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 2026-05-28 23:06
SnpEff version 
SnpEff 5.1d (build 2022-04-19 15:49), by Pablo Cingolani
Command line arguments 
SnpEff  GRCh38.105 -csvStats custom_Sig_18_tumor_normal.manta.diploid_sv_custom.ann_snpEff.csv custom_Sig_18_tumor_normal.manta.diploid_sv_custom.ann.vcf.gz
Warnings 2
Errors 0
Number of lines (input file) 6
Number of variants (before filter) 6
Number of not variants
(i.e. reference equals alternative) 		0
Number of variants processed
(i.e. after filter and non-variants) 		6
Number of known variants
(i.e. non-empty ID) 		4 ( 66.667% )
Number of multi-allelic VCF entries
(i.e. more than two alleles) 		0
Number of effects 19
Genome total length 63,147,197,748
Genome effective length 46,709,983
Variant rate 1 variant every 7,784,997 bases

Variants rate details

Chromosome Length Variants Variants rate
21 46,709,983 6 7,784,997
Total 46,709,983 6 7,784,997

Number variants by type

Type Total
SNP 0
MNP 0
INS 1
DEL 2
MIXED 1
INV 0
DUP 0
BND 2
INTERVAL 0
Total 6

Number of effects by impact

Type (alphabetical order)   Count Percent
HIGH   12 63.158%
MODERATE   1 5.263%
MODIFIER   6 31.579%

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
bidirectional_gene_fusion   12 63.158%
conservative_inframe_deletion   1 5.263%
downstream_gene_variant   1 5.263%
intragenic_variant   1 5.263%
intron_variant   2 10.526%
upstream_gene_variant   2 10.526%

Type (alphabetical order)   Count Percent
DOWNSTREAM   1 5.263%
EXON   1 5.263%
GENE   12 63.158%
INTRON   2 10.526%
TRANSCRIPT   1 5.263%
UPSTREAM   2 10.526%

Quality: 

	

		
 Min563 

		
 Max999 

		
 Mean786.667 

		
 Median798 

		
 Standard deviation232.931 

		
 Values563,597,999 

		
 Count2,1,3
Insertions and deletions length: 

	

		
 Min1 

		
 Max56 

		
 Mean19.333 

		
 Median1 

		
 Standard deviation31.754 

		
 Values1,56 

		
 Count2,1
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


Min50
Max100
Mean58.333
Median50
Standard deviation20.412
Values50,100
Count5,1

Allele Count


Min1
Max2
Mean1.167
Median1
Standard deviation0.408
Values1,2
Count5,1

Hom/Het per sample 




Sample_names , Sig_18_Blood
Reference , 0
Het , 5
Hom , 1
Missing , 0

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).

  - AAC ACC AGA AGC AGG AGT CAG CCC CGG CTC GAG GCG GGG GTG
-                              
AAC 1                            
ACC 2                            
AGA 1                            
AGC 11                            
AGG 1                            
AGT 1                            
CAG 7                            
CCC 4                            
CGG 1                            
CTC 1                            
GAG 1                            
GCG 1                            
GGG 2                            
GTG 1                            

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).

  - A E G L N P Q R S T V
-                        
A 1                      
E 1                      
G 2                      
L 1                      
N 1                      
P 4                      
Q 7                      
R 3                      
S 12                      
T 2                      
V 1                      

Variants by chromosome

		

		21, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000
21,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,2,2,0
Details by gene

Here you can find a tab-separated table.