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Detailed information for vg0911503277:

Variant ID: vg0911503277 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 11503277
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.86, G: 0.18, others allele: 0.00, population size: 28. )

Flanking Sequence (100 bp) in Reference Genome:

GTTTTGTTATTTCGAATTTATTCACGAAGTGGTTTTGGAGATGATTGGATTTCACAGGTGAATCTACAGGAAACTGCTGTCATTTTATGTGACCGGTTAG[A/G]
CCGGGCTCTGGTAACCGGTCAGACCGGTGGTATATGCGCGGTCAGACCGGCGCAGCCCGTGGTCTGACCGGCCGACTCTGTGTCGCTTTCGGTTTCGGTT

Reverse complement sequence

AACCGAAACCGAAAGCGACACAGAGTCGGCCGGTCAGACCACGGGCTGCGCCGGTCTGACCGCGCATATACCACCGGTCTGACCGGTTACCAGAGCCCGG[T/C]
CTAACCGGTCACATAAAATGACAGCAGTTTCCTGTAGATTCACCTGTGAAATCCAATCATCTCCAAAACCACTTCGTGAATAAATTCGAAATAACAAAAC

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	29.80%	25.10%	27.23%	17.80%	NA
All Indica	2759	8.70%	31.40%	38.13%	21.78%	NA
All Japonica	1512	68.60%	14.40%	5.29%	11.71%	NA
Aus	269	32.70%	1.50%	49.07%	16.73%	NA
Indica I	595	7.70%	61.20%	24.20%	6.89%	NA
Indica II	465	8.80%	23.90%	36.99%	30.32%	NA
Indica III	913	8.20%	20.00%	45.35%	26.40%	NA
Indica Intermediate	786	10.10%	26.30%	40.97%	22.65%	NA
Temperate Japonica	767	67.90%	6.60%	8.34%	17.08%	NA
Tropical Japonica	504	78.40%	13.90%	1.98%	5.75%	NA
Japonica Intermediate	241	50.20%	40.20%	2.49%	7.05%	NA
VI/Aromatic	96	5.20%	79.20%	9.38%	6.25%	NA
Intermediate	90	43.30%	27.80%	15.56%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0911503277	A -> G	LOC_Os09g19229.1	intron_variant ; MODIFIER	silent_mutation	Average:23.629; most accessible tissue: Zhenshan97 flag leaf, score: 67.31	N	N	N	N
vg0911503277	A -> DEL	N	N	silent_mutation	Average:23.629; most accessible tissue: Zhenshan97 flag leaf, score: 67.31	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0911503277	4.06E-06	NA	mr1852	Jap_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