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tih_rna_sample_00479_B23WHTKLT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0020/B23WHTKLT4/nfcore_rnafusion__3e501777--20260520-120107/QC/picard/tih_rna_sample_00479_B23WHTKLT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0020-3e501777
Published
May 21, 2026 2:13 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 tih_rna_sample_00479_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00479_B23WHTKLT4_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: Thu May 21 07:11:57 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
77990782344	77217207773	1920	70773137263	4589087355	1667766144	187215091	0	0	0	3372414	246562153	1136597	0.013493	0.986507	0	0.916546	0.059431	0.021598	0.002425	0.975977	0.966297	0	0.491747	0.505475	0.760026	0.801247			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.272057
1	0.306686
2	0.356557
3	0.415042
4	0.468472
5	0.518081
6	0.577978
7	0.626687
8	0.67919
9	0.72967
10	0.772827
11	0.816904
12	0.868921
13	0.911068
14	0.944167
15	0.982954
16	1.009066
17	1.039925
18	1.063671
19	1.08601
20	1.103909
21	1.120031
22	1.135172
23	1.146604
24	1.15338
25	1.163897
26	1.168097
27	1.165238
28	1.165097
29	1.164305
30	1.163442
31	1.161506
32	1.160264
33	1.165691
34	1.162818
35	1.170206
36	1.173158
37	1.171646
38	1.173323
39	1.170081
40	1.171419
41	1.178037
42	1.179206
43	1.184418
44	1.186495
45	1.185601
46	1.178126
47	1.181805
48	1.182152
49	1.187175
50	1.192662
51	1.196059
52	1.19906
53	1.202093
54	1.218061
55	1.222322
56	1.199321
57	1.197554
58	1.187565
59	1.179175
60	1.168631
61	1.16628
62	1.163424
63	1.158515
64	1.157611
65	1.154748
66	1.151417
67	1.140484
68	1.130174
69	1.117206
70	1.105606
71	1.09601
72	1.090647
73	1.081264
74	1.07479
75	1.064252
76	1.051687
77	1.036346
78	1.033464
79	1.022187
80	1.012552
81	0.999424
82	0.986146
83	0.967819
84	0.951369
85	0.933027
86	0.91303
87	0.89413
88	0.872127
89	0.852365
90	0.829049
91	0.801667
92	0.773541
93	0.743369
94	0.714844
95	0.686933
96	0.657444
97	0.62466
98	0.589578
99	0.55752
100	0.519691