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Detailed information for vg1003520346:

Variant ID: vg1003520346 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 3520346
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:


AAATCCTGGAGAGATTAACGAAATCACCATAGGCGCCTCGCTGTCGACGGGTATGTCGCCTACCACTGAAAGCACAACACCGTTAAATCTTAGAAAATTC[G/A]
CTCCCATGGGAAGTCGAACCCAGCACCTCATATCTAAATTCTTCTTGGAATAAAACCCATCAATGAACAATTTTTCTTTAGCACTAACATCACCGGACTG

Reverse complement sequence

CAGTCCGGTGATGTTAGTGCTAAAGAAAAATTGTTCATTGATGGGTTTTATTCCAAGAAGAATTTAGATATGAGGTGCTGGGTTCGACTTCCCATGGGAG[C/T]
GAATTTTCTAAGATTTAACGGTGTTGTGCTTTCAGTGGTAGGCGACATACCCGTCGACAGCGAGGCGCCTATGGTGATTTCGTTAATCTCTCCAGGATTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.00% 43.80% 0.17% 0.00% NA
All Indica  2759 49.70% 50.00% 0.25% 0.00% NA
All Japonica  1512 63.70% 36.20% 0.07% 0.00% NA
Aus  269 87.70% 12.30% 0.00% 0.00% NA
Indica I  595 47.70% 52.30% 0.00% 0.00% NA
Indica II  465 56.30% 43.40% 0.22% 0.00% NA
Indica III  913 53.00% 46.50% 0.44% 0.00% NA
Indica Intermediate  786 43.50% 56.20% 0.25% 0.00% NA
Temperate Japonica  767 91.80% 8.20% 0.00% 0.00% NA
Tropical Japonica  504 27.40% 72.40% 0.20% 0.00% NA
Japonica Intermediate  241 50.20% 49.80% 0.00% 0.00% NA
VI/Aromatic  96 26.00% 74.00% 0.00% 0.00% NA
Intermediate  90 56.70% 43.30% 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
vg1003520346 G -> A LOC_Os10g06760.1 downstream_gene_variant ; 1698.0bp to feature; MODIFIER silent_mutation Average:71.434; most accessible tissue: Zhenshan97 flower, score: 80.904 N N N N
vg1003520346 G -> A LOC_Os10g06760-LOC_Os10g06770 intergenic_region ; MODIFIER silent_mutation Average:71.434; most accessible tissue: Zhenshan97 flower, score: 80.904 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1003520346 NA 2.30E-06 mr1121 Jap_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
vg1003520346 2.47E-08 6.33E-11 mr1538 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
vg1003520346 1.02E-07 3.22E-07 mr1547 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
vg1003520346 1.20E-13 2.71E-17 mr1547 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
vg1003520346 4.56E-16 1.72E-20 mr1709 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
vg1003520346 7.94E-26 9.80E-34 mr1709 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
vg1003520346 NA 8.90E-06 mr1043_2 Jap_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
vg1003520346 2.12E-10 9.28E-15 mr1538_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
vg1003520346 3.00E-08 5.94E-11 mr1547_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
vg1003520346 7.23E-17 1.69E-25 mr1547_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
vg1003520346 2.20E-23 4.93E-25 mr1709_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
vg1003520346 7.35E-37 2.17E-50 mr1709_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