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Detailed information for vg0717886286:

Variant ID: vg0717886286 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 17886286
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.58, T: 0.40, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:


ACAGAAGGTAGCCTCTATGGACAATGTGAGGTTGTGGGCTAGTCCTACCATGAAAGTTTAAAGTGAATGTTAATAGCACACAGTAACAATAAAGAAGTGC[T/A]
GTTATGAGAGTATGGAAATCATATGACCATTCCCCATAAGTGTTGGGCTTTATCAAATCATGGATCGTGTGTCCATGAAACACATAGTTGTTCATCTAAT

Reverse complement sequence

ATTAGATGAACAACTATGTGTTTCATGGACACACGATCCATGATTTGATAAAGCCCAACACTTATGGGGAATGGTCATATGATTTCCATACTCTCATAAC[A/T]
GCACTTCTTTATTGTTACTGTGTGCTATTAACATTCACTTTAAACTTTCATGGTAGGACTAGCCCACAACCTCACATTGTCCATAGAGGCTACCTTCTGT

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 61.70% 38.20% 0.02% 0.00% NA
All Indica  2759 47.50% 52.50% 0.04% 0.00% NA
All Japonica  1512 83.10% 16.90% 0.00% 0.00% NA
Aus  269 71.00% 29.00% 0.00% 0.00% NA
Indica I  595 82.50% 17.30% 0.17% 0.00% NA
Indica II  465 22.40% 77.60% 0.00% 0.00% NA
Indica III  913 35.20% 64.80% 0.00% 0.00% NA
Indica Intermediate  786 50.10% 49.90% 0.00% 0.00% NA
Temperate Japonica  767 70.40% 29.60% 0.00% 0.00% NA
Tropical Japonica  504 96.40% 3.60% 0.00% 0.00% NA
Japonica Intermediate  241 95.90% 4.10% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 75.60% 24.40% 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
vg0717886286 T -> A LOC_Os07g30260.1 downstream_gene_variant ; 3870.0bp to feature; MODIFIER silent_mutation Average:52.473; most accessible tissue: Minghui63 flower, score: 68.171 N N N N
vg0717886286 T -> A LOC_Os07g30250.1 intron_variant ; MODIFIER silent_mutation Average:52.473; most accessible tissue: Minghui63 flower, score: 68.171 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0717886286 NA 7.02E-06 mr1138 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
vg0717886286 5.70E-07 5.70E-07 mr1181_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
vg0717886286 NA 8.73E-07 mr1354_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
vg0717886286 NA 5.38E-08 mr1952_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