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Detailed information for vg0422509805:

Variant ID: vg0422509805 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 22509805
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


TCCGGTGGAAACGGCTTCGGTTGAGAGGGTCTTGTCAGCTGTCTCTTATAAAGACAGATTTGCGAAACAAAATAGGGGATGAATGACTCAATGACTTGAT[G/A]
ATTTGCTACACTGAGAAGCAGATTTTTAGAAGTATTAGTGATGAAAACATCATCCAACACTTTTAAGAGATGAAAAAGCGCCGTATGCTAGTGCCTCAAC

Reverse complement sequence

GTTGAGGCACTAGCATACGGCGCTTTTTCATCTCTTAAAAGTGTTGGATGATGTTTTCATCACTAATACTTCTAAAAATCTGCTTCTCAGTGTAGCAAAT[C/T]
ATCAAGTCATTGAGTCATTCATCCCCTATTTTGTTTCGCAAATCTGTCTTTATAAGAGACAGCTGACAAGACCCTCTCAACCGAAGCCGTTTCCACCGGA

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 29.70% 2.50% 9.10% 58.68% NA
All Indica  2759 7.00% 4.10% 11.27% 77.60% NA
All Japonica  1512 72.70% 0.10% 7.01% 20.24% NA
Aus  269 1.50% 0.00% 1.12% 97.40% NA
Indica I  595 7.90% 1.70% 8.57% 81.85% NA
Indica II  465 1.70% 3.20% 5.81% 89.25% NA
Indica III  913 6.40% 7.80% 17.74% 68.13% NA
Indica Intermediate  786 10.20% 2.30% 9.03% 78.50% NA
Temperate Japonica  767 76.90% 0.00% 1.96% 21.12% NA
Tropical Japonica  504 67.50% 0.20% 14.09% 18.25% NA
Japonica Intermediate  241 70.10% 0.00% 8.30% 21.58% NA
VI/Aromatic  96 82.30% 0.00% 0.00% 17.71% NA
Intermediate  90 33.30% 3.30% 11.11% 52.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0422509805 G -> DEL N N silent_mutation Average:16.369; most accessible tissue: Callus, score: 49.78 N N N N
vg0422509805 G -> A LOC_Os04g37840-LOC_Os04g37850 intergenic_region ; MODIFIER silent_mutation Average:16.369; most accessible tissue: Callus, score: 49.78 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0422509805 NA 1.38E-06 mr1538 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
vg0422509805 2.08E-08 3.35E-10 mr1547 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
vg0422509805 8.54E-07 1.21E-08 mr1547 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
vg0422509805 2.81E-11 2.43E-14 mr1709 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
vg0422509805 3.44E-09 5.55E-17 mr1709 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
vg0422509805 NA 3.45E-07 mr1538_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
vg0422509805 1.46E-07 3.14E-09 mr1547_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
vg0422509805 1.41E-07 1.70E-09 mr1547_2 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
vg0422509805 2.99E-12 3.66E-24 mr1709_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
vg0422509805 4.85E-09 2.38E-21 mr1709_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