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Detailed information for vg0324100933:

Variant ID: vg0324100933 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 24100933
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 30. )

Flanking Sequence (100 bp) in Reference Genome:

CCGAGCCGATTGACTTCTCACCGGCCGATTAATATAACCTAAAAGGTATTCCTTTACGTGGAGGAATCAAAACTGGAGGAGAGCTAAGATATTCCTTAAT[A/G]
CTATCCAAAGCTTTCTGCTGCTTTGCCCCCCAAGCAAACTTTTGATCGGCTTTCAATCTTAGCAATGGTGTAAAAGGCTCTAACCTTCCAGACAAATTAG

Reverse complement sequence

CTAATTTGTCTGGAAGGTTAGAGCCTTTTACACCATTGCTAAGATTGAAAGCCGATCAAAAGTTTGCTTGGGGGGCAAAGCAGCAGAAAGCTTTGGATAG[T/C]
ATTAAGGAATATCTTAGCTCTCCTCCAGTTTTGATTCCTCCACGTAAAGGAATACCTTTTAGGTTATATTAATCGGCCGGTGAGAAGTCAATCGGCTCGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.30%	3.20%	24.46%	30.05%	NA
All Indica	2759	5.90%	5.10%	39.62%	49.37%	NA
All Japonica	1512	99.10%	0.00%	0.40%	0.46%	NA
Aus	269	77.00%	1.90%	10.41%	10.78%	NA
Indica I	595	8.60%	3.20%	24.87%	63.36%	NA
Indica II	465	3.40%	3.90%	30.32%	62.37%	NA
Indica III	913	2.10%	8.70%	56.85%	32.42%	NA
Indica Intermediate	786	9.90%	3.10%	36.26%	50.76%	NA
Temperate Japonica	767	99.50%	0.00%	0.26%	0.26%	NA
Tropical Japonica	504	99.00%	0.00%	0.40%	0.60%	NA
Japonica Intermediate	241	98.30%	0.00%	0.83%	0.83%	NA
VI/Aromatic	96	79.20%	4.20%	13.54%	3.12%	NA
Intermediate	90	57.80%	3.30%	17.78%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0324100933	A -> DEL	N	N	silent_mutation	Average:11.584; most accessible tissue: Zhenshan97 young leaf, score: 20.224	N	N	N	N
vg0324100933	A -> G	LOC_Os03g43210.1	downstream_gene_variant ; 2493.0bp to feature; MODIFIER	silent_mutation	Average:11.584; most accessible tissue: Zhenshan97 young leaf, score: 20.224	N	N	N	N
vg0324100933	A -> G	LOC_Os03g43220.1	intron_variant ; MODIFIER	silent_mutation	Average:11.584; most accessible tissue: Zhenshan97 young leaf, score: 20.224	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0324100933	NA	3.90E-41	mr1509	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
vg0324100933	NA	4.04E-24	mr1571	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
vg0324100933	NA	3.56E-81	mr1718	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
vg0324100933	5.63E-06	3.00E-07	mr1718	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
vg0324100933	4.38E-06	NA	mr1750	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
vg0324100933	2.78E-10	3.92E-12	mr1750	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
vg0324100933	7.32E-07	7.32E-07	mr1987	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