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Detailed information for vg1017269903:

Variant ID: vg1017269903 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 17269903
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.58, C: 0.42, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:


AATCATACTAAAATAATATATGATTTTGTTTGGGTGCTAGCCGCGTAATTGCGCGGGTCACCCAGCTAGTTAATAATAAGACCCTATTTAGTCTAAGTAA[T/C]
ACTATAGTTTTTCTTATTTCAACAAGTAGGTGATTTTGAAATTTGGGAGAGCTAATGGTGAAATTGAAGATTTGCTGAAAGGTAATAGTATAGATTATGA

Reverse complement sequence

TCATAATCTATACTATTACCTTTCAGCAAATCTTCAATTTCACCATTAGCTCTCCCAAATTTCAAAATCACCTACTTGTTGAAATAAGAAAAACTATAGT[A/G]
TTACTTAGACTAAATAGGGTCTTATTATTAACTAGCTGGGTGACCCGCGCAATTACGCGGCTAGCACCCAAACAAAATCATATATTATTTTAGTATGATT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.80% 42.10% 0.11% 0.00% NA
All Indica  2759 91.20% 8.70% 0.07% 0.00% NA
All Japonica  1512 8.50% 91.40% 0.13% 0.00% NA
Aus  269 7.80% 92.20% 0.00% 0.00% NA
Indica I  595 96.30% 3.50% 0.17% 0.00% NA
Indica II  465 92.70% 7.30% 0.00% 0.00% NA
Indica III  913 87.70% 12.20% 0.11% 0.00% NA
Indica Intermediate  786 90.50% 9.50% 0.00% 0.00% NA
Temperate Japonica  767 2.30% 97.70% 0.00% 0.00% NA
Tropical Japonica  504 6.00% 94.00% 0.00% 0.00% NA
Japonica Intermediate  241 33.20% 66.00% 0.83% 0.00% NA
VI/Aromatic  96 20.80% 79.20% 0.00% 0.00% NA
Intermediate  90 50.00% 48.90% 1.11% 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
vg1017269903 T -> C LOC_Os10g32980.1 downstream_gene_variant ; 3290.0bp to feature; MODIFIER silent_mutation Average:62.584; most accessible tissue: Zhenshan97 root, score: 78.911 N N N N
vg1017269903 T -> C LOC_Os10g32990.1 intron_variant ; MODIFIER silent_mutation Average:62.584; most accessible tissue: Zhenshan97 root, score: 78.911 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1017269903 NA 5.18E-07 mr1321 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
vg1017269903 NA 1.84E-07 mr1716 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
vg1017269903 NA 8.73E-06 mr1782 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
vg1017269903 NA 1.39E-06 mr1990 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
vg1017269903 NA 8.21E-13 mr1147_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
vg1017269903 6.71E-06 NA mr1653_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
vg1017269903 NA 3.49E-08 mr1700_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
vg1017269903 NA 4.94E-10 mr1782_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