File Info

Filename
tih_rna_sample_00473_B23WHTKLT4_2_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0020/B23WHTKLT4/nfcore_rnafusion__3e501777--20260520-120107/QC/picard/tih_rna_sample_00473_B23WHTKLT4_2_rna_metrics.txt
Size
2.8 KB
Workflow Run
dev_rna_exp0020-3e501777
Published
May 21, 2026 1:12 AM

Content

View in new tab 
## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT tih_rna_sample_00473_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00473_B23WHTKLT4_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 21 05:55:05 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
79137745349	78380771893	664	71676170917	5145077204	1384994195	174528913	0	0	0	2640080	249005480	1228786	0.010491	0.989509	0	0.914461	0.065642	0.01767	0.002227	0.980103	0.970728	0	0.498552	0.547296	0.731676	0.86843			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.294328
1	0.333217
2	0.384558
3	0.448358
4	0.505616
5	0.555593
6	0.614223
7	0.666524
8	0.722364
9	0.772652
10	0.822327
11	0.867851
12	0.909552
13	0.950778
14	0.977698
15	1.001937
16	1.028516
17	1.059576
18	1.075215
19	1.092821
20	1.109986
21	1.128613
22	1.146371
23	1.161966
24	1.172924
25	1.180562
26	1.187414
27	1.189436
28	1.192838
29	1.194367
30	1.192988
31	1.190111
32	1.18657
33	1.186257
34	1.194279
35	1.19797
36	1.198669
37	1.200729
38	1.200338
39	1.194112
40	1.193756
41	1.192578
42	1.195319
43	1.194402
44	1.190358
45	1.194421
46	1.190475
47	1.188823
48	1.181564
49	1.181116
50	1.177923
51	1.175391
52	1.169182
53	1.167233
54	1.170455
55	1.174153
56	1.17004
57	1.169573
58	1.159618
59	1.147188
60	1.146154
61	1.143473
62	1.147719
63	1.144336
64	1.143646
65	1.145354
66	1.132569
67	1.114792
68	1.104933
69	1.096956
70	1.085232
71	1.073519
72	1.065064
73	1.055915
74	1.046269
75	1.035677
76	1.024708
77	1.011765
78	1.005542
79	1.001369
80	0.978708
81	0.959968
82	0.945334
83	0.931798
84	0.920784
85	0.905257
86	0.882654
87	0.866694
88	0.847489
89	0.824285
90	0.806247
91	0.78893
92	0.76155
93	0.735603
94	0.706954
95	0.679128
96	0.649627
97	0.620345
98	0.585784
99	0.553601
100	0.521319