Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0816860448:

Variant ID: vg0816860448 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 16860448
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: 227. )

Flanking Sequence (100 bp) in Reference Genome:


TTTACCAAATTTCACTGTTAACAACAGGACATCATGACTTCACGGTTTTAGCTGTAGAACACTACATGAAGTGACTTTGGGGAGAAAACACTCTGTAAAC[A/G]
TGAAAATTAGATCATGGACACCGCGTCCATTAGAATATTTATTTTCGGTTAAATTGAAGAGAGAAATCATGTGAATTCTTTGAAATACCCTAGGTCCACA

Reverse complement sequence

TGTGGACCTAGGGTATTTCAAAGAATTCACATGATTTCTCTCTTCAATTTAACCGAAAATAAATATTCTAATGGACGCGGTGTCCATGATCTAATTTTCA[T/C]
GTTTACAGAGTGTTTTCTCCCCAAAGTCACTTCATGTAGTGTTCTACAGCTAAAACCGTGAAGTCATGATGTCCTGTTGTTAACAGTGAAATTTGGTAAA

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 52.80% 14.50% 4.87% 27.87% NA
All Indica  2759 28.20% 24.40% 7.83% 39.58% NA
All Japonica  1512 90.30% 0.20% 0.46% 9.06% NA
Aus  269 72.50% 0.70% 2.23% 24.54% NA
Indica I  595 46.70% 5.40% 4.37% 43.53% NA
Indica II  465 24.70% 26.90% 11.83% 36.56% NA
Indica III  913 16.00% 36.70% 7.12% 40.20% NA
Indica Intermediate  786 30.50% 22.90% 8.91% 37.66% NA
Temperate Japonica  767 98.20% 0.10% 0.26% 1.43% NA
Tropical Japonica  504 84.70% 0.40% 0.60% 14.29% NA
Japonica Intermediate  241 76.80% 0.00% 0.83% 22.41% NA
VI/Aromatic  96 97.90% 0.00% 0.00% 2.08% NA
Intermediate  90 67.80% 8.90% 1.11% 22.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0816860448 A -> G LOC_Os08g27660.1 upstream_gene_variant ; 2049.0bp to feature; MODIFIER silent_mutation Average:58.924; most accessible tissue: Minghui63 young leaf, score: 73.49 N N N N
vg0816860448 A -> G LOC_Os08g27672.1 downstream_gene_variant ; 2946.0bp to feature; MODIFIER silent_mutation Average:58.924; most accessible tissue: Minghui63 young leaf, score: 73.49 N N N N
vg0816860448 A -> G LOC_Os08g27674.1 downstream_gene_variant ; 2946.0bp to feature; MODIFIER silent_mutation Average:58.924; most accessible tissue: Minghui63 young leaf, score: 73.49 N N N N
vg0816860448 A -> G LOC_Os08g27650-LOC_Os08g27660 intergenic_region ; MODIFIER silent_mutation Average:58.924; most accessible tissue: Minghui63 young leaf, score: 73.49 N N N N
vg0816860448 A -> DEL N N silent_mutation Average:58.924; most accessible tissue: Minghui63 young leaf, score: 73.49 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0816860448 NA 8.40E-06 mr1041_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
vg0816860448 NA 9.37E-07 mr1184_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
vg0816860448 NA 4.13E-07 mr1278_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
vg0816860448 NA 3.74E-06 mr1293_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
vg0816860448 NA 8.53E-06 mr1329_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
vg0816860448 NA 4.27E-11 mr1338_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
vg0816860448 NA 2.42E-06 mr1373_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
vg0816860448 NA 1.75E-07 mr1418_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
vg0816860448 NA 1.46E-06 mr1419_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
vg0816860448 NA 1.66E-07 mr1420_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
vg0816860448 NA 5.81E-07 mr1467_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
vg0816860448 NA 1.15E-08 mr1488_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
vg0816860448 NA 1.38E-07 mr1492_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
vg0816860448 NA 9.48E-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
vg0816860448 NA 2.50E-09 mr1506_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
vg0816860448 NA 2.16E-06 mr1524_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
vg0816860448 NA 3.00E-07 mr1556_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
vg0816860448 9.24E-06 1.19E-06 mr1556_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
vg0816860448 NA 3.87E-07 mr1604_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
vg0816860448 NA 1.92E-07 mr1683_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
vg0816860448 NA 3.43E-08 mr1690_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
vg0816860448 NA 9.22E-06 mr1759_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
vg0816860448 NA 5.52E-07 mr1764_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
vg0816860448 3.37E-07 3.37E-07 mr1764_2 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
vg0816860448 NA 5.32E-08 mr1779_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
vg0816860448 NA 3.33E-06 mr1811_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
vg0816860448 NA 7.23E-07 mr1812_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
vg0816860448 2.56E-06 2.56E-06 mr1840_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
vg0816860448 NA 5.22E-06 mr1856_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
vg0816860448 NA 6.90E-08 mr1992_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