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Detailed information for vg1014597243:

Variant ID: vg1014597243 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 14597243
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

GGGTGGCCGTTTTAAAGTTGTGGCCGGGTGCCAATCCTGATTCAATCAAAGACTGATACATTACACATACTCCGACCGGACGAGACGCACTGTCTCATCC[G/A]
TGTCGTTTGAGAAGCACTCACTTAGTTGTTTCAAAAAGGAGTTTAAATAAAATCAATTGCAAAAACAACAGCCTTTCCTTTGAAGCCTGCATTAAACACT

Reverse complement sequence

AGTGTTTAATGCAGGCTTCAAAGGAAAGGCTGTTGTTTTTGCAATTGATTTTATTTAAACTCCTTTTTGAAACAACTAAGTGAGTGCTTCTCAAACGACA[C/T]
GGATGAGACAGTGCGTCTCGTCCGGTCGGAGTATGTGTAATGTATCAGTCTTTGATTGAATCAGGATTGGCACCCGGCCACAACTTTAAAACGGCCACCC

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	71.20%	24.20%	3.60%	1.06%	NA
All Indica	2759	51.70%	40.60%	5.98%	1.74%	NA
All Japonica	1512	99.40%	0.50%	0.07%	0.00%	NA
Aus	269	99.30%	0.00%	0.37%	0.37%	NA
Indica I	595	77.60%	15.50%	4.71%	2.18%	NA
Indica II	465	40.00%	52.30%	7.10%	0.65%	NA
Indica III	913	42.30%	48.70%	6.90%	2.08%	NA
Indica Intermediate	786	49.90%	43.30%	5.22%	1.65%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	0.80%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	78.90%	16.70%	3.33%	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
vg1014597243	G -> A	LOC_Os10g28094.1	upstream_gene_variant ; 2060.0bp to feature; MODIFIER	silent_mutation	Average:33.847; most accessible tissue: Zhenshan97 flag leaf, score: 55.285	N	N	N	N
vg1014597243	G -> A	LOC_Os10g28110.1	upstream_gene_variant ; 3860.0bp to feature; MODIFIER	silent_mutation	Average:33.847; most accessible tissue: Zhenshan97 flag leaf, score: 55.285	N	N	N	N
vg1014597243	G -> A	LOC_Os10g28094-LOC_Os10g28110	intergenic_region ; MODIFIER	silent_mutation	Average:33.847; most accessible tissue: Zhenshan97 flag leaf, score: 55.285	N	N	N	N
vg1014597243	G -> DEL	N	N	silent_mutation	Average:33.847; most accessible tissue: Zhenshan97 flag leaf, score: 55.285	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1014597243	NA	6.91E-06	mr1749	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
vg1014597243	2.07E-06	1.97E-06	mr1984	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
vg1014597243	NA	6.64E-06	mr1984	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