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Detailed information for vg1117079321:

Variant ID: vg1117079321 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 17079321
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.79, A: 0.21, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:


AGCAGCAAATAACCACGTTTAGAGAAAGTTTTCCCCAAGAGTGAGTTTATGGTATCCTATAGCTAAAACCATAGAGTCGCGATGTTATGTAGCAAAATTT[G/A]
CCTATAGTCATAGGTTCATATTACATATTGTCCCATACAACGTTACGTGATAAGGAAATTAAAAAAGCAACTCAAGTACATTTACGGTACGATCAATTCA

Reverse complement sequence

TGAATTGATCGTACCGTAAATGTACTTGAGTTGCTTTTTTAATTTCCTTATCACGTAACGTTGTATGGGACAATATGTAATATGAACCTATGACTATAGG[C/T]
AAATTTTGCTACATAACATCGCGACTCTATGGTTTTAGCTATAGGATACCATAAACTCACTCTTGGGGAAAACTTTCTCTAAACGTGGTTATTTGCTGCT

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 30.00% 25.70% 1.21% 43.08% NA
All Indica  2759 18.60% 34.10% 1.41% 45.92% NA
All Japonica  1512 45.80% 12.60% 0.79% 40.87% NA
Aus  269 68.80% 18.60% 1.12% 11.52% NA
Indica I  595 12.60% 27.90% 1.85% 57.65% NA
Indica II  465 19.60% 33.80% 1.08% 45.59% NA
Indica III  913 20.00% 39.00% 0.22% 40.74% NA
Indica Intermediate  786 20.70% 33.30% 2.67% 43.26% NA
Temperate Japonica  767 83.60% 2.50% 0.26% 13.69% NA
Tropical Japonica  504 2.00% 29.40% 1.59% 67.06% NA
Japonica Intermediate  241 17.00% 9.50% 0.83% 72.61% NA
VI/Aromatic  96 5.20% 2.10% 3.12% 89.58% NA
Intermediate  90 27.80% 34.40% 0.00% 37.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1117079321 G -> A LOC_Os11g29410.1 upstream_gene_variant ; 230.0bp to feature; MODIFIER silent_mutation Average:36.14; most accessible tissue: Callus, score: 63.408 N N N N
vg1117079321 G -> A LOC_Os11g29420.1 downstream_gene_variant ; 902.0bp to feature; MODIFIER silent_mutation Average:36.14; most accessible tissue: Callus, score: 63.408 N N N N
vg1117079321 G -> A LOC_Os11g29410-LOC_Os11g29420 intergenic_region ; MODIFIER silent_mutation Average:36.14; most accessible tissue: Callus, score: 63.408 N N N N
vg1117079321 G -> DEL N N silent_mutation Average:36.14; most accessible tissue: Callus, score: 63.408 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1117079321 NA 1.21E-08 mr1170 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
vg1117079321 NA 4.21E-07 mr1378 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
vg1117079321 7.83E-07 6.22E-10 mr1380 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
vg1117079321 6.97E-07 3.15E-08 mr1380 Ind_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
vg1117079321 NA 3.72E-06 mr1428 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
vg1117079321 NA 2.28E-06 mr1520 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
vg1117079321 NA 3.49E-09 mr1561 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
vg1117079321 1.79E-06 3.86E-08 mr1561 Ind_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
vg1117079321 NA 7.31E-06 mr1579 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
vg1117079321 NA 1.89E-06 mr1740 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
vg1117079321 NA 7.04E-07 mr1875 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
vg1117079321 NA 1.87E-06 mr1908 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
vg1117079321 NA 5.01E-08 mr1937 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
vg1117079321 NA 6.22E-07 mr1937 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
vg1117079321 NA 7.58E-06 mr1943 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
vg1117079321 NA 9.93E-08 mr1170_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