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Detailed information for vg0900167315:

Variant ID: vg0900167315 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 167315
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

CAAGTTGGTATCAGAGCTAGGTTTGACCGTAGGGCAAGCCAACTGGAAAACCTAAGAGCCCTCTGAACCCCTTTTCATATGCATATGCCTTTTTCACTTG[T/G]
ATTTGTTTCAGGAAAATTTGGGGTTTTGCCTCTTGGGTTTGTGGGAAAAATCTTGGTTGTTCATTCGGATCGGATTTTTAAAATTAGCTCAGTCTAGGGT

Reverse complement sequence

ACCCTAGACTGAGCTAATTTTAAAAATCCGATCCGAATGAACAACCAAGATTTTTCCCACAAACCCAAGAGGCAAAACCCCAAATTTTCCTGAAACAAAT[A/C]
CAAGTGAAAAAGGCATATGCATATGAAAAGGGGTTCAGAGGGCTCTTAGGTTTTCCAGTTGGCTTGCCCTACGGTCAAACCTAGCTCTGATACCAACTTG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	35.90%	13.90%	16.17%	34.02%	NA
All Indica	2759	9.20%	22.60%	25.05%	43.13%	NA
All Japonica	1512	84.30%	0.10%	0.26%	15.34%	NA
Aus	269	5.20%	12.30%	20.82%	61.71%	NA
Indica I	595	20.20%	20.20%	17.65%	42.02%	NA
Indica II	465	7.30%	4.70%	22.58%	65.38%	NA
Indica III	913	2.70%	34.00%	32.75%	30.56%	NA
Indica Intermediate	786	9.50%	21.90%	23.16%	45.42%	NA
Temperate Japonica	767	71.30%	0.10%	0.39%	28.16%	NA
Tropical Japonica	504	99.40%	0.00%	0.20%	0.40%	NA
Japonica Intermediate	241	94.20%	0.00%	0.00%	5.81%	NA
VI/Aromatic	96	95.80%	0.00%	4.17%	0.00%	NA
Intermediate	90	66.70%	1.10%	10.00%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0900167315	T -> G	LOC_Os09g01160.1	downstream_gene_variant ; 4120.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0900167315	T -> G	LOC_Os09g01180.1	downstream_gene_variant ; 2717.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0900167315	T -> G	LOC_Os09g01170.1	intron_variant ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0900167315	T -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0900167315	6.54E-07	NA	mr1165_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