File Info

Filename
aih-tih-sc-3270ab-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-3270ab-R1_A23YTGFLT4_1_rna_metrics.txt
Size
2.8 KB
Workflow Run
dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:50 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-3270ab-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-3270ab-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 20:35:05 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
74568735243	73765276588	9356	66879650931	4906411700	1773345759	205858842	0	0	0	3628033	244603804	1252052	0.014616	0.985384	0	0.906655	0.066514	0.02404	0.002791	0.973169	0.962683	0	0.517755	0.549547	0.715379	0.894078			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.29565
1	0.334291
2	0.388812
3	0.457665
4	0.518309
5	0.570905
6	0.631115
7	0.686833
8	0.747617
9	0.798671
10	0.840956
11	0.88168
12	0.931657
13	0.976668
14	1.010147
15	1.037723
16	1.064378
17	1.089663
18	1.104973
19	1.125885
20	1.143803
21	1.160256
22	1.1784
23	1.192337
24	1.200707
25	1.205003
26	1.207105
27	1.201783
28	1.200656
29	1.199846
30	1.202139
31	1.200468
32	1.191029
33	1.196337
34	1.187066
35	1.188473
36	1.187703
37	1.183235
38	1.184373
39	1.179976
40	1.170603
41	1.173873
42	1.179111
43	1.187875
44	1.182911
45	1.191221
46	1.183805
47	1.180717
48	1.173482
49	1.172012
50	1.175728
51	1.161551
52	1.150611
53	1.151061
54	1.152798
55	1.152646
56	1.146292
57	1.141906
58	1.134471
59	1.122427
60	1.113252
61	1.111867
62	1.112784
63	1.104067
64	1.108348
65	1.104944
66	1.097958
67	1.085788
68	1.083504
69	1.077205
70	1.06415
71	1.051811
72	1.048222
73	1.041196
74	1.032146
75	1.024706
76	1.021624
77	1.012378
78	1.006136
79	0.997347
80	0.984227
81	0.968303
82	0.956889
83	0.94607
84	0.929867
85	0.910622
86	0.889491
87	0.878147
88	0.86063
89	0.842146
90	0.81586
91	0.797144
92	0.770001
93	0.742642
94	0.716176
95	0.684089
96	0.650567
97	0.616852
98	0.580057
99	0.546657
100	0.511735