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Detailed information for vg1102378831:

Variant ID: vg1102378831 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 2378831
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: 117. )

Flanking Sequence (100 bp) in Reference Genome:

CATTTAAACATGCTACTAGTAATTCCTCGTAAACAAGCGATTCATTAATATTTACATTTCTCGATGCCCATGTAGCTAATCTTGTGTGGAAGAATGGAAA[G/A]
TCATGCATTAAATTCGAGAAAGTCATTAAGAAGATAGATTATTGGATTGAAATATGCCTATCAAAAATAGAATTTTCAGATTTAGAAATATGACTATCAA

Reverse complement sequence

TTGATAGTCATATTTCTAAATCTGAAAATTCTATTTTTGATAGGCATATTTCAATCCAATAATCTATCTTCTTAATGACTTTCTCGAATTTAATGCATGA[C/T]
TTTCCATTCTTCCACACAAGATTAGCTACATGGGCATCGAGAAATGTAAATATTAATGAATCGCTTGTTTACGAGGAATTACTAGTAGCATGTTTAAATG

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	73.60%	25.90%	0.51%	0.00%	NA
All Indica	2759	57.30%	42.20%	0.47%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	84.00%	14.10%	1.86%	0.00%	NA
Indica I	595	83.70%	16.10%	0.17%	0.00%	NA
Indica II	465	63.40%	36.10%	0.43%	0.00%	NA
Indica III	913	38.30%	61.60%	0.11%	0.00%	NA
Indica Intermediate	786	55.70%	43.10%	1.15%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	89.60%	4.20%	6.25%	0.00%	NA
Intermediate	90	88.90%	11.10%	0.00%	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
vg1102378831	G -> A	LOC_Os11g05350.1	upstream_gene_variant ; 2349.0bp to feature; MODIFIER	silent_mutation	Average:58.739; most accessible tissue: Zhenshan97 root, score: 81.351	N	N	N	N
vg1102378831	G -> A	LOC_Os11g05360.1	upstream_gene_variant ; 308.0bp to feature; MODIFIER	silent_mutation	Average:58.739; most accessible tissue: Zhenshan97 root, score: 81.351	N	N	N	N
vg1102378831	G -> A	LOC_Os11g05370.1	downstream_gene_variant ; 3353.0bp to feature; MODIFIER	silent_mutation	Average:58.739; most accessible tissue: Zhenshan97 root, score: 81.351	N	N	N	N
vg1102378831	G -> A	LOC_Os11g05350-LOC_Os11g05360	intergenic_region ; MODIFIER	silent_mutation	Average:58.739; most accessible tissue: Zhenshan97 root, score: 81.351	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1102378831	6.21E-07	NA	mr1218	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
vg1102378831	NA	2.66E-07	mr1218	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
vg1102378831	NA	9.89E-07	mr1090_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