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Detailed information for vg1124581657:

Variant ID: vg1124581657 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24581657
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCACCAAAGTTTTTTTGGAGCCCAACCAAACCTAATATAAAAATAATCTAATTTTCACTGCAAAAATAAATGGACAATCGTCAGTCCCTACAATACTAA[T/G]
AAAGTTAAGGGAGCATTGGCTAAAACGAGCCAGTAGGTGATCAATAGCCCTGAAATCTGCACTGTAGTGATTCCAGGAAAATTCAGAGATAGCAAGACAG

Reverse complement sequence

CTGTCTTGCTATCTCTGAATTTTCCTGGAATCACTACAGTGCAGATTTCAGGGCTATTGATCACCTACTGGCTCGTTTTAGCCAATGCTCCCTTAACTTT[A/C]
TTAGTATTGTAGGGACTGACGATTGTCCATTTATTTTTGCAGTGAAAATTAGATTATTTTTATATTAGGTTTGGTTGGGCTCCAAAAAAACTTTGGTGGT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.50%	17.50%	0.47%	17.52%	NA
All Indica	2759	86.40%	2.40%	0.29%	10.87%	NA
All Japonica	1512	28.40%	39.90%	0.79%	30.89%	NA
Aus	269	42.00%	46.10%	0.74%	11.15%	NA
Indica I	595	96.00%	3.50%	0.00%	0.50%	NA
Indica II	465	78.10%	1.90%	0.65%	19.35%	NA
Indica III	913	86.90%	1.50%	0.11%	11.50%	NA
Indica Intermediate	786	83.70%	2.80%	0.51%	12.98%	NA
Temperate Japonica	767	43.00%	37.50%	0.65%	18.77%	NA
Tropical Japonica	504	10.10%	47.40%	1.19%	41.27%	NA
Japonica Intermediate	241	19.90%	32.00%	0.41%	47.72%	NA
VI/Aromatic	96	70.80%	18.80%	0.00%	10.42%	NA
Intermediate	90	58.90%	17.80%	0.00%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1124581657	T -> DEL	N	N	silent_mutation	Average:23.685; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg1124581657	T -> G	LOC_Os11g41050.1	upstream_gene_variant ; 2213.0bp to feature; MODIFIER	silent_mutation	Average:23.685; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg1124581657	T -> G	LOC_Os11g41034-LOC_Os11g41050	intergenic_region ; MODIFIER	silent_mutation	Average:23.685; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124581657	2.89E-06	1.62E-09	mr1548_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