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Detailed information for vg0406946931:

Variant ID: vg0406946931 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 6946931
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

TGTTCACCCTAGAATAAACAAAACCCCAACTAGTGGGCGCTCTACTCATGGTTCCCCTAGTATGAATTTAGATAGATGCTTCGCTGATTAATAAGACAAC[A/T]
TTAGGTGGTTTTTATAACTTTAGACTTTGGGAATATTCATATCTCTTGGACTTTATGGAATGGTTGGACTATTGTGGAATTGGATGCACACCTCTCCCTC

Reverse complement sequence

GAGGGAGAGGTGTGCATCCAATTCCACAATAGTCCAACCATTCCATAAAGTCCAAGAGATATGAATATTCCCAAAGTCTAAAGTTATAAAAACCACCTAA[T/A]
GTTGTCTTATTAATCAGCGAAGCATCTATCTAAATTCATACTAGGGGAACCATGAGTAGAGCGCCCACTAGTTGGGGTTTTGTTTATTCTAGGGTGAACA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.20%	0.80%	7.85%	31.23%	NA
All Indica	2759	35.20%	1.30%	12.65%	50.82%	NA
All Japonica	1512	99.50%	0.00%	0.20%	0.26%	NA
Aus	269	80.70%	0.00%	3.72%	15.61%	NA
Indica I	595	7.70%	1.80%	6.22%	84.20%	NA
Indica II	465	34.60%	0.90%	18.06%	46.45%	NA
Indica III	913	56.50%	1.00%	14.35%	28.15%	NA
Indica Intermediate	786	31.70%	1.50%	12.34%	54.45%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	99.60%	0.00%	0.20%	0.20%	NA
Japonica Intermediate	241	98.30%	0.00%	0.41%	1.24%	NA
VI/Aromatic	96	85.40%	0.00%	6.25%	8.33%	NA
Intermediate	90	74.40%	0.00%	3.33%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0406946931	A -> DEL	N	N	silent_mutation	Average:10.844; most accessible tissue: Callus, score: 44.944	N	N	N	N
vg0406946931	A -> T	LOC_Os04g12540.1	upstream_gene_variant ; 4215.0bp to feature; MODIFIER	silent_mutation	Average:10.844; most accessible tissue: Callus, score: 44.944	N	N	N	N
vg0406946931	A -> T	LOC_Os04g12550.1	downstream_gene_variant ; 4410.0bp to feature; MODIFIER	silent_mutation	Average:10.844; most accessible tissue: Callus, score: 44.944	N	N	N	N
vg0406946931	A -> T	LOC_Os04g12540-LOC_Os04g12550	intergenic_region ; MODIFIER	silent_mutation	Average:10.844; most accessible tissue: Callus, score: 44.944	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0406946931	9.73E-07	NA	mr1722_2	Ind_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