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Detailed information for vg1000477711:

Variant ID: vg1000477711 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 477711
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.01, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

AGTTAGCACCCTTCTGGTGTCTATCCATTCTCTGTATTGACATCTCCTTGGTGGTTCCTGGGAGAAAAGAATAGATGTGAAGCGAGCAAAGTTAGTAAAT[G/A]
TTGTGAGAAAATAAGGATTCATGATAATCAAAATATTCTTACCATGAAATCGTTGTCGAGAATATTTGAACAAACAAAGAACCTTCGACCCAATATCGTA

Reverse complement sequence

TACGATATTGGGTCGAAGGTTCTTTGTTTGTTCAAATATTCTCGACAACGATTTCATGGTAAGAATATTTTGATTATCATGAATCCTTATTTTCTCACAA[C/T]
ATTTACTAACTTTGCTCGCTTCACATCTATTCTTTTCTCCCAGGAACCACCAAGGAGATGTCAATACAGAGAATGGATAGACACCAGAAGGGTGCTAACT

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	77.30%	15.40%	1.42%	5.95%	NA
All Indica	2759	70.10%	26.00%	0.83%	3.08%	NA
All Japonica	1512	99.30%	0.10%	0.13%	0.46%	NA
Aus	269	32.00%	1.10%	14.13%	52.79%	NA
Indica I	595	56.30%	43.70%	0.00%	0.00%	NA
Indica II	465	94.40%	4.70%	0.22%	0.65%	NA
Indica III	913	68.50%	25.40%	1.20%	4.93%	NA
Indica Intermediate	786	68.10%	25.80%	1.40%	4.71%	NA
Temperate Japonica	767	99.70%	0.10%	0.00%	0.13%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	96.70%	0.00%	0.83%	2.49%	NA
VI/Aromatic	96	56.20%	1.00%	2.08%	40.62%	NA
Intermediate	90	84.40%	4.40%	2.22%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1000477711	G -> A	LOC_Os10g01730.1	downstream_gene_variant ; 1657.0bp to feature; MODIFIER	silent_mutation	Average:22.831; most accessible tissue: Callus, score: 37.292	N	N	N	N
vg1000477711	G -> A	LOC_Os10g01750.1	downstream_gene_variant ; 4973.0bp to feature; MODIFIER	silent_mutation	Average:22.831; most accessible tissue: Callus, score: 37.292	N	N	N	N
vg1000477711	G -> A	LOC_Os10g01740.1	intron_variant ; MODIFIER	silent_mutation	Average:22.831; most accessible tissue: Callus, score: 37.292	N	N	N	N
vg1000477711	G -> DEL	N	N	silent_mutation	Average:22.831; most accessible tissue: Callus, score: 37.292	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1000477711	NA	1.54E-06	mr1655_2	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