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Detailed information for vg0910300794:

Variant ID: vg0910300794 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 10300794
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


TTATTAAACACATGTTTCAAAGGCCAATTCTAAGTGGGAGAATTGGCAAGTGGGCATATGCTTTGATAGAATATGATTTGGCTTATGAACCATTGAAATC[T/A]
ATGAAAGGCCAAATTGTATGTGATTTTATAGTGGACCATCATGTAGATATTGCTTATGAGGAAAAGGTCTGCTTAGTTGAAGTTATATCTTGGAAGATTT

Reverse complement sequence

AAATCTTCCAAGATATAACTTCAACTAAGCAGACCTTTTCCTCATAAGCAATATCTACATGATGGTCCACTATAAAATCACATACAATTTGGCCTTTCAT[A/T]
GATTTCAATGGTTCATAAGCCAAATCATATTCTATCAAAGCATATGCCCACTTGCCAATTCTCCCACTTAGAATTGGCCTTTGAAACATGTGTTTAATAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.20% 5.60% 0.13% 0.00% NA
All Indica  2759 90.70% 9.10% 0.22% 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 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 66.50% 32.70% 0.86% 0.00% NA
Indica III  913 99.20% 0.80% 0.00% 0.00% NA
Indica Intermediate  786 88.30% 11.50% 0.25% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 86.70% 13.30% 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
vg0910300794 T -> A LOC_Os09g16860.1 synonymous_variant ; p.Ser1333Ser; LOW synonymous_codon Average:18.909; most accessible tissue: Minghui63 flag leaf, score: 26.902 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0910300794 2.57E-06 NA mr1655 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
vg0910300794 5.22E-06 1.64E-07 mr1310_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
vg0910300794 NA 6.62E-06 mr1974_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