Home
Pipeline for SNP analysis
Pipeline V2 (from Fasta)
Pipeline V3 (from VCF)
SNiPlay Galaxy workflows
Tools
General statistics
VCFtools (stats)
Polyploid analysis
SNiPloid
Chromosome Viewer
Chromosome Viewer
SNP density
Diversity analysis
EggLib
VCFtools (sliding window)
Population stratification
sNMF
Admixture
IBD Kinship (Tassel)
PCA / IBS matrix (plink)
Distance tree (FastME)
Association Studies
GWAS Analysis
Others
Cytoscape
SNP Database
Public datasets
Download public datasets
Queries
SNP Queries V3
Documentation
Manual pipeline V2
Manual pipeline V3
How to cite
Login
SNP Queries V3
Choose a species:
Sorghum_v1
Rice_MSU7
Rice_MSU6
Grapevine
Coffee
Cassava_v6
Cassava_v4
Banana
Project:
Nelson_et_al_2011
Level:
Gene / all experiments
Export
Display SNP information
Display SNP count per gene
Export GFF
Export VCF
Export FASTA alignments
Export for Illumina VeraCode technology
Export for Phasing
Export HapMap for TASSEL
Individuals
:
0
Individual to be analyzed
:
Genes
:
0
Chromosomes
:
Filter/Display:
Accession
Assign individuals to groups/populations
Apply filters
Localisation within gene:
all
exon
intron
Utr5prime
Utr3prime
downstream
upstream
intergenic
Chromosome position: Min
Max
Synonymous / non-synonymous:
all
non synonymous
synonymous
Number of alleles:
Bi-allelic
Tri-allelic
Tetra-allelic
Type of variants:
All
SNP only
Indel only
Minor Allele Frequency (MAF) in %: Min
Max
Maximum authorized missing data ratio
%
Thin sites so that no two sites are within the specified distance from one another:
bp
Remove sites with a FILTER flag other than PASS