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Detailed information for vg1005177676:

Variant ID: vg1005177676 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 5177676
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.58, A: 0.42, others allele: 0.00, population size: 43. )

Flanking Sequence (100 bp) in Reference Genome:


AAGGCATATATAAAGGGGGGATCTTTAGTCCCGGTTGGTAACACCAACCGGGACTAAAGATCCCGGGGGCCCTGACAACGTCTGACATCTCTACAACCGG[A/G]
ACTAAAGATGATCTTTAATCCCAGTTGGTGTTACCAACCGGGACTAAAGATCTCATATGCCCGTTGTAGCCACTAACCGGGACTAAAGATCATCTTTAGT

Reverse complement sequence

ACTAAAGATGATCTTTAGTCCCGGTTAGTGGCTACAACGGGCATATGAGATCTTTAGTCCCGGTTGGTAACACCAACTGGGATTAAAGATCATCTTTAGT[T/C]
CCGGTTGTAGAGATGTCAGACGTTGTCAGGGCCCCCGGGATCTTTAGTCCCGGTTGGTGTTACCAACCGGGACTAAAGATCCCCCCTTTATATATGCCTT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 34.40% 23.70% 1.31% 40.56% NA
All Indica  2759 12.20% 31.80% 0.83% 55.20% NA
All Japonica  1512 79.30% 14.10% 0.99% 5.62% NA
Aus  269 1.50% 2.20% 1.49% 94.80% NA
Indica I  595 5.20% 20.70% 0.50% 73.61% NA
Indica II  465 15.30% 37.80% 1.08% 45.81% NA
Indica III  913 17.40% 37.20% 0.44% 44.91% NA
Indica Intermediate  786 9.70% 30.20% 1.40% 58.78% NA
Temperate Japonica  767 85.40% 6.60% 1.04% 6.91% NA
Tropical Japonica  504 70.40% 26.80% 0.79% 1.98% NA
Japonica Intermediate  241 78.40% 11.20% 1.24% 9.13% NA
VI/Aromatic  96 51.00% 4.20% 15.62% 29.17% NA
Intermediate  90 40.00% 25.60% 5.56% 28.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1005177676 A -> G LOC_Os10g09590.1 downstream_gene_variant ; 3302.0bp to feature; MODIFIER silent_mutation Average:28.476; most accessible tissue: Callus, score: 63.625 N N N N
vg1005177676 A -> G LOC_Os10g09570-LOC_Os10g09590 intergenic_region ; MODIFIER silent_mutation Average:28.476; most accessible tissue: Callus, score: 63.625 N N N N
vg1005177676 A -> DEL N N silent_mutation Average:28.476; most accessible tissue: Callus, score: 63.625 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1005177676 NA 3.22E-06 mr1608 Ind_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
vg1005177676 NA 7.36E-09 mr1658 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
vg1005177676 NA 9.50E-06 mr1884 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
vg1005177676 NA 9.73E-09 mr1050_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
vg1005177676 NA 7.15E-06 mr1379_2 Jap_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
vg1005177676 NA 6.53E-07 mr1608_2 Ind_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