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tih_rna_sample_00276_23LGNLLT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0002/A23LGNLLT4/nfcore_rnafusion_100M__5f1fa79--20260304-095416/QC/picard/tih_rna_sample_00276_23LGNLLT4_1_rna_metrics.txt
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2.8 KB
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dev_rna_exp0002_5f1fa79
Published
Mar 09, 2026 2:25 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_00276_23LGNLLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00276_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: Mon Mar 09 20:05:07 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
23967488868	23597679230	23818	20249840249	1529716948	1610006169	208092046	0	0	0	4402178	74165465	482695	0.05603	0.94397	0.000001	0.858128	0.064825	0.068227	0.008818	0.922953	0.908713	0	0.548096	0.473474	0.729912	0.724582			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.343574
1	0.379263
2	0.42779
3	0.479207
4	0.518336
5	0.556089
6	0.609687
7	0.664984
8	0.714493
9	0.753165
10	0.787595
11	0.824952
12	0.863906
13	0.901379
14	0.93268
15	0.960624
16	0.982918
17	1.009899
18	1.016419
19	1.028045
20	1.052915
21	1.07303
22	1.09435
23	1.105016
24	1.112629
25	1.123075
26	1.130953
27	1.136816
28	1.149211
29	1.154033
30	1.151782
31	1.152095
32	1.153481
33	1.155282
34	1.158894
35	1.167949
36	1.171788
37	1.165162
38	1.162228
39	1.162578
40	1.166533
41	1.166227
42	1.167413
43	1.169411
44	1.17222
45	1.164499
46	1.152088
47	1.149874
48	1.147221
49	1.144815
50	1.153865
51	1.147429
52	1.144077
53	1.142167
54	1.154947
55	1.157172
56	1.147995
57	1.139563
58	1.13352
59	1.129832
60	1.126169
61	1.12047
62	1.119163
63	1.121119
64	1.125028
65	1.124456
66	1.11837
67	1.10933
68	1.103827
69	1.097233
70	1.08763
71	1.078156
72	1.077391
73	1.075152
74	1.06541
75	1.059152
76	1.056032
77	1.052898
78	1.046541
79	1.043914
80	1.039195
81	1.027541
82	1.015374
83	0.999485
84	0.992918
85	0.983543
86	0.969916
87	0.961539
88	0.941575
89	0.923233
90	0.899278
91	0.878323
92	0.851924
93	0.823552
94	0.796841
95	0.767005
96	0.731662
97	0.698252
98	0.660783
99	0.619875
100	0.579194