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Detailed information for vg0704005849:

Variant ID: vg0704005849 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 4005849
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 134. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTTAACTCCTCTTTGGAAGGGTTTTGGAGGTACGAGATAATCTTGTTAATTTAACTAGTGTGGAAAGGCTCAATCTTGATCTGATTAACGTATATGGC[A/G]
CTGTTGATCGATCATTGGACCCAGCTTTTCAGAAAGGAGAGATAGAGAGATCTTGGGTATGTTCATATATGTCTCCAGCTCTCTGGAGGTCGTTGGAGCT

Reverse complement sequence

AGCTCCAACGACCTCCAGAGAGCTGGAGACATATATGAACATACCCAAGATCTCTCTATCTCTCCTTTCTGAAAAGCTGGGTCCAATGATCGATCAACAG[T/C]
GCCATATACGTTAATCAGATCAAGATTGAGCCTTTCCACACTAGTTAAATTAACAAGATTATCTCGTACCTCCAAAACCCTTCCAAAGAGGAGTTAAAAA

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 95.90% 3.10% 1.02% 0.00% NA
All Indica  2759 93.30% 5.30% 1.41% 0.00% NA
All Japonica  1512 99.40% 0.00% 0.60% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.50% 0.00% 1.51% 0.00% NA
Indica II  465 82.40% 13.50% 4.09% 0.00% NA
Indica III  913 98.00% 1.60% 0.33% 0.00% NA
Indica Intermediate  786 90.20% 8.80% 1.02% 0.00% NA
Temperate Japonica  767 99.10% 0.00% 0.91% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 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
vg0704005849 A -> G LOC_Os07g07960.1 upstream_gene_variant ; 870.0bp to feature; MODIFIER silent_mutation Average:69.056; most accessible tissue: Zhenshan97 panicle, score: 86.058 N N N N
vg0704005849 A -> G LOC_Os07g07960-LOC_Os07g07974 intergenic_region ; MODIFIER silent_mutation Average:69.056; most accessible tissue: Zhenshan97 panicle, score: 86.058 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0704005849 NA 2.46E-06 mr1598 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
vg0704005849 3.81E-07 NA mr1319_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
vg0704005849 1.67E-06 NA mr1319_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