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Detailed information for vg0211784502:

Variant ID: vg0211784502 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 11784502
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


TGTTGAATCTACAGATTTACAGATTCTGAATAATTCTTACATCACCATTGTGCCAAAAAAAAACTTCTCCAGAAACAGTTAATGATTTCAGGCCAATTTC[T/C]
CTAATGGGTTTGAGCCTTAAGTTCCTTACCAAATTGATGGCTGATAGATTGCAAGGTGTGATTCTCAAAGTGGTTAGTGAAAACCAATATGGATTCATCA

Reverse complement sequence

TGATGAATCCATATTGGTTTTCACTAACCACTTTGAGAATCACACCTTGCAATCTATCAGCCATCAATTTGGTAAGGAACTTAAGGCTCAAACCCATTAG[A/G]
GAAATTGGCCTGAAATCATTAACTGTTTCTGGAGAAGTTTTTTTTTGGCACAATGGTGATGTAAGAATTATTCAGAATCTGTAAATCTGTAGATTCAACA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 43.00% 16.60% 5.99% 34.41% NA
All Indica  2759 10.60% 22.80% 9.64% 56.94% NA
All Japonica  1512 98.30% 0.10% 0.13% 1.46% NA
Aus  269 39.40% 53.50% 3.72% 3.35% NA
Indica I  595 6.10% 19.30% 5.55% 69.08% NA
Indica II  465 8.40% 34.20% 6.88% 50.54% NA
Indica III  913 13.80% 20.30% 14.35% 51.59% NA
Indica Intermediate  786 11.70% 21.60% 8.91% 57.76% NA
Temperate Japonica  767 99.00% 0.10% 0.00% 0.91% NA
Tropical Japonica  504 97.40% 0.20% 0.20% 2.18% NA
Japonica Intermediate  241 97.90% 0.00% 0.41% 1.66% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 58.90% 8.90% 5.56% 26.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0211784502 T -> DEL LOC_Os02g20010.1 N frameshift_variant Average:14.621; most accessible tissue: Callus, score: 35.53 N N N N
vg0211784502 T -> C LOC_Os02g20010.1 synonymous_variant ; p.Ser784Ser; LOW synonymous_codon Average:14.621; most accessible tissue: Callus, score: 35.53 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0211784502 NA 3.13E-06 mr1538 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
vg0211784502 5.24E-06 6.18E-07 mr1547 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
vg0211784502 1.61E-06 6.46E-09 mr1547 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
vg0211784502 3.29E-08 3.69E-14 mr1709 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
vg0211784502 3.46E-07 5.31E-12 mr1709 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
vg0211784502 NA 9.30E-07 mr1547_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
vg0211784502 8.08E-07 2.31E-15 mr1709_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
vg0211784502 NA 8.68E-13 mr1709_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