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Filename
ColoN_FFPE_L01_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_L01_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_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT ColoN_FFPE_L01_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 08:39:06 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
2783768389	2693443349	168979	2139939424	198065456	308340603	46928887	0	0	0	869545	9725511	69054	0.082071	0.917929	0.000063	0.7945	0.073536	0.114478	0.017423	0.868036	0.83987	0	0.793186	0.337775	0.555742	0.459336			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.275834
1	0.310552
2	0.366162
3	0.428361
4	0.483578
5	0.542882
6	0.606477
7	0.664344
8	0.723212
9	0.781532
10	0.820251
11	0.854195
12	0.868928
13	0.902148
14	0.934569
15	0.951856
16	0.969989
17	0.972466
18	0.984952
19	1.009534
20	1.027626
21	1.040007
22	1.047501
23	1.061556
24	1.064295
25	1.066741
26	1.068409
27	1.071022
28	1.087411
29	1.088725
30	1.08986
31	1.097647
32	1.112262
33	1.125827
34	1.13043
35	1.147445
36	1.161704
37	1.170251
38	1.177449
39	1.178269
40	1.171206
41	1.184817
42	1.175046
43	1.166687
44	1.166992
45	1.164274
46	1.151145
47	1.143929
48	1.147239
49	1.150778
50	1.156885
51	1.161559
52	1.156202
53	1.161001
54	1.163865
55	1.154802
56	1.158336
57	1.161876
58	1.155819
59	1.149291
60	1.151413
61	1.151595
62	1.156639
63	1.14713
64	1.154952
65	1.163445
66	1.156594
67	1.147062
68	1.140666
69	1.129028
70	1.122471
71	1.101003
72	1.0916
73	1.088872
74	1.09658
75	1.094714
76	1.102324
77	1.102045
78	1.084063
79	1.062124
80	1.052804
81	1.040057
82	1.021638
83	1.012254
84	1.004955
85	0.992962
86	0.994735
87	0.986397
88	0.978781
89	0.977544
90	0.953708
91	0.932222
92	0.896895
93	0.842008
94	0.80188
95	0.759044
96	0.716764
97	0.67132
98	0.617884
99	0.565433
100	0.514693