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Detailed information for vg0727529174:

Variant ID: vg0727529174 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 27529174
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.90, G: 0.07, others allele: 0.00, population size: 41. )

Flanking Sequence (100 bp) in Reference Genome:


TGGTCTTTAGTTCCTAATTTTTTTTCCAAAAACATCACATCAAATCTTTGGATATATGCATGGACAGTAAAGAGATCTCAACATTAAATATAGATAAAAA[T/G]
AAAAAACTACTTGCACAATTTGCAATGGAAATCGCGGGATGAATCTTTTGAGCCTAATTGGTCCATGACTAGCTATAAGTGCTACAGTAACCCACATTTG

Reverse complement sequence

CAAATGTGGGTTACTGTAGCACTTATAGCTAGTCATGGACCAATTAGGCTCAAAAGATTCATCCCGCGATTTCCATTGCAAATTGTGCAAGTAGTTTTTT[A/C]
TTTTTATCTATATTTAATGTTGAGATCTCTTTACTGTCCATGCATATATCCAAAGATTTGATGTGATGTTTTTGGAAAAAAAATTAGGAACTAAAGACCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 31.20% 19.90% 0.99% 47.84% NA
All Indica  2759 50.10% 5.90% 1.27% 42.73% NA
All Japonica  1512 1.50% 42.90% 0.53% 55.09% NA
Aus  269 16.70% 1.10% 0.74% 81.41% NA
Indica I  595 40.30% 3.50% 0.67% 55.46% NA
Indica II  465 83.00% 2.60% 2.58% 11.83% NA
Indica III  913 42.10% 7.70% 0.99% 49.29% NA
Indica Intermediate  786 47.30% 7.60% 1.27% 43.77% NA
Temperate Japonica  767 1.60% 66.20% 0.26% 31.94% NA
Tropical Japonica  504 1.00% 13.10% 0.99% 84.92% NA
Japonica Intermediate  241 2.10% 31.10% 0.41% 66.39% NA
VI/Aromatic  96 4.20% 89.60% 0.00% 6.25% NA
Intermediate  90 25.60% 45.60% 2.22% 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
vg0727529174 T -> DEL N N silent_mutation Average:28.575; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N
vg0727529174 T -> G LOC_Os07g46120.1 downstream_gene_variant ; 1758.0bp to feature; MODIFIER silent_mutation Average:28.575; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N
vg0727529174 T -> G LOC_Os07g46130.1 intron_variant ; MODIFIER silent_mutation Average:28.575; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0727529174 NA 5.03E-06 mr1032 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
vg0727529174 NA 6.96E-07 mr1165 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
vg0727529174 NA 3.45E-07 mr1291 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
vg0727529174 NA 1.35E-06 mr1478 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
vg0727529174 NA 3.00E-06 mr1502 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
vg0727529174 NA 3.42E-06 mr1543 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
vg0727529174 NA 6.34E-06 mr1608 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
vg0727529174 NA 3.13E-06 mr1720 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
vg0727529174 NA 6.51E-06 mr1888 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
vg0727529174 NA 2.91E-06 mr1950 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
vg0727529174 NA 8.64E-06 mr1975 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
vg0727529174 NA 7.71E-06 mr1227_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
vg0727529174 6.51E-06 NA mr1362_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
vg0727529174 NA 2.44E-06 mr1497_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
vg0727529174 NA 6.76E-07 mr1730_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
vg0727529174 NA 7.59E-06 mr1960_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