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 ebola_zaire
Date 2018-11-14 15:49
SnpEff version 
SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani
Command line arguments 
SnpEff  ebola_zaire -s all_effects_report.html
Warnings 0
Errors 0
Number of lines (input file) 24
Number of variants (before filter) 24
Number of not variants
(i.e. reference equals alternative) 		0
Number of variants processed
(i.e. after filter and non-variants) 		24
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 117
Genome total length 18,959
Genome effective length 18,959
Variant rate 1 variant every 789 bases

Variants rate details

Chromosome Length Variants Variants rate
KJ660346 18,959 24 789
Total 18,959 24 789

Number variants by type

Type Total
SNP 24
MNP 0
INS 0
DEL 0
MIXED 0
INV 0
DUP 0
BND 0
INTERVAL 0
Total 24

Number of effects by impact

Type (alphabetical order)   Count Percent
LOW   12 10.256%
MODERATE   12 10.256%
MODIFIER   93 79.487%

Number of effects by functional class

Type (alphabetical order)   Count Percent
MISSENSE   12 50%
SILENT   12 50%

Missense / Silent ratio: 1

Number of effects by type and region

Type Region
Type (alphabetical order)   Count Percent
downstream_gene_variant   57 48.718%
intergenic_region   6 5.128%
missense_variant   12 10.256%
synonymous_variant   12 10.256%
upstream_gene_variant   30 25.641%

Type (alphabetical order)   Count Percent
DOWNSTREAM   57 48.718%
EXON   24 20.513%
INTERGENIC   6 5.128%
UPSTREAM   30 25.641%

Quality: 

	

		
 Min3 

		
 Max670 

		
 Mean260 

		
 Median135 

		
 Standard deviation257.674 

		
 Values3,4,22,23,51,95,108,162,353,430,463,472,484,509,571,587,604,612,670 

		
 Count4,3,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
Insertions and deletions length:
Base changes (SNPs)

  A C G T
A 0 2 3 0
C 1 0 0 5
G 5 0 0 2
T 1 4 1 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 35
Transversions 11
Ts/Tv ratio 3.1818

All variants: 

Sample ,bam/SRR1972917.bam,bam/SRR1972918.bam,bam/SRR1972919.bam,bam/SRR1972920.bam,bam/SRR1972921.bam,Total
Transitions ,10,10,2,3,10,35
Transversions ,4,2,3,1,1,11
Ts/Tv ,2.500,5.000,0.667,3.000,10.000,3.182

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

No results available (empty input?)
Allele frequency


Min10
Max50
Mean28.042
Median20.5
Standard deviation16.897
Values10,12,16,25,30,33,50
Count2,5,5,2,1,1,8

Allele Count


Min1
Max5
Mean1.917
Median1
Standard deviation1.213
Values1,2,3,4,5
Count13,4,4,2,1

Hom/Het per sample 




Sample_names , bam/SRR1972917.bam, bam/SRR1972918.bam, bam/SRR1972919.bam, bam/SRR1972920.bam, bam/SRR1972921.bam
Reference , 5, 12, 2, 7, 13
Het , 14, 12, 5, 4, 11
Hom , 0, 0, 0, 0, 0
Missing , 5, 0, 17, 13, 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).

  AAA AAG AGC ATA ATC ATG ATT CAA CAG CCA CCC CCT CGT CTA CTG GAC GAT GCA GCG GTA GTC GTG GTT TGT TTC TTT
AAA                                                    
AAG 1                                                  
AGC         1                                          
ATA                                                    
ATC             1                                      
ATG       1                                            
ATT                                                    
CAA                                                    
CAG               1                                    
CCA                     1                              
CCC                                                    
CCT                     1                              
CGT                                               1    
CTA                   3                                
CTG                           1                        
GAC                                                    
GAT                               1                    
GCA                                       1            
GCG                                           3        
GTA                                           1        
GTC                               1             3      
GTG                                                    
GTT                                                   1
TGT                                                    
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 C D F I K L M P Q R S V
A                         4
C                          
D     1                    
F       1                  
I         1                
K           1              
L             1   3        
M         1                
P                 2        
Q                   1      
R   1                      
S         1                
V     1 1                 4

Variants by chromosome

		

		KJ660346, 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
KJ660346,Count,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,1,0,0,2,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,1,0,0,0,1,0,0,1,0,0,0,0,0,0,1,0,1,0,1,0,0,0,0
Details by gene

Here you can find a tab-separated table.