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Hs746T_FFPE_RNA_0001_B23LG7FLT4_2_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0008/B23LG7FLT4/nfcore_rnafusion_100M__1bb6229e--20260226-142939/QC/picard/Hs746T_FFPE_RNA_0001_B23LG7FLT4_2_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0008_1bb6229e
Published
Feb 26, 2026 11:22 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 Hs746T_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT Hs746T_FFPE_RNA_0001_B23LG7FLT4_2_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: Fri Feb 27 06:42:56 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
24930523616	24472772517	22680	21567898279	1651453337	1111688697	141709524	0	0	0	2881305	76579524	480926	0.036261	0.963739	0.000001	0.881302	0.067481	0.045426	0.00579	0.948783	0.931362	0	0.513117	0.587274	0.751056	0.897902			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.285291
1	0.323926
2	0.370533
3	0.429249
4	0.50079
5	0.570818
6	0.629542
7	0.689147
8	0.746691
9	0.79851
10	0.850025
11	0.902508
12	0.948464
13	0.98968
14	1.024382
15	1.058862
16	1.074695
17	1.09689
18	1.109336
19	1.12467
20	1.15035
21	1.172293
22	1.185772
23	1.196722
24	1.210381
25	1.213851
26	1.217622
27	1.217371
28	1.214468
29	1.208634
30	1.206762
31	1.207554
32	1.205226
33	1.203502
34	1.197974
35	1.195591
36	1.191758
37	1.185787
38	1.187085
39	1.184301
40	1.182812
41	1.179678
42	1.177468
43	1.176678
44	1.171259
45	1.171246
46	1.161645
47	1.155774
48	1.154322
49	1.156606
50	1.151277
51	1.146272
52	1.143717
53	1.142102
54	1.145724
55	1.141979
56	1.135984
57	1.133325
58	1.123118
59	1.114113
60	1.112431
61	1.10985
62	1.107426
63	1.103244
64	1.096573
65	1.09579
66	1.089143
67	1.077754
68	1.068394
69	1.062752
70	1.059604
71	1.053149
72	1.05301
73	1.042254
74	1.029447
75	1.025442
76	1.01868
77	1.006435
78	0.999032
79	0.99164
80	0.976127
81	0.957078
82	0.943371
83	0.92586
84	0.912929
85	0.904007
86	0.885173
87	0.872509
88	0.862009
89	0.841355
90	0.824012
91	0.800896
92	0.775288
93	0.751218
94	0.724939
95	0.701315
96	0.675424
97	0.647758
98	0.617113
99	0.586305
100	0.551251