SnpEff: Variant analysis

Contents
Summary
Variant rate by chromosome
Variants by type
Number of variants by impact
Number of variants by functional class
Number of variants by effect
Quality histogram
InDel length histogram
Base variant table
Transition vs transversions (ts/tv)
Allele frequency
Allele Count
Codon change table
Amino acid change table
Chromosome variants plots
Details by gene
Summary

Genome GRCh38.105
Date 2026-06-04 19:36
SnpEff version 
SnpEff 5.1d (build 2022-04-19 15:49), by Pablo Cingolani
Command line arguments 
SnpEff  GRCh38.105 -csvStats HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff.csv HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann.vcf.gz
Warnings 0
Errors 0
Number of lines (input file) 0
Number of variants (before filter) 0
Number of not variants
(i.e. reference equals alternative) 		0
Number of variants processed
(i.e. after filter and non-variants) 		0
Number of known variants
(i.e. non-empty ID) 		0 ( 0% )
Number of multi-allelic VCF entries
(i.e. more than two alleles) 		0
Number of effects 0
Genome total length 63,147,197,748
Genome effective length 0
Variant rate 1 variant every 0 bases

Variants rate details

Chromosome Length Variants Variants rate
Total 0 0 0

Number variants by type

Type Total
SNP 0
MNP 0
INS 0
DEL 0
MIXED 0
INV 0
DUP 0
BND 0
INTERVAL 0
Total 0

Number of effects by impact

Type (alphabetical order)   Count Percent

Number of effects by functional class

Type (alphabetical order)   Count Percent

Missense / Silent ratio: 0

Number of effects by type and region

Type Region
Type (alphabetical order)   Count Percent

Type (alphabetical order)   Count Percent

Quality:
Insertions and deletions length:
Base changes (SNPs)

  A C G T
A 0 0 0 0
C 0 0 0 0
G 0 0 0 0
T 0 0 0 0

Ts/Tv (transitions / transversions)

Note: Only SNPs are used for this statistic.
Note: This Ts/Tv ratio is a 'raw' ratio (ratio of observed events).

Transitions 0
Transversions 0
Ts/Tv ratio 0

All variants: 

No results available (empty input?)

Only known variants (i.e. the ones having a non-empty ID field): 

No results available (empty input?)
Allele frequency


Allele Count


Hom/Het per sample 









	

 



 Codon changes 


	

		How to read this table: 

		- Rows are reference codons and columns are changed codons. E.g. Row 'AAA' column 'TAA' indicates how many 'AAA' codons have been replaced by 'TAA' codons.

		- Red background colors indicate that more changes happened (heat-map).

		- Diagonals are indicated using grey background color 
 
		- WARNING: This table may include different translation codon tables (e.g. mamalian DNA and mitochondrial DNA).

		

	


  


	
		
 
			   
			
		

	








 



 Amino acid changes
 

	

		How to read this table: 

		- Rows are reference amino acids and columns are changed amino acids. E.g. Row 'A' column 'E' indicates how many 'A' amino acids have been replaced by 'E' amino acids.

		- Red background colors indicate that more changes happened (heat-map).

		- Diagonals are indicated using grey background color 
 
		- WARNING: This table may include different translation codon tables (e.g. mamalian DNA and mitochondrial DNA).

		

	




	
		
 
			   
			
		

	








 



 Variants by chromosome
 










	

	 Details by gene 

	

	Here you can find a tab-separated table.