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Detailed information for vg0507940286:

Variant ID: vg0507940286 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 7940286
Reference Allele: T	Alternative Allele: G
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.00, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:

ACTATGTGGCAAGAGAGTTAATGAGGAGAGAGGTAAAAATATGAAGAAACCATTCTCATGCAAGAAACCATCTCTACACAAGTAACAAGAATGAAAACAA[T/G]
GGGATATGTGGATAAAAGGAGAGAGAAGAAAGATGATTGGCTAATAATTGAATTTGAAGACAACATCCATCGGATATACTAGATGAATACCCCGCCACGT

Reverse complement sequence

ACGTGGCGGGGTATTCATCTAGTATATCCGATGGATGTTGTCTTCAAATTCAATTATTAGCCAATCATCTTTCTTCTCTCTCCTTTTATCCACATATCCC[A/C]
TTGTTTTCATTCTTGTTACTTGTGTAGAGATGGTTTCTTGCATGAGAATGGTTTCTTCATATTTTTACCTCTCTCCTCATTAACTCTCTTGCCACATAGT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.50%	31.60%	0.15%	1.74%	NA
All Indica	2759	94.60%	4.60%	0.14%	0.65%	NA
All Japonica	1512	18.50%	81.40%	0.07%	0.00%	NA
Aus	269	74.70%	1.90%	0.74%	22.68%	NA
Indica I	595	97.10%	2.00%	0.17%	0.67%	NA
Indica II	465	95.50%	4.10%	0.22%	0.22%	NA
Indica III	913	94.00%	5.10%	0.00%	0.88%	NA
Indica Intermediate	786	92.70%	6.40%	0.25%	0.64%	NA
Temperate Japonica	767	32.60%	67.40%	0.00%	0.00%	NA
Tropical Japonica	504	3.20%	96.80%	0.00%	0.00%	NA
Japonica Intermediate	241	5.80%	93.80%	0.41%	0.00%	NA
VI/Aromatic	96	1.00%	99.00%	0.00%	0.00%	NA
Intermediate	90	58.90%	37.80%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0507940286	T -> DEL	N	N	silent_mutation	Average:38.095; most accessible tissue: Callus, score: 53.748	N	N	N	N
vg0507940286	T -> G	LOC_Os05g14170.1	downstream_gene_variant ; 3873.0bp to feature; MODIFIER	silent_mutation	Average:38.095; most accessible tissue: Callus, score: 53.748	N	N	N	N
vg0507940286	T -> G	LOC_Os05g14170-LOC_Os05g14180	intergenic_region ; MODIFIER	silent_mutation	Average:38.095; most accessible tissue: Callus, score: 53.748	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0507940286	NA	2.10E-06	mr1182	Jap_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
vg0507940286	2.16E-06	6.47E-14	mr1657	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
vg0507940286	NA	1.26E-12	mr1521_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
vg0507940286	NA	6.34E-15	mr1686_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