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Detailed information for vg1004831241:

Variant ID: vg1004831241 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4831241
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.79, A: 0.21, others allele: 0.00, population size: 34. )

Flanking Sequence (100 bp) in Reference Genome:

CACCACGTGTCAGTTTAGCAAGCTGCATGTCTGCCCTTCTTCATACAACGACTTCCTTGCAATGGTTGCGATGAAGCCTGGAATATATCTGGGCGGGACT[A/G]
ACGTGCCAACTCCAGGAGCTAGCACGCCGGCTCCGGCTAGGGACGAGTGCCTGGAGGCTCTCATCAATCCGACGGGACGGGGCGAGGCGTGTGTCAGGCC

Reverse complement sequence

GGCCTGACACACGCCTCGCCCCGTCCCGTCGGATTGATGAGAGCCTCCAGGCACTCGTCCCTAGCCGGAGCCGGCGTGCTAGCTCCTGGAGTTGGCACGT[T/C]
AGTCCCGCCCAGATATATTCCAGGCTTCATCGCAACCATTGCAAGGAAGTCGTTGTATGAAGAAGGGCAGACATGCAGCTTGCTAAACTGACACGTGGTG

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	50.00%	0.30%	11.36%	38.30%	NA
All Indica	2759	44.80%	0.40%	9.79%	45.02%	NA
All Japonica	1512	68.30%	0.10%	5.03%	26.59%	NA
Aus	269	4.10%	0.70%	59.48%	35.69%	NA
Indica I	595	43.40%	0.80%	10.92%	44.87%	NA
Indica II	465	48.20%	0.20%	6.67%	44.95%	NA
Indica III	913	45.90%	0.10%	10.19%	43.81%	NA
Indica Intermediate	786	42.70%	0.40%	10.31%	46.56%	NA
Temperate Japonica	767	70.70%	0.10%	7.56%	21.64%	NA
Tropical Japonica	504	68.70%	0.00%	1.98%	29.37%	NA
Japonica Intermediate	241	60.20%	0.00%	3.32%	36.51%	NA
VI/Aromatic	96	28.10%	0.00%	21.88%	50.00%	NA
Intermediate	90	63.30%	1.10%	11.11%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1004831241	A -> G	LOC_Os10g08920.1	upstream_gene_variant ; 844.0bp to feature; MODIFIER	silent_mutation	Average:31.099; most accessible tissue: Zhenshan97 panicle, score: 74.671	N	N	N	N
vg1004831241	A -> G	LOC_Os10g08930.1	upstream_gene_variant ; 813.0bp to feature; MODIFIER	silent_mutation	Average:31.099; most accessible tissue: Zhenshan97 panicle, score: 74.671	N	N	N	N
vg1004831241	A -> G	LOC_Os10g08940.1	upstream_gene_variant ; 4644.0bp to feature; MODIFIER	silent_mutation	Average:31.099; most accessible tissue: Zhenshan97 panicle, score: 74.671	N	N	N	N
vg1004831241	A -> G	LOC_Os10g08940.2	upstream_gene_variant ; 4665.0bp to feature; MODIFIER	silent_mutation	Average:31.099; most accessible tissue: Zhenshan97 panicle, score: 74.671	N	N	N	N
vg1004831241	A -> G	LOC_Os10g08920-LOC_Os10g08930	intergenic_region ; MODIFIER	silent_mutation	Average:31.099; most accessible tissue: Zhenshan97 panicle, score: 74.671	N	N	N	N
vg1004831241	A -> DEL	N	N	silent_mutation	Average:31.099; most accessible tissue: Zhenshan97 panicle, score: 74.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004831241	1.59E-06	NA	mr1771	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