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Detailed information for vg0224285609:

Variant ID: vg0224285609 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24285609
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.85, T: 0.13, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

TGTGTTGTTCTTAAACCATCGACTCGTTCAACTAGATATATTGGCTAAATAATAACACCTTCACACTTTTACGCCCCCACATTTTTTGTTGTTAGTATAT[T/C]
ACTTCTGTGAAAAAAAAATGAAATGCATTGAAATTTTGTTTCGGCATATAAAAGTTAATGATCAGTATAACCTTGAATACGACGATTATAATCTTTTTAG

Reverse complement sequence

CTAAAAAGATTATAATCGTCGTATTCAAGGTTATACTGATCATTAACTTTTATATGCCGAAACAAAATTTCAATGCATTTCATTTTTTTTTCACAGAAGT[A/G]
ATATACTAACAACAAAAAATGTGGGGGCGTAAAAGTGTGAAGGTGTTATTATTTAGCCAATATATCTAGTTGAACGAGTCGATGGTTTAAGAACAACACA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.30%	24.60%	0.11%	0.00%	NA
All Indica	2759	73.50%	26.40%	0.11%	0.00%	NA
All Japonica	1512	78.80%	21.10%	0.13%	0.00%	NA
Aus	269	77.30%	22.70%	0.00%	0.00%	NA
Indica I	595	49.90%	49.90%	0.17%	0.00%	NA
Indica II	465	84.10%	15.90%	0.00%	0.00%	NA
Indica III	913	82.50%	17.50%	0.00%	0.00%	NA
Indica Intermediate	786	74.70%	25.10%	0.25%	0.00%	NA
Temperate Japonica	767	70.40%	29.50%	0.13%	0.00%	NA
Tropical Japonica	504	90.30%	9.70%	0.00%	0.00%	NA
Japonica Intermediate	241	81.30%	18.30%	0.41%	0.00%	NA
VI/Aromatic	96	62.50%	37.50%	0.00%	0.00%	NA
Intermediate	90	80.00%	20.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0224285609	T -> C	LOC_Os02g40110.1	upstream_gene_variant ; 805.0bp to feature; MODIFIER	silent_mutation	Average:41.031; most accessible tissue: Zhenshan97 root, score: 72.188	N	N	N	N
vg0224285609	T -> C	LOC_Os02g40100.1	downstream_gene_variant ; 4568.0bp to feature; MODIFIER	silent_mutation	Average:41.031; most accessible tissue: Zhenshan97 root, score: 72.188	N	N	N	N
vg0224285609	T -> C	LOC_Os02g40120.1	downstream_gene_variant ; 3210.0bp to feature; MODIFIER	silent_mutation	Average:41.031; most accessible tissue: Zhenshan97 root, score: 72.188	N	N	N	N
vg0224285609	T -> C	LOC_Os02g40110-LOC_Os02g40120	intergenic_region ; MODIFIER	silent_mutation	Average:41.031; most accessible tissue: Zhenshan97 root, score: 72.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224285609	3.09E-06	NA	mr1065	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