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SW780_FFPE_RNA_0001_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/SW780_FFPE_RNA_0001_B23LG7FLT4_1_rna_metrics.txt
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2.9 KB
Workflow Run
dev_rna_exp0008_exp0011-e7be3c7a_b
Published
May 28, 2026 6:04 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 SW780_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT SW780_FFPE_RNA_0001_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 22:49:16 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
74700150076	73792205728	72586	63940782360	5345373920	3910804239	595172623	0	0	0	5855918	231990090	1449650	0.024621	0.975379	0.000001	0.866498	0.072438	0.052998	0.008066	0.938936	0.927524	0	0.504169	0.565626	0.762237	0.799683			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.280742
1	0.311929
2	0.359739
3	0.411741
4	0.474611
5	0.537761
6	0.602023
7	0.663204
8	0.718913
9	0.772102
10	0.821416
11	0.869247
12	0.911068
13	0.952754
14	0.986739
15	1.016826
16	1.046943
17	1.068378
18	1.080553
19	1.094815
20	1.111921
21	1.128479
22	1.138734
23	1.151596
24	1.156107
25	1.159181
26	1.161537
27	1.159296
28	1.156385
29	1.149959
30	1.14478
31	1.14183
32	1.141524
33	1.135682
34	1.127882
35	1.128471
36	1.1312
37	1.124002
38	1.119722
39	1.11688
40	1.118297
41	1.124669
42	1.132025
43	1.139864
44	1.138139
45	1.138829
46	1.129107
47	1.118458
48	1.121069
49	1.130048
50	1.134029
51	1.133442
52	1.141568
53	1.144704
54	1.151188
55	1.152909
56	1.152177
57	1.151768
58	1.146531
59	1.140352
60	1.132782
61	1.132284
62	1.134866
63	1.124832
64	1.120904
65	1.123092
66	1.117451
67	1.110807
68	1.104025
69	1.102608
70	1.101247
71	1.096209
72	1.099216
73	1.100723
74	1.093937
75	1.094797
76	1.089187
77	1.078453
78	1.078825
79	1.072882
80	1.058222
81	1.045115
82	1.033424
83	1.016055
84	1.000502
85	0.989866
86	0.972543
87	0.954872
88	0.931289
89	0.911866
90	0.884784
91	0.858212
92	0.833597
93	0.798217
94	0.761336
95	0.727686
96	0.691247
97	0.657567
98	0.618763
99	0.577699
100	0.531592