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EndoN_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/EndoN_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 5:59 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 EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT EndoN_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 22:44:28 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
64910845571	63892087958	92536	56163808435	4294219526	2979145884	454821577	0	0	0	10368632	227062108	1250443	0.04367	0.95633	0.000001	0.879042	0.067211	0.046628	0.007119	0.946252	0.931401	0	0.716454	0.351894	0.581184	0.697881			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.30916
1	0.338627
2	0.390178
3	0.448595
4	0.494249
5	0.534246
6	0.582843
7	0.631933
8	0.686447
9	0.733298
10	0.761298
11	0.798775
12	0.843168
13	0.878009
14	0.907369
15	0.928813
16	0.943808
17	0.947281
18	0.954913
19	0.976276
20	0.993895
21	1.008001
22	1.032715
23	1.054063
24	1.069956
25	1.077948
26	1.079746
27	1.082807
28	1.098448
29	1.101155
30	1.092406
31	1.107853
32	1.115166
33	1.122504
34	1.117796
35	1.11892
36	1.123264
37	1.132696
38	1.147865
39	1.154807
40	1.161186
41	1.172986
42	1.178167
43	1.177765
44	1.173914
45	1.176972
46	1.162788
47	1.156648
48	1.15648
49	1.16807
50	1.188106
51	1.195451
52	1.194539
53	1.200893
54	1.204284
55	1.196766
56	1.201353
57	1.201753
58	1.19499
59	1.199378
60	1.212603
61	1.214855
62	1.210386
63	1.195051
64	1.185445
65	1.170177
66	1.157494
67	1.149095
68	1.146117
69	1.145371
70	1.133691
71	1.122615
72	1.113268
73	1.10811
74	1.114436
75	1.120154
76	1.130739
77	1.127094
78	1.109476
79	1.088353
80	1.069298
81	1.047609
82	1.034653
83	1.018695
84	1.010965
85	1.000016
86	0.990349
87	0.981013
88	0.96322
89	0.936964
90	0.904554
91	0.86652
92	0.828937
93	0.791587
94	0.759725
95	0.728755
96	0.689947
97	0.645369
98	0.598016
99	0.551414
100	0.505823