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tih_rna_sample_00501_23LGNLLT4_1_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0005/A23LGNLLT4/nfcore_rnafusion__2cae617--20260515-145204/QC/picard/tih_rna_sample_00501_23LGNLLT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0005_2cae617
Published
May 16, 2026 6:01 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_00501_23LGNLLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00501_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: Sat May 16 10:00:40 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
78885168307	77895091538	60206	66307076251	6232771099	4651309327	703874655	0	0	0	11998608	226240045	1041670	0.050364	0.949636	0.000001	0.851236	0.080015	0.059712	0.009036	0.931251	0.919563	0	0.543553	0.540445	0.729841	0.824209			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.334384
1	0.374433
2	0.425845
3	0.484013
4	0.550762
5	0.61224
6	0.665278
7	0.714954
8	0.771393
9	0.818605
10	0.856505
11	0.894898
12	0.931805
13	0.96296
14	0.984922
15	1.000603
16	1.020277
17	1.043863
18	1.048011
19	1.060132
20	1.078717
21	1.095451
22	1.111248
23	1.118398
24	1.124768
25	1.128302
26	1.134986
27	1.138154
28	1.142627
29	1.147687
30	1.151397
31	1.165102
32	1.18028
33	1.192343
34	1.193905
35	1.191748
36	1.191716
37	1.187397
38	1.182367
39	1.17007
40	1.164844
41	1.165834
42	1.161337
43	1.16388
44	1.165934
45	1.167231
46	1.159571
47	1.144707
48	1.139329
49	1.13667
50	1.135537
51	1.129588
52	1.128908
53	1.13625
54	1.145077
55	1.143465
56	1.141714
57	1.139481
58	1.133247
59	1.130394
60	1.128421
61	1.13054
62	1.129998
63	1.119199
64	1.120814
65	1.126072
66	1.133165
67	1.129886
68	1.122242
69	1.109354
70	1.100951
71	1.08648
72	1.078452
73	1.070902
74	1.060351
75	1.055401
76	1.043938
77	1.029226
78	1.017454
79	1.007056
80	0.993122
81	0.978808
82	0.955979
83	0.936392
84	0.922158
85	0.911537
86	0.897173
87	0.888956
88	0.878622
89	0.860717
90	0.843043
91	0.833073
92	0.811372
93	0.781287
94	0.755391
95	0.733054
96	0.707137
97	0.67621
98	0.644042
99	0.609206
100	0.566311