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Detailed information for vg0508237720:

Variant ID: vg0508237720 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 8237720
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.70, G: 0.29, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

CCTTCCAACCCGGCGCGTGATTCTTCGCTGCAATAGTCGTGGGGACCTCTACACTCTACCTACTACTGTCCCTGCCATCACCGCCCACAGCTTCCTCGCC[A/G]
AGTCATCCACCTTATGGCATCATCGCCTTGGTCACCCCAGTCCAGCCGCAGTCCAAACTCTTCATAAATTAGCTATTCTTTCTTGTACTAGGTCTAATAA

Reverse complement sequence

TTATTAGACCTAGTACAAGAAAGAATAGCTAATTTATGAAGAGTTTGGACTGCGGCTGGACTGGGGTGACCAAGGCGATGATGCCATAAGGTGGATGACT[T/C]
GGCGAGGAAGCTGTGGGCGGTGATGGCAGGGACAGTAGTAGGTAGAGTGTAGAGGTCCCCACGACTATTGCAGCGAAGAATCACGCGCCGGGTTGGAAGG

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	56.60%	43.00%	0.06%	0.34%	NA
All Indica	2759	35.30%	64.20%	0.11%	0.47%	NA
All Japonica	1512	98.90%	1.10%	0.00%	0.00%	NA
Aus	269	20.40%	79.60%	0.00%	0.00%	NA
Indica I	595	41.20%	58.30%	0.00%	0.50%	NA
Indica II	465	55.50%	43.90%	0.43%	0.22%	NA
Indica III	913	25.30%	74.20%	0.00%	0.55%	NA
Indica Intermediate	786	30.40%	69.00%	0.13%	0.51%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	97.80%	2.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	60.00%	36.70%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0508237720	A -> DEL	N	N	silent_mutation	Average:47.926; most accessible tissue: Zhenshan97 young leaf, score: 63.653	N	N	N	N
vg0508237720	A -> G	LOC_Os05g14520-LOC_Os05g14540	intergenic_region ; MODIFIER	silent_mutation	Average:47.926; most accessible tissue: Zhenshan97 young leaf, score: 63.653	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0508237720	NA	6.04E-11	mr1593	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
vg0508237720	NA	1.18E-19	mr1195_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
vg0508237720	7.16E-06	2.12E-15	mr1593_2	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