SNP and InDel
Phenotype and GWAS information
Variation map
Haplotype network
ANOVA of haplotypes
Sequence maker
Phylogenetic tree
Visualization of variant frequency

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

gwas

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)

Ignore missing allele in MAF filtering?

Yes No

Groups

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

Region or GeneID

Embed sample names in figure

Yes No

Flanking region length (bp)

gwas

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

Note: consensus sequences are generated by substituting variants based on the reference genome.

Consensus sequence(s)

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)

Groups

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

Region or GeneID

Flanking region length (bp)

Maxium feature tracks