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Detailed information for vg0712947265:

Variant ID: vg0712947265 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 12947265
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : CT (evidence from allele frequency in Oryza rufipogon: CT: 1.00, others allele: 0.00, population size: 43. )

Flanking Sequence (100 bp) in Reference Genome:


CAGAGATGTACCACTGTACCCACAAGACACAGCCCCACAACATGTCACCATGTGCCTCAATACCACCACGGTACCTCGGAAAGGAGCTGTGACAGTACCC[C/T]
CGCACAACACAATCCACCACAGCGCACCTTTCCTGGATCATAATCACCCCCTTATAAACAAGGCATGGACTCCCCAGCGACCCCCGTGGGCTTATCTCCG

Reverse complement sequence

CGGAGATAAGCCCACGGGGGTCGCTGGGGAGTCCATGCCTTGTTTATAAGGGGGTGATTATGATCCAGGAAAGGTGCGCTGTGGTGGATTGTGTTGTGCG[G/A]
GGGTACTGTCACAGCTCCTTTCCGAGGTACCGTGGTGGTATTGAGGCACATGGTGACATGTTGTGGGGCTGTGTCTTGTGGGTACAGTGGTACATCTCTG

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 37.80% 0.40% 35.36% 26.51% NA
All Indica  2759 15.90% 0.60% 52.27% 31.24% NA
All Japonica  1512 82.10% 0.00% 1.06% 16.87% NA
Aus  269 17.10% 0.00% 62.83% 20.07% NA
Indica I  595 22.50% 0.80% 32.61% 44.03% NA
Indica II  465 25.60% 0.40% 38.92% 35.05% NA
Indica III  913 3.10% 0.10% 72.62% 24.21% NA
Indica Intermediate  786 20.00% 1.10% 51.40% 27.48% NA
Temperate Japonica  767 79.00% 0.00% 0.65% 20.34% NA
Tropical Japonica  504 87.10% 0.00% 0.60% 12.30% NA
Japonica Intermediate  241 81.30% 0.00% 3.32% 15.35% NA
VI/Aromatic  96 10.40% 0.00% 21.88% 67.71% NA
Intermediate  90 55.60% 0.00% 25.56% 18.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0712947265 C -> DEL N N silent_mutation Average:11.597; most accessible tissue: Zhenshan97 panicle, score: 20.424 N N N N
vg0712947265 C -> T LOC_Os07g22960.1 intron_variant ; MODIFIER silent_mutation Average:11.597; most accessible tissue: Zhenshan97 panicle, score: 20.424 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0712947265 NA 5.95E-06 mr1192 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
vg0712947265 NA 3.23E-07 mr1167_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
vg0712947265 NA 1.09E-07 mr1624_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
vg0712947265 NA 8.81E-07 mr1693_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
vg0712947265 NA 9.93E-08 mr1726_2 Jap_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
vg0712947265 NA 2.58E-06 mr1741_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
vg0712947265 NA 9.31E-08 mr1765_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
vg0712947265 NA 7.89E-06 mr1887_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