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Detailed information for vg0910004814:

Variant ID: vg0910004814 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 10004814
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.77, C: 0.24, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


ACCGGGGTGAGTCCATTGTAAAAATTCTGCAGGATTAGCCAGTCGTCCATCCCATGATGAGGACAGGCGGCCACGTACTCCTGCAGTTGTTCCCATGCTT[T/C]
CGGAATAGACTCATCCCTTATCTGCTAGAAACTTGAAATCCTTCCATAAAGGGCATTGGTTTTGCCCATCGGGAAGAATTTTGAGAGGAATGCCATCAAG

Reverse complement sequence

CTTGATGGCATTCCTCTCAAAATTCTTCCCGATGGGCAAAACCAATGCCCTTTATGGAAGGATTTCAAGTTTCTAGCAGATAAGGGATGAGTCTATTCCG[A/G]
AAGCATGGGAACAACTGCAGGAGTACGTGGCCGCCTGTCCTCATCATGGGATGGACGACTGGCTAATCCTGCAGAATTTTTACAATGGACTCACCCCGGT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 24.30% 4.40% 4.00% 67.35% NA
All Indica  2759 5.00% 5.00% 4.24% 85.79% NA
All Japonica  1512 61.80% 2.10% 3.51% 32.54% NA
Aus  269 13.00% 4.50% 3.72% 78.81% NA
Indica I  595 10.90% 1.50% 4.54% 83.03% NA
Indica II  465 3.20% 2.40% 3.01% 91.40% NA
Indica III  913 0.40% 9.20% 5.04% 85.32% NA
Indica Intermediate  786 6.70% 4.30% 3.82% 85.11% NA
Temperate Japonica  767 94.50% 0.00% 0.13% 5.35% NA
Tropical Japonica  504 7.70% 5.80% 9.33% 77.18% NA
Japonica Intermediate  241 71.00% 1.20% 2.07% 25.73% NA
VI/Aromatic  96 21.90% 18.80% 3.12% 56.25% NA
Intermediate  90 22.20% 6.70% 6.67% 64.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0910004814 T -> DEL N N silent_mutation Average:16.608; most accessible tissue: Callus, score: 33.189 N N N N
vg0910004814 T -> C LOC_Os09g16380.1 downstream_gene_variant ; 4024.0bp to feature; MODIFIER silent_mutation Average:16.608; most accessible tissue: Callus, score: 33.189 N N N N
vg0910004814 T -> C LOC_Os09g16370.1 intron_variant ; MODIFIER silent_mutation Average:16.608; most accessible tissue: Callus, score: 33.189 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0910004814 NA 4.89E-06 mr1011 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
vg0910004814 1.23E-06 1.23E-06 mr1370 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
vg0910004814 NA 5.52E-06 mr1425 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
vg0910004814 NA 5.09E-12 mr1471 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
vg0910004814 NA 3.08E-06 mr1471 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
vg0910004814 NA 1.67E-20 mr1679 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
vg0910004814 NA 6.98E-10 mr1679 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
vg0910004814 NA 2.94E-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
vg0910004814 NA 8.98E-22 mr1679_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
vg0910004814 NA 7.17E-09 mr1679_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
vg0910004814 NA 7.91E-17 mr1699_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