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Detailed information for vg0140617467:

Variant ID: vg0140617467 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 40617467
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


ATCAGAGCATAAAAATGTGCCAGATGCTCAGGTTGGGGGTTTGGGAATTGCTAAAAAACTGTTGCAAGTTTTTTAAGGTGAAAAAACCTTACAGTATAAC[C/T]
ATAGTATAATTGTAATATAATTACCCTACAACTACATTGTAGCTAGAGATCCACATGATCAGTTTCAGCGTCAGTTTTTCAGTTCATAAACAGCAAACCT

Reverse complement sequence

AGGTTTGCTGTTTATGAACTGAAAAACTGACGCTGAAACTGATCATGTGGATCTCTAGCTACAATGTAGTTGTAGGGTAATTATATTACAATTATACTAT[G/A]
GTTATACTGTAAGGTTTTTTCACCTTAAAAAACTTGCAACAGTTTTTTAGCAATTCCCAAACCCCCAACCTGAGCATCTGGCACATTTTTATGCTCTGAT

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 97.10% 2.90% 0.04% 0.00% NA
All Indica  2759 95.20% 4.70% 0.07% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 88.40% 11.40% 0.17% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.10% 0.90% 0.00% 0.00% NA
Indica Intermediate  786 93.00% 6.90% 0.13% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 0.00% 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
vg0140617467 C -> T LOC_Os01g70170.1 upstream_gene_variant ; 4004.0bp to feature; MODIFIER silent_mutation Average:71.517; most accessible tissue: Zhenshan97 flower, score: 86.702 N N N N
vg0140617467 C -> T LOC_Os01g70180.2 upstream_gene_variant ; 238.0bp to feature; MODIFIER silent_mutation Average:71.517; most accessible tissue: Zhenshan97 flower, score: 86.702 N N N N
vg0140617467 C -> T LOC_Os01g70180.1 intron_variant ; MODIFIER silent_mutation Average:71.517; most accessible tissue: Zhenshan97 flower, score: 86.702 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0140617467 1.04E-06 1.32E-07 mr1228 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
vg0140617467 NA 6.01E-06 mr1457 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
vg0140617467 NA 7.67E-06 mr1531 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
vg0140617467 1.94E-06 3.76E-07 mr1574 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
vg0140617467 NA 2.66E-06 mr1749 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
vg0140617467 NA 1.92E-09 mr1860 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
vg0140617467 NA 3.11E-07 mr1887 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