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A673_FFPE_RNA_0001_B23LG7FLT4_2_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0008_exp0011/B23LG7FLT4/nfcore_rnafusion__e7be3c7a--20260528-111100/QC/picard/A673_FFPE_RNA_0001_B23LG7FLT4_2_rna_metrics.txt
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2.9 KB
Workflow Run
dev_rna_exp0008_exp0011-e7be3c7a_b
Published
May 28, 2026 6:32 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 A673_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT A673_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: Thu May 28 22:29:53 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
73512628841	72663627768	51628	63401253105	4907562830	3772507766	582252439	0	0	0	4262143	232994193	1478218	0.017964	0.982036	0.000001	0.872531	0.067538	0.051917	0.008013	0.940069	0.929212	0	0.522925	0.568471	0.738335	0.855042			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.265351
1	0.303736
2	0.358457
3	0.424417
4	0.499753
5	0.567696
6	0.634558
7	0.697342
8	0.758177
9	0.812681
10	0.863417
11	0.910421
12	0.957356
13	0.996806
14	1.031007
15	1.056095
16	1.086471
17	1.108444
18	1.114296
19	1.126032
20	1.140215
21	1.155113
22	1.164137
23	1.177132
24	1.179018
25	1.180686
26	1.180834
27	1.184669
28	1.182176
29	1.173978
30	1.162687
31	1.155112
32	1.160863
33	1.15579
34	1.151099
35	1.150131
36	1.148389
37	1.141318
38	1.140379
39	1.143678
40	1.146425
41	1.149027
42	1.154927
43	1.15557
44	1.149062
45	1.141804
46	1.126414
47	1.1203
48	1.121004
49	1.125158
50	1.130781
51	1.127355
52	1.133137
53	1.134197
54	1.139103
55	1.139917
56	1.133411
57	1.135535
58	1.135754
59	1.132471
60	1.128708
61	1.130469
62	1.130235
63	1.125516
64	1.122841
65	1.115269
66	1.109845
67	1.107018
68	1.108608
69	1.111656
70	1.102182
71	1.093159
72	1.084916
73	1.075781
74	1.073888
75	1.065911
76	1.054233
77	1.041258
78	1.034734
79	1.027252
80	1.016666
81	1.005578
82	0.994881
83	0.970117
84	0.956029
85	0.945741
86	0.932703
87	0.917167
88	0.896243
89	0.872992
90	0.850966
91	0.826483
92	0.797893
93	0.765276
94	0.724927
95	0.695001
96	0.66132
97	0.624251
98	0.583773
99	0.540376
100	0.496561