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Detailed information for vg0721709577:

Variant ID: vg0721709577 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 21709577
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GATCTAAATATATTTTCATGCTTTTATGTCCCTAGCACAACCTTACTTGTTCCTAGCTAACTAAATATGTGATTAACACAATTTAATTAGCTATTATATA[T/A]
AAATATCATCACACAGTTACATTAACCACCATAAATAGATCGATAGACCAGTGTTTTTGGTAATACAACTTGTGTTATACTCTAATTATTTATTTCGTGA

Reverse complement sequence

TCACGAAATAAATAATTAGAGTATAACACAAGTTGTATTACCAAAAACACTGGTCTATCGATCTATTTATGGTGGTTAATGTAACTGTGTGATGATATTT[A/T]
TATATAATAGCTAATTAAATTGTGTTAATCACATATTTAGTTAGCTAGGAACAAGTAAGGTTGTGCTAGGGACATAAAAGCATGAAAATATATTTAGATC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.30% 6.70% 0.02% 0.00% NA
All Indica  2759 93.30% 6.70% 0.04% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 52.00% 48.00% 0.00% 0.00% NA
Indica I  595 96.60% 3.40% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 89.60% 10.40% 0.00% 0.00% NA
Indica Intermediate  786 91.60% 8.30% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0721709577 T -> A LOC_Os07g36290.1 downstream_gene_variant ; 3910.0bp to feature; MODIFIER silent_mutation Average:29.179; most accessible tissue: Callus, score: 58.012 N N N N
vg0721709577 T -> A LOC_Os07g36300.1 intron_variant ; MODIFIER silent_mutation Average:29.179; most accessible tissue: Callus, score: 58.012 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0721709577 4.76E-06 NA mr1098_2 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0721709577 6.36E-06 NA mr1123_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251