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Detailed information for vg1104344322:

Variant ID: vg1104344322 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 4344322
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.75, A: 0.26, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

CGAAAATGTTTCAATCGTTTAAATCGGGCGTTGTTTCACTTTATATAAAAACAATGTTTCAGCAAATATGGAAAGAATGTTTCAATTCACTGGAACATTT[A/G]
ATCCATACATAGTGAAACATTATAAGTACACTAAGTGAAACATTTTTTGGTAGAACAAAAAAAATAAAACGAATTCTCTTAATAGAGGGTTTCCAAAATA

Reverse complement sequence

TATTTTGGAAACCCTCTATTAAGAGAATTCGTTTTATTTTTTTTGTTCTACCAAAAAATGTTTCACTTAGTGTACTTATAATGTTTCACTATGTATGGAT[T/C]
AAATGTTCCAGTGAATTGAAACATTCTTTCCATATTTGCTGAAACATTGTTTTTATATAAAGTGAAACAACGCCCGATTTAAACGATTGAAACATTTTCG

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	60.60%	39.30%	0.08%	0.00%	NA
All Indica	2759	90.10%	9.70%	0.11%	0.00%	NA
All Japonica	1512	15.10%	84.90%	0.00%	0.00%	NA
Aus	269	22.70%	77.30%	0.00%	0.00%	NA
Indica I	595	79.70%	20.00%	0.34%	0.00%	NA
Indica II	465	96.30%	3.70%	0.00%	0.00%	NA
Indica III	913	94.20%	5.80%	0.00%	0.00%	NA
Indica Intermediate	786	89.70%	10.20%	0.13%	0.00%	NA
Temperate Japonica	767	2.90%	97.10%	0.00%	0.00%	NA
Tropical Japonica	504	34.10%	65.90%	0.00%	0.00%	NA
Japonica Intermediate	241	14.10%	85.90%	0.00%	0.00%	NA
VI/Aromatic	96	32.30%	67.70%	0.00%	0.00%	NA
Intermediate	90	62.20%	36.70%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1104344322	A -> G	LOC_Os11g08285.1	upstream_gene_variant ; 1531.0bp to feature; MODIFIER	silent_mutation	Average:19.652; most accessible tissue: Callus, score: 29.104	N	N	N	N
vg1104344322	A -> G	LOC_Os11g08280.1	downstream_gene_variant ; 1507.0bp to feature; MODIFIER	silent_mutation	Average:19.652; most accessible tissue: Callus, score: 29.104	N	N	N	N
vg1104344322	A -> G	LOC_Os11g08280-LOC_Os11g08285	intergenic_region ; MODIFIER	silent_mutation	Average:19.652; most accessible tissue: Callus, score: 29.104	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1104344322	1.45E-07	1.45E-07	mr1487	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
vg1104344322	7.96E-06	NA	mr1549	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
vg1104344322	1.08E-12	1.60E-40	mr1638	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
vg1104344322	6.07E-12	3.75E-14	mr1638	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