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EndoN_FFPE_L06_RNA_01_B23LG7FLT4_1_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0008_exp0011/B23LG7FLT4/nfcore_rnafusion__e7be3c7a--20260528-111100/QC/picard/EndoN_FFPE_L06_RNA_01_B23LG7FLT4_1_rna_metrics.txt
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2.9 KB
Workflow Run
dev_rna_exp0008_exp0011-e7be3c7a_b
Published
May 28, 2026 5:19 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 EndoN_FFPE_L06_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT EndoN_FFPE_L06_RNA_01_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 22:48:27 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
43603994671	42711556821	152969	36703929363	2833758302	2657936063	515780124	0	0	0	7884831	158712506	881017	0.047329	0.952671	0.000004	0.859344	0.066346	0.06223	0.012076	0.925691	0.906745	0	0.797436	0.357286	0.500213	0.764853			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.323361
1	0.36201
2	0.422895
3	0.490938
4	0.545219
5	0.595126
6	0.639388
7	0.679944
8	0.734295
9	0.783239
10	0.813191
11	0.848384
12	0.887267
13	0.92431
14	0.955161
15	0.974402
16	0.984963
17	0.989651
18	0.99699
19	1.010612
20	1.027679
21	1.040782
22	1.059228
23	1.071724
24	1.076242
25	1.085703
26	1.090046
27	1.103068
28	1.117557
29	1.11169
30	1.108896
31	1.123627
32	1.126086
33	1.133222
34	1.131499
35	1.137202
36	1.143515
37	1.14568
38	1.150316
39	1.153829
40	1.168269
41	1.183118
42	1.186095
43	1.182585
44	1.173882
45	1.165272
46	1.153492
47	1.146259
48	1.137578
49	1.132471
50	1.14613
51	1.152974
52	1.159848
53	1.170334
54	1.180335
55	1.176918
56	1.177678
57	1.172019
58	1.165339
59	1.171249
60	1.19037
61	1.200175
62	1.201951
63	1.181509
64	1.178927
65	1.172887
66	1.160872
67	1.1471
68	1.132826
69	1.128161
70	1.114158
71	1.109015
72	1.105859
73	1.104962
74	1.111066
75	1.111534
76	1.120645
77	1.123728
78	1.112205
79	1.081231
80	1.058932
81	1.032782
82	1.009395
83	0.991601
84	0.983096
85	0.964214
86	0.948138
87	0.938337
88	0.923366
89	0.894976
90	0.861743
91	0.829266
92	0.79795
93	0.767803
94	0.736213
95	0.700676
96	0.656386
97	0.613516
98	0.569101
99	0.518291
100	0.471735