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Detailed information for vg0817768586:

Variant ID: vg0817768586 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 17768586
Reference Allele: AAlternative Allele: C,T
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.86, C: 0.14, others allele: 0.00, population size: 28. )

Flanking Sequence (100 bp) in Reference Genome:


CGAGCGGTAAAAAAAAGTCAATTGTGTTACTTGTAATAATCATAGTCTAAGCAGGGGTTAAGATAAATCAAGTGTAGAGTGACATACAAGCAGGGAGCTA[A/C,T]
TCATTCTCATACTAAAATATCTAAGCTAAGTGGAAAGAAAATAGAAAGAGAATCTATTCCTATACTTCTAGTATACATAATATACATACATTCTAGTTAT

Reverse complement sequence

ATAACTAGAATGTATGTATATTATGTATACTAGAAGTATAGGAATAGATTCTCTTTCTATTTTCTTTCCACTTAGCTTAGATATTTTAGTATGAGAATGA[T/G,A]
TAGCTCCCTGCTTGTATGTCACTCTACACTTGATTTATCTTAACCCCTGCTTAGACTATGATTATTACAAGTAACACAATTGACTTTTTTTTACCGCTCG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 32.20% 10.80% 3.22% 53.75% NA
All Indica  2759 20.60% 7.90% 3.12% 68.36% NA
All Japonica  1512 60.60% 2.20% 2.98% 34.19% NA
Aus  269 3.70% 86.60% 1.12% 8.55% NA
Indica I  595 37.10% 3.20% 3.87% 55.80% NA
Indica II  465 26.70% 11.00% 4.09% 58.28% NA
Indica III  913 2.20% 8.00% 2.85% 86.97% NA
Indica Intermediate  786 25.80% 9.70% 2.29% 62.21% NA
Temperate Japonica  767 83.30% 0.30% 1.69% 14.73% NA
Tropical Japonica  504 35.10% 5.00% 3.77% 56.15% NA
Japonica Intermediate  241 41.90% 2.50% 5.39% 50.21% NA
VI/Aromatic  96 2.10% 10.40% 14.58% 72.92% NA
Intermediate  90 30.00% 16.70% 4.44% 48.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0817768586 A -> C LOC_Os08g29020.1 3_prime_UTR_variant ; 1406.0bp to feature; MODIFIER silent_mutation Average:18.38; most accessible tissue: Callus, score: 78.505 N N N N
vg0817768586 A -> T LOC_Os08g29020.1 3_prime_UTR_variant ; 1406.0bp to feature; MODIFIER N Average:18.38; most accessible tissue: Callus, score: 78.505 N N N N
vg0817768586 A -> DEL N N silent_mutation Average:18.38; most accessible tissue: Callus, score: 78.505 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0817768586 NA 4.29E-06 mr1321_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
vg0817768586 5.65E-08 3.44E-09 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
vg0817768586 4.42E-06 1.29E-06 mr1338_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
vg0817768586 NA 4.70E-06 mr1579_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