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Detailed information for vg0314422629:

Variant ID: vg0314422629 (JBrowse)Variation Type: INDEL
Chromosome: chr03Position: 14422629
Reference Allele: TAlternative Allele: A,TAC
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, A: 0.01, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:


TTAATGAAAGAGGCTGAAACCTGTTGATATATCTGGTTCATTGGCCACCATCGATTCCGTCCAAACTATTGTTCTTTGATGTGGAATGAATCCCTCCAAA[T/A,TAC]
ACACTTGATTATTGTTTCGAATTATAGTTGCAAAGTGTTAACTTTTGAAGTTAATTTTAACTTGCATGTTTGTGTAGTGATATATTACATATTGATCTAT

Reverse complement sequence

ATAGATCAATATGTAATATATCACTACACAAACATGCAAGTTAAAATTAACTTCAAAAGTTAACACTTTGCAACTATAATTCGAAACAATAATCAAGTGT[A/T,GTA]
TTTGGAGGGATTCATTCCACATCAAAGAACAATAGTTTGGACGGAATCGATGGTGGCCAATGAACCAGATATATCAACAGGTTTCAGCCTCTTTCATTAA

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 49.60% 31.90% 11.21% 7.30% NA
All Indica  2759 18.50% 51.50% 18.16% 11.78% NA
All Japonica  1512 99.50% 0.20% 0.07% 0.20% NA
Aus  269 69.50% 18.60% 7.43% 4.46% NA
Indica I  595 16.00% 42.70% 23.36% 17.98% NA
Indica II  465 3.40% 64.10% 21.08% 11.40% NA
Indica III  913 25.20% 46.70% 17.20% 10.95% NA
Indica Intermediate  786 21.60% 56.50% 13.61% 8.27% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.20% 0.20% 0.20% NA
Japonica Intermediate  241 98.80% 0.40% 0.00% 0.83% NA
VI/Aromatic  96 92.70% 6.20% 0.00% 1.04% NA
Intermediate  90 58.90% 27.80% 8.89% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0314422629 T -> A LOC_Os03g25260.1 upstream_gene_variant ; 2000.0bp to feature; MODIFIER silent_mutation Average:33.165; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0314422629 T -> A LOC_Os03g25240.1 downstream_gene_variant ; 2267.0bp to feature; MODIFIER silent_mutation Average:33.165; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0314422629 T -> A LOC_Os03g25250.1 downstream_gene_variant ; 353.0bp to feature; MODIFIER silent_mutation Average:33.165; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0314422629 T -> A LOC_Os03g25240-LOC_Os03g25250 intergenic_region ; MODIFIER silent_mutation Average:33.165; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0314422629 T -> DEL N N silent_mutation Average:33.165; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0314422629 T -> TAC LOC_Os03g25260.1 upstream_gene_variant ; 1999.0bp to feature; MODIFIER N Average:33.165; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0314422629 T -> TAC LOC_Os03g25240.1 downstream_gene_variant ; 2268.0bp to feature; MODIFIER N Average:33.165; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0314422629 T -> TAC LOC_Os03g25250.1 downstream_gene_variant ; 352.0bp to feature; MODIFIER N Average:33.165; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0314422629 T -> TAC LOC_Os03g25240-LOC_Os03g25250 intergenic_region ; MODIFIER N Average:33.165; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0314422629 NA 3.08E-32 mr1037 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
vg0314422629 NA 7.26E-09 mr1037 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
vg0314422629 NA 2.03E-36 mr1064 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
vg0314422629 NA 2.25E-22 mr1155 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
vg0314422629 NA 3.55E-11 mr1713 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
vg0314422629 NA 5.58E-09 mr1770 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
vg0314422629 NA 8.05E-07 mr1785 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
vg0314422629 NA 1.90E-51 mr1798 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
vg0314422629 NA 8.13E-09 mr1798 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
vg0314422629 NA 1.30E-22 mr1888 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
vg0314422629 2.40E-06 2.40E-06 mr1926 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
vg0314422629 NA 2.32E-33 mr1037_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
vg0314422629 NA 3.00E-08 mr1798_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