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Pipeline for SNP analysis
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Pipeline V3 (from VCF)
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SNP Queries V3
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SNP Queries V3
Choose a species:
oryza_sativa_MSU7
Project:
3K_RGP
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
Other identifier
Assign individuals to groups/populations
Apply filters
Localisation within gene:
all
gene
exon
Utr5prime
Utr3prime
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
Generate flanking sequences
bp, respecting an absence of genetic variation in
bp around the SNP
Enter a list of positions
Enter a list of genomic positions separated by comma
(ex: chr1:43897,chr1:57489,chr2:87660)