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Detailed information for vg0226196512:

Variant ID: vg0226196512 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 26196512
Reference Allele: T	Alternative Allele: G
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.78, G: 0.22, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:

GAATCACCCGTTTAACTTGCTTGGCCTCGGTTTGCATGCCAAACCGACAGACCTACCTAGTAGTCGCACTAATTCCTGTAGGCTATACTACCCTGACTCC[T/G]
TGTAGCTCCACCTTTGTGGTACCTCGGTATCCATGTTCTTTGAGCGCGTATACCAAATATCCTACATACACCGTTGTTTGTCGAAAACTTGGGAAATGGG

Reverse complement sequence

CCCATTTCCCAAGTTTTCGACAAACAACGGTGTATGTAGGATATTTGGTATACGCGCTCAAAGAACATGGATACCGAGGTACCACAAAGGTGGAGCTACA[A/C]
GGAGTCAGGGTAGTATAGCCTACAGGAATTAGTGCGACTACTAGGTAGGTCTGTCGGTTTGGCATGCAAACCGAGGCCAAGCAAGTTAAACGGGTGATTC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.50%	30.70%	0.55%	4.19%	NA
All Indica	2759	97.90%	1.90%	0.14%	0.07%	NA
All Japonica	1512	2.80%	82.90%	1.46%	12.83%	NA
Aus	269	98.10%	1.90%	0.00%	0.00%	NA
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	98.70%	1.30%	0.00%	0.00%	NA
Indica III	913	99.10%	0.90%	0.00%	0.00%	NA
Indica Intermediate	786	94.70%	4.60%	0.51%	0.25%	NA
Temperate Japonica	767	0.90%	82.00%	2.09%	14.99%	NA
Tropical Japonica	504	6.00%	90.50%	0.20%	3.37%	NA
Japonica Intermediate	241	2.50%	69.70%	2.07%	25.73%	NA
VI/Aromatic	96	4.20%	95.80%	0.00%	0.00%	NA
Intermediate	90	43.30%	54.40%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0226196512	T -> G	LOC_Os02g43400.1	upstream_gene_variant ; 1575.0bp to feature; MODIFIER	silent_mutation	Average:20.917; most accessible tissue: Minghui63 young leaf, score: 32.638	N	N	N	N
vg0226196512	T -> G	LOC_Os02g43410.1	downstream_gene_variant ; 3501.0bp to feature; MODIFIER	silent_mutation	Average:20.917; most accessible tissue: Minghui63 young leaf, score: 32.638	N	N	N	N
vg0226196512	T -> G	LOC_Os02g43410.2	downstream_gene_variant ; 3501.0bp to feature; MODIFIER	silent_mutation	Average:20.917; most accessible tissue: Minghui63 young leaf, score: 32.638	N	N	N	N
vg0226196512	T -> G	LOC_Os02g43400-LOC_Os02g43410	intergenic_region ; MODIFIER	silent_mutation	Average:20.917; most accessible tissue: Minghui63 young leaf, score: 32.638	N	N	N	N
vg0226196512	T -> DEL	N	N	silent_mutation	Average:20.917; most accessible tissue: Minghui63 young leaf, score: 32.638	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0226196512	NA	5.45E-15	mr1324_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
vg0226196512	6.19E-06	NA	mr1425_2	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