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 nCoV-2019.reference
Date 2024-04-26 12:25
SnpEff version
SnpEff 5.0e (build 2021-03-09 06:01), by Pablo Cingolani
Command line arguments
SnpEff  nCoV-2019.reference SAMPLE2_PE.vcf.gz -csvStats SAMPLE2_PE.snpeff.csv 
Warnings 6
Errors 0
Number of lines (input file) 8
Number of variants (before filter) 8
Number of not variants
(i.e. reference equals alternative)
0
Number of variants processed
(i.e. after filter and non-variants)
8
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 49
Genome total length 29,903
Genome effective length 29,903
Variant rate 1 variant every 3,737 bases


Variants rate details

Chromosome Length Variants Variants rate
MN908947.3 29,903 8 3,737
Total 29,903 8 3,737


Number variants by type

Type Total
SNP 7
MNP 0
INS 1
DEL 0
MIXED 0
INV 0
DUP 0
BND 0
INTERVAL 0
Total 8


Number of effects by impact

Type (alphabetical order)   Count Percent
HIGH   1 2.041%
LOW   1 2.041%
MODERATE   6 12.245%
MODIFIER   41 83.673%


Number of effects by functional class

Type (alphabetical order)   Count Percent
MISSENSE   6 85.714%
SILENT   1 14.286%

Missense / Silent ratio: 6


Number of effects by type and region

Type Region
Type (alphabetical order)   Count Percent
downstream_gene_variant   23 46.939%
frameshift_variant   1 2.041%
missense_variant   6 12.245%
synonymous_variant   1 2.041%
upstream_gene_variant   18 36.735%

Type (alphabetical order)   Count Percent
DOWNSTREAM   23 46.939%
EXON   8 16.327%
UPSTREAM   18 36.735%


Quality:

	

Insertions and deletions length:

	
Min0
Max0
Mean0
Median0
Standard deviation0
Values0
Count1


Base changes (SNPs)

  A C G T
A 0 0 0 0
C 0 0 0 4
G 0 0 0 1
T 1 1 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 5
Transversions 2
Ts/Tv ratio 2.5

All variants:

Sample ,SAMPLE2_PE,Total
Transitions ,5,5
Transversions ,2,2
Ts/Tv ,2.500,2.500

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

No results available (empty input?)


Allele frequency


Min50
Max50
Mean50
Median50
Standard deviation0
Values50
Count8


Allele Count


Min1
Max1
Mean1
Median1
Standard deviation0
Values1
Count8


Hom/Het per sample




Sample_names , SAMPLE2_PE
Reference , 0
Het , 8
Hom , 0
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).

  ACT ATT GAC GAT GCA GGA GTA TAT TCA TTA TTC TTT
ACT   1                    
ATT                        
GAC       1                
GAT                        
GCA             1          
GGA             1          
GTA                        
TAT                        
TCA                   1 1  
TTA                 1      
TTC                        
TTT               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 D F G I L S T V Y
-   1                    
?                        
A                     1  
D       1                
F                       1
G                     1  
I                        
L                 1      
S         1     1        
T             1          
V                        
Y                        


Variants by chromosome

		
MN908947.3, Position,0,100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500,1600,1700,1800,1900,2000,2100,2200,2300,2400,2500,2600,2700,2800,2900,3000,3100,3200,3300,3400,3500,3600,3700,3800,3900,4000,4100,4200,4300,4400,4500,4600,4700,4800,4900,5000,5100,5200,5300,5400,5500,5600,5700,5800,5900,6000,6100,6200,6300,6400,6500,6600,6700,6800,6900,7000,7100,7200,7300,7400,7500,7600,7700,7800,7900,8000,8100,8200,8300,8400,8500,8600,8700,8800,8900,9000,9100,9200,9300,9400,9500,9600,9700,9800,9900,10000,10100,10200,10300,10400,10500,10600,10700,10800,10900,11000,11100,11200,11300,11400,11500,11600,11700,11800,11900,12000,12100,12200,12300,12400,12500,12600,12700,12800,12900,13000,13100,13200,13300,13400,13500,13600,13700,13800,13900,14000,14100,14200,14300,14400,14500,14600,14700,14800,14900,15000,15100,15200,15300,15400,15500,15600,15700,15800,15900,16000,16100,16200,16300,16400,16500,16600,16700,16800,16900,17000,17100,17200,17300,17400,17500,17600,17700,17800,17900,18000,18100,18200,18300,18400,18500,18600,18700,18800,18900,19000,19100,19200,19300,19400,19500,19600,19700,19800,19900,20000,20100,20200,20300,20400,20500,20600,20700,20800,20900,21000,21100,21200,21300,21400,21500,21600,21700,21800,21900,22000,22100,22200,22300,22400,22500,22600,22700,22800,22900,23000,23100,23200,23300,23400,23500,23600,23700,23800,23900,24000,24100,24200,24300,24400,24500,24600,24700,24800,24900,25000,25100,25200,25300,25400,25500,25600,25700,25800,25900,26000,26100,26200,26300,26400,26500,26600,26700,26800,26900,27000,27100,27200,27300,27400,27500,27600,27700,27800,27900,28000,28100,28200,28300,28400,28500,28600,28700,28800,28900,29000,29100,29200,29300,29400,29500,29600,29700,29800,29900 MN908947.3,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0

Details by gene

Here you can find a tab-separated table.