File Info

Filename
tih_rna_sample_00566_23LGNLLT4_1_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0005/A23LGNLLT4/nfcore_rnafusion__2cae617--20260515-145204/QC/picard/tih_rna_sample_00566_23LGNLLT4_1_rna_metrics.txt
Size
2.8 KB
Workflow Run
dev_rna_exp0005_2cae617
Published
May 16, 2026 6:07 AM

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 tih_rna_sample_00566_23LGNLLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00566_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: Sat May 16 10:04:40 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
78008837624	77112567243	56233	66602671544	5599013212	4277797477	633028777	0	0	0	9367397	218343271	829430	0.041137	0.958863	0.000001	0.863707	0.072608	0.055475	0.008209	0.936315	0.925558	0	0.516175	0.549897	0.687429	0.960158			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.274879
1	0.317944
2	0.380882
3	0.449901
4	0.518933
5	0.584991
6	0.645651
7	0.701825
8	0.759111
9	0.809915
10	0.859375
11	0.910438
12	0.960163
13	0.995757
14	1.018861
15	1.048804
16	1.073275
17	1.103472
18	1.11485
19	1.123702
20	1.138577
21	1.153522
22	1.171801
23	1.190785
24	1.196837
25	1.197604
26	1.193883
27	1.19155
28	1.185132
29	1.183531
30	1.184369
31	1.185427
32	1.183358
33	1.184658
34	1.177249
35	1.180479
36	1.179715
37	1.180052
38	1.179435
39	1.170791
40	1.164296
41	1.164612
42	1.167769
43	1.168083
44	1.165143
45	1.168146
46	1.157989
47	1.153324
48	1.153337
49	1.149051
50	1.150218
51	1.148851
52	1.140362
53	1.137829
54	1.146194
55	1.147111
56	1.146606
57	1.14229
58	1.139844
59	1.12669
60	1.120791
61	1.123991
62	1.134628
63	1.127727
64	1.125365
65	1.128076
66	1.12331
67	1.119534
68	1.111479
69	1.103372
70	1.093164
71	1.08222
72	1.075224
73	1.068209
74	1.054962
75	1.047693
76	1.036963
77	1.018087
78	1.012418
79	1.011995
80	0.999557
81	0.98066
82	0.966736
83	0.941429
84	0.921308
85	0.904139
86	0.885505
87	0.865865
88	0.845451
89	0.82214
90	0.799481
91	0.775331
92	0.749805
93	0.72272
94	0.696435
95	0.67105
96	0.644769
97	0.61231
98	0.577797
99	0.544797
100	0.511438