SnpEff: Variant analysis

Contents
Summary
Change rate by chromosome
Variants by type
Number of variants by impact
Number of variants by functional class
Number of variants by effect
Quality histogram
Coverage histogram
Base change table
Transition vs transversions (ts/tv)
Frequency of alleles
Codon change table
Amino acid change table
Chromosome change plots
Details by gene
Summary

Genome Slyc2.40
Date 2014-04-29 21:59
SnpEff version 
SnpEff 3.4i (build 2014-01-16), by Pablo Cingolani
Command line arguments 
SnpEff  -no-upstream -no-downstream Slyc2.40
Warnings 2
Number of lines (input file) 35
Number of variants (before filter) 35
Filter
Number of variants filtered out 0
Number of not variants
(i.e. reference equals alternative) 		0
Number of variants processed
(i.e. after filter and non-variants) 		35
Number of known variants
(i.e. non-empty ID) 		0 ( 0% )
Number of effects 66
Genome total length 781,666,411
Genome effective length 65,021,438
Change rate 1 change every 1,857,755 bases

Change rate details

Chromosome Length Changes Change rate
SL2.40ch05 65,021,438 35 1,857,755
Total 65,021,438 35 1,857,755

Number changes by type

Type Total Homo Hetero
SNP 26 24 2
MNP 0 0 0
INS 5 5 0
DEL 4 3 1
MIXED 0 0 0
Interval 0 0 0
Total 35 32 3

Number of effects by impact

Type (alphabetical order)   Count Percent
LOW   2 3.03%
MODERATE   1 1.515%
MODIFIER   63 95.455%

Number of effects by functional class

Type (alphabetical order)   Count Percent
MISSENSE   1 33.333%
SILENT   2 66.667%

Missense / Silent ratio: 0.5

Number of effects by type and region

Type Region
Type (alphabetical order)   Count Percent
DOWNSTREAM   25 37.879%
INTERGENIC   6 9.091%
INTRON   23 34.848%
NON_SYNONYMOUS_CODING   1 1.515%
SYNONYMOUS_CODING   2 3.03%
UPSTREAM   6 9.091%
UTR_3_PRIME   3 4.545%

Type (alphabetical order)   Count Percent
DOWNSTREAM   25 37.879%
EXON   3 4.545%
INTERGENIC   6 9.091%
INTRON   23 34.848%
UPSTREAM   6 9.091%
UTR_3_PRIME   3 4.545%

Quality: 

	

		
 Min30 

		
 Max222 

		
 Mean163.971 

		
 Median185 

		
 Standard deviation70.129 

		
 Values30,38,54,63,67,83,86,93,131,135,142,173,174,183,185,212,214,222 

		
 Count1,2,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,16
Coverage: 

	

		
 Min5 

		
 Max68 

		
 Mean23.514 

		
 Median21 

		
 Standard deviation13.238 

		
 Values5,6,7,10,12,13,14,15,16,17,19,20,21,22,23,27,28,29,31,32,33,35,36,46,51,68 

		
 Count1,1,1,2,2,1,1,2,1,1,2,1,1,2,2,2,2,1,2,1,1,1,1,1,1,1
Insertions and deletions length: 

	

		
 Min-14 

		
 Max3 

		
 Mean-1.222 

		
 Median-1 

		
 Standard deviation5.019 

		
 Values-14,-2,-1,1,3 

		
 Count1,1,2,4,1
Base changes (SNPs)

  A C G T
A 0 0 8 1
C 0 0 1 3
G 7 1 0 1
T 1 1 2 0

Ts/Tv (transitions / transversions)

Note: Only SNPs are used for this statistic.
Note: This Ts/Tv ratio is a 'raw' ratio. Some people prefer to use a ratio of rates, not observed events. In that case, you need to multiply by 2.0 (since there are twice as many possible transitions than transversions, E[Ts/Tv] ratio is twice the ratio of events).

Transitions 19
Transversions 7
Ts/Tv ratio 2.7143

All variants: 

Sample ,/ifshk5/PC_PA_EU/PMO/Tomato_reseq/01.BWA/SZAXPI009328-129,Total
Transitions ,37,37
Transversions ,13,13
Ts/Tv ,2.846,2.846

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

No results available (empty input?)
Frequency of alleles

Note: Number of times an allele appears once (singleton), twice (doubletons), etc.

All variants:
Min1
Max2
Mean1.923
Median2
Standard deviation0.272
Values1,2
Count2,24

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

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).

  AAC ACC ACT TAC TGC TGT
AAC       1    
ACC     1      
ACT            
TAC            
TGC           1
TGT            

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).

  C N T Y
C 1      
N       1
T     1  
Y        

Changes by chromosome

		

		SL2.40ch05, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000,60000000,61000000,62000000,63000000,64000000,65000000
SL2.40ch05,Count,1,4,2,6,4,18,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
Details by gene

Here you can find a tab-separated table.