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ColoN_FFPE_L01_RNA_01_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/ColoN_FFPE_L01_RNA_01_B23LG7FLT4_2_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0008_exp0011-e7be3c7a_b
Published
May 28, 2026 5:34 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 ColoN_FFPE_L01_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT ColoN_FFPE_L01_RNA_01_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 23:20:43 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
56761207306	55306523980	105311	48496876852	4026578131	2089452194	693511492	0	0	0	24667815	165626026	1026884	0.12963	0.87037	0.000002	0.876874	0.072805	0.037779	0.012539	0.949679	0.925341	0	0.723922	0.371341	0.545485	0.68523			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.266165
1	0.298882
2	0.354021
3	0.416918
4	0.481854
5	0.554294
6	0.621565
7	0.677243
8	0.734293
9	0.780035
10	0.82826
11	0.872173
12	0.920653
13	0.970143
14	1.015508
15	1.049507
16	1.070384
17	1.081603
18	1.088048
19	1.094825
20	1.117212
21	1.128006
22	1.134201
23	1.141824
24	1.156299
25	1.167156
26	1.175845
27	1.181711
28	1.1905
29	1.178989
30	1.168631
31	1.165304
32	1.167716
33	1.161866
34	1.155848
35	1.16283
36	1.162431
37	1.149289
38	1.146759
39	1.149877
40	1.15197
41	1.161692
42	1.166396
43	1.175935
44	1.183438
45	1.184954
46	1.189151
47	1.193222
48	1.18526
49	1.187088
50	1.177729
51	1.178315
52	1.167795
53	1.16351
54	1.164828
55	1.172832
56	1.167908
57	1.154289
58	1.15399
59	1.155255
60	1.154697
61	1.160057
62	1.168874
63	1.151252
64	1.146639
65	1.131084
66	1.118491
67	1.113101
68	1.104772
69	1.097585
70	1.084536
71	1.070678
72	1.065929
73	1.064659
74	1.059827
75	1.063522
76	1.066444
77	1.059727
78	1.045669
79	1.032527
80	1.015088
81	0.996518
82	0.976149
83	0.966178
84	0.94498
85	0.919005
86	0.892277
87	0.879418
88	0.866333
89	0.846636
90	0.824494
91	0.797901
92	0.772579
93	0.742902
94	0.71374
95	0.675229
96	0.63674
97	0.613025
98	0.577642
99	0.545329
100	0.512918