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Detailed information for vg1119716424:

Variant ID: vg1119716424 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 19716424
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


GATTGCACAAAAACAAACAAGCCACAAAAGTTAGTCAGAAACAACATTGTTCAGAATAAAATAGAAAACTAAACATGAGTAGTGCTATGCAATGTGGATC[A/G]
ACAAATAACTAAACCCATTCTCTCTAATCATTGAAGAATTGGCATAGTTAATAATTTTTTTCACTAGCAAAATAAAAACCTCAAGTTGGTCTTTAAATTT

Reverse complement sequence

AAATTTAAAGACCAACTTGAGGTTTTTATTTTGCTAGTGAAAAAAATTATTAACTATGCCAATTCTTCAATGATTAGAGAGAATGGGTTTAGTTATTTGT[T/C]
GATCCACATTGCATAGCACTACTCATGTTTAGTTTTCTATTTTATTCTGAACAATGTTGTTTCTGACTAACTTTTGTGGCTTGTTTGTTTTTGTGCAATC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 81.60% 18.20% 0.15% 0.00% NA
All Indica  2759 72.10% 27.90% 0.04% 0.00% NA
All Japonica  1512 97.40% 2.40% 0.26% 0.00% NA
Aus  269 87.70% 12.30% 0.00% 0.00% NA
Indica I  595 88.40% 11.60% 0.00% 0.00% NA
Indica II  465 38.70% 61.30% 0.00% 0.00% NA
Indica III  913 81.80% 18.10% 0.11% 0.00% NA
Indica Intermediate  786 68.20% 31.80% 0.00% 0.00% NA
Temperate Japonica  767 96.70% 3.30% 0.00% 0.00% NA
Tropical Japonica  504 98.20% 1.20% 0.60% 0.00% NA
Japonica Intermediate  241 97.50% 2.10% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 72.20% 25.60% 2.22% 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
vg1119716424 A -> G LOC_Os11g33330.1 intron_variant ; MODIFIER silent_mutation Average:45.417; 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
vg1119716424 NA 8.33E-07 mr1220 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
vg1119716424 NA 1.83E-08 mr1829 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
vg1119716424 NA 7.96E-06 mr1842 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
vg1119716424 NA 6.59E-14 mr1902 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
vg1119716424 NA 2.14E-10 mr1829_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
vg1119716424 NA 1.40E-10 mr1902_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