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Detailed information for vg0109353965:

Variant ID: vg0109353965 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 9353965
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


AGCCTAAATTGAATTTTTAATTGGCCTCAAGAAAATATCGGTGTAAAAGCAAGAGAGAAACCCTAAATAAATTAATGCGAATAATAATCGGAATTGGCAT[A/G]
TGGAATTTTTCTTGAGTTCTACATGTCGAAATGTGCTAACAAGATTTTTAGTGGAATTTTCAGAGCTCTAGAAATAATTTTAACCAATTAAAATCGAGCA

Reverse complement sequence

TGCTCGATTTTAATTGGTTAAAATTATTTCTAGAGCTCTGAAAATTCCACTAAAAATCTTGTTAGCACATTTCGACATGTAGAACTCAAGAAAAATTCCA[T/C]
ATGCCAATTCCGATTATTATTCGCATTAATTTATTTAGGGTTTCTCTCTTGCTTTTACACCGATATTTTCTTGAGGCCAATTAAAAATTCAATTTAGGCT

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 27.00% 16.80% 8.55% 47.67% NA
All Indica  2759 3.10% 23.70% 4.82% 68.43% NA
All Japonica  1512 72.50% 1.30% 15.54% 10.65% NA
Aus  269 0.70% 41.60% 3.35% 54.28% NA
Indica I  595 3.40% 14.80% 4.03% 77.82% NA
Indica II  465 3.00% 16.60% 2.58% 77.85% NA
Indica III  913 2.00% 35.80% 7.67% 54.55% NA
Indica Intermediate  786 4.20% 20.50% 3.44% 71.88% NA
Temperate Japonica  767 67.00% 0.30% 15.38% 17.34% NA
Tropical Japonica  504 82.30% 3.20% 11.51% 2.98% NA
Japonica Intermediate  241 69.30% 0.80% 24.48% 5.39% NA
VI/Aromatic  96 68.80% 0.00% 18.75% 12.50% NA
Intermediate  90 31.10% 7.80% 10.00% 51.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0109353965 A -> G LOC_Os01g16470.1 downstream_gene_variant ; 2629.0bp to feature; MODIFIER silent_mutation Average:51.55; most accessible tissue: Zhenshan97 flag leaf, score: 65.3 N N N N
vg0109353965 A -> G LOC_Os01g16480.1 intron_variant ; MODIFIER silent_mutation Average:51.55; most accessible tissue: Zhenshan97 flag leaf, score: 65.3 N N N N
vg0109353965 A -> DEL N N silent_mutation Average:51.55; most accessible tissue: Zhenshan97 flag leaf, score: 65.3 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0109353965 3.18E-06 NA mr1301 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
vg0109353965 1.41E-06 1.41E-06 mr1347 Jap_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
vg0109353965 4.59E-06 NA mr1382 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
vg0109353965 NA 2.24E-06 mr1382 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
vg0109353965 4.56E-06 3.62E-08 mr1398 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
vg0109353965 NA 2.96E-07 mr1398 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
vg0109353965 1.63E-09 NA mr1422 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
vg0109353965 5.87E-06 3.40E-08 mr1422 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
vg0109353965 NA 1.11E-07 mr1554 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
vg0109353965 NA 3.50E-06 mr1602 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
vg0109353965 8.46E-06 NA mr1696 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
vg0109353965 NA 2.76E-07 mr1993 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
vg0109353965 NA 9.39E-08 mr1084_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
vg0109353965 NA 2.35E-06 mr1206_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
vg0109353965 NA 7.89E-06 mr1405_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
vg0109353965 NA 6.36E-06 mr1419_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
vg0109353965 NA 6.15E-08 mr1668_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