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Detailed information for vg1011521268:

Variant ID: vg1011521268 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 11521268
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

TTTATTCAACTAATCACATAGTCGGGGGCTACACCTAATTAGGTGCATCTAGTCGATGCACCTGATTTTTTATTTTAGCCCTTCACAGTCTTTGATTCAA[G/A]
TACTCGGGAGACCAAGGCAGGAATAATTGAAGCACTCGGATTATCATCTTGAAGACTTCAAGAGAAGATTATTTCGTCGACTATAAAGGTCTCAGGGGTT

Reverse complement sequence

AACCCCTGAGACCTTTATAGTCGACGAAATAATCTTCTCTTGAAGTCTTCAAGATGATAATCCGAGTGCTTCAATTATTCCTGCCTTGGTCTCCCGAGTA[C/T]
TTGAATCAAAGACTGTGAAGGGCTAAAATAAAAAATCAGGTGCATCGACTAGATGCACCTAATTAGGTGTAGCCCCCGACTATGTGATTAGTTGAATAAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	85.50%	2.30%	0.85%	11.32%	NA
All Indica	2759	98.00%	1.20%	0.51%	0.25%	NA
All Japonica	1512	59.40%	4.80%	1.65%	34.19%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.30%	0.50%	0.00%	0.17%	NA
Indica II	465	98.50%	1.10%	0.43%	0.00%	NA
Indica III	913	96.80%	2.00%	0.88%	0.33%	NA
Indica Intermediate	786	98.20%	0.90%	0.51%	0.38%	NA
Temperate Japonica	767	79.10%	0.80%	0.39%	19.69%	NA
Tropical Japonica	504	36.30%	11.30%	3.77%	48.61%	NA
Japonica Intermediate	241	44.80%	3.70%	1.24%	50.21%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	85.60%	2.20%	1.11%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1011521268	G -> A	LOC_Os10g22260.1	upstream_gene_variant ; 935.0bp to feature; MODIFIER	silent_mutation	Average:17.314; most accessible tissue: Callus, score: 42.419	N	N	N	N
vg1011521268	G -> A	LOC_Os10g22290.1	upstream_gene_variant ; 4540.0bp to feature; MODIFIER	silent_mutation	Average:17.314; most accessible tissue: Callus, score: 42.419	N	N	N	N
vg1011521268	G -> A	LOC_Os10g22270.1	downstream_gene_variant ; 1754.0bp to feature; MODIFIER	silent_mutation	Average:17.314; most accessible tissue: Callus, score: 42.419	N	N	N	N
vg1011521268	G -> A	LOC_Os10g22260-LOC_Os10g22270	intergenic_region ; MODIFIER	silent_mutation	Average:17.314; most accessible tissue: Callus, score: 42.419	N	N	N	N
vg1011521268	G -> DEL	N	N	silent_mutation	Average:17.314; most accessible tissue: Callus, score: 42.419	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1011521268	4.78E-06	4.79E-06	mr1760_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