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 16:39
SnpEff version
SnpEff 4.3u (build 2018-03-26 14:13), by Pablo Cingolani
Command line arguments
SnpEff  H1N1_10 varscan/full_AF_0.05_frac_0.002_varscan.vcf 
Warnings 0
Errors 0
Number of lines (input file) 115
Number of variants (before filter) 115
Number of not variants
(i.e. reference equals alternative)
0
Number of variants processed
(i.e. after filter and non-variants)
115
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 129
Genome total length 13,133
Genome effective length 13,133
Variant rate 1 variant every 114 bases


Variants rate details

Chromosome Length Variants Variants rate
H1N1_HA 1,701 9 189
H1N1_MP 982 10 98
H1N1_NA 1,410 11 128
H1N1_NP 1,497 15 99
H1N1_NS 838 4 209
H1N1_PA 2,151 28 76
H1N1_PB1 2,274 20 113
H1N1_PB2 2,280 18 126
Total 13,133 115 114


Number variants by type

Type Total
SNP 115
MNP 0
INS 0
DEL 0
MIXED 0
INV 0
DUP 0
BND 0
INTERVAL 0
Total 115


Number of effects by impact

Type (alphabetical order)   Count Percent
HIGH   1 0.775%
LOW   34 26.357%
MODERATE   82 63.566%
MODIFIER   12 9.302%


Number of effects by functional class

Type (alphabetical order)   Count Percent
MISSENSE   82 70.69%
SILENT   34 29.31%

Missense / Silent ratio: 2.4118


Number of effects by type and region

Type Region
Type (alphabetical order)   Count Percent
downstream_gene_variant   2 1.538%
intron_variant   11 8.462%
missense_variant   82 63.077%
splice_acceptor_variant   1 0.769%
synonymous_variant   34 26.154%

Type (alphabetical order)   Count Percent
DOWNSTREAM   2 1.55%
EXON   116 89.922%
INTRON   10 7.752%
SPLICE_SITE_ACCEPTOR   1 0.775%


Quality:

	

Insertions and deletions length:

	

Base changes (SNPs)

  A C G T
A 0 8 26 3
C 4 0 0 14
G 34 1 0 4
T 2 15 4 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 89
Transversions 26
Ts/Tv ratio 3.4231

All variants:

Sample ,sample,Total
Transitions ,89,89
Transversions ,26,26
Ts/Tv ,3.423,3.423

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
Count115


Allele Count


Min1
Max1
Mean1
Median1
Standard deviation0
Values1
Count115


Hom/Het per sample




Sample_names , sample
Reference , 0
Het , 115
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 AGC AGG AGT ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT CGA CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT TAC TAT TCA TCC TCG TCT TGC TGT TTA TTC TTG TTT
AAA     3           1               2                             1                                                      
AAC 1                 1               1                                                                                  
AAG       1             2                                                                                                
AAT               1       1               1                                                                              
ACA             1           1                                                                                            
ACC         1                                                                                                            
ACG                                                                                                                      
ACT         1                     1               1                             1                                        
AGA 3                   1                                                         1                                      
AGC   1                                                                             1                                    
AGG     1                                                                                                                
AGT       1           2                                                                                         1        
ATA                             1 1                                                       1                              
ATC           1                                                                                                          
ATG                         1                                 1                               1                          
ATT                                                                                                                      
CAA                                         1                                                                            
CAC                                                                                                                      
CAG                                 3                                                                                    
CAT                                     1                                                                                
CCA                                             1                                                                        
CCC                                               1                                                                      
CCG                                                                                                                      
CCT                                       1                                                                 1            
CGA                                 1                                                                                    
CGG                                                 1         1                                                          
CGT                                                                                                             2        
CTA                                         1                 1                                                   1      
CTC                                           1                                                                     1    
CTG                                                                                                                      
CTT                                                         1 1                                                          
GAA 1                                                                 1           3                                      
GAC   1                                                                                                                  
GAG     4                                                         1                   2                                  
GAT                                                                                             1                        
GCA         1                                                                                         1                  
GCC                                                                                                     1                
GCG                                                                       1                                              
GCT                                               1                         1 1                                          
GGA                                                                                   1                                  
GGC                                                                                                                      
GGG                                                                   3                                                  
GGT                       2                                             1             1                                  
GTA                         2                                             1                   1                          
GTC                                                                                             2                        
GTG                             1                                                         2                              
GTT                               1                                                                                      
TAC                                   1                                                                                  
TAT                                                                                                                      
TCA                                         1                                                                            
TCC                                                                                                                 2    
TCG                                                                                                                      
TCT                                               1                                                                     1
TGC                                                                                                                      
TGT                                                                                                 1         1          
TTA                                                                                                                      
TTC                                                         1                                                     1     1
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 Y
A 3                       1     2 1    
C   1                                 1
D                       1           1  
E       2   5     5                    
F         1         4                  
G     1 3   2                   2      
H                           1          
I               1     1           1 1  
K       1         3     1   2 3        
L         1         4     2     1      
M               1   1               1  
N             2   1             2 1    
P             1           2     1      
Q                         1 3          
R   2       1     4 1       1 2        
S   1     3 1           2 2     2      
T 1             2         1       3    
V 1             3     1             5  
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,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
		
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,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,1,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0
		
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,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,1,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,1,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
		
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,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0
		
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,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
		
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,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,1,2,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,1,1,0,1,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,1,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
		
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,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0
		
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,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0

Details by gene

Here you can find a tab-separated table.