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 H3N2
Date 2023-01-09 19:10
SnpEff version 
SnpEff 4.3u (build 2018-03-26 14:13), by Pablo Cingolani
Command line arguments 
SnpEff  H3N2 HK3GMBGXL_Flu09_E01_FluA_Rep2_Plate2.fas_BWA_timo_custom.vcf
Warnings 56
Errors 0
Number of lines (input file) 124
Number of variants (before filter) 124
Number of not variants
(i.e. reference equals alternative) 		0
Number of variants processed
(i.e. after filter and non-variants) 		73
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 157
Genome total length 13,133
Genome effective length 13,133
Variant rate 1 variant every 179 bases

Variants rate details

Chromosome Length Variants Variants rate
H3N2_HA 1,701 9 189
H3N2_M2 982 12 81
H3N2_NA 1,410 4 352
H3N2_NP 1,497 9 166
H3N2_NS2 838 16 52
H3N2_PA 2,151 9 239
H3N2_PB1 2,274 8 284
H3N2_PB2 2,280 6 380
Total 13,133 73 179

Number variants by type

Type Total
SNP 73
MNP 0
INS 0
DEL 0
MIXED 0
INV 0
DUP 0
BND 0
INTERVAL 0
Total 73

Number of effects by impact

Type (alphabetical order)   Count Percent
LOW   38 24.204%
MODERATE   37 23.567%
MODIFIER   82 52.229%

Number of effects by functional class

Type (alphabetical order)   Count Percent
MISSENSE   37 49.333%
SILENT   38 50.667%

Missense / Silent ratio: 0.9737

Number of effects by type and region

Type Region
Type (alphabetical order)   Count Percent
downstream_gene_variant   35 22.293%
missense_variant   37 23.567%
synonymous_variant   38 24.204%
upstream_gene_variant   47 29.936%

Type (alphabetical order)   Count Percent
DOWNSTREAM   35 22.293%
EXON   75 47.771%
UPSTREAM   47 29.936%

Quality: 

	

		
 Min0 

		
 Max0 

		
 Mean0 

		
 Median0 

		
 Standard deviation0 

		
 Values0 

		
 Count51
Insertions and deletions length:
Base changes (SNPs)

  A C G T
A 0 1 37 0
C 4 0 1 5
G 11 0 0 1
T 0 12 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 65
Transversions 8
Ts/Tv ratio 8.125

All variants: 

Sample ,sample,Total
Transitions ,65,65
Transversions ,8,8
Ts/Tv ,8.125,8.125

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
Count73

Allele Count


Min1
Max1
Mean1
Median1
Standard deviation0
Values1
Count73

Hom/Het per sample 




Sample_names , sample
Reference , 0
Het , 73
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 ACG ACT AGA AGG AGT ATA ATC ATG ATT CAA CAG CCA CCC CCT CGC CNN CTC GAA GAC GAG GCA GCC GCG GCT GGA GGC GGG GGT GNN GTA GTG GTT NAN NGN NNG NNN TCA TCC TCG TCT TGC TGG TGT TTA TTC TTG TTT
AAA     3           1                                                                                        
AAC                                                                                                          
AAG 1                                                                                                        
AAT   1                                                                                                      
ACA             1                                                                                            
ACC                                                       3                                                  
ACG                                                                                                          
ACT       1                     1                                                                            
AGA                   5                                         1                                            
AGG                                                                                                          
AGT       3                                                           1                                      
ATA                                                                                                          
ATC                                                                                                          
ATG                       2                                                                                  
ATT                                                                                                          
CAA                                 1                                                                        
CAG                                                                                                          
CCA                                                                                                          
CCC                                                                                                          
CCT                                     1                                                     2              
CGC                                                                                             1            
CNN                                                                                                          
CTC                         1                                                                                
GAA 1                                                 1                                                      
GAC                                                       1       4                                          
GAG                                                                 3                                        
GCA                                                         3                                                
GCC                                                                                                          
GCG                                                                                                          
GCT                                                       1                   1                              
GGA                                                                 4                                        
GGC                                                             1                                            
GGG                                                                                                          
GGT                     1                                         1                                          
GNN                                                                                                          
GTA                                                                                                          
GTG                                                                 1     1   1                              
GTT                             1                                                                            
NAN                                                                                                          
NGN                                                                                                          
NNG                                                                                                          
NNN                                           1                         1       2 4 1                        
TCA                                   2                                                                      
TCC                                                                                                          
TCG                                                                                               1          
TCT                                                                                                          
TGC                                         2                                                                
TGG                                                                                                          
TGT                                                                                             1            
TTA                                                                                                       1  
TTC                                                                                       1           1      
TTG                                                                                                          
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 E F G I K L M N P Q R S T V W
? 9                                    
A   4                               1  
C     1                       2        
D   1         4                        
E         1   3   1                    
F           1       1           1      
G             6                 1      
I                                      
K                 4           1        
L               1   1                  
M               2                      
N                       1              
P                         1     2      
Q                           1          
R     1       1               5        
S             1         3 2           1
T   3           1       1         1    
V             1 1                   2  
W                                      

Variants by chromosome

		

		H3N2_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
H3N2_HA,Count,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0

	
		

		H3N2_M2, 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
H3N2_M2,Count,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,1,0,0,0,1,0,0

	
		

		H3N2_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
H3N2_NA,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0

	
		

		H3N2_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
H3N2_NP,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0

	
		

		H3N2_NS2, 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
H3N2_NS2,Count,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,1,0,2,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,1,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,2,0,0

	
		

		H3N2_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
H3N2_PA,Count,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0

	
		

		H3N2_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
H3N2_PB1,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0

	
		

		H3N2_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
H3N2_PB2,Count,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0
Details by gene

Here you can find a tab-separated table.