Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0711420049:

Variant ID: vg0711420049 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 11420049
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.02, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


GTGGTTGGCGACTCCATATCACCGCAAGGCGTTTAGGTGTTGCGATCGTGCTTGTCGACTTGTCAAAAAAGTTGCCAACACGATTTTTGGCGACTCCGCT[G/A]
GGGACTAGATCTACATATTACGGCCGAATTTGCTTTAACCTAGTCGCTTCGTCGAATTAATAGTTTCGGCCAAGCGGCCGAAATTAATCTACGCATCACG

Reverse complement sequence

CGTGATGCGTAGATTAATTTCGGCCGCTTGGCCGAAACTATTAATTCGACGAAGCGACTAGGTTAAAGCAAATTCGGCCGTAATATGTAGATCTAGTCCC[C/T]
AGCGGAGTCGCCAAAAATCGTGTTGGCAACTTTTTTGACAAGTCGACAAGCACGATCGCAACACCTAAACGCCTTGCGGTGATATGGAGTCGCCAACCAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.60% 8.40% 34.49% 3.55% NA
All Indica  2759 27.80% 9.50% 57.09% 5.65% NA
All Japonica  1512 94.40% 4.50% 0.66% 0.46% NA
Aus  269 76.20% 17.10% 6.32% 0.37% NA
Indica I  595 38.50% 2.40% 53.45% 5.71% NA
Indica II  465 15.50% 12.30% 65.16% 7.10% NA
Indica III  913 21.70% 12.60% 60.13% 5.59% NA
Indica Intermediate  786 34.00% 9.70% 51.53% 4.83% NA
Temperate Japonica  767 98.30% 0.10% 0.78% 0.78% NA
Tropical Japonica  504 86.70% 12.70% 0.60% 0.00% NA
Japonica Intermediate  241 97.90% 1.20% 0.41% 0.41% NA
VI/Aromatic  96 83.30% 8.30% 8.33% 0.00% NA
Intermediate  90 60.00% 13.30% 22.22% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0711420049 G -> DEL N N silent_mutation Average:30.395; most accessible tissue: Zhenshan97 flower, score: 45.068 N N N N
vg0711420049 G -> A LOC_Os07g19300.1 upstream_gene_variant ; 507.0bp to feature; MODIFIER silent_mutation Average:30.395; most accessible tissue: Zhenshan97 flower, score: 45.068 N N N N
vg0711420049 G -> A LOC_Os07g19290.1 downstream_gene_variant ; 512.0bp to feature; MODIFIER silent_mutation Average:30.395; most accessible tissue: Zhenshan97 flower, score: 45.068 N N N N
vg0711420049 G -> A LOC_Os07g19290-LOC_Os07g19300 intergenic_region ; MODIFIER silent_mutation Average:30.395; most accessible tissue: Zhenshan97 flower, score: 45.068 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0711420049 2.47E-06 NA mr1890 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