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 H1N1_10
Date 2021-05-26 16:42
SnpEff version 
SnpEff 4.3u (build 2018-03-26 14:13), by Pablo Cingolani
Command line arguments 
SnpEff  H1N1_10 freebayes/full_AF_0.1_frac_0.1_freebayes-default.vcf
Warnings 0
Errors 0
Number of lines (input file) 110
Number of variants (before filter) 110
Number of not variants
(i.e. reference equals alternative) 		0
Number of variants processed
(i.e. after filter and non-variants) 		110
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 124
Genome total length 13,133
Genome effective length 13,133
Variant rate 1 variant every 119 bases

Variants rate details

Chromosome Length Variants Variants rate
H1N1_HA 1,701 13 130
H1N1_MP 982 8 122
H1N1_NA 1,410 12 117
H1N1_NP 1,497 11 136
H1N1_NS 838 6 139
H1N1_PA 2,151 27 79
H1N1_PB1 2,274 16 142
H1N1_PB2 2,280 17 134
Total 13,133 110 119

Number variants by type

Type Total
SNP 107
MNP 3
INS 0
DEL 0
MIXED 0
INV 0
DUP 0
BND 0
INTERVAL 0
Total 110

Number of effects by impact

Type (alphabetical order)   Count Percent
LOW   32 25.806%
MODERATE   79 63.71%
MODIFIER   13 10.484%

Number of effects by functional class

Type (alphabetical order)   Count Percent
MISSENSE   77 71.296%
SILENT   31 28.704%

Missense / Silent ratio: 2.4839

Number of effects by type and region

Type Region
Type (alphabetical order)   Count Percent
downstream_gene_variant   4 3.226%
intron_variant   9 7.258%
missense_variant   79 63.71%
synonymous_variant   32 25.806%

Type (alphabetical order)   Count Percent
DOWNSTREAM   4 3.226%
EXON   111 89.516%
INTRON   9 7.258%

Quality: 

	

		
 Min0 

		
 Max0 

		
 Mean0 

		
 Median0 

		
 Standard deviation0 

		
 Values0 

		
 Count110
Insertions and deletions length:
Base changes (SNPs)

  A C G T
A 0 4 23 3
C 5 0 1 16
G 35 0 0 4
T 1 14 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 0
Transversions 0
Ts/Tv ratio 0

All variants: 

Sample ,full_AF_0.1_frac_0.1,Total
Transitions ,0,0
Transversions ,0,0
Ts/Tv ,NaN,NaN

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

No results available (empty input?)
Allele frequency


Min0
Max0
Mean0
Median0
Standard deviation0
Values0
Count110

Allele Count


Min0
Max0
Mean0
Median0
Standard deviation0
Values0
Count110

Hom/Het per sample 




Sample_names , full_AF_0.1_frac_0.1
Reference , 110
Het , 0
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).

  AAA AAC AAG AAT ACA ACC ACT AGA AGC AGG AGT ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT CGA CGG CGT CTA CTC CTT GAA GAC GAG GAT GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT TAC TAT TCA TCC TCG TCT TGC TGG TGT TTA TTC TTG TTT
AAA     2         1               1                           1                                                        
AAC 1               1                                                                                                  
AAG       1           2                                                                                                
AAT                     1                                                                                              
ACA 1                     1                                                                                            
ACC         1                                                                                                          
ACT         1                   1               1                           1                                          
AGA 4                 1                                                       1                                        
AGC   1                                                                         1                                      
AGG     1                                                                                                              
AGT       1         2                                                                                         1        
ATA                         1 1 1                                                     1                                
ATC           1                                                                                                        
ATG                       1                                                               1                            
ATT                                                                                                                    
CAA                                       1                   1                                                        
CAC                                                                                                                    
CAG                               2                                                                                    
CAT                                                                                                                    
CCA                                           1                                                                        
CCC                                             1                                                                      
CCG                                                                                                                    
CCT                                     1                                                               1              
CGA                               2                                                                                    
CGG                                               1                                                                    
CGT                                                                                                           2        
CTA                                       1                                                                         1  
CTC                                         1                                                                     2    
CTT                                                       1                                                            
GAA 1                                                             1           3                                        
GAC                                                                 1                                                  
GAG     4                                                     1                   2                                    
GAT                                                                                         1                          
GCA         1                                                                                     1                    
GCC                                                                                                 1                  
GCG                                                                   1                                                
GCT                                             1                       1                                              
GGA                                                                               1                                    
GGC                                                                                                                    
GGG                                                               3           2                                        
GGT                     2                                           1             1                                    
GTA                       2                                           1                   1                            
GTC                                                                                         2                          
GTG                           1                                                       2   1                            
GTT                             1                                                                                      
TAC                                 1                                                                                  
TAT                                                                                                                    
TCA                                       1                                                                            
TCC                                                                                                               2    
TCG                                                                                                                    
TCT                                             1                                                                     1
TGC                                                                                                                    
TGG                                                                                                           1        
TGT                                                                                             1         1            
TTA                                                                                                                    
TTC                                                       1                                                     1     2
TTG                                                                                                   1                
TTT                                                         1                                                   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 E F G H I K L M N P Q R S T V W Y
A 2                       1     2 1      
C   1                                   1
D     1                             1    
E       2   5     5                      
F         2         4                    
G     1 3   4                   2        
H                                        
I               2     1           1 1    
K       1         2     1   1 3          
L         2         2     2     1        
M               1                   1    
N                 1             2        
P             1           2     1        
Q       1                 1 2            
R   2       1     5         2 2          
S   1     3 1           2 2     2        
T 1             2 1       1       2      
V 1             3     1             6    
W   1                                    
Y             1                          

Variants by chromosome

		

		H1N1_HA, Position,0,10,20,30,40,50,60,70,80,90,100,110,120,130,140,150,160,170,180,190,200,210,220,230,240,250,260,270,280,290,300,310,320,330,340,350,360,370,380,390,400,410,420,430,440,450,460,470,480,490,500,510,520,530,540,550,560,570,580,590,600,610,620,630,640,650,660,670,680,690,700,710,720,730,740,750,760,770,780,790,800,810,820,830,840,850,860,870,880,890,900,910,920,930,940,950,960,970,980,990,1000,1010,1020,1030,1040,1050,1060,1070,1080,1090,1100,1110,1120,1130,1140,1150,1160,1170,1180,1190,1200,1210,1220,1230,1240,1250,1260,1270,1280,1290,1300,1310,1320,1330,1340,1350,1360,1370,1380,1390,1400,1410,1420,1430,1440,1450,1460,1470,1480,1490,1500,1510,1520,1530,1540,1550,1560,1570,1580,1590,1600,1610,1620,1630,1640,1650,1660,1670,1680,1690,1700
H1N1_HA,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0

	
		

		H1N1_MP, Position,0,10,20,30,40,50,60,70,80,90,100,110,120,130,140,150,160,170,180,190,200,210,220,230,240,250,260,270,280,290,300,310,320,330,340,350,360,370,380,390,400,410,420,430,440,450,460,470,480,490,500,510,520,530,540,550,560,570,580,590,600,610,620,630,640,650,660,670,680,690,700,710,720,730,740,750,760,770,780,790,800,810,820,830,840,850,860,870,880,890,900,910,920,930,940,950,960,970,980
H1N1_MP,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,1,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0

	
		

		H1N1_NA, Position,0,10,20,30,40,50,60,70,80,90,100,110,120,130,140,150,160,170,180,190,200,210,220,230,240,250,260,270,280,290,300,310,320,330,340,350,360,370,380,390,400,410,420,430,440,450,460,470,480,490,500,510,520,530,540,550,560,570,580,590,600,610,620,630,640,650,660,670,680,690,700,710,720,730,740,750,760,770,780,790,800,810,820,830,840,850,860,870,880,890,900,910,920,930,940,950,960,970,980,990,1000,1010,1020,1030,1040,1050,1060,1070,1080,1090,1100,1110,1120,1130,1140,1150,1160,1170,1180,1190,1200,1210,1220,1230,1240,1250,1260,1270,1280,1290,1300,1310,1320,1330,1340,1350,1360,1370,1380,1390,1400,1410
H1N1_NA,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,1,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0

	
		

		H1N1_NP, Position,0,10,20,30,40,50,60,70,80,90,100,110,120,130,140,150,160,170,180,190,200,210,220,230,240,250,260,270,280,290,300,310,320,330,340,350,360,370,380,390,400,410,420,430,440,450,460,470,480,490,500,510,520,530,540,550,560,570,580,590,600,610,620,630,640,650,660,670,680,690,700,710,720,730,740,750,760,770,780,790,800,810,820,830,840,850,860,870,880,890,900,910,920,930,940,950,960,970,980,990,1000,1010,1020,1030,1040,1050,1060,1070,1080,1090,1100,1110,1120,1130,1140,1150,1160,1170,1180,1190,1200,1210,1220,1230,1240,1250,1260,1270,1280,1290,1300,1310,1320,1330,1340,1350,1360,1370,1380,1390,1400,1410,1420,1430,1440,1450,1460,1470,1480,1490
H1N1_NP,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0

	
		

		H1N1_NS, Position,0,10,20,30,40,50,60,70,80,90,100,110,120,130,140,150,160,170,180,190,200,210,220,230,240,250,260,270,280,290,300,310,320,330,340,350,360,370,380,390,400,410,420,430,440,450,460,470,480,490,500,510,520,530,540,550,560,570,580,590,600,610,620,630,640,650,660,670,680,690,700,710,720,730,740,750,760,770,780,790,800,810,820,830
H1N1_NS,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0

	
		

		H1N1_PA, Position,0,10,20,30,40,50,60,70,80,90,100,110,120,130,140,150,160,170,180,190,200,210,220,230,240,250,260,270,280,290,300,310,320,330,340,350,360,370,380,390,400,410,420,430,440,450,460,470,480,490,500,510,520,530,540,550,560,570,580,590,600,610,620,630,640,650,660,670,680,690,700,710,720,730,740,750,760,770,780,790,800,810,820,830,840,850,860,870,880,890,900,910,920,930,940,950,960,970,980,990,1000,1010,1020,1030,1040,1050,1060,1070,1080,1090,1100,1110,1120,1130,1140,1150,1160,1170,1180,1190,1200,1210,1220,1230,1240,1250,1260,1270,1280,1290,1300,1310,1320,1330,1340,1350,1360,1370,1380,1390,1400,1410,1420,1430,1440,1450,1460,1470,1480,1490,1500,1510,1520,1530,1540,1550,1560,1570,1580,1590,1600,1610,1620,1630,1640,1650,1660,1670,1680,1690,1700,1710,1720,1730,1740,1750,1760,1770,1780,1790,1800,1810,1820,1830,1840,1850,1860,1870,1880,1890,1900,1910,1920,1930,1940,1950,1960,1970,1980,1990,2000,2010,2020,2030,2040,2050,2060,2070,2080,2090,2100,2110,2120,2130,2140,2150
H1N1_PA,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,1,2,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0

	
		

		H1N1_PB1, Position,0,10,20,30,40,50,60,70,80,90,100,110,120,130,140,150,160,170,180,190,200,210,220,230,240,250,260,270,280,290,300,310,320,330,340,350,360,370,380,390,400,410,420,430,440,450,460,470,480,490,500,510,520,530,540,550,560,570,580,590,600,610,620,630,640,650,660,670,680,690,700,710,720,730,740,750,760,770,780,790,800,810,820,830,840,850,860,870,880,890,900,910,920,930,940,950,960,970,980,990,1000,1010,1020,1030,1040,1050,1060,1070,1080,1090,1100,1110,1120,1130,1140,1150,1160,1170,1180,1190,1200,1210,1220,1230,1240,1250,1260,1270,1280,1290,1300,1310,1320,1330,1340,1350,1360,1370,1380,1390,1400,1410,1420,1430,1440,1450,1460,1470,1480,1490,1500,1510,1520,1530,1540,1550,1560,1570,1580,1590,1600,1610,1620,1630,1640,1650,1660,1670,1680,1690,1700,1710,1720,1730,1740,1750,1760,1770,1780,1790,1800,1810,1820,1830,1840,1850,1860,1870,1880,1890,1900,1910,1920,1930,1940,1950,1960,1970,1980,1990,2000,2010,2020,2030,2040,2050,2060,2070,2080,2090,2100,2110,2120,2130,2140,2150,2160,2170,2180,2190,2200,2210,2220,2230,2240,2250,2260,2270
H1N1_PB1,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0

	
		

		H1N1_PB2, Position,0,10,20,30,40,50,60,70,80,90,100,110,120,130,140,150,160,170,180,190,200,210,220,230,240,250,260,270,280,290,300,310,320,330,340,350,360,370,380,390,400,410,420,430,440,450,460,470,480,490,500,510,520,530,540,550,560,570,580,590,600,610,620,630,640,650,660,670,680,690,700,710,720,730,740,750,760,770,780,790,800,810,820,830,840,850,860,870,880,890,900,910,920,930,940,950,960,970,980,990,1000,1010,1020,1030,1040,1050,1060,1070,1080,1090,1100,1110,1120,1130,1140,1150,1160,1170,1180,1190,1200,1210,1220,1230,1240,1250,1260,1270,1280,1290,1300,1310,1320,1330,1340,1350,1360,1370,1380,1390,1400,1410,1420,1430,1440,1450,1460,1470,1480,1490,1500,1510,1520,1530,1540,1550,1560,1570,1580,1590,1600,1610,1620,1630,1640,1650,1660,1670,1680,1690,1700,1710,1720,1730,1740,1750,1760,1770,1780,1790,1800,1810,1820,1830,1840,1850,1860,1870,1880,1890,1900,1910,1920,1930,1940,1950,1960,1970,1980,1990,2000,2010,2020,2030,2040,2050,2060,2070,2080,2090,2100,2110,2120,2130,2140,2150,2160,2170,2180,2190,2200,2210,2220,2230,2240,2250,2260,2270,2280
H1N1_PB2,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0
Details by gene

Here you can find a tab-separated table.