File Info

Filename
tih_rna_sample_00149_23KMKGLT4_1_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0004/B23KMKGLT4/nfcore_rnafusion_100M__5f1fa79--20260304-101508/QC/picard/tih_rna_sample_00149_23KMKGLT4_1_rna_metrics.txt
Size
2.8 KB
Workflow Run
dev_rna_exp0004_5f1fa79
Published
Mar 04, 2026 4:40 PM

Content

View in new tab 
## 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_00149_23KMKGLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00149_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 23:36:17 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
23682363695	23378663035	12412	20076368842	1710041468	1437739383	154500930	0	0	0	2641380	76579857	252195	0.033342	0.966658	0.000001	0.858748	0.073145	0.061498	0.006609	0.931893	0.919942	0	0.559965	0.529428	0.745194	0.804245			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.286187
1	0.320799
2	0.373675
3	0.437828
4	0.494737
5	0.553544
6	0.608698
7	0.663658
8	0.712901
9	0.762287
10	0.806329
11	0.854648
12	0.897963
13	0.931887
14	0.966944
15	0.995567
16	1.018037
17	1.036338
18	1.048336
19	1.058993
20	1.079425
21	1.098201
22	1.115744
23	1.134025
24	1.138926
25	1.139076
26	1.14618
27	1.157842
28	1.166383
29	1.16688
30	1.165929
31	1.162399
32	1.164584
33	1.169974
34	1.17193
35	1.177378
36	1.180219
37	1.179964
38	1.1819
39	1.180849
40	1.178171
41	1.179198
42	1.179921
43	1.178468
44	1.176861
45	1.182176
46	1.178227
47	1.174946
48	1.173654
49	1.17487
50	1.176452
51	1.167624
52	1.152262
53	1.141315
54	1.145247
55	1.144334
56	1.145445
57	1.141308
58	1.137447
59	1.129296
60	1.12739
61	1.133161
62	1.128555
63	1.122622
64	1.123584
65	1.125425
66	1.121206
67	1.110958
68	1.106768
69	1.106679
70	1.096536
71	1.087641
72	1.080168
73	1.06777
74	1.055699
75	1.047148
76	1.046127
77	1.041195
78	1.037107
79	1.027686
80	1.022066
81	1.010169
82	0.996981
83	0.981049
84	0.975036
85	0.963825
86	0.942636
87	0.928342
88	0.910977
89	0.896599
90	0.871054
91	0.842352
92	0.81677
93	0.78508
94	0.752685
95	0.722416
96	0.691215
97	0.656895
98	0.6205
99	0.585951
100	0.543581