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aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0021/A23YTGFLT4/nfcore_rnafusion__d2190e45--20260603-105009/QC/picard/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1_rna_metrics.txt
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2.8 KB
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:35 PM

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## 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-6d9e6f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-6d9e6f-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 20:18:02 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
73559277077	72784507561	7206	65171433383	5159945224	2201778263	251343485	0	0	0	7403834	240142674	1130818	0.029909	0.970091	0	0.895403	0.070893	0.030251	0.003453	0.966296	0.956118	0	0.508972	0.511955	0.764562	0.751917			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.261917
1	0.296521
2	0.343965
3	0.406309
4	0.471588
5	0.533628
6	0.591698
7	0.63892
8	0.689498
9	0.739658
10	0.78738
11	0.829978
12	0.877198
13	0.919629
14	0.955845
15	0.98993
16	1.01976
17	1.040782
18	1.059249
19	1.075584
20	1.09353
21	1.113139
22	1.128086
23	1.148372
24	1.158353
25	1.164216
26	1.168851
27	1.170515
28	1.169019
29	1.166218
30	1.164124
31	1.162363
32	1.158929
33	1.161132
34	1.156364
35	1.157562
36	1.157799
37	1.155744
38	1.149875
39	1.14886
40	1.146052
41	1.146607
42	1.154858
43	1.169252
44	1.174035
45	1.181622
46	1.179904
47	1.190022
48	1.186781
49	1.182909
50	1.167017
51	1.163926
52	1.159166
53	1.15633
54	1.159574
55	1.157121
56	1.154092
57	1.144678
58	1.136489
59	1.133267
60	1.129513
61	1.135277
62	1.136494
63	1.132551
64	1.131936
65	1.135102
66	1.127811
67	1.120779
68	1.119938
69	1.121092
70	1.113299
71	1.107179
72	1.102618
73	1.100639
74	1.096147
75	1.089925
76	1.07547
77	1.064479
78	1.05701
79	1.042981
80	1.026831
81	1.015696
82	1.004766
83	0.987304
84	0.970713
85	0.952863
86	0.932755
87	0.922169
88	0.906694
89	0.890167
90	0.86692
91	0.8438
92	0.819764
93	0.786879
94	0.758256
95	0.728665
96	0.692741
97	0.655686
98	0.615419
99	0.577503
100	0.54169