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Detailed information for vg0200349177:

Variant ID: vg0200349177 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 349177
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.71, A: 0.29, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

TTTCTTCATGTCAAATTAATGCTAGAAAATGTGGATTGGCACTTCTGCTGTGCTGTCAAAACTTGCCTCCCAACCAGGCAACCACCATGTAACTAATTTA[A/G]
CAAAGGCTAATCAGAACTACCTTCCTGAAACACAGAATTATGATTTCATAAACACACCTCTTTTCAACCCTGCACCTGCAGGGAACATGAGAATTCTTAC

Reverse complement sequence

GTAAGAATTCTCATGTTCCCTGCAGGTGCAGGGTTGAAAAGAGGTGTGTTTATGAAATCATAATTCTGTGTTTCAGGAAGGTAGTTCTGATTAGCCTTTG[T/C]
TAAATTAGTTACATGGTGGTTGCCTGGTTGGGAGGCAAGTTTTGACAGCACAGCAGAAGTGCCAATCCACATTTTCTAGCATTAATTTGACATGAAGAAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.50%	44.10%	0.08%	0.30%	NA
All Indica	2759	30.00%	69.40%	0.07%	0.47%	NA
All Japonica	1512	98.50%	1.50%	0.00%	0.00%	NA
Aus	269	72.50%	27.10%	0.37%	0.00%	NA
Indica I	595	34.50%	65.00%	0.17%	0.34%	NA
Indica II	465	29.70%	69.70%	0.00%	0.65%	NA
Indica III	913	26.40%	73.50%	0.00%	0.11%	NA
Indica Intermediate	786	31.00%	67.90%	0.13%	0.89%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	96.60%	3.40%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	54.20%	45.80%	0.00%	0.00%	NA
Intermediate	90	65.60%	32.20%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0200349177	A -> G	LOC_Os02g01590.1	downstream_gene_variant ; 1981.0bp to feature; MODIFIER	silent_mutation	Average:66.906; most accessible tissue: Callus, score: 80.094	N	N	N	N
vg0200349177	A -> G	LOC_Os02g01610.1	downstream_gene_variant ; 1614.0bp to feature; MODIFIER	silent_mutation	Average:66.906; most accessible tissue: Callus, score: 80.094	N	N	N	N
vg0200349177	A -> G	LOC_Os02g01590.2	downstream_gene_variant ; 1981.0bp to feature; MODIFIER	silent_mutation	Average:66.906; most accessible tissue: Callus, score: 80.094	N	N	N	N
vg0200349177	A -> G	LOC_Os02g01610.2	downstream_gene_variant ; 356.0bp to feature; MODIFIER	silent_mutation	Average:66.906; most accessible tissue: Callus, score: 80.094	N	N	N	N
vg0200349177	A -> G	LOC_Os02g01590-LOC_Os02g01610	intergenic_region ; MODIFIER	silent_mutation	Average:66.906; most accessible tissue: Callus, score: 80.094	N	N	N	N
vg0200349177	A -> DEL	N	N	silent_mutation	Average:66.906; most accessible tissue: Callus, score: 80.094	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0200349177	6.24E-06	NA	mr1291_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
vg0200349177	NA	1.62E-06	mr1291_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
vg0200349177	NA	8.39E-06	mr1479_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