SampleInfo
VarTable
Heatmap
HapNet
PhyloTree
HapMap
SnpFreq
SeqMaker
Available samples
Available chromosomes
Pre-defined sample groups
Other system information
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)
Minimum allele frequency (MAF)
Ignore missing allele in MAF filtering?
Yes
No
Advanced options
Run
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)
Ignore missing allele in MAF filtering?
Yes
No
Draw
Download options
Groups
Ex: Group1{Sample1,Sample2},Group2{Sample3,Sample4}
Region or GeneID
Embed sample names in figure
Yes
No
Flanking region length (bp)
Draw
Download options
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)
Draw
Download options
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
Draw
Download Options
Groups
Ex: Group1{Sample1,Sample2},Group2{Sample3,Sample4}
Region or GeneID
Flanking region length (bp)
Maxium feature tracks
Draw
Download Options
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
Run
Download as fasta
Note:
consensus sequences are generated by substituting variants based on the reference genome.
Consensus sequence(s)