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Detailed information for vg0407913349:

Variant ID: vg0407913349 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 7913349
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


TGACAAAATGGATTCCGGTAGAAAAACATAATATACTCTTACTTGCACCGTGTATATTATATATTTACCTCGAGCATAGTAACAGATTCAATTTCTATCT[C/T]
GAATGGTGCTTCAAACAATATATACGTGGGGTTGTTTTTTTGGCCCTTATCTTTTTTAATCTTCCTTCCTCTTTTCTCTGTGTAAAAATATACGATGCAG

Reverse complement sequence

CTGCATCGTATATTTTTACACAGAGAAAAGAGGAAGGAAGATTAAAAAAGATAAGGGCCAAAAAAACAACCCCACGTATATATTGTTTGAAGCACCATTC[G/A]
AGATAGAAATTGAATCTGTTACTATGCTCGAGGTAAATATATAATATACACGGTGCAAGTAAGAGTATATTATGTTTTTCTACCGGAATCCATTTTGTCA

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 94.20% 5.80% 0.02% 0.00% NA
All Indica  2759 96.60% 3.40% 0.04% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 37.50% 62.50% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 95.40% 4.60% 0.00% 0.00% NA
Indica Intermediate  786 93.50% 6.40% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 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
vg0407913349 C -> T LOC_Os04g14140.1 upstream_gene_variant ; 4974.0bp to feature; MODIFIER silent_mutation Average:37.307; most accessible tissue: Minghui63 flower, score: 49.234 N N N N
vg0407913349 C -> T LOC_Os04g14150.1 upstream_gene_variant ; 418.0bp to feature; MODIFIER silent_mutation Average:37.307; most accessible tissue: Minghui63 flower, score: 49.234 N N N N
vg0407913349 C -> T LOC_Os04g14160.1 upstream_gene_variant ; 2724.0bp to feature; MODIFIER silent_mutation Average:37.307; most accessible tissue: Minghui63 flower, score: 49.234 N N N N
vg0407913349 C -> T LOC_Os04g14140-LOC_Os04g14150 intergenic_region ; MODIFIER silent_mutation Average:37.307; most accessible tissue: Minghui63 flower, score: 49.234 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0407913349 NA 2.22E-06 mr1236_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
vg0407913349 8.02E-06 NA mr1666_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