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Detailed information for vg0703432636:

Variant ID: vg0703432636 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 3432636
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.90, G: 0.10, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

ACCAAAAATAATGACAATGGTCAGAAGAGAAGGCTCGGCACAATACTGACCTTGAAACAACAGCGTGGGAGGAATCACTTGCAGAGAGCTTAGACACTAT[A/G]
TCACCCATGTAATGTTCATTATGTGATAAAGTAAGTCTTATTGTCTTAGGTTCATCCTCCATCATACAAGGAACAAAAATCCCATCTACTTCTATGGGAT

Reverse complement sequence

ATCCCATAGAAGTAGATGGGATTTTTGTTCCTTGTATGATGGAGGATGAACCTAAGACAATAAGACTTACTTTATCACATAATGAACATTACATGGGTGA[T/C]
ATAGTGTCTAAGCTCTCTGCAAGTGATTCCTCCCACGCTGTTGTTTCAAGGTCAGTATTGTGCCGAGCCTTCTCTTCTGACCATTGTCATTATTTTTGGT

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	55.90%	43.60%	0.11%	0.34%	NA
All Indica	2759	35.80%	63.60%	0.07%	0.51%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	3.30%	96.70%	0.00%	0.00%	NA
Indica I	595	84.70%	15.00%	0.00%	0.34%	NA
Indica II	465	15.10%	84.10%	0.22%	0.65%	NA
Indica III	913	15.90%	83.70%	0.11%	0.33%	NA
Indica Intermediate	786	34.20%	65.00%	0.00%	0.76%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	90.60%	9.40%	0.00%	0.00%	NA
Intermediate	90	58.90%	35.60%	3.33%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0703432636	A -> DEL	LOC_Os07g06970.1	N	frameshift_variant	Average:59.972; most accessible tissue: Minghui63 flower, score: 70.849	N	N	N	N
vg0703432636	A -> G	LOC_Os07g06970.1	synonymous_variant ; p.Asp264Asp; LOW	synonymous_codon	Average:59.972; most accessible tissue: Minghui63 flower, score: 70.849	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0703432636	NA	3.82E-07	mr1291	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
vg0703432636	NA	1.34E-17	mr1557	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
vg0703432636	NA	7.22E-06	mr1904	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
vg0703432636	NA	7.90E-06	mr1974_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