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Detailed information for vg0710140235:

Variant ID: vg0710140235 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 10140235
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

GACTGCATTTGCTTCAGAAACGTCCATGTGGATAGGCACGAAGGTGCTCTTATGATAGTTCTTTTTCAAACCCGAGAAGTCAACAAAGGAATCTCGGATG[T/A]
CTTTTAGAGTTTAGCCTGTTGAACATATCCCTGAATTAAGATCAAAGTTTCATCTGCATACTGCAAGGAAAGGCAGCGTGGTTTGTATTTGGAGAGGGTG

Reverse complement sequence

CACCCTCTCCAAATACAAACCACGCTGCCTTTCCTTGCAGTATGCAGATGAAACTTTGATCTTAATTCAGGGATATGTTCAACAGGCTAAACTCTAAAAG[A/T]
CATCCGAGATTCCTTTGTTGACTTCTCGGGTTTGAAAAAGAACTATCATAAGAGCACCTTCGTGCCTATCCACATGGACGTTTCTGAAGCAAATGCAGTC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.70%	3.20%	1.14%	0.00%	NA
All Indica	2759	99.80%	0.20%	0.00%	0.00%	NA
All Japonica	1512	87.80%	8.60%	3.57%	0.00%	NA
Aus	269	95.50%	4.50%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.40%	0.00%	0.00%	NA
Temperate Japonica	767	92.20%	1.80%	6.00%	0.00%	NA
Tropical Japonica	504	95.40%	4.60%	0.00%	0.00%	NA
Japonica Intermediate	241	58.10%	38.60%	3.32%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg0710140235	T -> A	LOC_Os07g17210.1	upstream_gene_variant ; 2761.0bp to feature; MODIFIER	silent_mutation	Average:73.041; most accessible tissue: Callus, score: 81.898	N	N	N	N
vg0710140235	T -> A	LOC_Os07g17220.1	downstream_gene_variant ; 2054.0bp to feature; MODIFIER	silent_mutation	Average:73.041; most accessible tissue: Callus, score: 81.898	N	N	N	N
vg0710140235	T -> A	LOC_Os07g17220.2	downstream_gene_variant ; 2054.0bp to feature; MODIFIER	silent_mutation	Average:73.041; most accessible tissue: Callus, score: 81.898	N	N	N	N
vg0710140235	T -> A	LOC_Os07g17210-LOC_Os07g17220	intergenic_region ; MODIFIER	silent_mutation	Average:73.041; most accessible tissue: Callus, score: 81.898	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0710140235	3.52E-06	NA	mr1672_2	Jap_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