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Detailed information for vg0905621415:

Variant ID: vg0905621415 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 5621415
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:

GACAAGCATGAATATAATCTCTTCCTCCAGCTTCAAACATCATTGATGGAAGGTCTTCACGATCACTAGTCAACGTCATGCGAACACGACTATTCTCCTC[A/G]
TTGGGGTCATGGGGAATTTGGCGATACTCGGGGACAATGTTGTAGCCTACTTCAAATGCCATCATTCTCAGCTCCCTGACGAATCCTACTGCATCGATCA

Reverse complement sequence

TGATCGATGCAGTAGGATTCGTCAGGGAGCTGAGAATGATGGCATTTGAAGTAGGCTACAACATTGTCCCCGAGTATCGCCAAATTCCCCATGACCCCAA[T/C]
GAGGAGAATAGTCGTGTTCGCATGACGTTGACTAGTGATCGTGAAGACCTTCCATCAATGATGTTTGAAGCTGGAGGAAGAGATTATATTCATGCTTGTC

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	82.40%	17.60%	0.00%	0.00%	NA
All Indica	2759	90.00%	10.00%	0.00%	0.00%	NA
All Japonica	1512	81.00%	19.00%	0.00%	0.00%	NA
Aus	269	25.30%	74.70%	0.00%	0.00%	NA
Indica I	595	93.60%	6.40%	0.00%	0.00%	NA
Indica II	465	86.20%	13.80%	0.00%	0.00%	NA
Indica III	913	93.20%	6.80%	0.00%	0.00%	NA
Indica Intermediate	786	85.60%	14.40%	0.00%	0.00%	NA
Temperate Japonica	767	90.60%	9.40%	0.00%	0.00%	NA
Tropical Japonica	504	82.10%	17.90%	0.00%	0.00%	NA
Japonica Intermediate	241	47.70%	52.30%	0.00%	0.00%	NA
VI/Aromatic	96	41.70%	58.30%	0.00%	0.00%	NA
Intermediate	90	87.80%	12.20%	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
vg0905621415	A -> G	LOC_Os09g10310.1	synonymous_variant ; p.Asn38Asn; LOW	synonymous_codon	Average:39.814; most accessible tissue: Zhenshan97 flag leaf, score: 58.104	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0905621415	NA	7.28E-06	mr1064	Jap_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