File Info

Filename
aih-tih-sc-6c4b48-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-6c4b48-R1_A23YTGFLT4_1_rna_metrics.txt
Size
2.8 KB
Workflow Run
dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:40 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 aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-6c4b48-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 20:22:07 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
79247989640	78529302965	2462	70637618348	5487776129	2165623457	238282569	0	0	0	7434231	241617999	1332688	0.02985	0.97015	0	0.899506	0.069882	0.027577	0.003034	0.969388	0.960597	0	0.498217	0.596707	0.745924	0.90233			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.265117
1	0.308126
2	0.364672
3	0.431332
4	0.504062
5	0.579338
6	0.648206
7	0.709812
8	0.763369
9	0.81491
10	0.861997
11	0.9056
12	0.950168
13	0.995012
14	1.031414
15	1.062315
16	1.089026
17	1.117338
18	1.137582
19	1.155853
20	1.173259
21	1.184118
22	1.190691
23	1.200586
24	1.205638
25	1.202239
26	1.200632
27	1.201734
28	1.203578
29	1.20629
30	1.2049
31	1.201817
32	1.193407
33	1.1934
34	1.189756
35	1.189839
36	1.191927
37	1.182222
38	1.173279
39	1.164971
40	1.160536
41	1.163524
42	1.161508
43	1.170755
44	1.170404
45	1.181086
46	1.181624
47	1.178803
48	1.174006
49	1.17292
50	1.159958
51	1.156888
52	1.15106
53	1.152625
54	1.153174
55	1.148677
56	1.141839
57	1.136337
58	1.129575
59	1.126225
60	1.116709
61	1.111413
62	1.109485
63	1.103138
64	1.093246
65	1.087904
66	1.088251
67	1.078174
68	1.067603
69	1.056516
70	1.050216
71	1.043207
72	1.039332
73	1.031872
74	1.027494
75	1.021249
76	1.008181
77	0.993859
78	0.990512
79	0.976775
80	0.966831
81	0.955055
82	0.94254
83	0.934025
84	0.920436
85	0.908591
86	0.893057
87	0.883017
88	0.862575
89	0.840316
90	0.816073
91	0.791656
92	0.76991
93	0.7462
94	0.718904
95	0.691259
96	0.662559
97	0.633534
98	0.600429
99	0.571709
100	0.536384