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SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0008_exp0011/B23LG7FLT4/nfcore_rnafusion__e7be3c7a--20260528-111100/QC/picard/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1_rna_metrics.txt
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2.9 KB
Workflow Run
dev_rna_exp0008_exp0011-e7be3c7a_b
Published
May 28, 2026 5:26 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 SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_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: Thu May 28 21:23:52 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
75344628536	74427998074	72779	65850235117	4980918776	3099796002	496975400	0	0	0	10042638	234467890	1526581	0.041072	0.958928	0.000001	0.884751	0.066923	0.041648	0.006677	0.951674	0.940096	0	0.517626	0.58716	0.74194	0.908483			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.272407
1	0.317648
2	0.378152
3	0.445349
4	0.516388
5	0.585534
6	0.65378
7	0.722694
8	0.782861
9	0.834225
10	0.885383
11	0.937589
12	0.986399
13	1.025357
14	1.059917
15	1.090303
16	1.120821
17	1.142894
18	1.157504
19	1.166508
20	1.174425
21	1.194112
22	1.206205
23	1.211898
24	1.215186
25	1.211661
26	1.216368
27	1.213946
28	1.212933
29	1.20405
30	1.202095
31	1.200992
32	1.200878
33	1.203604
34	1.193918
35	1.192645
36	1.191337
37	1.178201
38	1.170272
39	1.159252
40	1.155731
41	1.149221
42	1.146573
43	1.161609
44	1.159375
45	1.158549
46	1.156339
47	1.151172
48	1.152836
49	1.158772
50	1.145753
51	1.146955
52	1.14566
53	1.139074
54	1.14137
55	1.137316
56	1.128542
57	1.119543
58	1.110514
59	1.104507
60	1.099665
61	1.099563
62	1.104405
63	1.097496
64	1.092713
65	1.091057
66	1.098845
67	1.089668
68	1.084629
69	1.075118
70	1.065158
71	1.050953
72	1.04926
73	1.044613
74	1.032571
75	1.017774
76	1.002105
77	0.989507
78	0.985579
79	0.972982
80	0.959134
81	0.942456
82	0.923715
83	0.908474
84	0.886661
85	0.8736
86	0.858143
87	0.847048
88	0.832519
89	0.81659
90	0.797238
91	0.782097
92	0.765185
93	0.74082
94	0.71768
95	0.693255
96	0.671219
97	0.648186
98	0.621407
99	0.588516
100	0.54863