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Detailed information for vg0129761733:

Variant ID: vg0129761733 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 29761733
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.02, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


TTGAATCAACGATGGTTGTCAGACTGGCAGGTATGTCCTCATGGTAGGCTGCTTTCCATATCTATGTAGCCTCACCGGTCCAGTCTAAGCACTTGTATAT[G/A]
TATATAGTGAAATTACTGTCAAGTGTCAATGCAACCCCTTAATCTTTATTTGGCTTCGATTAGAGGAAATTATAAACAGGTTCATTATGAAAAATTCTTA

Reverse complement sequence

TAAGAATTTTTCATAATGAACCTGTTTATAATTTCCTCTAATCGAAGCCAAATAAAGATTAAGGGGTTGCATTGACACTTGACAGTAATTTCACTATATA[C/T]
ATATACAAGTGCTTAGACTGGACCGGTGAGGCTACATAGATATGGAAAGCAGCCTACCATGAGGACATACCTGCCAGTCTGACAACCATCGTTGATTCAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.50% 6.50% 0.00% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 81.30% 18.70% 0.00% 0.00% NA
Aus  269 96.30% 3.70% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 47.60% 52.40% 0.00% 0.00% NA
Japonica Intermediate  241 94.20% 5.80% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0129761733 G -> A LOC_Os01g51754.1 5_prime_UTR_variant ; 2007.0bp to feature; MODIFIER silent_mutation Average:58.556; most accessible tissue: Callus, score: 84.647 N N N N
vg0129761733 G -> A LOC_Os01g51754.2 5_prime_UTR_variant ; 2007.0bp to feature; MODIFIER silent_mutation Average:58.556; most accessible tissue: Callus, score: 84.647 N N N N
vg0129761733 G -> A LOC_Os01g51754.3 upstream_gene_variant ; 645.0bp to feature; MODIFIER silent_mutation Average:58.556; most accessible tissue: Callus, score: 84.647 N N N N
vg0129761733 G -> A LOC_Os01g51754.4 intron_variant ; MODIFIER silent_mutation Average:58.556; most accessible tissue: Callus, score: 84.647 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0129761733 4.73E-06 NA mr1539_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