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Detailed information for vg0331370140:

Variant ID: vg0331370140 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 31370140
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


CATGAATCAATCCGAAGGAAAATTAAAGGAGACATTCCTTTCCTGTGGAATCAATAGAGAAACAAAGAAAAATTTACATCCACTCCTACCTCATTTTTTC[C/T]
ATTTCCTACGTTTTTACTCTGTCTATCCGAACACATGTTTACCAATCATAGCTACAGAATTTCTGTGTTTTTCAATCCTCTATTTTATCTATGCATTCCT

Reverse complement sequence

AGGAATGCATAGATAAAATAGAGGATTGAAAAACACAGAAATTCTGTAGCTATGATTGGTAAACATGTGTTCGGATAGACAGAGTAAAAACGTAGGAAAT[G/A]
GAAAAAATGAGGTAGGAGTGGATGTAAATTTTTCTTTGTTTCTCTATTGATTCCACAGGAAAGGAATGTCTCCTTTAATTTTCCTTCGGATTGATTCATG

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 97.30% 2.60% 0.06% 0.00% NA
All Indica  2759 95.80% 4.20% 0.07% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 83.20% 16.80% 0.00% 0.00% NA
Indica III  913 99.00% 1.00% 0.00% 0.00% NA
Indica Intermediate  786 96.20% 3.60% 0.25% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 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 93.30% 5.60% 1.11% 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
vg0331370140 C -> T LOC_Os03g55120-LOC_Os03g55130 intergenic_region ; MODIFIER silent_mutation Average:41.193; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0331370140 NA 9.79E-06 mr1415 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
vg0331370140 NA 9.79E-06 mr1567 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
vg0331370140 7.05E-06 2.03E-08 mr1806 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
vg0331370140 1.87E-06 4.62E-14 mr1829 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
vg0331370140 NA 7.24E-09 mr1902 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
vg0331370140 NA 6.80E-07 mr1806_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
vg0331370140 NA 3.98E-14 mr1829_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
vg0331370140 NA 6.34E-07 mr1842_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
vg0331370140 NA 1.35E-12 mr1902_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