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Detailed information for vg1207556909:

Variant ID: vg1207556909 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 7556909
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.80, C: 0.20, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:


GGTTCAAAAGAGGCACGACACTTTATGATCTTTAGTCAGATTGGTGTTATCAACCTGGACTAAATATCATTTTTAGTCCTGGTTTAACACGTTGTCAGGC[T/C]
GTGTCAGGCCCTCCACTATTTTTAGTCCCGGTTGTTTATACCAGCCGGGACCAAAGATTGAAAAAAAAACCGCTCCCACACGCACCTCCTCTTCTCCTTT

Reverse complement sequence

AAAGGAGAAGAGGAGGTGCGTGTGGGAGCGGTTTTTTTTTCAATCTTTGGTCCCGGCTGGTATAAACAACCGGGACTAAAAATAGTGGAGGGCCTGACAC[A/G]
GCCTGACAACGTGTTAAACCAGGACTAAAAATGATATTTAGTCCAGGTTGATAACACCAATCTGACTAAAGATCATAAAGTGTCGTGCCTCTTTTGAACC

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 56.00% 43.70% 0.23% 0.00% NA
All Indica  2759 89.10% 10.60% 0.33% 0.00% NA
All Japonica  1512 5.00% 95.00% 0.00% 0.00% NA
Aus  269 29.70% 70.30% 0.00% 0.00% NA
Indica I  595 91.10% 8.20% 0.67% 0.00% NA
Indica II  465 88.80% 11.20% 0.00% 0.00% NA
Indica III  913 91.00% 9.00% 0.00% 0.00% NA
Indica Intermediate  786 85.40% 14.00% 0.64% 0.00% NA
Temperate Japonica  767 5.20% 94.80% 0.00% 0.00% NA
Tropical Japonica  504 5.80% 94.20% 0.00% 0.00% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 9.40% 90.60% 0.00% 0.00% NA
Intermediate  90 30.00% 67.80% 2.22% 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
vg1207556909 T -> C LOC_Os12g13460.1 downstream_gene_variant ; 2602.0bp to feature; MODIFIER silent_mutation Average:62.114; most accessible tissue: Callus, score: 88.417 N N N N
vg1207556909 T -> C LOC_Os12g13470.1 downstream_gene_variant ; 4990.0bp to feature; MODIFIER silent_mutation Average:62.114; most accessible tissue: Callus, score: 88.417 N N N N
vg1207556909 T -> C LOC_Os12g13460-LOC_Os12g13470 intergenic_region ; MODIFIER silent_mutation Average:62.114; most accessible tissue: Callus, score: 88.417 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1207556909 NA 8.34E-10 mr1151 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
vg1207556909 NA 1.09E-13 mr1218 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
vg1207556909 NA 2.77E-09 mr1249 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
vg1207556909 2.93E-06 8.77E-07 mr1350 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
vg1207556909 NA 4.62E-12 mr1151_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
vg1207556909 NA 6.19E-07 mr1855_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