\

Search for Variation information by Variation ID:

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

Detailed information for vg0421066643:

Variant ID: vg0421066643 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 21066643
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:


TTTAAAAATCAATTATGAAAAGTAAATTACGATAGAAGTCTCAAAATCATCTTAAACAATTAAGTTCTAAAAATTTTTTTACAGCGACTTATTAGTTGTA[G/T]
GGAAAATGATTAGAGTTTTTAGGCAAGTAAATTAACACTCTCACATGTGTGGAACTGAGTAAAATAGTACTGATGTCTTTACAGGTAGAAGACATAGATG

Reverse complement sequence

CATCTATGTCTTCTACCTGTAAAGACATCAGTACTATTTTACTCAGTTCCACACATGTGAGAGTGTTAATTTACTTGCCTAAAAACTCTAATCATTTTCC[C/A]
TACAACTAATAAGTCGCTGTAAAAAAATTTTTAGAACTTAATTGTTTAAGATGATTTTGAGACTTCTATCGTAATTTACTTTTCATAATTGATTTTTAAA

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 62.80% 18.20% 0.49% 18.49% NA
All Indica  2759 38.60% 29.20% 0.83% 31.32% NA
All Japonica  1512 99.70% 0.10% 0.00% 0.20% NA
Aus  269 83.30% 16.70% 0.00% 0.00% NA
Indica I  595 44.20% 6.70% 1.51% 47.56% NA
Indica II  465 15.50% 26.00% 1.51% 56.99% NA
Indica III  913 49.50% 38.10% 0.11% 12.27% NA
Indica Intermediate  786 35.40% 37.90% 0.76% 25.95% NA
Temperate Japonica  767 99.70% 0.00% 0.00% 0.26% NA
Tropical Japonica  504 99.60% 0.20% 0.00% 0.20% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 85.60% 6.70% 0.00% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0421066643 G -> DEL N N silent_mutation Average:8.798; most accessible tissue: Callus, score: 40.511 N N N N
vg0421066643 G -> T LOC_Os04g34760-LOC_Os04g34780 intergenic_region ; MODIFIER silent_mutation Average:8.798; most accessible tissue: Callus, score: 40.511 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0421066643 NA 1.16E-07 mr1182 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
vg0421066643 NA 4.25E-13 mr1183 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
vg0421066643 NA 3.02E-13 mr1503 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
vg0421066643 8.42E-06 1.59E-08 mr1158_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
vg0421066643 NA 8.65E-07 mr1167_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
vg0421066643 NA 3.21E-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
vg0421066643 NA 2.94E-06 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
vg0421066643 NA 1.40E-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
vg0421066643 NA 1.14E-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
vg0421066643 NA 9.54E-10 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
vg0421066643 NA 3.73E-06 mr1508_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
vg0421066643 NA 7.51E-07 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
vg0421066643 NA 1.02E-06 mr1549_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
vg0421066643 NA 6.35E-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
vg0421066643 NA 1.13E-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
vg0421066643 NA 3.98E-06 mr1950_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