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Detailed information for vg0922610630:

Variant ID: vg0922610630 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 22610630
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


TACGTTCCCTGATTTCGCGGAGGAATACATCCGTCACTCCTTCCTGGTTAGGCTTACCCAATCTTCGGATGCCAGGGTGGCCGAGAGGTTCATGCAGTTT[C/T]
TGGTCAAGTATGTTCTTTTCTCATTTACCTTCTTTGCGAATCTATCCATATGATGTATATTTGACTTAATATTTCTATTTCTATAGCTACACTGCCCCCG

Reverse complement sequence

CGGGGGCAGTGTAGCTATAGAAATAGAAATATTAAGTCAAATATACATCATATGGATAGATTCGCAAAGAAGGTAAATGAGAAAAGAACATACTTGACCA[G/A]
AAACTGCATGAACCTCTCGGCCACCCTGGCATCCGAAGATTGGGTAAGCCTAACCAGGAAGGAGTGACGGATGTATTCCTCCGCGAAATCAGGGAACGTA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.50% 42.10% 0.36% 0.00% NA
All Indica  2759 29.80% 69.60% 0.58% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 83.60% 16.40% 0.00% 0.00% NA
Indica I  595 32.40% 66.70% 0.84% 0.00% NA
Indica II  465 24.50% 74.80% 0.65% 0.00% NA
Indica III  913 25.80% 73.70% 0.44% 0.00% NA
Indica Intermediate  786 35.50% 64.00% 0.51% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 78.90% 20.00% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0922610630 C -> T LOC_Os09g39330.1 synonymous_variant ; p.Leu79Leu; LOW synonymous_codon Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0922610630 NA 2.45E-11 mr1195 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
vg0922610630 NA 1.39E-06 mr1344 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
vg0922610630 NA 3.03E-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
vg0922610630 9.90E-16 NA mr1865 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
vg0922610630 3.99E-15 6.39E-17 mr1865 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
vg0922610630 NA 1.18E-06 mr1925 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
vg0922610630 9.36E-11 NA mr1865_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
vg0922610630 1.70E-11 3.76E-13 mr1865_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