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Detailed information for vg0104049262:

Variant ID: vg0104049262 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 4049262
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


ATTGATTCAACTATGGCCGCTGCGATGCTCACACATGGCCAACACCTCTTCTTGACCTTTGGAGAAGAGAAGCGATTCAACTCAATTCAGGCCAAGTTTT[C/T]
CAAACTTTTTCTTCAAACTTCCAACTTTTCCATCACATCAAAACTTTACTACACACACAAACTTCCAATTTTTCCGTTACATCATTCCAATTTTAATCAA

Reverse complement sequence

TTGATTAAAATTGGAATGATGTAACGGAAAAATTGGAAGTTTGTGTGTGTAGTAAAGTTTTGATGTGATGGAAAAGTTGGAAGTTTGAAGAAAAAGTTTG[G/A]
AAAACTTGGCCTGAATTGAGTTGAATCGCTTCTCTTCTCCAAAGGTCAAGAAGAGGTGTTGGCCATGTGTGAGCATCGCAGCGGCCATAGTTGAATCAAT

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 97.60% 2.30% 0.11% 0.00% NA
All Indica  2759 95.90% 4.00% 0.18% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 91.40% 8.20% 0.34% 0.00% NA
Indica II  465 99.40% 0.40% 0.22% 0.00% NA
Indica III  913 98.00% 2.00% 0.00% 0.00% NA
Indica Intermediate  786 94.70% 5.10% 0.25% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% 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  90 100.00% 0.00% 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
vg0104049262 C -> T LOC_Os01g08270.1 downstream_gene_variant ; 2594.0bp to feature; MODIFIER silent_mutation Average:59.694; most accessible tissue: Callus, score: 89.265 N N N N
vg0104049262 C -> T LOC_Os01g08270.4 downstream_gene_variant ; 2594.0bp to feature; MODIFIER silent_mutation Average:59.694; most accessible tissue: Callus, score: 89.265 N N N N
vg0104049262 C -> T LOC_Os01g08260-LOC_Os01g08270 intergenic_region ; MODIFIER silent_mutation Average:59.694; most accessible tissue: Callus, score: 89.265 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0104049262 2.11E-06 2.76E-09 mr1177 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
vg0104049262 NA 2.03E-06 mr1180 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
vg0104049262 NA 4.00E-06 mr1261 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
vg0104049262 NA 2.38E-06 mr1327 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
vg0104049262 NA 2.11E-06 mr1336 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
vg0104049262 2.99E-06 2.21E-07 mr1480 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
vg0104049262 4.76E-06 4.76E-06 mr1540 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
vg0104049262 NA 1.31E-06 mr1627 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
vg0104049262 4.04E-06 3.37E-10 mr1692 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
vg0104049262 5.30E-06 4.46E-06 mr1732 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
vg0104049262 NA 5.45E-06 mr1839 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
vg0104049262 NA 5.29E-06 mr1128_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
vg0104049262 NA 7.04E-06 mr1336_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
vg0104049262 NA 6.66E-06 mr1454_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
vg0104049262 NA 7.13E-06 mr1864_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