.155316
21	1.170062
22	1.182428
23	1.193815
24	1.202459
25	1.209474
26	1.219602
27	1.219548
28	1.21655
29	1.212235
30	1.207317
31	1.205712
32	1.192219
33	1.192988
34	1.192258
35	1.189417
36	1.189724
37	1.18347
38	1.173422
39	1.171401
40	1.16455
41	1.163579
42	1.16614
43	1.16435
44	1.160347
45	1.168045
46	1.166506
47	1.162828
48	1.155786
49	1.154026
50	1.157156
51	1.152402
52	1.148894
53	1.146484
54	1.148668
55	1.14667
56	1.143145
57	1.138013
58	1.133277
59	1.13269
60	1.131082
61	1.129822
62	1.123371
63	1.113393
64	1.109128
65	1.105678
66	1.103404
67	1.100104
68	1.088546
69	1.076753
70	1.065712
71	1.055877
72	1.049744
73	1.040854
74	1.036623
75	1.028081
76	1.015604
77	0.997631
78	0.989201
79	0.981414
80	0.954053
81	0.931437
82	0.926056
83	0.915371
84	0.899891
85	0.888968
86	0.874013
87	0.868374
88	0.856919
89	0.837948
90	0.816011
91	0.793173
92	0.773403
93	0.750058
94	0.724935
95	0.694154
96	0.657952
97	0.623496
98	0.587595
99	0.548629
100	0.509348