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 GRCh38.105
Date 2026-02-02 21:45
SnpEff version 
SnpEff 5.1d (build 2022-04-19 15:49), by Pablo Cingolani
Command line arguments 
SnpEff  GRCh38.105 -csvStats Sig_18_tissue_vs_Sig_18_Blood.tiddit_sv_merge_custom.ann_snpEff.csv Sig_18_tissue_vs_Sig_18_Blood.tiddit_sv_merge_custom.ann.vcf.gz
Warnings 0
Errors 0
Number of lines (input file) 9
Number of variants (before filter) 9
Number of not variants
(i.e. reference equals alternative) 		0
Number of variants processed
(i.e. after filter and non-variants) 		9
Number of known variants
(i.e. non-empty ID) 		8 ( 88.889% )
Number of multi-allelic VCF entries
(i.e. more than two alleles) 		0
Number of effects 35
Genome total length 63,147,197,748
Genome effective length 46,709,983
Variant rate 1 variant every 5,189,998 bases

Variants rate details

Chromosome Length Variants Variants rate
21 46,709,983 9 5,189,998
Total 46,709,983 9 5,189,998

Number variants by type

Type Total
SNP 0
MNP 0
INS 0
DEL 1
MIXED 0
INV 0
DUP 7
BND 1
INTERVAL 0
Total 9

Number of effects by impact

Type (alphabetical order)   Count Percent
HIGH   16 45.714%
MODIFIER   19 54.286%

Number of effects by functional class

Type (alphabetical order)   Count Percent

Missense / Silent ratio: 0

Number of effects by type and region

Type Region
Type (alphabetical order)   Count Percent
bidirectional_gene_fusion   8 20.513%
downstream_gene_variant   3 7.692%
frameshift_variant   4 10.256%
gene_fusion   8 20.513%
intragenic_variant   6 15.385%
intron_variant   5 12.821%
non_coding_transcript_exon_variant   1 2.564%
upstream_gene_variant   4 10.256%

Type (alphabetical order)   Count Percent
DOWNSTREAM   3 8.571%
EXON   1 2.857%
GENE   16 45.714%
INTRON   5 14.286%
TRANSCRIPT   6 17.143%
UPSTREAM   4 11.429%

Quality: 

	

		
 Min20 

		
 Max80 

		
 Mean57.222 

		
 Median50 

		
 Standard deviation23.333 

		
 Values20,35,40,50,80 

		
 Count1,1,1,2,4
Insertions and deletions length: 

	

		
 Min1 

		
 Max1 

		
 Mean1 

		
 Median0.5 

		
 Standard deviation0 

		
 Values1 

		
 Count1
Base changes (SNPs)

  A C G T
A 0 0 0 0
C 0 0 0 0
G 0 0 0 0
T 0 0 0 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: 

No results available (empty input?)

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

No results available (empty input?)
Allele frequency


Min50
Max100
Mean88.889
Median100
Standard deviation22.048
Values50,100
Count2,7

Allele Count


Min1
Max4
Mean2
Median2
Standard deviation0.866
Values1,2,4
Count2,6,1

Hom/Het per sample 




Sample_names , Sig_18_Sig_18_Blood, Sig_18_Sig_18_tissue
Reference , 0, 0
Het , 1, 1
Hom , 5, 3
Missing , 3, 5

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).

 

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).

 

Variants by chromosome

		

		21, 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
21,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,2,2,3,0
Details by gene

Here you can find a tab-separated table.