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Detailed information for vg1000702985:

Variant ID: vg1000702985 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 702985
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


TGACCAGTTTCCTCGAGGAAAAACCAGATTTTTGCCACTTTGATTTTGCAAAAGCAATCTCTCTCTCCATTTTCTGTTTATGAGCTAATCTGAAACAAAA[A/G]
CCAACAATATGTCCATCTTTGCCACAAAAAGAACAAGTATATTTTTCACGATGATTAGACACATTGGTAGCACTAGTAGATTTAGCAACATGAGCAACAA

Reverse complement sequence

TTGTTGCTCATGTTGCTAAATCTACTAGTGCTACCAATGTGTCTAATCATCGTGAAAAATATACTTGTTCTTTTTGTGGCAAAGATGGACATATTGTTGG[T/C]
TTTTGTTTCAGATTAGCTCATAAACAGAAAATGGAGAGAGAGATTGCTTTTGCAAAATCAAAGTGGCAAAAATCTGGTTTTTCCTCGAGGAAACTGGTCA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 83.00% 12.90% 4.13% 0.00% NA
All Indica  2759 71.30% 21.60% 7.03% 0.00% NA
All Japonica  1512 99.40% 0.60% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 56.80% 27.70% 15.46% 0.00% NA
Indica II  465 83.00% 13.10% 3.87% 0.00% NA
Indica III  913 73.70% 22.60% 3.72% 0.00% NA
Indica Intermediate  786 72.60% 21.00% 6.36% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 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 96.70% 2.20% 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
vg1000702985 A -> G LOC_Os10g02120.1 intron_variant ; MODIFIER silent_mutation Average:46.426; most accessible tissue: Minghui63 young leaf, score: 71.839 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1000702985 1.66E-06 7.04E-06 mr1245_2 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
vg1000702985 8.77E-06 5.84E-06 mr1245_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
vg1000702985 3.08E-06 2.01E-08 mr1332_2 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
vg1000702985 1.15E-06 5.59E-08 mr1332_2 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
vg1000702985 1.89E-06 4.39E-06 mr1373_2 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
vg1000702985 9.46E-06 1.89E-06 mr1373_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
vg1000702985 NA 2.36E-06 mr1648_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
vg1000702985 NA 2.31E-06 mr1648_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
vg1000702985 NA 2.38E-07 mr1655_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
vg1000702985 NA 5.37E-06 mr1669_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