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Detailed information for vg1003864522:

Variant ID: vg1003864522 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 3864522
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:

AAATATAAAATTACAGTCTTATATAACTAAAATTACATATGTAAATTTAGTTGATATGACATGTAAGTGCACTGTAATTTTGATGACATGTAAGTGCACT[G/T]
TAATTTTGATGAAAATATTGTGTAAGTAAATTTGCATTAGTTATTTTATTTCAAATATAAAATTACAGTCCTATATAACTAAAATTACATTGTAAATTTA

Reverse complement sequence

TAAATTTACAATGTAATTTTAGTTATATAGGACTGTAATTTTATATTTGAAATAAAATAACTAATGCAAATTTACTTACACAATATTTTCATCAAAATTA[C/A]
AGTGCACTTACATGTCATCAAAATTACAGTGCACTTACATGTCATATCAACTAAATTTACATATGTAATTTTAGTTATATAAGACTGTAATTTTATATTT

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	45.10%	15.60%	5.61%	33.75%	NA
All Indica	2759	23.00%	26.20%	9.17%	41.57%	NA
All Japonica	1512	86.00%	0.30%	0.20%	13.56%	NA
Aus	269	45.70%	0.00%	1.12%	53.16%	NA
Indica I	595	25.90%	16.00%	10.08%	48.07%	NA
Indica II	465	30.80%	26.00%	7.31%	35.91%	NA
Indica III	913	20.00%	37.30%	9.75%	32.86%	NA
Indica Intermediate	786	19.70%	21.20%	8.91%	50.13%	NA
Temperate Japonica	767	94.10%	0.30%	0.13%	5.48%	NA
Tropical Japonica	504	79.40%	0.00%	0.20%	20.44%	NA
Japonica Intermediate	241	73.90%	0.80%	0.41%	24.90%	NA
VI/Aromatic	96	22.90%	1.00%	0.00%	76.04%	NA
Intermediate	90	55.60%	7.80%	6.67%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1003864522	G -> T	LOC_Os10g07340.1	upstream_gene_variant ; 3718.0bp to feature; MODIFIER	silent_mutation	Average:17.238; most accessible tissue: Callus, score: 33.898	N	N	N	N
vg1003864522	G -> T	LOC_Os10g07310.1	downstream_gene_variant ; 3213.0bp to feature; MODIFIER	silent_mutation	Average:17.238; most accessible tissue: Callus, score: 33.898	N	N	N	N
vg1003864522	G -> T	LOC_Os10g07320.1	downstream_gene_variant ; 463.0bp to feature; MODIFIER	silent_mutation	Average:17.238; most accessible tissue: Callus, score: 33.898	N	N	N	N
vg1003864522	G -> T	LOC_Os10g07320-LOC_Os10g07340	intergenic_region ; MODIFIER	silent_mutation	Average:17.238; most accessible tissue: Callus, score: 33.898	N	N	N	N
vg1003864522	G -> DEL	N	N	silent_mutation	Average:17.238; most accessible tissue: Callus, score: 33.898	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1003864522	4.79E-06	8.59E-06	mr1398_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