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659_b7Z-T1-TRNA-1_B23MHV2LT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0009_exp0010/B23MHV2LT4/nfcore_rnafusion__04da504a--20260522-114016/QC/picard/659_b7Z-T1-TRNA-1_B23MHV2LT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp09_10-04da504a
Published
May 22, 2026 7:30 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 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_b7Z-T1-TRNA-1_B23MHV2LT4_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 23 00:23:00 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
79635603766	78716295065	4451	70210706229	6744632569	1509617982	251333834	0	0	0	6189148	238598895	1375644	0.025284	0.974716	0	0.891946	0.085683	0.019178	0.003193	0.977629	0.966343	0	0.500773	0.576196	0.733903	0.858646			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.246964
1	0.286537
2	0.344556
3	0.416885
4	0.486409
5	0.550062
6	0.610912
7	0.66139
8	0.715007
9	0.767675
10	0.817473
11	0.856997
12	0.887124
13	0.927762
14	0.964819
15	0.990824
16	1.014313
17	1.040945
18	1.06131
19	1.076896
20	1.097366
21	1.121405
22	1.136501
23	1.14821
24	1.158303
25	1.160185
26	1.164277
27	1.161702
28	1.163295
29	1.164537
30	1.168195
31	1.167791
32	1.162755
33	1.164153
34	1.160492
35	1.166973
36	1.169066
37	1.167002
38	1.169038
39	1.169018
40	1.168169
41	1.168852
42	1.172414
43	1.17956
44	1.176501
45	1.187772
46	1.191051
47	1.191817
48	1.186929
49	1.184504
50	1.175965
51	1.170377
52	1.168017
53	1.171831
54	1.181773
55	1.181486
56	1.177228
57	1.177033
58	1.176049
59	1.165859
60	1.154922
61	1.155657
62	1.154089
63	1.14508
64	1.146088
65	1.145459
66	1.138486
67	1.132121
68	1.125995
69	1.113592
70	1.104062
71	1.096089
72	1.092862
73	1.089312
74	1.081492
75	1.074784
76	1.06255
77	1.048714
78	1.041098
79	1.028927
80	1.00792
81	0.993946
82	0.981619
83	0.969721
84	0.955545
85	0.938572
86	0.912301
87	0.895897
88	0.877514
89	0.857068
90	0.833672
91	0.801511
92	0.775371
93	0.744978
94	0.714685
95	0.684231
96	0.652754
97	0.62982
98	0.592714
99	0.559112
100	0.520699