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Detailed information for vg0207033828:

Variant ID: vg0207033828 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 7033828
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

AGGTACACTAACTAGTAAGATTTAAAGAGGATTAAGTGTACTAAAATTAACACGCAGATTCATTCACTTGTCTAGTTGTCTTACCGCAAGGAAAGTTTGA[A/G]
CTTCATTGTTCATGAAAATACTACTCCCTCAGGTCAATATTAGCAAATTCTACTAAGCGCAAGTCAATTCCACTGTCTGAAACATCATATATTTCGGTCC

Reverse complement sequence

GGACCGAAATATATGATGTTTCAGACAGTGGAATTGACTTGCGCTTAGTAGAATTTGCTAATATTGACCTGAGGGAGTAGTATTTTCATGAACAATGAAG[T/C]
TCAAACTTTCCTTGCGGTAAGACAACTAGACAAGTGAATGAATCTGCGTGTTAATTTTAGTACACTTAATCCTCTTTAAATCTTACTAGTTAGTGTACCT

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	91.20%	8.80%	0.00%	0.00%	NA
All Indica	2759	94.30%	5.70%	0.00%	0.00%	NA
All Japonica	1512	99.30%	0.70%	0.00%	0.00%	NA
Aus	269	32.70%	67.30%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	86.90%	13.10%	0.00%	0.00%	NA
Indica III	913	96.70%	3.30%	0.00%	0.00%	NA
Indica Intermediate	786	91.60%	8.40%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	97.50%	2.50%	0.00%	0.00%	NA
VI/Aromatic	96	38.50%	61.50%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	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
vg0207033828	A -> G	LOC_Os02g13200.1	intron_variant ; MODIFIER	silent_mutation	Average:57.289; most accessible tissue: Minghui63 flower, score: 72.895	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0207033828	NA	9.88E-11	mr1570	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
vg0207033828	NA	3.77E-07	mr1126_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
vg0207033828	NA	5.52E-10	mr1612_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