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Detailed information for vg1124463257:

Variant ID: vg1124463257 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24463257
Reference Allele: A	Alternative Allele: T,C
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.79, A: 0.19, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:

CGGAACGGTCCATTAGCGCATGATTAATTAAGTATTAGCTAATTTTTTTAAAATGTATCAATATTAATTTTTTAAGCAACTTTCATACAGAAACTTTTTT[A/T,C]
AAAAAAACGCACCGTTTAGCAATTTGAAAAGCGTGTGCGTGAAAAACGAGGGAGATAAGTTGTAAAACTTGGAGTAAGAACACAGCCGTAGTCGCTGTAG

Reverse complement sequence

CTACAGCGACTACGGCTGTGTTCTTACTCCAAGTTTTACAACTTATCTCCCTCGTTTTTCACGCACACGCTTTTCAAATTGCTAAACGGTGCGTTTTTTT[T/A,G]
AAAAAAGTTTCTGTATGAAAGTTGCTTAAAAAATTAATATTGATACATTTTAAAAAAATTAGCTAATACTTAATTAATCATGCGCTAATGGACCGTTCCG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	33.70%	31.70%	0.93%	33.54%	C: 0.15%
All Indica	2759	33.10%	39.00%	0.33%	27.58%	NA
All Japonica	1512	34.00%	15.10%	1.92%	48.94%	NA
Aus	269	31.20%	43.10%	1.12%	23.79%	C: 0.74%
Indica I	595	27.90%	40.50%	0.17%	31.43%	NA
Indica II	465	38.70%	55.70%	0.22%	5.38%	NA
Indica III	913	27.80%	33.40%	0.11%	38.66%	NA
Indica Intermediate	786	39.70%	34.60%	0.76%	24.94%	NA
Temperate Japonica	767	37.50%	12.80%	1.17%	48.50%	NA
Tropical Japonica	504	35.90%	17.70%	1.79%	44.64%	NA
Japonica Intermediate	241	18.70%	17.40%	4.56%	59.34%	NA
VI/Aromatic	96	58.30%	31.20%	1.04%	5.21%	C: 4.17%
Intermediate	90	28.90%	51.10%	2.22%	16.67%	C: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1124463257	A -> T	LOC_Os11g40870-LOC_Os11g40890	intergenic_region ; MODIFIER	silent_mutation	Average:29.047; most accessible tissue: Callus, score: 50.82	N	N	N	N
vg1124463257	A -> DEL	N	N	silent_mutation	Average:29.047; most accessible tissue: Callus, score: 50.82	N	N	N	N
vg1124463257	A -> C	LOC_Os11g40870-LOC_Os11g40890	intergenic_region ; MODIFIER	silent_mutation	Average:29.047; most accessible tissue: Callus, score: 50.82	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124463257	1.20E-07	1.30E-08	mr1309	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
vg1124463257	NA	4.48E-06	mr1477_2	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
vg1124463257	NA	2.11E-06	mr1609_2	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