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Filename
EndoN_FFPE_L02_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/EndoN_FFPE_L02_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 EndoN_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT EndoN_FFPE_L02_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 08:39:07 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
2611502049	2514553801	153662	1710038364	201378349	531663273	71320153	0	0	0	602150	7933369	58714	0.070546	0.929454	0.000061	0.680056	0.080085	0.211434	0.028363	0.760142	0.731922	0	0.855217	0.330799	0.502427	0.538701			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.345624
1	0.393507
2	0.44907
3	0.508174
4	0.560232
5	0.614928
6	0.660606
7	0.69751
8	0.732585
9	0.783253
10	0.811671
11	0.841877
12	0.882539
13	0.931359
14	0.968165
15	0.982736
16	1.000595
17	0.999378
18	0.994285
19	1.007235
20	1.02865
21	1.038496
22	1.035513
23	1.045381
24	1.055634
25	1.057015
26	1.054673
27	1.060716
28	1.068506
29	1.058952
30	1.05595
31	1.066414
32	1.078862
33	1.08797
34	1.08088
35	1.08521
36	1.095871
37	1.103684
38	1.111059
39	1.110044
40	1.138617
41	1.167531
42	1.170749
43	1.183958
44	1.202599
45	1.206147
46	1.198133
47	1.185105
48	1.171132
49	1.164178
50	1.153259
51	1.147324
52	1.144438
53	1.138849
54	1.134366
55	1.13557
56	1.143093
57	1.148647
58	1.142754
59	1.136258
60	1.153185
61	1.153508
62	1.148678
63	1.145252
64	1.154943
65	1.164215
66	1.160634
67	1.138521
68	1.126028
69	1.134558
70	1.122611
71	1.109274
72	1.104066
73	1.092053
74	1.096002
75	1.10152
76	1.110881
77	1.114225
78	1.108414
79	1.093449
80	1.084838
81	1.064909
82	1.051386
83	1.034711
84	1.018461
85	1.000422
86	0.995326
87	0.979569
88	0.962395
89	0.94472
90	0.918595
91	0.893317
92	0.866019
93	0.832119
94	0.798766
95	0.752725
96	0.701134
97	0.648543
98	0.60144
99	0.54271
100	0.48844