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Detailed information for vg0501763185:

Variant ID: vg0501763185 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 1763185
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

CGGGGAAAAGGGAATATATTACTCCTCACAAACAAGGTGAGAGATGAAATTACAACTGTTTTCAAGCCAGAAATTAGACATAGACTCACATCGTGCCTTA[T/G]
TTGCTAAGATATGGCTAACACGATTTTGGTTGCGATGGCTAACACGAAGAAGCAATTAGTATGTGAAGAAAGGGATAAGAAAGAATCAGGTGGAGAGGAA

Reverse complement sequence

TTCCTCTCCACCTGATTCTTTCTTATCCCTTTCTTCACATACTAATTGCTTCTTCGTGTTAGCCATCGCAACCAAAATCGTGTTAGCCATATCTTAGCAA[A/C]
TAAGGCACGATGTGAGTCTATGTCTAATTTCTGGCTTGAAAACAGTTGTAATTTCATCTCTCACCTTGTTTGTGAGGAGTAATATATTCCCTTTTCCCCG

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	84.20%	4.60%	0.97%	10.24%	NA
All Indica	2759	91.60%	7.80%	0.11%	0.58%	NA
All Japonica	1512	66.90%	0.10%	2.78%	30.22%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.00%	1.00%	0.00%	0.00%	NA
Indica II	465	95.30%	3.40%	0.00%	1.29%	NA
Indica III	913	84.10%	15.70%	0.11%	0.11%	NA
Indica Intermediate	786	92.40%	6.20%	0.25%	1.15%	NA
Temperate Japonica	767	86.30%	0.10%	1.30%	12.26%	NA
Tropical Japonica	504	45.40%	0.00%	4.37%	50.20%	NA
Japonica Intermediate	241	50.20%	0.00%	4.15%	45.64%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	85.60%	1.10%	1.11%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0501763185	T -> DEL	N	N	silent_mutation	Average:51.064; most accessible tissue: Zhenshan97 flower, score: 76.106	N	N	N	N
vg0501763185	T -> G	LOC_Os05g03940.1	upstream_gene_variant ; 3498.0bp to feature; MODIFIER	silent_mutation	Average:51.064; most accessible tissue: Zhenshan97 flower, score: 76.106	N	N	N	N
vg0501763185	T -> G	LOC_Os05g03930.1	downstream_gene_variant ; 4152.0bp to feature; MODIFIER	silent_mutation	Average:51.064; most accessible tissue: Zhenshan97 flower, score: 76.106	N	N	N	N
vg0501763185	T -> G	LOC_Os05g03934.1	downstream_gene_variant ; 429.0bp to feature; MODIFIER	silent_mutation	Average:51.064; most accessible tissue: Zhenshan97 flower, score: 76.106	N	N	N	N
vg0501763185	T -> G	LOC_Os05g03934-LOC_Os05g03940	intergenic_region ; MODIFIER	silent_mutation	Average:51.064; most accessible tissue: Zhenshan97 flower, score: 76.106	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0501763185	4.97E-06	4.97E-06	mr1427_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