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Detailed information for vg0605312569:

Variant ID: vg0605312569 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 5312569
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


TTCAAATTTTGGTTTATAAAATTTATTCAAAATTTACCGGTTTTCCACCGAATTTCGTGAAATTCCGAATTCCGCCGGTGCCCGAAACGGAAGGGCTGTC[G/A]
GAATCGGAAACCTGCTCCAGTTAGCATTTCGCAATTCAAAGCTGTAGCAGATGACGAAACGGCGGTGATGTTGAGTACTTCTCTTCTGTGTGTATATGCA

Reverse complement sequence

TGCATATACACACAGAAGAGAAGTACTCAACATCACCGCCGTTTCGTCATCTGCTACAGCTTTGAATTGCGAAATGCTAACTGGAGCAGGTTTCCGATTC[C/T]
GACAGCCCTTCCGTTTCGGGCACCGGCGGAATTCGGAATTTCACGAAATTCGGTGGAAAACCGGTAAATTTTGAATAAATTTTATAAACCAAAATTTGAA

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 90.20% 8.10% 1.69% 0.00% NA
All Indica  2759 97.60% 1.30% 1.05% 0.00% NA
All Japonica  1512 77.80% 19.30% 2.91% 0.00% NA
Aus  269 84.00% 14.90% 1.12% 0.00% NA
Indica I  595 97.50% 0.00% 2.52% 0.00% NA
Indica II  465 98.50% 1.30% 0.22% 0.00% NA
Indica III  913 99.60% 0.30% 0.11% 0.00% NA
Indica Intermediate  786 95.00% 3.40% 1.53% 0.00% NA
Temperate Japonica  767 95.30% 1.70% 3.00% 0.00% NA
Tropical Japonica  504 55.20% 42.10% 2.78% 0.00% NA
Japonica Intermediate  241 69.30% 27.80% 2.90% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 81.10% 14.40% 4.44% 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
vg0605312569 G -> A LOC_Os06g10350.1 upstream_gene_variant ; 2609.0bp to feature; MODIFIER silent_mutation Average:44.514; most accessible tissue: Callus, score: 86.622 N N N N
vg0605312569 G -> A LOC_Os06g10330.1 downstream_gene_variant ; 4822.0bp to feature; MODIFIER silent_mutation Average:44.514; most accessible tissue: Callus, score: 86.622 N N N N
vg0605312569 G -> A LOC_Os06g10340.1 downstream_gene_variant ; 1967.0bp to feature; MODIFIER silent_mutation Average:44.514; most accessible tissue: Callus, score: 86.622 N N N N
vg0605312569 G -> A LOC_Os06g10355.1 downstream_gene_variant ; 4909.0bp to feature; MODIFIER silent_mutation Average:44.514; most accessible tissue: Callus, score: 86.622 N N N N
vg0605312569 G -> A LOC_Os06g10340-LOC_Os06g10350 intergenic_region ; MODIFIER silent_mutation Average:44.514; most accessible tissue: Callus, score: 86.622 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0605312569 9.63E-07 NA mr1201 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
vg0605312569 2.08E-06 1.75E-06 mr1219 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
vg0605312569 4.88E-07 1.61E-06 mr1274 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
vg0605312569 NA 9.98E-06 mr1006_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
vg0605312569 NA 4.27E-06 mr1020_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
vg0605312569 5.40E-09 2.48E-07 mr1201_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
vg0605312569 2.32E-08 1.77E-08 mr1219_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
vg0605312569 NA 9.20E-06 mr1269_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
vg0605312569 5.11E-11 1.28E-07 mr1274_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
vg0605312569 NA 8.59E-06 mr1289_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
vg0605312569 NA 6.73E-06 mr1359_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
vg0605312569 NA 2.34E-06 mr1470_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
vg0605312569 NA 7.54E-07 mr1786_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