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Detailed information for vg0324945119:

Variant ID: vg0324945119 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 24945119
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

GAATTCTCTTCTTTGTTAGCTGCCCGTCAACTTCTCCTGGATCGTCTCGTCTAATCTTGTATTGTAGTGCTTTGCAAACAAGGCATGCTTCTAGGTTCTC[A/G]
TACTCCTCACCACGATATAGGATACAATCATTCGGACATGCGTGAATCTTCTGAACTTCCAGTCCTAGAGGGCAAACTATCTTCTTAGCCTCGTACGTTG

Reverse complement sequence

CAACGTACGAGGCTAAGAAGATAGTTTGCCCTCTAGGACTGGAAGTTCAGAAGATTCACGCATGTCCGAATGATTGTATCCTATATCGTGGTGAGGAGTA[T/C]
GAGAACCTAGAAGCATGCCTTGTTTGCAAAGCACTACAATACAAGATTAGACGAGACGATCCAGGAGAAGTTGACGGGCAGCTAACAAAGAAGAGAATTC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.90%	46.80%	0.25%	0.04%	NA
All Indica	2759	80.10%	19.40%	0.40%	0.07%	NA
All Japonica	1512	0.90%	99.10%	0.00%	0.00%	NA
Aus	269	83.60%	16.40%	0.00%	0.00%	NA
Indica I	595	71.40%	27.70%	0.84%	0.00%	NA
Indica II	465	96.30%	3.70%	0.00%	0.00%	NA
Indica III	913	84.00%	15.80%	0.11%	0.11%	NA
Indica Intermediate	786	72.60%	26.60%	0.64%	0.13%	NA
Temperate Japonica	767	0.70%	99.30%	0.00%	0.00%	NA
Tropical Japonica	504	0.80%	99.20%	0.00%	0.00%	NA
Japonica Intermediate	241	1.70%	98.30%	0.00%	0.00%	NA
VI/Aromatic	96	9.40%	90.60%	0.00%	0.00%	NA
Intermediate	90	45.60%	53.30%	1.11%	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
vg0324945119	A -> DEL	LOC_Os03g44370.1	N	frameshift_variant	Average:27.024; most accessible tissue: Zhenshan97 flower, score: 42.409	N	N	N	N
vg0324945119	A -> G	LOC_Os03g44370.1	synonymous_variant ; p.Tyr295Tyr; LOW	synonymous_codon	Average:27.024; most accessible tissue: Zhenshan97 flower, score: 42.409	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0324945119	NA	7.73E-12	mr1281	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
vg0324945119	6.17E-08	NA	mr1671	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
vg0324945119	2.60E-06	1.88E-10	mr1671	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
vg0324945119	NA	4.44E-06	mr1733	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
vg0324945119	NA	3.77E-06	mr1821	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
vg0324945119	NA	4.33E-07	mr1915	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
vg0324945119	1.21E-06	NA	mr1031_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
vg0324945119	NA	9.38E-07	mr1212_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
vg0324945119	NA	1.51E-06	mr1671_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