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tih_rna_sample_00067_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_00067_23LGNLLT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
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_00067_23LGNLLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00067_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 20:21:07 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
23399395861	22466893498	26284	19636082546	1488873327	1212295361	129615980	0	0	0	6105932	70513543	428485	0.079692	0.920308	0.000001	0.874001	0.06627	0.053959	0.005769	0.94027	0.902799	0	0.564289	0.513978	0.692791	0.840178			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.277428
1	0.321782
2	0.374089
3	0.437202
4	0.504399
5	0.566995
6	0.621172
7	0.671015
8	0.723928
9	0.772081
10	0.819596
11	0.870311
12	0.920237
13	0.965258
14	0.992625
15	1.021402
16	1.045149
17	1.070719
18	1.097367
19	1.107412
20	1.116175
21	1.127459
22	1.139772
23	1.161173
24	1.172905
25	1.173789
26	1.176565
27	1.1753
28	1.179734
29	1.184426
30	1.186315
31	1.180599
32	1.176333
33	1.179745
34	1.171249
35	1.182251
36	1.190634
37	1.186134
38	1.185481
39	1.17717
40	1.172295
41	1.173498
42	1.183004
43	1.197175
44	1.201387
45	1.206609
46	1.207282
47	1.207622
48	1.204182
49	1.199681
50	1.18399
51	1.177172
52	1.171568
53	1.153625
54	1.148296
55	1.141407
56	1.129319
57	1.124874
58	1.116239
59	1.103032
60	1.104371
61	1.108264
62	1.107262
63	1.096862
64	1.098496
65	1.09608
66	1.091745
67	1.084263
68	1.083415
69	1.088123
70	1.080034
71	1.066051
72	1.066132
73	1.062885
74	1.052255
75	1.049059
76	1.046562
77	1.040053
78	1.03084
79	1.020588
80	1.008274
81	0.994813
82	0.978019
83	0.960182
84	0.949398
85	0.935389
86	0.912901
87	0.8943
88	0.876592
89	0.855228
90	0.834666
91	0.816449
92	0.787085
93	0.7552
94	0.726685
95	0.697012
96	0.669199
97	0.641192
98	0.602987
99	0.565795
100	0.527403