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Filename
ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0011/B23LG7FLT4/nfcore_rnafusion__2cae617--20260515-145204/QC/picard/ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0011-2cae617
Published
May 16, 2026 1:54 AM

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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 ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT ColoN_FFPE_L06_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: Sat May 16 08:38:26 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
1873887217	1791474927	301650	1346102358	151619391	235315138	58136390	0	0	0	408256	6158453	56577	0.062171	0.937829	0.000168	0.751393	0.084634	0.131353	0.032452	0.836027	0.799259	0	0.898374	0.337879	0.39689	0.479552			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.31616
1	0.359503
2	0.431498
3	0.507597
4	0.579535
5	0.649564
6	0.694369
7	0.743487
8	0.79396
9	0.838848
10	0.875731
11	0.917833
12	0.954513
13	0.988751
14	1.023473
15	1.026473
16	1.034586
17	1.027728
18	1.019664
19	1.032745
20	1.050621
21	1.07422
22	1.083046
23	1.10568
24	1.119183
25	1.121403
26	1.130098
27	1.136207
28	1.145611
29	1.139222
30	1.144012
31	1.148845
32	1.147904
33	1.156961
34	1.147455
35	1.142568
36	1.136163
37	1.136985
38	1.135709
39	1.134354
40	1.131663
41	1.149003
42	1.150917
43	1.152159
44	1.150433
45	1.151847
46	1.133016
47	1.126222
48	1.130103
49	1.123643
50	1.110917
51	1.106396
52	1.105178
53	1.120391
54	1.139978
55	1.14316
56	1.143217
57	1.135918
58	1.120925
59	1.112433
60	1.104776
61	1.111447
62	1.109092
63	1.093018
64	1.090679
65	1.08881
66	1.094825
67	1.090883
68	1.095665
69	1.095131
70	1.084969
71	1.071837
72	1.075734
73	1.071022
74	1.072881
75	1.076975
76	1.069887
77	1.056882
78	1.049919
79	1.036988
80	1.024985
81	1.020569
82	1.016652
83	1.018585
84	1.023529
85	1.017181
86	0.996579
87	0.974321
88	0.950296
89	0.92375
90	0.892581
91	0.87738
92	0.833047
93	0.788951
94	0.755273
95	0.720964
96	0.683618
97	0.640674
98	0.591576
99	0.547672
100	0.560766