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Detailed information for vg1014702877:

Variant ID: vg1014702877 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 14702877
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.00, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTGAATGTGATTGGCAGTGTTTTTAACCTGACTCTGGCAAGAGATATCAAGCATCTTTTAGGAGGTTGGCTTTGTGATTTAATAAAGAAGATAAAAAG[G/T]
TAGTGGTAGTTGGGATTGCTGCTGTTCTTTGGGTTATTTGGAAAGCCAGGAATGCTGCATGCTTTAAAAAGGAAAAATTGAATGACCCGGTGGAACTAAT

Reverse complement sequence

ATTAGTTCCACCGGGTCATTCAATTTTTCCTTTTTAAAGCATGCAGCATTCCTGGCTTTCCAAATAACCCAAAGAACAGCAGCAATCCCAACTACCACTA[C/A]
CTTTTTATCTTCTTTATTAAATCACAAAGCCAACCTCCTAAAAGATGCTTGATATCTCTTGCCAGAGTCAGGTTAAAAACACTGCCAATCACATTCAAAA

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 84.30% 15.60% 0.15% 0.00% NA
All Indica  2759 73.30% 26.50% 0.25% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 71.10% 28.10% 0.84% 0.00% NA
Indica II  465 87.10% 12.70% 0.22% 0.00% NA
Indica III  913 66.60% 33.30% 0.11% 0.00% NA
Indica Intermediate  786 74.60% 25.40% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg1014702877 G -> T LOC_Os10g28260.1 splice_donor_variant&intron_variant ; HIGH splice_donor_variant Average:51.275; most accessible tissue: Zhenshan97 flower, score: 84.504 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1014702877 NA 2.93E-06 mr1189 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
vg1014702877 NA 6.22E-06 mr1346 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
vg1014702877 NA 2.66E-06 mr1625 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
vg1014702877 4.64E-06 4.65E-06 mr1966 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
vg1014702877 5.07E-06 5.07E-06 mr1966 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
vg1014702877 NA 1.40E-06 mr1990 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