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Detailed information for vg1127835781:

Variant ID: vg1127835781 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 27835781
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:


GATTGGAAATAAATTAATTATGAACACTCAATATATCCATTCTCTAATTATTTTCTGTATTTGTTCACAATGCTTTTCATGATAATTTGATGATTGATCA[G/A]
TGCCATATGATATATCACTGCTAGAGAAAGGCTCTTTAATCCCGGTTTGCAACCCCTTTAGTCTTGGGTTGCAAATCGGGACTACTAATACGGGACTAAA

Reverse complement sequence

TTTAGTCCCGTATTAGTAGTCCCGATTTGCAACCCAAGACTAAAGGGGTTGCAAACCGGGATTAAAGAGCCTTTCTCTAGCAGTGATATATCATATGGCA[C/T]
TGATCAATCATCAAATTATCATGAAAAGCATTGTGAACAAATACAGAAAATAATTAGAGAATGGATATATTGAGTGTTCATAATTAATTTATTTCCAATC

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 83.50% 16.40% 0.06% 0.00% NA
All Indica  2759 76.10% 23.80% 0.11% 0.00% NA
All Japonica  1512 95.00% 5.00% 0.00% 0.00% NA
Aus  269 91.10% 8.90% 0.00% 0.00% NA
Indica I  595 73.40% 26.40% 0.17% 0.00% NA
Indica II  465 68.00% 32.00% 0.00% 0.00% NA
Indica III  913 81.60% 18.30% 0.11% 0.00% NA
Indica Intermediate  786 76.50% 23.40% 0.13% 0.00% NA
Temperate Japonica  767 97.30% 2.70% 0.00% 0.00% NA
Tropical Japonica  504 90.30% 9.70% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 2.50% 0.00% 0.00% NA
VI/Aromatic  96 89.60% 10.40% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg1127835781 G -> A LOC_Os11g45990.1 downstream_gene_variant ; 535.0bp to feature; MODIFIER silent_mutation Average:36.242; most accessible tissue: Zhenshan97 panicle, score: 61.671 N N N N
vg1127835781 G -> A LOC_Os11g45990-LOC_Os11g46000 intergenic_region ; MODIFIER silent_mutation Average:36.242; most accessible tissue: Zhenshan97 panicle, score: 61.671 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127835781 NA 2.20E-06 mr1191_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
vg1127835781 4.29E-06 1.04E-08 mr1698_2 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