File Info

Filename
aih-tih-sc-ec2fd6-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-ec2fd6-R1_A23YTGFLT4_1_rna_metrics.txt
Size
2.8 KB
Workflow Run
dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:37 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-ec2fd6-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-ec2fd6-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 20:29:01 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
67603787337	66848412494	4350	60473297111	4273687764	1885876307	215546962	0	0	0	3375572	231349655	949270	0.014381	0.985619	0	0.904633	0.063931	0.028211	0.003224	0.968564	0.957742	0	0.529624	0.482356	0.772608	0.725082			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.258626
1	0.287196
2	0.325999
3	0.3816
4	0.44224
5	0.50689
6	0.56356
7	0.615026
8	0.662304
9	0.714915
10	0.766028
11	0.812371
12	0.861813
13	0.909597
14	0.941879
15	0.969852
16	0.997614
17	1.021043
18	1.036096
19	1.056822
20	1.07904
21	1.094366
22	1.100856
23	1.115923
24	1.117524
25	1.125979
26	1.131129
27	1.131687
28	1.137104
29	1.139372
30	1.141706
31	1.143461
32	1.140263
33	1.146303
34	1.146142
35	1.155204
36	1.158535
37	1.156716
38	1.159431
39	1.160585
40	1.158664
41	1.158287
42	1.162719
43	1.164151
44	1.169429
45	1.177274
46	1.17473
47	1.178375
48	1.185395
49	1.18943
50	1.188368
51	1.187126
52	1.177999
53	1.171583
54	1.170684
55	1.166989
56	1.16493
57	1.161921
58	1.155813
59	1.149838
60	1.145138
61	1.143542
62	1.140121
63	1.134241
64	1.133203
65	1.142236
66	1.13905
67	1.144647
68	1.148375
69	1.147459
70	1.144792
71	1.13832
72	1.128824
73	1.121246
74	1.119232
75	1.112441
76	1.100156
77	1.087015
78	1.077709
79	1.063244
80	1.051052
81	1.034466
82	1.022599
83	1.0068
84	0.990056
85	0.971198
86	0.950134
87	0.937606
88	0.91514
89	0.892149
90	0.871206
91	0.8449
92	0.822429
93	0.795347
94	0.767471
95	0.734375
96	0.700454
97	0.665226
98	0.624762
99	0.585038
100	0.539014