File Info

Filename
aih-tih-sc-89f3a3-R1_A23YTGFLT4_1_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0021/A23YTGFLT4/nfcore_rnafusion__d2190e45--20260603-105009/QC/picard/aih-tih-sc-89f3a3-R1_A23YTGFLT4_1_rna_metrics.txt
Size
2.8 KB
Workflow Run
dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:43 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 aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-89f3a3-R1_A23YTGFLT4_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 Jun 03 20:21:02 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
77590076565	76833312336	4364	68620080392	5480273610	2428706273	304247697	0	0	0	7046020	241073693	1214025	0.028398	0.971602	0	0.893103	0.071327	0.03161	0.00396	0.96443	0.955024	0	0.504238	0.583628	0.731471	0.892171			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.315862
1	0.357459
2	0.40849
3	0.46703
4	0.534436
5	0.600063
6	0.659686
7	0.716128
8	0.771902
9	0.820328
10	0.869617
11	0.918867
12	0.966683
13	1.006274
14	1.037207
15	1.061486
16	1.085344
17	1.100645
18	1.112704
19	1.126748
20	1.141711
21	1.159893
22	1.176172
23	1.19138
24	1.195841
25	1.199012
26	1.202141
27	1.20778
28	1.21261
29	1.216632
30	1.217325
31	1.219132
32	1.197289
33	1.188366
34	1.186272
35	1.183686
36	1.1767
37	1.171499
38	1.170948
39	1.165169
40	1.164848
41	1.170853
42	1.169041
43	1.158649
44	1.155996
45	1.159369
46	1.152181
47	1.148313
48	1.143622
49	1.141065
50	1.13436
51	1.126998
52	1.120871
53	1.121352
54	1.12295
55	1.125136
56	1.119819
57	1.114941
58	1.111259
59	1.107098
60	1.10464
61	1.107893
62	1.110816
63	1.102021
64	1.100638
65	1.100712
66	1.096402
67	1.0885
68	1.082305
69	1.069508
70	1.05655
71	1.043001
72	1.036191
73	1.029999
74	1.028666
75	1.023993
76	1.014607
77	1.005292
78	1.000337
79	0.990477
80	0.97551
81	0.962522
82	0.950805
83	0.941138
84	0.926419
85	0.914075
86	0.893224
87	0.881971
88	0.862506
89	0.844062
90	0.821739
91	0.806665
92	0.783417
93	0.756088
94	0.728302
95	0.701857
96	0.674805
97	0.645221
98	0.6125
99	0.582525
100	0.546779