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Detailed information for vg0722037727:

Variant ID: vg0722037727 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 22037727
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:

GCACACCACTGATCCACTCAGGCGCAAGGTAACCCCTTGTCCCTCTCATTGTTGTCAAAACACGGCTGAAATCCCGCCCTAAGAGCTTTGCTAGACCAAA[G/A]
TCAGACACTTTGGGTACAAATGACTCATCCAAAAGTATGTTATCTGGCTTAACATCACAGTGTATTATGCAATCCCTACATTTTTCATGCAGGTAATTTA

Reverse complement sequence

TAAATTACCTGCATGAAAAATGTAGGGATTGCATAATACACTGTGATGTTAAGCCAGATAACATACTTTTGGATGAGTCATTTGTACCCAAAGTGTCTGA[C/T]
TTTGGTCTAGCAAAGCTCTTAGGGCGGGATTTCAGCCGTGTTTTGACAACAATGAGAGGGACAAGGGGTTACCTTGCGCCTGAGTGGATCAGTGGTGTGC

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	59.70%	40.20%	0.06%	0.00%	NA
All Indica	2759	35.00%	64.90%	0.11%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	68.40%	31.60%	0.00%	0.00%	NA
Indica I	595	6.60%	93.10%	0.34%	0.00%	NA
Indica II	465	43.40%	56.60%	0.00%	0.00%	NA
Indica III	913	48.40%	51.60%	0.00%	0.00%	NA
Indica Intermediate	786	35.90%	64.00%	0.13%	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	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	74.40%	25.60%	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
vg0722037727	G -> A	LOC_Os07g36780.1	synonymous_variant ; p.Asp636Asp; LOW	synonymous_codon	Average:75.174; most accessible tissue: Callus, score: 87.696	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0722037727	NA	3.59E-08	mr1717	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