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 2026-06-04 19:40
SnpEff version 
SnpEff 5.1d (build 2022-04-19 15:49), by Pablo Cingolani
Command line arguments 
SnpEff  GRCh38.105 -csvStats HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff.csv HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann.vcf.gz
Warnings 17
Errors 0
Number of lines (input file) 35
Number of variants (before filter) 35
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 multi-allelic VCF entries
(i.e. more than two alleles) 		0
Number of effects 56
Genome total length 63,147,197,748
Genome effective length 46,709,983
Variant rate 1 variant every 1,334,570 bases

Variants rate details

Chromosome Length Variants Variants rate
21 46,709,983 35 1,334,570
Total 46,709,983 35 1,334,570

Number variants by type

Type Total
SNP 0
MNP 0
INS 15
DEL 20
MIXED 0
INV 0
DUP 0
BND 0
INTERVAL 0
Total 35

Number of effects by impact

Type (alphabetical order)   Count Percent
LOW   5 8.929%
MODERATE   3 5.357%
MODIFIER   48 85.714%

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
3_prime_UTR_variant   3 4.918%
conservative_inframe_deletion   1 1.639%
disruptive_inframe_deletion   1 1.639%
disruptive_inframe_insertion   1 1.639%
downstream_gene_variant   8 13.115%
intragenic_variant   3 4.918%
intron_variant   29 47.541%
non_coding_transcript_exon_variant   2 3.279%
splice_region_variant   5 8.197%
upstream_gene_variant   8 13.115%

Type (alphabetical order)   Count Percent
DOWNSTREAM   8 14.286%
EXON   5 8.929%
INTRON   24 42.857%
SPLICE_SITE_REGION   5 8.929%
TRANSCRIPT   3 5.357%
UPSTREAM   8 14.286%
UTR_3_PRIME   3 5.357%

Quality:
Insertions and deletions length: 

	

		
 Min0 

		
 Max2 

		
 Mean0.657 

		
 Median1 

		
 Standard deviation0.539 

		
 Values0,1,2 

		
 Count13,21,1
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


Min0
Max0
Mean0
Median0
Standard deviation0
Values0
Count35

Allele Count


Min0
Max0
Mean0
Median0
Standard deviation0
Values0
Count35

Hom/Het per sample 




Sample_names , NORMAL, TUMOR
Reference , 0, 0
Het , 0, 0
Hom , 0, 0
Missing , 35, 35

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).

  - CAC CAT CCG CTA GCC GCG GCT GGG
-     1            
CAC                  
CAT   1              
CCG 1                
CTA 1                
GCC 2           1    
GCG 2                
GCT 1                
GGG 2                

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 G H L P
-       1    
A 5 1        
G 2          
H       1    
L 1          
P 1          

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,0,0,0,0,0,0,0,0,0,0,2,0,0,0,1,0,0,0,0,0,0,1,0,0,0,1,0,0,1,3,0,0,2,3,4,0,3,1,0,0,0,1,0,2,2,1,7
Details by gene

Here you can find a tab-separated table.