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Detailed information for vg0922029772:

Variant ID: vg0922029772 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 22029772
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:


CGGGCTAAGCAGTCAAGGTTTAAAGCAACAAAGGGCTTGGTTATCAATCTCCTCGCCATTTTCGGAAGCATGCTTTTCTGTGAGCAATCTTACCTTTCTC[A/T]
GTGATTATTTACTTGTATGAGATTTCCTTTTAAAGTGTTCTGAACATATTCTGATTTTATGGCTTTTTTGGCAGAGGCCTGCATATAGCTTTATAAATGC

Reverse complement sequence

GCATTTATAAAGCTATATGCAGGCCTCTGCCAAAAAAGCCATAAAATCAGAATATGTTCAGAACACTTTAAAAGGAAATCTCATACAAGTAAATAATCAC[T/A]
GAGAAAGGTAAGATTGCTCACAGAAAAGCATGCTTCCGAAAATGGCGAGGAGATTGATAACCAAGCCCTTTGTTGCTTTAAACCTTGACTGCTTAGCCCG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.40% 4.70% 1.93% 0.00% NA
All Indica  2759 88.90% 7.90% 3.23% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 99.30% 0.00% 0.74% 0.00% NA
Indica I  595 90.80% 3.20% 6.05% 0.00% NA
Indica II  465 82.60% 12.30% 5.16% 0.00% NA
Indica III  913 91.60% 8.30% 0.11% 0.00% NA
Indica Intermediate  786 88.00% 8.40% 3.56% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 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  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0922029772 A -> T LOC_Os09g38300.1 upstream_gene_variant ; 4772.0bp to feature; MODIFIER silent_mutation Average:50.266; most accessible tissue: Zhenshan97 flower, score: 72.578 N N N N
vg0922029772 A -> T LOC_Os09g38268.1 intron_variant ; MODIFIER silent_mutation Average:50.266; most accessible tissue: Zhenshan97 flower, score: 72.578 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0922029772 3.05E-07 NA mr1022_2 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
vg0922029772 3.07E-06 NA mr1079_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
vg0922029772 2.46E-06 NA mr1178_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
vg0922029772 5.23E-06 NA mr1390_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
vg0922029772 3.41E-06 NA mr1490_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