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tih_rna_sample_00154_23KMKGLT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0004/B23KMKGLT4/nfcore_rnafusion_100M__5f1fa79--20260304-101508/QC/picard/tih_rna_sample_00154_23KMKGLT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0004_5f1fa79
Published
Mar 04, 2026 4:52 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_00154_23KMKGLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00154_23KMKGLT4_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: Wed Mar 04 23:54:27 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
25258035573	24829476935	19358	21687807220	1798649391	1198037369	144963597	0	0	0	3051524	77234462	333978	0.038008	0.961992	0.000001	0.87347	0.07244	0.048251	0.005838	0.94591	0.929861	0	0.499231	0.58829	0.749379	0.877777			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.331026
1	0.375305
2	0.423269
3	0.479348
4	0.533328
5	0.591956
6	0.651738
7	0.704018
8	0.751014
9	0.803284
10	0.852843
11	0.899847
12	0.949874
13	0.996574
14	1.02839
15	1.05325
16	1.072201
17	1.095491
18	1.110475
19	1.119154
20	1.129776
21	1.130914
22	1.136555
23	1.150284
24	1.157726
25	1.158967
26	1.155015
27	1.159217
28	1.15947
29	1.158256
30	1.160248
31	1.158617
32	1.157186
33	1.159085
34	1.151406
35	1.155859
36	1.149891
37	1.147386
38	1.147585
39	1.14596
40	1.138523
41	1.135937
42	1.137281
43	1.138245
44	1.13612
45	1.150371
46	1.152107
47	1.147151
48	1.141739
49	1.147867
50	1.142428
51	1.137877
52	1.129583
53	1.124592
54	1.125577
55	1.132711
56	1.128778
57	1.127666
58	1.118497
59	1.102575
60	1.097642
61	1.101391
62	1.101672
63	1.096176
64	1.100461
65	1.102126
66	1.097348
67	1.091121
68	1.089447
69	1.086688
70	1.077077
71	1.062013
72	1.055201
73	1.047012
74	1.044839
75	1.048819
76	1.049129
77	1.04405
78	1.041134
79	1.03467
80	1.026049
81	1.012094
82	0.998571
83	0.984852
84	0.975285
85	0.962793
86	0.942149
87	0.930875
88	0.907947
89	0.888698
90	0.866165
91	0.845175
92	0.81956
93	0.78743
94	0.749906
95	0.717633
96	0.683837
97	0.65415
98	0.613522
99	0.57545
100	0.533126