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Detailed information for vg0224011069:

Variant ID: vg0224011069 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24011069
Reference Allele: T	Alternative Allele: C,A,G
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

TCGATAACAGTTACTCCAATGTCTGCGCGCAGTTGAGAATATGAATTCGTTCATTTGCATCGAAGTCGGGGGCTACTGTCAGGGTTATGGATACCACATA[T/C,A,G]
CTAATAGTAGTTGACTAAATCTCGGCAGGATCCACCACATACCATATCTTATACGGAAACTGACCTCGAGGGAGTTCCGGATAAGGAAAGACAACCAGAG

Reverse complement sequence

CTCTGGTTGTCTTTCCTTATCCGGAACTCCCTCGAGGTCAGTTTCCGTATAAGATATGGTATGTGGTGGATCCTGCCGAGATTTAGTCAACTACTATTAG[A/G,T,C]
TATGTGGTATCCATAACCCTGACAGTAGCCCCCGACTTCGATGCAAATGAACGAATTCATATTCTCAACTGCGCGCAGACATTGGAGTAACTGTTATCGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	76.40%	12.40%	10.60%	0.57%	G: 0.02%
All Indica	2759	70.40%	18.40%	10.84%	0.40%	NA
All Japonica	1512	96.80%	0.60%	2.38%	0.20%	G: 0.07%
Aus	269	36.10%	17.80%	44.61%	1.49%	NA
Indica I	595	85.20%	11.10%	3.70%	0.00%	NA
Indica II	465	57.40%	17.60%	23.44%	1.51%	NA
Indica III	913	72.40%	20.60%	6.79%	0.22%	NA
Indica Intermediate	786	64.40%	21.90%	13.49%	0.25%	NA
Temperate Japonica	767	98.70%	0.70%	0.65%	0.00%	NA
Tropical Japonica	504	93.30%	0.60%	5.56%	0.60%	NA
Japonica Intermediate	241	97.90%	0.40%	1.24%	0.00%	G: 0.41%
VI/Aromatic	96	39.60%	12.50%	40.62%	7.29%	NA
Intermediate	90	82.20%	7.80%	7.78%	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
vg0224011069	T -> A	LOC_Os02g39750.1	upstream_gene_variant ; 4230.0bp to feature; MODIFIER	N	Average:30.602; most accessible tissue: Minghui63 root, score: 51.763	N	N	N	N
vg0224011069	T -> A	LOC_Os02g39750-LOC_Os02g39764	intergenic_region ; MODIFIER	N	Average:30.602; most accessible tissue: Minghui63 root, score: 51.763	N	N	N	N
vg0224011069	T -> G	LOC_Os02g39750.1	upstream_gene_variant ; 4230.0bp to feature; MODIFIER	silent_mutation	Average:30.602; most accessible tissue: Minghui63 root, score: 51.763	N	N	N	N
vg0224011069	T -> G	LOC_Os02g39750-LOC_Os02g39764	intergenic_region ; MODIFIER	silent_mutation	Average:30.602; most accessible tissue: Minghui63 root, score: 51.763	N	N	N	N
vg0224011069	T -> DEL	N	N	silent_mutation	Average:30.602; most accessible tissue: Minghui63 root, score: 51.763	N	N	N	N
vg0224011069	T -> C	LOC_Os02g39750.1	upstream_gene_variant ; 4230.0bp to feature; MODIFIER	silent_mutation	Average:30.602; most accessible tissue: Minghui63 root, score: 51.763	N	N	N	N
vg0224011069	T -> C	LOC_Os02g39750-LOC_Os02g39764	intergenic_region ; MODIFIER	silent_mutation	Average:30.602; most accessible tissue: Minghui63 root, score: 51.763	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224011069	1.10E-06	5.57E-06	mr1865_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