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Detailed information for vg0719546836:

Variant ID: vg0719546836 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 19546836
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAGATTTAATGTTGCAGCGAATTAAAATACTCTTTTGCAACAATAAAAACCCACATATTTTGGAAACTCTTTATTAAGGGAATTTGGTTTATTTATTATT[A/C]
TACAAAAAATGTTTCTTCTAGTGTACGCACAATGTTTCACTATGTATAGATCTAATGTTGTAGTGAACTGAAATACTCCATTGCAAAAAAAAACCCACAT

Reverse complement sequence

ATGTGGGTTTTTTTTTGCAATGGAGTATTTCAGTTCACTACAACATTAGATCTATACATAGTGAAACATTGTGCGTACACTAGAAGAAACATTTTTTGTA[T/G]
AATAATAAATAAACCAAATTCCCTTAATAAAGAGTTTCCAAAATATGTGGGTTTTTATTGTTGCAAAAGAGTATTTTAATTCGCTGCAACATTAAATCTA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.50% 19.50% 7.85% 14.20% NA
All Indica  2759 74.30% 0.70% 12.36% 12.69% NA
All Japonica  1512 21.20% 58.90% 1.19% 18.78% NA
Aus  269 91.40% 0.00% 0.74% 7.81% NA
Indica I  595 85.00% 0.20% 7.73% 7.06% NA
Indica II  465 84.30% 1.10% 13.55% 1.08% NA
Indica III  913 62.70% 0.00% 16.32% 21.03% NA
Indica Intermediate  786 73.80% 1.50% 10.56% 14.12% NA
Temperate Japonica  767 4.30% 92.80% 0.26% 2.61% NA
Tropical Japonica  504 53.40% 10.70% 1.19% 34.72% NA
Japonica Intermediate  241 7.50% 51.50% 4.15% 36.93% NA
VI/Aromatic  96 94.80% 0.00% 1.04% 4.17% NA
Intermediate  90 63.30% 13.30% 10.00% 13.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0719546836 A -> DEL N N silent_mutation Average:66.137; most accessible tissue: Zhenshan97 flower, score: 81.593 N N N N
vg0719546836 A -> C LOC_Os07g32730.1 downstream_gene_variant ; 1030.0bp to feature; MODIFIER silent_mutation Average:66.137; most accessible tissue: Zhenshan97 flower, score: 81.593 N N N N
vg0719546836 A -> C LOC_Os07g32730-LOC_Os07g32740 intergenic_region ; MODIFIER silent_mutation Average:66.137; most accessible tissue: Zhenshan97 flower, score: 81.593 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0719546836 NA 5.41E-07 mr1082 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
vg0719546836 NA 4.97E-06 mr1083 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
vg0719546836 NA 1.83E-06 mr1226 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
vg0719546836 NA 3.23E-06 mr1291 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
vg0719546836 NA 9.84E-14 mr1653 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
vg0719546836 NA 1.55E-06 mr1815 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
vg0719546836 NA 9.46E-07 mr1082_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
vg0719546836 NA 3.74E-06 mr1083_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
vg0719546836 NA 1.63E-06 mr1153_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
vg0719546836 3.01E-06 NA mr1155_2 Jap_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
vg0719546836 NA 2.54E-13 mr1217_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
vg0719546836 NA 1.15E-06 mr1226_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
vg0719546836 NA 1.49E-10 mr1232_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
vg0719546836 NA 1.58E-16 mr1557_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
vg0719546836 NA 5.00E-10 mr1806_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
vg0719546836 NA 9.58E-08 mr1909_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