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 2026-06-08 20:34
SnpEff version 
SnpEff 5.1d (build 2022-04-19 15:49), by Pablo Cingolani
Command line arguments 
SnpEff  GRCh38.105 -csvStats HCC1395_BL.tnseq_tumor_only.filtered_snpEff.csv HCC1395_BL.tnseq_tumor_only.filtered.vcf.gz
Warnings 55
Errors 0
Number of lines (input file) 180
Number of variants (before filter) 250
Number of not variants
(i.e. reference equals alternative) 		0
Number of variants processed
(i.e. after filter and non-variants) 		250
Number of known variants
(i.e. non-empty ID) 		0 ( 0% )
Number of multi-allelic VCF entries
(i.e. more than two alleles) 		29
Number of effects 362
Genome total length 63,147,197,748
Genome effective length 46,709,983
Variant rate 1 variant every 186,839 bases

Variants rate details

Chromosome Length Variants Variants rate
21 46,709,983 250 186,839
Total 46,709,983 250 186,839

Number variants by type

Type Total
SNP 91
MNP 4
INS 64
DEL 91
MIXED 0
INV 0
DUP 0
BND 0
INTERVAL 0
Total 250

Number of effects by impact

Type (alphabetical order)   Count Percent
HIGH   2 0.552%
LOW   14 3.867%
MODERATE   26 7.182%
MODIFIER   320 88.398%

Number of effects by functional class

Type (alphabetical order)   Count Percent
MISSENSE   19 67.857%
SILENT   9 32.143%

Missense / Silent ratio: 2.1111

Number of effects by type and region

Type Region
Type (alphabetical order)   Count Percent
3_prime_UTR_variant   17 4.632%
5_prime_UTR_premature_start_codon_gain_variant   1 0.272%
5_prime_UTR_variant   8 2.18%
conservative_inframe_insertion   1 0.272%
disruptive_inframe_deletion   1 0.272%
disruptive_inframe_insertion   3 0.817%
downstream_gene_variant   36 9.809%
frameshift_variant   1 0.272%
intragenic_variant   24 6.54%
intron_variant   203 55.313%
missense_variant   21 5.722%
non_coding_transcript_exon_variant   8 2.18%
splice_acceptor_variant   1 0.272%
splice_region_variant   4 1.09%
synonymous_variant   9 2.452%
upstream_gene_variant   29 7.902%

Type (alphabetical order)   Count Percent
DOWNSTREAM   36 9.945%
EXON   43 11.878%
INTRON   199 54.972%
SPLICE_SITE_ACCEPTOR   1 0.276%
SPLICE_SITE_REGION   4 1.105%
TRANSCRIPT   24 6.63%
UPSTREAM   29 8.011%
UTR_3_PRIME   17 4.696%
UTR_5_PRIME   9 2.486%

Quality:
Insertions and deletions length: 

	

		
 Min0 

		
 Max32 

		
 Mean2.148 

		
 Median1 

		
 Standard deviation3.934 

		
 Values0,1,2,3,4,5,6,7,9,11,12,13,17,18,32 

		
 Count25,102,2,5,1,4,1,4,2,4,1,1,1,1,1
Base changes (SNPs)

  A C G T
A 0 1 15 1
C 7 0 3 14
G 18 3 0 10
T 3 9 7 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 56
Transversions 35
Ts/Tv ratio 1.6

All variants: 

Sample ,HCC1395_BL,Total
Transitions ,56,56
Transversions ,35,35
Ts/Tv ,1.600,1.600

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

No results available (empty input?)
Allele frequency


Min50
Max450
Mean69.444
Median50
Standard deviation57.99
Values50,100,150,200,250,300,350,450
Count151,14,5,3,2,3,1,1

Allele Count


Min1
Max9
Mean1.389
Median1
Standard deviation1.16
Values1,2,3,4,5,6,7,9
Count151,14,5,3,2,3,1,1

Hom/Het per sample 




Sample_names , HCC1395_BL
Reference , 0
Het , 151
Hom , 14
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).

  - AAT ACA ACC ACG ACT AGC AGT ATA ATC ATG CAA CAC CAG CAT CCA CCC CCG CGC CTC CTG GAA GAG GCA GCG GGA GGC GGG GTG GTT TCC TCG TGC TGT TTG
-   1       1                 1               2                        
AAT               1                                                      
ACA                                                                      
ACC                                 1                                    
ACG           1                                                          
ACT                                                                      
AGC                                                     1                
AGT                                                                      
ATA     1                                                                
ATC       1                                                              
ATG                                                                      
CAA                                                                      
CAC                       1     2                                        
CAG                                                                      
CAT                         1                                            
CCA 2                                                                    
CCC                               2                             1        
CCG                                         1                            
CGC                         1                                            
CTC                                 2                                    
CTG                                                                      
GAA                                                                      
GAG                           1               2     1                    
GCA     1                                                                
GCG                     1                       1 1                      
GGA                                                                      
GGC 1                                                                    
GGG                                                   1                  
GTG                     2                                                
GTT                                                           1          
TCC                                     1                                
TCG                                                                     1
TGC                                                     1             2  
TGT                                                                 2    
TTG                                                                      

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 C E G H I L M N P Q R S T V
-   1     2   1       1         1  
?                                  
A     1   1         1           1  
C       4   1                      
E     1   2               1        
G 1         1                      
H             3           1        
I                               2  
L                       2          
M                                  
N                             1    
P 2               1     2     1    
Q                                  
R             1                    
S           1     1         1      
T                       1       1  
V                   2             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,0,0,0,0,0,1,0,0,0,0,18,0,0,0,3,2,0,1,7,0,0,2,0,0,0,3,0,0,6,1,2,6,13,8,13,4,8,7,3,10,2,56,2,3,30,17,22
Details by gene

Here you can find a tab-separated table.