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Detailed information for vg0509650627:

Variant ID: vg0509650627 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 9650627
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


ACTAAATTTTGTTATGGGCAGATATATTGTTGTACAGGATAACACTTCAATCTTTCAATAACAGGTACATCGATAGTTGTGGATTCAGTGGTCCGTTCCC[T/G]
TCAACATTCTCAAAACTTCAGAACCTGAAGATCTTGTACGGTCAATACCATAGCCTTAGACATTATATATGTTCGTCATGTTTTCATGCTAAATGTCTAA

Reverse complement sequence

TTAGACATTTAGCATGAAAACATGACGAACATATATAATGTCTAAGGCTATGGTATTGACCGTACAAGATCTTCAGGTTCTGAAGTTTTGAGAATGTTGA[A/C]
GGGAACGGACCACTGAATCCACAACTATCGATGTACCTGTTATTGAAAGATTGAAGTGTTATCCTGTACAACAATATATCTGCCCATAACAAAATTTAGT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.50% 5.60% 0.89% 0.00% NA
All Indica  2759 89.10% 9.50% 1.45% 0.00% NA
All Japonica  1512 99.80% 0.10% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.00% 1.00% 1.01% 0.00% NA
Indica II  465 71.60% 24.70% 3.66% 0.00% NA
Indica III  913 86.70% 13.00% 0.22% 0.00% NA
Indica Intermediate  786 95.30% 2.80% 1.91% 0.00% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 0.00% 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
vg0509650627 T -> G LOC_Os05g16930.1 synonymous_variant ; p.Pro140Pro; LOW synonymous_codon Average:59.743; most accessible tissue: Zhenshan97 young leaf, score: 71.497 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0509650627 8.07E-14 7.46E-39 mr1039 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
vg0509650627 3.57E-10 1.80E-22 mr1039 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
vg0509650627 8.29E-07 NA mr1632 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
vg0509650627 6.01E-06 1.39E-09 mr1632 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
vg0509650627 2.69E-16 1.97E-40 mr1039_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
vg0509650627 6.49E-12 6.32E-23 mr1039_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
vg0509650627 NA 8.80E-06 mr1159_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
vg0509650627 2.02E-06 NA mr1514_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
vg0509650627 8.41E-06 NA mr1514_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
vg0509650627 8.43E-14 NA mr1632_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
vg0509650627 5.06E-12 5.04E-18 mr1632_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