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tih_rna_sample_00512_23LGNLLT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0005/A23LGNLLT4/nfcore_rnafusion_100M__5f1fa79--20260304-095416/QC/picard/tih_rna_sample_00512_23LGNLLT4_1_rna_metrics.txt
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2.8 KB
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dev_rna_exp0005_5f1fa79
Published
Mar 09, 2026 6:38 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 tih_rna_sample_00512_23LGNLLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00512_23LGNLLT4_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 Mar 10 00:24:43 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
25304622915	24949262704	22831	21623267352	1705609873	1475275596	145087052	0	0	0	2730352	77522623	208193	0.034022	0.965978	0.000001	0.86669	0.068363	0.059131	0.005815	0.935053	0.921922	0	0.551553	0.480055	0.718416	0.760412			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.270266
1	0.30135
2	0.349477
3	0.409934
4	0.46478
5	0.509028
6	0.568737
7	0.624621
8	0.681411
9	0.744221
10	0.799646
11	0.85451
12	0.910181
13	0.956287
14	0.989225
15	1.014856
16	1.038182
17	1.065953
18	1.081019
19	1.08552
20	1.099918
21	1.117946
22	1.134681
23	1.150439
24	1.153648
25	1.156028
26	1.152414
27	1.151232
28	1.156442
29	1.15873
30	1.169611
31	1.171656
32	1.169894
33	1.170962
34	1.166298
35	1.179196
36	1.183227
37	1.17535
38	1.177682
39	1.174226
40	1.173315
41	1.169959
42	1.18322
43	1.195733
44	1.19682
45	1.20762
46	1.211556
47	1.207498
48	1.208552
49	1.209531
50	1.200288
51	1.196486
52	1.190356
53	1.1833
54	1.179776
55	1.17873
56	1.177613
57	1.172538
58	1.163198
59	1.152866
60	1.143147
61	1.145809
62	1.142527
63	1.131693
64	1.128927
65	1.129642
66	1.121448
67	1.114016
68	1.112809
69	1.110045
70	1.103672
71	1.092211
72	1.087166
73	1.076344
74	1.058491
75	1.050086
76	1.038205
77	1.029478
78	1.028075
79	1.013215
80	0.997462
81	0.982362
82	0.972483
83	0.953502
84	0.937522
85	0.922979
86	0.904573
87	0.893242
88	0.87967
89	0.864431
90	0.844093
91	0.815101
92	0.787428
93	0.758076
94	0.728557
95	0.699218
96	0.668406
97	0.637146
98	0.60626
99	0.572508
100	0.534713