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Detailed information for vg0604095633:

Variant ID: vg0604095633 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 4095633
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.65, A: 0.34, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


TCTATTAGAGGAGGAACAAAGAAAGGCAAAGGCAATAGGTTAGTATGGTAACTAATACTAGTACTTCTGCTGTTTGAGTACTTACTGTCCAAAAAGGCTG[A/T]
CATTTGTCCGCTTCTTTACTTCCAGCAGCTGTTCCTTCATATCATTTTTATTCGATGACATCTGTCAAAGTGCTTAGCGTTTTAACTTTTAAGAGAGCCC

Reverse complement sequence

GGGCTCTCTTAAAAGTTAAAACGCTAAGCACTTTGACAGATGTCATCGAATAAAAATGATATGAAGGAACAGCTGCTGGAAGTAAAGAAGCGGACAAATG[T/A]
CAGCCTTTTTGGACAGTAAGTACTCAAACAGCAGAAGTACTAGTATTAGTTACCATACTAACCTATTGCCTTTGCCTTTCTTTGTTCCTCCTCTAATAGA

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 59.60% 40.30% 0.02% 0.00% NA
All Indica  2759 90.60% 9.40% 0.00% 0.00% NA
All Japonica  1512 0.90% 99.10% 0.00% 0.00% NA
Aus  269 98.50% 1.10% 0.37% 0.00% NA
Indica I  595 99.00% 1.00% 0.00% 0.00% NA
Indica II  465 66.70% 33.30% 0.00% 0.00% NA
Indica III  913 98.50% 1.50% 0.00% 0.00% NA
Indica Intermediate  786 89.40% 10.60% 0.00% 0.00% NA
Temperate Japonica  767 0.40% 99.60% 0.00% 0.00% NA
Tropical Japonica  504 1.60% 98.40% 0.00% 0.00% NA
Japonica Intermediate  241 1.20% 98.80% 0.00% 0.00% NA
VI/Aromatic  96 3.10% 96.90% 0.00% 0.00% NA
Intermediate  90 40.00% 60.00% 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
vg0604095633 A -> T LOC_Os06g08390.1 downstream_gene_variant ; 3388.0bp to feature; MODIFIER silent_mutation Average:33.246; most accessible tissue: Callus, score: 49.495 N N N N
vg0604095633 A -> T LOC_Os06g08400.1 intron_variant ; MODIFIER silent_mutation Average:33.246; most accessible tissue: Callus, score: 49.495 N N N N
vg0604095633 A -> T LOC_Os06g08400.2 intron_variant ; MODIFIER silent_mutation Average:33.246; most accessible tissue: Callus, score: 49.495 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0604095633 NA 4.89E-09 mr1050 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
vg0604095633 NA 1.45E-21 mr1122 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
vg0604095633 NA 1.76E-59 mr1141 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
vg0604095633 NA 2.31E-19 mr1141 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
vg0604095633 NA 4.58E-26 mr1903 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
vg0604095633 NA 2.54E-70 mr1141_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
vg0604095633 NA 3.15E-17 mr1141_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
vg0604095633 NA 3.93E-26 mr1149_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
vg0604095633 NA 4.07E-27 mr1441_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
vg0604095633 NA 6.45E-07 mr1654_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
vg0604095633 4.83E-07 NA mr1750_2 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
vg0604095633 NA 6.99E-09 mr1835_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
vg0604095633 NA 7.42E-06 mr1860_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
vg0604095633 NA 6.62E-08 mr1889_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
vg0604095633 NA 4.78E-13 mr1904_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
vg0604095633 NA 1.55E-09 mr1907_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
vg0604095633 NA 1.56E-10 mr1934_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