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Detailed information for vg1104309736:

Variant ID: vg1104309736 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 4309736
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


GTGATTATAGAATACCACGTGGTGATTTAGGAGCGTTTGTAGAAGGCCATATGGTGGCTTGAGAGTATTTATTGGAAGTTTAATTAACTTTTATTATATA[T/A]
GTCCCTTAAACTTTTTAGAAAAAATAGCTGTCACGTGACACTCATATAAAAGCTTGTAGGTCACCACATGTCATATCTCTCAATTAAAAGAATTATTAAA

Reverse complement sequence

TTTAATAATTCTTTTAATTGAGAGATATGACATGTGGTGACCTACAAGCTTTTATATGAGTGTCACGTGACAGCTATTTTTTCTAAAAAGTTTAAGGGAC[A/T]
TATATAATAAAAGTTAATTAAACTTCCAATAAATACTCTCAAGCCACCATATGGCCTTCTACAAACGCTCCTAAATCACCACGTGGTATTCTATAATCAC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 47.90% 40.60% 7.02% 4.40% NA
All Indica  2759 22.70% 60.70% 10.66% 6.02% NA
All Japonica  1512 89.50% 7.20% 1.26% 2.05% NA
Aus  269 58.70% 37.90% 2.97% 0.37% NA
Indica I  595 22.90% 68.10% 7.73% 1.34% NA
Indica II  465 13.30% 58.70% 11.40% 16.56% NA
Indica III  913 27.50% 57.40% 11.72% 3.40% NA
Indica Intermediate  786 22.40% 60.10% 11.20% 6.36% NA
Temperate Japonica  767 98.80% 0.70% 0.26% 0.26% NA
Tropical Japonica  504 73.80% 18.30% 3.17% 4.76% NA
Japonica Intermediate  241 92.50% 5.00% 0.41% 2.07% NA
VI/Aromatic  96 89.60% 8.30% 2.08% 0.00% NA
Intermediate  90 48.90% 30.00% 10.00% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1104309736 T -> A LOC_Os11g08210-LOC_Os11g08220 intergenic_region ; MODIFIER silent_mutation Average:15.956; most accessible tissue: Callus, score: 30.97 N N N N
vg1104309736 T -> DEL N N silent_mutation Average:15.956; most accessible tissue: Callus, score: 30.97 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1104309736 NA 1.86E-06 mr1583 Jap_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
vg1104309736 5.06E-13 7.18E-46 mr1638 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
vg1104309736 4.14E-09 3.14E-11 mr1638 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
vg1104309736 NA 2.27E-06 mr1068_2 Jap_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
vg1104309736 NA 9.37E-06 mr1091_2 Jap_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
vg1104309736 NA 5.20E-07 mr1096_2 Jap_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
vg1104309736 NA 3.77E-06 mr1110_2 Jap_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
vg1104309736 NA 2.13E-06 mr1112_2 Jap_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
vg1104309736 5.50E-07 1.58E-08 mr1121_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
vg1104309736 4.42E-06 6.24E-06 mr1200_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
vg1104309736 2.51E-06 2.51E-06 mr1234_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
vg1104309736 NA 7.35E-06 mr1329_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