SnpHub

About

This dataset contains genome variants information of two samples, by mapping resequencing reads to barley Morex genome.

Snphub

SnpHub, a Shiny-based server framework for retrieving, analyzing and visualizing the large genomic variations data in a lab.

Homepage

SnpHub homepage

Documentation

SnpHub manual

Avaliable samples

Avaliable chromosomes

Pre-defined sample groups

Other system informations

Variation type

snp indel snp+indel

Optional information

ANN DP GQ

Show genotype in nucleotide

Yes No

Samples, must have variant

Samples, must NOT have variant

Samples, independent of having variant

Use #ALL for all samples Use #GroupName to use pre-defined groups as samples

Region or GeneID

Flanking region length (bp)

Download raw results as CSV Download genotype in nucleotide as CSV

Results

Groups

Ex: Group1{Sample1,Sample2},Group2{Sample3,Sample4}

Region or GeneID

Flanking region length (bp)

Cluster samples according to their genotypes

Yes No

Flip x and y axis

Yes No

Minimum allele frequency (MAF)

Type

NJ-tree MDS

Delete missing site while calculating distance matrix?

Yes No

Choose NO here may reduce the accuracy of distance.

Groups

Ex: Group1{Sample1,Sample2},Group2{Sample3,Sample4}

Region or GeneID

Flanking region length (bp)

Samples

Use #GroupName to use pre-defined groups as samples

Site

Input should be a single site (Ex: chr1A:220037)

Draw type missing on plot

Yes No

Longitude range

Latitude range

Diatance merge range

Pie zoom factor

Variation type to be replaced

snp indel both

Replace homozygous/heterozygous?

homo_only all

Samples

Use #RAW for raw reference genome sequence. Use #GroupName to use pre-defined groups as samples

Region or GeneID

Download as fasta

About

Snphub

Homepage

Documentation

Avaliable samples

Avaliable chromosomes

Pre-defined sample groups

Other system informations

Results

Consensus sequence(s)