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SkinN_FFPE_L09_RNA_01_B23LG7FLT4_1_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/SkinN_FFPE_L09_RNA_01_B23LG7FLT4_1_rna_metrics.txt
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2.9 KB
Workflow Run
dev_rna_exp0008_exp0011-e7be3c7a_b
Published
May 28, 2026 6:01 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 SkinN_FFPE_L09_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT SkinN_FFPE_L09_RNA_01_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 23:35:01 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
60532185165	58908613975	7249492	48151988859	3618385435	4760779646	2370210543	0	0	0	13617951	193694209	1313859	0.065688	0.934312	0.000123	0.817401	0.061424	0.080816	0.040235	0.878825	0.855254	0	0.814759	0.348267	0.496042	0.77043			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.293902
1	0.327359
2	0.381457
3	0.430485
4	0.478551
5	0.537229
6	0.595841
7	0.640408
8	0.699311
9	0.747753
10	0.784931
11	0.827033
12	0.861844
13	0.895916
14	0.937087
15	0.963813
16	0.979303
17	0.991866
18	1.00871
19	1.028828
20	1.046504
21	1.071867
22	1.082505
23	1.092119
24	1.099776
25	1.111161
26	1.118654
27	1.136051
28	1.156695
29	1.154671
30	1.152708
31	1.157494
32	1.169022
33	1.187456
34	1.18336
35	1.17764
36	1.172967
37	1.174522
38	1.184127
39	1.177103
40	1.169001
41	1.190058
42	1.198713
43	1.197877
44	1.201682
45	1.215418
46	1.214393
47	1.216686
48	1.209167
49	1.199987
50	1.198535
51	1.196583
52	1.195534
53	1.19181
54	1.189726
55	1.178061
56	1.165141
57	1.15533
58	1.145952
59	1.144718
60	1.155558
61	1.158132
62	1.146913
63	1.134234
64	1.129244
65	1.130688
66	1.126603
67	1.115744
68	1.113194
69	1.114188
70	1.1161
71	1.106592
72	1.095276
73	1.088412
74	1.082905
75	1.072883
76	1.074092
77	1.06935
78	1.055346
79	1.040191
80	1.020553
81	1.007327
82	0.99805
83	0.991105
84	0.980479
85	0.97026
86	0.959837
87	0.95317
88	0.93785
89	0.921846
90	0.888661
91	0.854333
92	0.813307
93	0.77323
94	0.724596
95	0.687544
96	0.647911
97	0.612998
98	0.572917
99	0.527617
100	0.483995