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 16:40
SnpEff version
SnpEff 4.3u (build 2018-03-26 14:13), by Pablo Cingolani
Command line arguments
SnpEff  H1N1_10 tims-pipeline/full_AF_0.02_frac_0.001_tims.vcf 
Warnings 0
Errors 0
Number of lines (input file) 30
Number of variants (before filter) 30
Number of not variants
(i.e. reference equals alternative)
0
Number of variants processed
(i.e. after filter and non-variants)
30
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 34
Genome total length 13,133
Genome effective length 13,133
Variant rate 1 variant every 437 bases


Variants rate details

Chromosome Length Variants Variants rate
H1N1_HA 1,701 3 567
H1N1_MP 982 2 491
H1N1_NA 1,410 3 470
H1N1_NP 1,497 3 499
H1N1_NS 838 2 419
H1N1_PA 2,151 12 179
H1N1_PB1 2,274 2 1,137
H1N1_PB2 2,280 3 760
Total 13,133 30 437


Number variants by type

Type Total
SNP 30
MNP 0
INS 0
DEL 0
MIXED 0
INV 0
DUP 0
BND 0
INTERVAL 0
Total 30


Number of effects by impact

Type (alphabetical order)   Count Percent
LOW   11 32.353%
MODERATE   19 55.882%
MODIFIER   4 11.765%


Number of effects by functional class

Type (alphabetical order)   Count Percent
MISSENSE   19 63.333%
SILENT   11 36.667%

Missense / Silent ratio: 1.7273


Number of effects by type and region

Type Region
Type (alphabetical order)   Count Percent
downstream_gene_variant   1 2.941%
intron_variant   3 8.824%
missense_variant   19 55.882%
synonymous_variant   11 32.353%

Type (alphabetical order)   Count Percent
DOWNSTREAM   1 2.941%
EXON   30 88.235%
INTRON   3 8.824%


Quality:

	

Insertions and deletions length:

	

Base changes (SNPs)

  A C G T
A 0 3 8 2
C 0 0 0 3
G 7 1 0 0
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 22
Transversions 8
Ts/Tv ratio 2.75

All variants:

Sample ,sample,Total
Transitions ,22,22
Transversions ,8,8
Ts/Tv ,2.750,2.750

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
Count30


Allele Count


Min1
Max1
Mean1
Median1
Standard deviation0
Values1
Count30


Hom/Het per sample




Sample_names , sample
Reference , 0
Het , 30
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 AAG ACC ACT AGA AGC AGG AGT ATA ATC ATG CAA CAC CCA CCG CCT CGT CTA CTG GAA GAC GAG GAT GCA GCC GCG GCT GGA GGG GGT GTA GTG GTT TAC TGT TTA TTT
AAA         1             1                                                  
AAG             1                                                            
ACC                                                                          
ACT                               1                                          
AGA                                                                          
AGC                                                                          
AGG   1                                                                      
AGT           1                                                         1    
ATA                     1                                       1            
ATC     1                                                                    
ATG                                                                          
CAA                                                                          
CAC                                                                          
CCA                             1                                            
CCG                                                                          
CCT                                                                          
CGT                                                                     1    
CTA                                     1                                 1  
CTG                                                                          
GAA 1                                       1             1                  
GAC                                             1                            
GAG   1                                                                      
GAT                                                                 1        
GCA                                                                          
GCC                                                                          
GCG                                               1                          
GCT                               1                 1                        
GGA                                                         1                
GGG                                                       1                  
GGT                                                         1                
GTA                 1                                                        
GTG                                                             1            
GTT                                                                          
TAC                         1                                                
TGT                                                                          
TTA                                                                          
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 H I K L M P Q R S T V Y
A 2                     1            
C                                    
D     1                           1  
E     1     1     2                  
F                   1                
G           3                        
H                                    
I                     1         1 1  
K                         1 2        
L                   2                
M                                    
P                       1            
Q                                    
R   1             1                  
S   1                         1      
T                       1            
V               1                 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,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
		
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,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0
		
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,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
		
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,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
		
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,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
		
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,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,2,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
		
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,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
		
H1N1_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,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0

Details by gene

Here you can find a tab-separated table.