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aih-tih-sc-965752-R1_A23WJ53LT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0019/A23WJ53LT4/nfcore_rnafusion__3e501777--20260519-110950/QC/picard/aih-tih-sc-965752-R1_A23WJ53LT4_1_rna_metrics.txt
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2.8 KB
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dev_rna_exp0019_2-3e501777
Published
May 19, 2026 4:59 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 aih-tih-sc-965752-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-965752-R1_A23WJ53LT4_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: Tue May 19 21:20:04 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
72566177225	71695300788	1766	65611147850	4381756141	1520548087	181846944	0	0	0	10377763	244021654	1106332	0.040793	0.959207	0	0.915139	0.061116	0.021208	0.002536	0.976255	0.964539	0	0.531542	0.50878	0.745553	0.754256			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.285752
1	0.319623
2	0.367949
3	0.420329
4	0.473767
5	0.522168
6	0.584964
7	0.640172
8	0.697533
9	0.745665
10	0.791821
11	0.837201
12	0.879696
13	0.918101
14	0.956373
15	0.978675
16	1.002308
17	1.031036
18	1.047693
19	1.066318
20	1.080805
21	1.097957
22	1.11756
23	1.130212
24	1.139133
25	1.144274
26	1.149917
27	1.156378
28	1.156314
29	1.157078
30	1.167794
31	1.174946
32	1.171547
33	1.176221
34	1.171575
35	1.172061
36	1.173279
37	1.177816
38	1.178508
39	1.177939
40	1.173041
41	1.170361
42	1.174533
43	1.185802
44	1.184396
45	1.193141
46	1.192716
47	1.192551
48	1.194104
49	1.200498
50	1.188584
51	1.184455
52	1.17691
53	1.169067
54	1.165195
55	1.15735
56	1.152123
57	1.147771
58	1.133371
59	1.123648
60	1.119223
61	1.119292
62	1.127411
63	1.124289
64	1.122325
65	1.124433
66	1.130178
67	1.121708
68	1.117447
69	1.112645
70	1.096047
71	1.085642
72	1.077671
73	1.072419
74	1.066829
75	1.061977
76	1.052412
77	1.044907
78	1.042991
79	1.032503
80	1.021319
81	1.009149
82	0.997979
83	0.984891
84	0.971796
85	0.954119
86	0.933254
87	0.918534
88	0.897753
89	0.877263
90	0.860622
91	0.847747
92	0.819605
93	0.792714
94	0.762744
95	0.732761
96	0.702622
97	0.667559
98	0.629371
99	0.590712
100	0.552279