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Detailed information for vg1124459457:

Variant ID: vg1124459457 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24459457
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

ACACCAACCGGGACTAAAGATCATATTTAAGTCCCGGTTGTGAATGTGTCAGAAGTTGTTACTAATCGGGACAAAAGATTAATATTAATCCATCAGTTCT[C/T]
ATTTTTTCACTTGCAGTTGCATGATCCGTAAATGGCTTATTGACATTGGAACTATCAAACATGACGGAAATAGCTAATGGCAGATAAGAACGTCTATGAA

Reverse complement sequence

TTCATAGACGTTCTTATCTGCCATTAGCTATTTCCGTCATGTTTGATAGTTCCAATGTCAATAAGCCATTTACGGATCATGCAACTGCAAGTGAAAAAAT[G/A]
AGAACTGATGGATTAATATTAATCTTTTGTCCCGATTAGTAACAACTTCTGACACATTCACAACCGGGACTTAAATATGATCTTTAGTCCCGGTTGGTGT

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	40.40%	25.50%	0.83%	33.22%	NA
All Indica	2759	35.40%	36.30%	0.98%	27.33%	NA
All Japonica	1512	48.80%	2.20%	0.60%	48.41%	NA
Aus	269	46.80%	28.60%	1.12%	23.42%	NA
Indica I	595	30.30%	38.20%	0.17%	31.43%	NA
Indica II	465	30.80%	63.90%	0.00%	5.38%	NA
Indica III	913	37.20%	22.00%	2.52%	38.23%	NA
Indica Intermediate	786	39.80%	35.20%	0.38%	24.55%	NA
Temperate Japonica	767	50.20%	1.70%	0.39%	47.72%	NA
Tropical Japonica	504	52.80%	2.80%	0.60%	43.85%	NA
Japonica Intermediate	241	36.10%	2.50%	1.24%	60.17%	NA
VI/Aromatic	96	33.30%	60.40%	0.00%	6.25%	NA
Intermediate	90	42.20%	41.10%	0.00%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1124459457	C -> T	LOC_Os11g40870-LOC_Os11g40890	intergenic_region ; MODIFIER	silent_mutation	Average:41.608; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg1124459457	C -> DEL	N	N	silent_mutation	Average:41.608; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124459457	1.51E-06	1.36E-07	mr1662	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
vg1124459457	1.34E-06	3.78E-10	mr1662_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