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Detailed information for vg1004892287:

Variant ID: vg1004892287 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4892287
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, C: 0.02, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

TATTTTCTTCCCCATGGATTATAAGGATGGATCGTATTGTGGGAATGATATTGTTATTAGTTTAACTTATAATTGTCTGTCGTGGATGTCCGTATTTACA[G/C]
GGGAGACTCTGCCGTAATTTCTAATAATTTTGGAAGTTAGTGGTTTGAGTGGTTTTTGGTGTGGCACTCTTGGTACGTGGTTATCTGGTGTGTTACAATT

Reverse complement sequence

AATTGTAACACACCAGATAACCACGTACCAAGAGTGCCACACCAAAAACCACTCAAACCACTAACTTCCAAAATTATTAGAAATTACGGCAGAGTCTCCC[C/G]
TGTAAATACGGACATCCACGACAGACAATTATAAGTTAAACTAATAACAATATCATTCCCACAATACGATCCATCCTTATAATCCATGGGGAAGAAAATA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.80%	48.50%	0.74%	0.00%	NA
All Indica	2759	37.80%	61.20%	0.98%	0.00%	NA
All Japonica	1512	81.00%	18.80%	0.20%	0.00%	NA
Aus	269	3.30%	95.90%	0.74%	0.00%	NA
Indica I	595	31.40%	67.20%	1.34%	0.00%	NA
Indica II	465	38.50%	60.90%	0.65%	0.00%	NA
Indica III	913	44.40%	54.80%	0.88%	0.00%	NA
Indica Intermediate	786	34.70%	64.20%	1.02%	0.00%	NA
Temperate Japonica	767	93.20%	6.80%	0.00%	0.00%	NA
Tropical Japonica	504	68.80%	30.80%	0.40%	0.00%	NA
Japonica Intermediate	241	67.20%	32.40%	0.41%	0.00%	NA
VI/Aromatic	96	64.60%	35.40%	0.00%	0.00%	NA
Intermediate	90	66.70%	30.00%	3.33%	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
vg1004892287	G -> C	LOC_Os10g09030.1	upstream_gene_variant ; 3532.0bp to feature; MODIFIER	silent_mutation	Average:33.448; most accessible tissue: Callus, score: 47.708	N	N	N	N
vg1004892287	G -> C	LOC_Os10g09040.1	upstream_gene_variant ; 1228.0bp to feature; MODIFIER	silent_mutation	Average:33.448; most accessible tissue: Callus, score: 47.708	N	N	N	N
vg1004892287	G -> C	LOC_Os10g09040-LOC_Os10g09060	intergenic_region ; MODIFIER	silent_mutation	Average:33.448; most accessible tissue: Callus, score: 47.708	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004892287	NA	4.00E-06	mr1847	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
vg1004892287	NA	9.96E-06	mr1053_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
vg1004892287	NA	7.49E-06	mr1128_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
vg1004892287	5.37E-07	5.37E-07	mr1151_2	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
vg1004892287	NA	7.10E-07	mr1705_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