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Detailed information for vg0801223463:

Variant ID: vg0801223463 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 1223463
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAAATTCCTAGTGATTAAATCCGAATTTCTACCGTGAATCGATTACTTATAGAGATTACCCAAAAATAATCTATAATAGTCTATAAGAATTCATCTAATT[G/T]
TTTAGTTATTAATTACATTTAAATTACTACCGCGAATTGATTTCTTATGGAAATTACCAAGAATAATCTATAATAATCTATGATTATAGTATCATTTTGC

Reverse complement sequence

GCAAAATGATACTATAATCATAGATTATTATAGATTATTCTTGGTAATTTCCATAAGAAATCAATTCGCGGTAGTAATTTAAATGTAATTAATAACTAAA[C/A]
AATTAGATGAATTCTTATAGACTATTATAGATTATTTTTGGGTAATCTCTATAAGTAATCGATTCACGGTAGAAATTCGGATTTAATCACTAGGAATTTC

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	89.00%	6.60%	3.96%	0.51%	NA
All Indica	2759	82.50%	11.00%	6.20%	0.25%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	90.70%	0.00%	3.35%	5.95%	NA
Indica I	595	75.00%	17.60%	7.39%	0.00%	NA
Indica II	465	98.30%	1.10%	0.65%	0.00%	NA
Indica III	913	74.00%	15.90%	9.86%	0.22%	NA
Indica Intermediate	786	88.80%	6.20%	4.33%	0.64%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	1.00%	2.08%	0.00%	NA
Intermediate	90	90.00%	3.30%	5.56%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0801223463	G -> T	LOC_Os08g02870.1	downstream_gene_variant ; 1877.0bp to feature; MODIFIER	silent_mutation	Average:29.567; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0801223463	G -> T	LOC_Os08g02870-LOC_Os08g02880	intergenic_region ; MODIFIER	silent_mutation	Average:29.567; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0801223463	G -> DEL	N	N	silent_mutation	Average:29.567; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0801223463	1.06E-06	NA	mr1277	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
vg0801223463	6.93E-06	2.92E-06	mr1277	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