\

Search for Variation information by Variation ID:

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

Detailed information for vg0406835352:

Variant ID: vg0406835352 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 6835352
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, T: 0.10, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:


TATTTATTATTTCCTTTAAAATATAAAATTACAATTCTATAGACCTAATATTACATTTGTAAGTTAAGTTGATATGACATGTAAGTGTATTGTAATTTCA[C/T]
TATAGTTATACTGTAATTACAATGTAACTATAATAGAATTACACTGTAACTTTTAGTGTAATTGCAGTGTAACTATAGTGAAATTTATCTTCTATGCATT

Reverse complement sequence

AATGCATAGAAGATAAATTTCACTATAGTTACACTGCAATTACACTAAAAGTTACAGTGTAATTCTATTATAGTTACATTGTAATTACAGTATAACTATA[G/A]
TGAAATTACAATACACTTACATGTCATATCAACTTAACTTACAAATGTAATATTAGGTCTATAGAATTGTAATTTTATATTTTAAAGGAAATAATAAATA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 78.50% 12.80% 0.32% 8.40% NA
All Indica  2759 68.10% 19.80% 0.40% 11.71% NA
All Japonica  1512 99.20% 0.50% 0.07% 0.26% NA
Aus  269 82.90% 0.40% 0.74% 15.99% NA
Indica I  595 85.20% 6.10% 0.00% 8.74% NA
Indica II  465 71.80% 15.70% 0.86% 11.61% NA
Indica III  913 57.30% 27.80% 0.55% 14.35% NA
Indica Intermediate  786 65.60% 23.20% 0.25% 10.94% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 0.80% 0.20% 0.00% NA
Japonica Intermediate  241 97.50% 0.80% 0.00% 1.66% NA
VI/Aromatic  96 40.60% 35.40% 1.04% 22.92% NA
Intermediate  90 75.60% 18.90% 0.00% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0406835352 C -> DEL N N silent_mutation Average:28.957; most accessible tissue: Callus, score: 62.597 N N N N
vg0406835352 C -> T LOC_Os04g12390.1 intron_variant ; MODIFIER silent_mutation Average:28.957; most accessible tissue: Callus, score: 62.597 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0406835352 NA 6.31E-07 mr1015 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
vg0406835352 NA 6.65E-06 mr1233 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
vg0406835352 NA 6.62E-07 mr1305 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
vg0406835352 NA 8.07E-06 mr1314 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
vg0406835352 NA 3.71E-07 mr1409 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
vg0406835352 NA 9.54E-06 mr1426 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
vg0406835352 NA 6.73E-07 mr1515 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
vg0406835352 3.08E-06 NA mr1537 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
vg0406835352 NA 3.21E-06 mr1537 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
vg0406835352 NA 6.71E-06 mr1574 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
vg0406835352 NA 5.32E-06 mr1586 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